Daily Papers

Table Structure Recognition (TSR) is vital for various downstream tasks like information retrieval, table reconstruction, and document understanding. While most state-of-the-art (SOTA) research predominantly focuses on TSR in English documents, the need for similar capabilities in other languages is evident, considering the global diversity of data. Moreover, creating substantial labeled data in non-English languages and training these SOTA models from scratch is costly and time-consuming. We propose TSR as a language-agnostic cell arrangement prediction and introduce SPRINT, Script-agnostic Structure Recognition in Tables. SPRINT uses recently introduced Optimized Table Structure Language (OTSL) sequences to predict table structures. We show that when coupled with a pre-trained table grid estimator, SPRINT can improve the overall tree edit distance-based similarity structure scores of tables even for non-English documents. We experimentally evaluate our performance across benchmark TSR datasets including PubTabNet, FinTabNet, and PubTables-1M. Our findings reveal that SPRINT not only matches SOTA models in performance on standard datasets but also demonstrates lower latency. Additionally, SPRINT excels in accurately identifying table structures in non-English documents, surpassing current leading models by showing an absolute average increase of 11.12%. We also present an algorithm for converting valid OTSL predictions into a widely used HTML-based table representation. To encourage further research, we release our code and Multilingual Scanned and Scene Table Structure Recognition Dataset, MUSTARD labeled with OTSL sequences for 1428 tables in thirteen languages encompassing several scripts at https://github.com/IITB-LEAP-OCR/SPRINT

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Optical Chemical Structure Recognition (OCSR) is crucial for digitizing chemical knowledge by converting molecular images into machine-readable formats. While recent vision-language models (VLMs) have shown potential in this task, their image-captioning approach often struggles with complex molecular structures and inconsistent annotations. To overcome these challenges, we introduce GTR-Mol-VLM, a novel framework featuring two key innovations: (1) the Graph Traversal as Visual Chain of Thought mechanism that emulates human reasoning by incrementally parsing molecular graphs through sequential atom-bond predictions, and (2) the data-centric principle of Faithfully Recognize What You've Seen, which addresses the mismatch between abbreviated structures in images and their expanded annotations. To support model development, we constructed GTR-CoT-1.3M, a large-scale instruction-tuning dataset with meticulously corrected annotations, and introduced MolRec-Bench, the first benchmark designed for a fine-grained evaluation of graph-parsing accuracy in OCSR. Comprehensive experiments demonstrate that GTR-Mol-VLM achieves superior results compared to specialist models, chemistry-domain VLMs, and commercial general-purpose VLMs. Notably, in scenarios involving molecular images with functional group abbreviations, GTR-Mol-VLM outperforms the second-best baseline by approximately 14 percentage points, both in SMILES-based and graph-based metrics. We hope that this work will drive OCSR technology to more effectively meet real-world needs, thereby advancing the fields of cheminformatics and AI for Science. We will release GTR-CoT at https://github.com/opendatalab/GTR-CoT.

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental molecule-language interface tasks: language-prompted molecular structure recognition, editing, and generation. To ensure high-quality, unambiguous, and deterministic outputs, we construct the recognition tasks using automated cheminformatics tools, and curate editing and generation tasks through rigorous expert annotation and validation. MolLangBench supports the evaluation of models that interface language with different molecular representations, including linear strings, molecular images, and molecular graphs. Evaluations of state-of-the-art models reveal significant limitations: the strongest model (o3) achieves 79.2% and 78.5% accuracy on recognition and editing tasks, which are intuitively simple for humans, and performs even worse on the generation task, reaching only 29.0% accuracy. These results highlight the shortcomings of current AI systems in handling even preliminary molecular recognition and manipulation tasks. We hope MolLangBench will catalyze further research toward more effective and reliable AI systems for chemical applications.

All tables can be represented as grids. Based on this observation, we propose GridFormer, a novel approach for interpreting unconstrained table structures by predicting the vertex and edge of a grid. First, we propose a flexible table representation in the form of an MXN grid. In this representation, the vertexes and edges of the grid store the localization and adjacency information of the table. Then, we introduce a DETR-style table structure recognizer to efficiently predict this multi-objective information of the grid in a single shot. Specifically, given a set of learned row and column queries, the recognizer directly outputs the vertexes and edges information of the corresponding rows and columns. Extensive experiments on five challenging benchmarks which include wired, wireless, multi-merge-cell, oriented, and distorted tables demonstrate the competitive performance of our model over other methods.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Benchmark datasets for table structure recognition (TSR) must be carefully processed to ensure they are annotated consistently. However, even if a dataset's annotations are self-consistent, there may be significant inconsistency across datasets, which can harm the performance of models trained and evaluated on them. In this work, we show that aligning these benchmarksx2014removing both errors and inconsistency between themx2014improves model performance significantly. We demonstrate this through a data-centric approach where we adopt a single model architecture, the Table Transformer (TATR), that we hold fixed throughout. Baseline exact match accuracy for TATR evaluated on the ICDAR-2013 benchmark is 65% when trained on PubTables-1M, 42% when trained on FinTabNet, and 69% combined. After reducing annotation mistakes and inter-dataset inconsistency, performance of TATR evaluated on ICDAR-2013 increases substantially to 75% when trained on PubTables-1M, 65% when trained on FinTabNet, and 81% combined. We show through ablations over the modification steps that canonicalization of the table annotations has a significantly positive effect on performance, while other choices balance necessary trade-offs that arise when deciding a benchmark dataset's final composition. Overall we believe our work has significant implications for benchmark design for TSR and potentially other tasks as well. All dataset processing and training code will be released.

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table separation line prediction as a line regression problem instead of an image segmentation problem and propose a new two-stage DETR based separator prediction approach, dubbed Separator REgression TRansformer (SepRETR), to predict separation lines from table images directly. To make the two-stage DETR framework work efficiently and effectively for the separation line prediction task, we propose two improvements: 1) A prior-enhanced matching strategy to solve the slow convergence issue of DETR; 2) A new cross attention module to sample features from a high-resolution convolutional feature map directly so that high localization accuracy is achieved with low computational cost. After separation line prediction, a simple relation network based cell merging module is used to recover spanning cells. With these new techniques, our TSRFormer achieves state-of-the-art performance on several benchmark datasets, including SciTSR, PubTabNet and WTW. Furthermore, we have validated the robustness of our approach to tables with complex structures, borderless cells, large blank spaces, empty or spanning cells as well as distorted or even curved shapes on a more challenging real-world in-house dataset.

Extracting tables from documents is a crucial task in any document conversion pipeline. Recently, transformer-based models have demonstrated that table-structure can be recognized with impressive accuracy using Image-to-Markup-Sequence (Im2Seq) approaches. Taking only the image of a table, such models predict a sequence of tokens (e.g. in HTML, LaTeX) which represent the structure of the table. Since the token representation of the table structure has a significant impact on the accuracy and run-time performance of any Im2Seq model, we investigate in this paper how table-structure representation can be optimised. We propose a new, optimised table-structure language (OTSL) with a minimized vocabulary and specific rules. The benefits of OTSL are that it reduces the number of tokens to 5 (HTML needs 28+) and shortens the sequence length to half of HTML on average. Consequently, model accuracy improves significantly, inference time is halved compared to HTML-based models, and the predicted table structures are always syntactically correct. This in turn eliminates most post-processing needs.

An automatic table recognition method for interpretation of tabular data in document images majorly involves solving two problems of table detection and table structure recognition. The prior work involved solving both problems independently using two separate approaches. More recent works signify the use of deep learning-based solutions while also attempting to design an end to end solution. In this paper, we present an improved deep learning-based end to end approach for solving both problems of table detection and structure recognition using a single Convolution Neural Network (CNN) model. We propose CascadeTabNet: a Cascade mask Region-based CNN High-Resolution Network (Cascade mask R-CNN HRNet) based model that detects the regions of tables and recognizes the structural body cells from the detected tables at the same time. We evaluate our results on ICDAR 2013, ICDAR 2019 and TableBank public datasets. We achieved 3rd rank in ICDAR 2019 post-competition results for table detection while attaining the best accuracy results for the ICDAR 2013 and TableBank dataset. We also attain the highest accuracy results on the ICDAR 2019 table structure recognition dataset. Additionally, we demonstrate effective transfer learning and image augmentation techniques that enable CNNs to achieve very accurate table detection results. Code and dataset has been made available at: https://github.com/DevashishPrasad/CascadeTabNet

We introduce MonkeyOCR, a vision-language model for document parsing that advances the state of the art by leveraging a Structure-Recognition-Relation (SRR) triplet paradigm. This design simplifies what would otherwise be a complex multi-tool pipeline (as in MinerU's modular approach) and avoids the inefficiencies of processing full pages with giant end-to-end models (e.g., large multimodal LLMs like Qwen-VL). In SRR, document parsing is abstracted into three fundamental questions - "Where is it?" (structure), "What is it?" (recognition), and "How is it organized?" (relation) - corresponding to layout analysis, content identification, and logical ordering. This focused decomposition balances accuracy and speed: it enables efficient, scalable processing without sacrificing precision. To train and evaluate this approach, we introduce the MonkeyDoc (the most comprehensive document parsing dataset to date), with 3.9 million instances spanning over ten document types in both Chinese and English. Experiments show that MonkeyOCR outperforms MinerU by an average of 5.1%, with particularly notable improvements on challenging content such as formulas (+15.0%) and tables (+8.6%). Remarkably, our 3B-parameter model surpasses much larger and top-performing models, including Qwen2.5-VL (72B) and Gemini 2.5 Pro, achieving state-of-the-art average performance on English document parsing tasks. In addition, MonkeyOCR processes multi-page documents significantly faster (0.84 pages per second compared to 0.65 for MinerU and 0.12 for Qwen2.5-VL-7B). The 3B model can be efficiently deployed for inference on a single NVIDIA 3090 GPU. Code and models will be released at https://github.com/Yuliang-Liu/MonkeyOCR.

In this paper, we propose a new class of metric for table structure recognition (TSR) evaluation, called grid table similarity (GriTS). Unlike prior metrics, GriTS evaluates the correctness of a predicted table directly in its natural form as a matrix. To create a similarity measure between matrices, we generalize the two-dimensional largest common substructure (2D-LCS) problem, which is NP-hard, to the 2D most similar substructures (2D-MSS) problem and propose a polynomial-time heuristic for solving it. This algorithm produces both an upper and a lower bound on the true similarity between matrices. We show using evaluation on a large real-world dataset that in practice there is almost no difference between these bounds. We compare GriTS to other metrics and empirically validate that matrix similarity exhibits more desirable behavior than alternatives for TSR performance evaluation. Finally, GriTS unifies all three subtasks of cell topology recognition, cell location recognition, and cell content recognition within the same framework, which simplifies the evaluation and enables more meaningful comparisons across different types of TSR approaches. Code will be released at https://github.com/microsoft/table-transformer.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Table structure recognition is a key task in document analysis. However, the geometric deformation in deformed tables causes a weak correlation between content information and structure, resulting in downstream tasks not being able to obtain accurate content information. To obtain fine-grained spatial coordinates of cells, we propose the OG-HFYOLO model, which enhances the edge response by Gradient Orientation-aware Extractor, combines a Heterogeneous Kernel Cross Fusion module and a scale-aware loss function to adapt to multi-scale objective features, and introduces mask-driven non-maximal suppression in the post-processing, which replaces the traditional bounding box suppression mechanism. Furthermore, we also propose a data generator, filling the gap in the dataset for fine-grained deformation table cell spatial coordinate localization, and derive a large-scale dataset named Deformation Wired Table (DWTAL). Experiments show that our proposed model demonstrates excellent segmentation accuracy on all mainstream instance segmentation models. The dataset and the source code are open source: https://github.com/justliulong/OGHFYOLO.

We introduce Docling, an easy-to-use, self-contained, MIT-licensed, open-source toolkit for document conversion, that can parse several types of popular document formats into a unified, richly structured representation. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table structure recognition (TableFormer), and runs efficiently on commodity hardware in a small resource budget. Docling is released as a Python package and can be used as a Python API or as a CLI tool. Docling's modular architecture and efficient document representation make it easy to implement extensions, new features, models, and customizations. Docling has been already integrated in other popular open-source frameworks (e.g., LangChain, LlamaIndex, spaCy), making it a natural fit for the processing of documents and the development of high-end applications. The open-source community has fully engaged in using, promoting, and developing for Docling, which gathered 10k stars on GitHub in less than a month and was reported as the No. 1 trending repository in GitHub worldwide in November 2024.

This technical report introduces Docling, an easy to use, self-contained, MIT-licensed open-source package for PDF document conversion. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table structure recognition (TableFormer), and runs efficiently on commodity hardware in a small resource budget. The code interface allows for easy extensibility and addition of new features and models.

Recently, significant progress has been made applying machine learning to the problem of table structure inference and extraction from unstructured documents. However, one of the greatest challenges remains the creation of datasets with complete, unambiguous ground truth at scale. To address this, we develop a new, more comprehensive dataset for table extraction, called PubTables-1M. PubTables-1M contains nearly one million tables from scientific articles, supports multiple input modalities, and contains detailed header and location information for table structures, making it useful for a wide variety of modeling approaches. It also addresses a significant source of ground truth inconsistency observed in prior datasets called oversegmentation, using a novel canonicalization procedure. We demonstrate that these improvements lead to a significant increase in training performance and a more reliable estimate of model performance at evaluation for table structure recognition. Further, we show that transformer-based object detection models trained on PubTables-1M produce excellent results for all three tasks of detection, structure recognition, and functional analysis without the need for any special customization for these tasks. Data and code will be released at https://github.com/microsoft/table-transformer.

PaliGemma 2 is an upgrade of the PaliGemma open Vision-Language Model (VLM) based on the Gemma 2 family of language models. We combine the SigLIP-So400m vision encoder that was also used by PaliGemma with the whole range of Gemma 2 models, from the 2B one all the way up to the 27B model. We train these models at three resolutions (224px, 448px, and 896px) in multiple stages to equip them with broad knowledge for transfer via fine-tuning. The resulting family of base models covering different model sizes and resolutions allows us to investigate factors impacting transfer performance (such as learning rate) and to analyze the interplay between the type of task, model size, and resolution. We further increase the number and breadth of transfer tasks beyond the scope of PaliGemma including different OCR-related tasks such as table structure recognition, molecular structure recognition, music score recognition, as well as long fine-grained captioning and radiography report generation, on which PaliGemma 2 obtains state-of-the-art results.

Recent large language models (LLMs) have advanced table understanding capabilities but rely on converting tables into text sequences. While multimodal large language models (MLLMs) enable direct visual processing, they face limitations in handling scientific tables due to fixed input image resolutions and insufficient numerical reasoning capabilities. We present a comprehensive framework for multimodal scientific table understanding and reasoning with dynamic input image resolutions. Our framework consists of three key components: (1) MMSci-Pre, a domain-specific table structure learning dataset of 52K scientific table structure recognition samples, (2) MMSci-Ins, an instruction tuning dataset with 12K samples across three table-based tasks, and (3) MMSci-Eval, a benchmark with 3,114 testing samples specifically designed to evaluate numerical reasoning capabilities. Extensive experiments demonstrate that our domain-specific approach with 52K scientific table images achieves superior performance compared to 150K general-domain tables, highlighting the importance of data quality over quantity. Our proposed table-based MLLMs with dynamic input resolutions show significant improvements in both general table understanding and numerical reasoning capabilities, with strong generalisation to held-out datasets. Our code and data are publicly available at https://github.com/Bernard-Yang/MMSci_Table.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep learning framework that unifies molecule detection, reaction diagram parsing, and optical chemical structure recognition (OCSR) into a single pipeline for automating the extraction of chemical data directly from page-level documents. Recognizing the lack of a standard page-level benchmark and evaluation metric, we also present a testset of 550 pages annotated with molecule bounding boxes, reaction labels, and MOLfiles, along with a novel evaluation metric. Experimental results demonstrate that MolMole outperforms existing toolkits on both our benchmark and public datasets. The benchmark testset will be publicly available, and the MolMole toolkit will be accessible soon through an interactive demo on the LG AI Research website. For commercial inquiries, please contact us at mailto:[email protected]{contact\[email protected]}.

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both tasks in a unified way. We define the task of Contextualized Table Extraction (CTE), which aims to extract and define the structure of tables considering the textual context of the document. The dataset comprises 75k fully annotated pages of scientific papers, including more than 35k tables. Data are gathered from PubMed Central, merging the information provided by annotations in the PubTables-1M and PubLayNet datasets. The dataset can support CTE and adds new classes to the original ones. The generated annotations can be used to develop end-to-end pipelines for various tasks, including document layout analysis, table detection, structure recognition, and functional analysis. We formally define CTE and evaluation metrics, showing which subtasks can be tackled, describing advantages, limitations, and future works of this collection of data. Annotations and code will be accessible a https://github.com/AILab-UniFI/cte-dataset.

Tables contain factual and quantitative data accompanied by various structures and contents that pose challenges for machine comprehension. Previous methods generally design task-specific architectures and objectives for individual tasks, resulting in modal isolation and intricate workflows. In this paper, we present a novel large vision-language model, TabPedia, equipped with a concept synergy mechanism. In this mechanism, all the involved diverse visual table understanding (VTU) tasks and multi-source visual embeddings are abstracted as concepts. This unified framework allows TabPedia to seamlessly integrate VTU tasks, such as table detection, table structure recognition, table querying, and table question answering, by leveraging the capabilities of large language models (LLMs). Moreover, the concept synergy mechanism enables table perception-related and comprehension-related tasks to work in harmony, as they can effectively leverage the needed clues from the corresponding source perception embeddings. Furthermore, to better evaluate the VTU task in real-world scenarios, we establish a new and comprehensive table VQA benchmark, ComTQA, featuring approximately 9,000 QA pairs. Extensive quantitative and qualitative experiments on both table perception and comprehension tasks, conducted across various public benchmarks, validate the effectiveness of our TabPedia. The superior performance further confirms the feasibility of using LLMs for understanding visual tables when all concepts work in synergy. The benchmark ComTQA has been open-sourced at https://huggingface.co/datasets/ByteDance/ComTQA. The source code and model will be released later.

In this paper, we establish a benchmark for table visual question answering, referred to as the TableVQA-Bench, derived from pre-existing table question-answering (QA) and table structure recognition datasets. It is important to note that existing datasets have not incorporated images or QA pairs, which are two crucial components of TableVQA. As such, the primary objective of this paper is to obtain these necessary components. Specifically, images are sourced either through the application of a stylesheet or by employing the proposed table rendering system. QA pairs are generated by exploiting the large language model (LLM) where the input is a text-formatted table. Ultimately, the completed TableVQA-Bench comprises 1,500 QA pairs. We comprehensively compare the performance of various multi-modal large language models (MLLMs) on TableVQA-Bench. GPT-4V achieves the highest accuracy among commercial and open-sourced MLLMs from our experiments. Moreover, we discover that the number of vision queries plays a significant role in TableVQA performance. To further analyze the capabilities of MLLMs in comparison to their LLM backbones, we investigate by presenting image-formatted tables to MLLMs and text-formatted tables to LLMs, respectively. Our findings suggest that processing visual inputs is more challenging than text inputs, as evidenced by the lower performance of MLLMs, despite generally requiring higher computational costs than LLMs. The proposed TableVQA-Bench and evaluation codes are available at https://github.com/naver-ai/tablevqabench{https://github.com/naver-ai/tablevqabench}.

In this paper, we present StrucTexTv2, an effective document image pre-training framework, by performing masked visual-textual prediction. It consists of two self-supervised pre-training tasks: masked image modeling and masked language modeling, based on text region-level image masking. The proposed method randomly masks some image regions according to the bounding box coordinates of text words. The objectives of our pre-training tasks are reconstructing the pixels of masked image regions and the corresponding masked tokens simultaneously. Hence the pre-trained encoder can capture more textual semantics in comparison to the masked image modeling that usually predicts the masked image patches. Compared to the masked multi-modal modeling methods for document image understanding that rely on both the image and text modalities, StrucTexTv2 models image-only input and potentially deals with more application scenarios free from OCR pre-processing. Extensive experiments on mainstream benchmarks of document image understanding demonstrate the effectiveness of StrucTexTv2. It achieves competitive or even new state-of-the-art performance in various downstream tasks such as image classification, layout analysis, table structure recognition, document OCR, and information extraction under the end-to-end scenario.

Spoken language understanding (SLU) is a structure prediction task in the field of speech. Recently, many works on SLU that treat it as a sequence-to-sequence task have achieved great success. However, This method is not suitable for simultaneous speech recognition and understanding. In this paper, we propose a joint speech recognition and structure learning framework (JSRSL), an end-to-end SLU model based on span, which can accurately transcribe speech and extract structured content simultaneously. We conduct experiments on name entity recognition and intent classification using the Chinese dataset AISHELL-NER and the English dataset SLURP. The results show that our proposed method not only outperforms the traditional sequence-to-sequence method in both transcription and extraction capabilities but also achieves state-of-the-art performance on the two datasets.

Existing visual place recognition (VPR) datasets predominantly rely on vehicle-mounted imagery, lack multimodal diversity and underrepresent dense, mixed-use street-level spaces, especially in non-Western urban contexts. To address these gaps, we introduce MMS-VPR, a large-scale multimodal dataset for street-level place recognition in complex, pedestrian-only environments. The dataset comprises 78,575 annotated images and 2,512 video clips captured across 207 locations in a ~70,800 m^2 open-air commercial district in Chengdu, China. Each image is labeled with precise GPS coordinates, timestamp, and textual metadata, and covers varied lighting conditions, viewpoints, and timeframes. MMS-VPR follows a systematic and replicable data collection protocol with minimal device requirements, lowering the barrier for scalable dataset creation. Importantly, the dataset forms an inherent spatial graph with 125 edges, 81 nodes, and 1 subgraph, enabling structure-aware place recognition. We further define two application-specific subsets -- Dataset_Edges and Dataset_Points -- to support fine-grained and graph-based evaluation tasks. Extensive benchmarks using conventional VPR models, graph neural networks, and multimodal baselines show substantial improvements when leveraging multimodal and structural cues. MMS-VPR facilitates future research at the intersection of computer vision, geospatial understanding, and multimodal reasoning. The dataset is publicly available at https://huggingface.co/datasets/Yiwei-Ou/MMS-VPR.

Existing skeleton-based action recognition methods typically follow a centralized learning paradigm, which can pose privacy concerns when exposing human-related videos. Federated Learning (FL) has attracted much attention due to its outstanding advantages in privacy-preserving. However, directly applying FL approaches to skeleton videos suffers from unstable training. In this paper, we investigate and discover that the heterogeneous human topology graph structure is the crucial factor hindering training stability. To address this limitation, we pioneer a novel Federated Skeleton-based Action Recognition (FSAR) paradigm, which enables the construction of a globally generalized model without accessing local sensitive data. Specifically, we introduce an Adaptive Topology Structure (ATS), separating generalization and personalization by learning a domain-invariant topology shared across clients and a domain-specific topology decoupled from global model aggregation.Furthermore, we explore Multi-grain Knowledge Distillation (MKD) to mitigate the discrepancy between clients and server caused by distinct updating patterns through aligning shallow block-wise motion features. Extensive experiments on multiple datasets demonstrate that FSAR outperforms state-of-the-art FL-based methods while inherently protecting privacy.

Understanding objects is a central building block of artificial intelligence, especially for embodied AI. Even though object recognition excels with deep learning, current machines still struggle to learn higher-level knowledge, e.g., what attributes an object has, and what can we do with an object. In this work, we propose a challenging Object Concept Learning (OCL) task to push the envelope of object understanding. It requires machines to reason out object affordances and simultaneously give the reason: what attributes make an object possesses these affordances. To support OCL, we build a densely annotated knowledge base including extensive labels for three levels of object concept (category, attribute, affordance), and the causal relations of three levels. By analyzing the causal structure of OCL, we present a baseline, Object Concept Reasoning Network (OCRN). It leverages causal intervention and concept instantiation to infer the three levels following their causal relations. In experiments, OCRN effectively infers the object knowledge while following the causalities well. Our data and code are available at https://mvig-rhos.com/ocl.

Formula recognition presents significant challenges due to the complicated structure and varied notation of mathematical expressions. Despite continuous advancements in formula recognition models, the evaluation metrics employed by these models, such as BLEU and Edit Distance, still exhibit notable limitations. They overlook the fact that the same formula has diverse representations and is highly sensitive to the distribution of training data, thereby causing the unfairness in formula recognition evaluation. To this end, we propose a Character Detection Matching (CDM) metric, ensuring the evaluation objectivity by designing a image-level rather than LaTex-level metric score. Specifically, CDM renders both the model-predicted LaTeX and the ground-truth LaTeX formulas into image-formatted formulas, then employs visual feature extraction and localization techniques for precise character-level matching, incorporating spatial position information. Such a spatially-aware and character-matching method offers a more accurate and equitable evaluation compared with previous BLEU and Edit Distance metrics that rely solely on text-based character matching. Experimentally, we evaluated various formula recognition models using CDM, BLEU, and ExpRate metrics. Their results demonstrate that the CDM aligns more closely with human evaluation standards and provides a fairer comparison across different models by eliminating discrepancies caused by diverse formula representations.

To overcome the limitations and challenges of current automatic table data annotation methods and random table data synthesis approaches, we propose a novel method for synthesizing annotation data specifically designed for table recognition. This method utilizes the structure and content of existing complex tables, facilitating the efficient creation of tables that closely replicate the authentic styles found in the target domain. By leveraging the actual structure and content of tables from Chinese financial announcements, we have developed the first extensive table annotation dataset in this domain. We used this dataset to train several recent deep learning-based end-to-end table recognition models. Additionally, we have established the inaugural benchmark for real-world complex tables in the Chinese financial announcement domain, using it to assess the performance of models trained on our synthetic data, thereby effectively validating our method's practicality and effectiveness. Furthermore, we applied our synthesis method to augment the FinTabNet dataset, extracted from English financial announcements, by increasing the proportion of tables with multiple spanning cells to introduce greater complexity. Our experiments show that models trained on this augmented dataset achieve comprehensive improvements in performance, especially in the recognition of tables with multiple spanning cells.

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

Convolution is a broadly useful operation with applications including signal processing, machine learning, probability, optics, polynomial multiplication, and efficient parsing. Usually, however, this operation is understood and implemented in more specialized forms, hiding commonalities and limiting usefulness. This paper formulates convolution in the common algebraic framework of semirings and semimodules and populates that framework with various representation types. One of those types is the grand abstract template and itself generalizes to the free semimodule monad. Other representations serve varied uses and performance trade-offs, with implementations calculated from simple and regular specifications. Of particular interest is Brzozowski's method for regular expression matching. Uncovering the method's essence frees it from syntactic manipulations, while generalizing from boolean to weighted membership (such as multisets and probability distributions) and from sets to n-ary relations. The classic trie data structure then provides an elegant and efficient alternative to syntax. Pleasantly, polynomial arithmetic requires no additional implementation effort, works correctly with a variety of representations, and handles multivariate polynomials and power series with ease. Image convolution also falls out as a special case.

Typical text recognition methods rely on an encoder-decoder structure, in which the encoder extracts features from an image, and the decoder produces recognized text from these features. In this study, we propose a simpler and more effective method for text recognition, known as the Decoder-only Transformer for Optical Character Recognition (DTrOCR). This method uses a decoder-only Transformer to take advantage of a generative language model that is pre-trained on a large corpus. We examined whether a generative language model that has been successful in natural language processing can also be effective for text recognition in computer vision. Our experiments demonstrated that DTrOCR outperforms current state-of-the-art methods by a large margin in the recognition of printed, handwritten, and scene text in both English and Chinese.

Video-based gait recognition has achieved impressive results in constrained scenarios. However, visual cameras neglect human 3D structure information, which limits the feasibility of gait recognition in the 3D wild world. Instead of extracting gait features from images, this work explores precise 3D gait features from point clouds and proposes a simple yet efficient 3D gait recognition framework, termed LidarGait. Our proposed approach projects sparse point clouds into depth maps to learn the representations with 3D geometry information, which outperforms existing point-wise and camera-based methods by a significant margin. Due to the lack of point cloud datasets, we built the first large-scale LiDAR-based gait recognition dataset, SUSTech1K, collected by a LiDAR sensor and an RGB camera. The dataset contains 25,239 sequences from 1,050 subjects and covers many variations, including visibility, views, occlusions, clothing, carrying, and scenes. Extensive experiments show that (1) 3D structure information serves as a significant feature for gait recognition. (2) LidarGait outperforms existing point-based and silhouette-based methods by a significant margin, while it also offers stable cross-view results. (3) The LiDAR sensor is superior to the RGB camera for gait recognition in the outdoor environment. The source code and dataset have been made available at https://lidargait.github.io.

Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target labels is unknown. Residual network is a new structure of convolutional neural network and works well in various computer vision tasks. In this paper, we take advantage of the architectures mentioned above to create a new network for handwritten digit string recognition. First we design a residual network to extract features from input images, then we employ a RNN to model the contextual information within feature sequences and predict recognition results. At the top of this network, a standard CTC is applied to calculate the loss and yield the final results. These three parts compose an end-to-end trainable network. The proposed new architecture achieves the highest performances on ORAND-CAR-A and ORAND-CAR-B with recognition rates 89.75% and 91.14%, respectively. In addition, the experiments on a generated captcha dataset which has much longer string length show the potential of the proposed network to handle long strings.

The widely studied task of Natural Language Inference (NLI) requires a system to recognize whether one piece of text is textually entailed by another, i.e. whether the entirety of its meaning can be inferred from the other. In current NLI datasets and models, textual entailment relations are typically defined on the sentence- or paragraph-level. However, even a simple sentence often contains multiple propositions, i.e. distinct units of meaning conveyed by the sentence. As these propositions can carry different truth values in the context of a given premise, we argue for the need to recognize the textual entailment relation of each proposition in a sentence individually. We propose PropSegmEnt, a corpus of over 35K propositions annotated by expert human raters. Our dataset structure resembles the tasks of (1) segmenting sentences within a document to the set of propositions, and (2) classifying the entailment relation of each proposition with respect to a different yet topically-aligned document, i.e. documents describing the same event or entity. We establish strong baselines for the segmentation and entailment tasks. Through case studies on summary hallucination detection and document-level NLI, we demonstrate that our conceptual framework is potentially useful for understanding and explaining the compositionality of NLI labels.

Low-resource speech recognition has been long-suffering from insufficient training data. In this paper, we propose an approach that leverages neighboring languages to improve low-resource scenario performance, founded on the hypothesis that similar linguistic units in neighboring languages exhibit comparable term frequency distributions, which enables us to construct a Huffman tree for performing multilingual hierarchical Softmax decoding. This hierarchical structure enables cross-lingual knowledge sharing among similar tokens, thereby enhancing low-resource training outcomes. Empirical analyses demonstrate that our method is effective in improving the accuracy and efficiency of low-resource speech recognition.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

Nowadays, Natural Language Processing (NLP) is an important tool for most people's daily life routines, ranging from understanding speech, translation, named entity recognition (NER), and text categorization, to generative text models such as ChatGPT. Due to the existence of big data and consequently large corpora for widely used languages like English, Spanish, Turkish, Persian, and many more, these applications have been developed accurately. However, the Kurdish language still requires more corpora and large datasets to be included in NLP applications. This is because Kurdish has a rich linguistic structure, varied dialects, and a limited dataset, which poses unique challenges for Kurdish NLP (KNLP) application development. While several studies have been conducted in KNLP for various applications, Kurdish NER (KNER) remains a challenge for many KNLP tasks, including text analysis and classification. In this work, we address this limitation by proposing a methodology for fine-tuning the pre-trained RoBERTa model for KNER. To this end, we first create a Kurdish corpus, followed by designing a modified model architecture and implementing the training procedures. To evaluate the trained model, a set of experiments is conducted to demonstrate the performance of the KNER model using different tokenization methods and trained models. The experimental results show that fine-tuned RoBERTa with the SentencePiece tokenization method substantially improves KNER performance, achieving a 12.8% improvement in F1-score compared to traditional models, and consequently establishes a new benchmark for KNLP.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Recent progress in using recurrent neural networks (RNNs) for image description has motivated the exploration of their application for video description. However, while images are static, working with videos requires modeling their dynamic temporal structure and then properly integrating that information into a natural language description. In this context, we propose an approach that successfully takes into account both the local and global temporal structure of videos to produce descriptions. First, our approach incorporates a spatial temporal 3-D convolutional neural network (3-D CNN) representation of the short temporal dynamics. The 3-D CNN representation is trained on video action recognition tasks, so as to produce a representation that is tuned to human motion and behavior. Second we propose a temporal attention mechanism that allows to go beyond local temporal modeling and learns to automatically select the most relevant temporal segments given the text-generating RNN. Our approach exceeds the current state-of-art for both BLEU and METEOR metrics on the Youtube2Text dataset. We also present results on a new, larger and more challenging dataset of paired video and natural language descriptions.

Underwater acoustic target recognition is a difficult task owing to the intricate nature of underwater acoustic signals. The complex underwater environments, unpredictable transmission channels, and dynamic motion states greatly impact the real-world underwater acoustic signals, and may even obscure the intrinsic characteristics related to targets. Consequently, the data distribution of underwater acoustic signals exhibits high intra-class diversity, thereby compromising the accuracy and robustness of recognition systems.To address these issues, this work proposes a convolution-based mixture of experts (CMoE) that recognizes underwater targets in a fine-grained manner. The proposed technique introduces multiple expert layers as independent learners, along with a routing layer that determines the assignment of experts according to the characteristics of inputs. This design allows the model to utilize independent parameter spaces, facilitating the learning of complex underwater signals with high intra-class diversity. Furthermore, this work optimizes the CMoE structure by balancing regularization and an optional residual module. To validate the efficacy of our proposed techniques, we conducted detailed experiments and visualization analyses on three underwater acoustic databases across several acoustic features. The experimental results demonstrate that our CMoE consistently achieves significant performance improvements, delivering superior recognition accuracy when compared to existing advanced methods.

Recently, MLP-based vision backbones have achieved promising performance in several visual recognition tasks. However, the existing MLP-based methods directly aggregate tokens with static weights, leaving the adaptability to different images untouched. Moreover, Recent research demonstrates that MLP-Transformer is great at creating long-range dependencies but ineffective at catching high frequencies that primarily transmit local information, which prevents it from applying to the downstream dense prediction tasks, such as semantic segmentation. To address these challenges, we propose a content-adaptive yet computationally efficient structure, dubbed Dynamic Spectrum Mixer (DSM). The DSM represents token interactions in the frequency domain by employing the Discrete Cosine Transform, which can learn long-term spatial dependencies with log-linear complexity. Furthermore, a dynamic spectrum weight generation layer is proposed as the spectrum bands selector, which could emphasize the informative frequency bands while diminishing others. To this end, the technique can efficiently learn detailed features from visual input that contains both high- and low-frequency information. Extensive experiments show that DSM is a powerful and adaptable backbone for a range of visual recognition tasks. Particularly, DSM outperforms previous transformer-based and MLP-based models, on image classification, object detection, and semantic segmentation tasks, such as 83.8 \% top-1 accuracy on ImageNet, and 49.9 \% mIoU on ADE20K.

Model pre-training is essential in human-centric perception. In this paper, we first introduce masked image modeling (MIM) as a pre-training approach for this task. Upon revisiting the MIM training strategy, we reveal that human structure priors offer significant potential. Motivated by this insight, we further incorporate an intuitive human structure prior - human parts - into pre-training. Specifically, we employ this prior to guide the mask sampling process. Image patches, corresponding to human part regions, have high priority to be masked out. This encourages the model to concentrate more on body structure information during pre-training, yielding substantial benefits across a range of human-centric perception tasks. To further capture human characteristics, we propose a structure-invariant alignment loss that enforces different masked views, guided by the human part prior, to be closely aligned for the same image. We term the entire method as HAP. HAP simply uses a plain ViT as the encoder yet establishes new state-of-the-art performance on 11 human-centric benchmarks, and on-par result on one dataset. For example, HAP achieves 78.1% mAP on MSMT17 for person re-identification, 86.54% mA on PA-100K for pedestrian attribute recognition, 78.2% AP on MS COCO for 2D pose estimation, and 56.0 PA-MPJPE on 3DPW for 3D pose and shape estimation.

The Conformer has become the most popular encoder model for automatic speech recognition (ASR). It adds convolution modules to a transformer to learn both local and global dependencies. In this work we describe a faster, more memory-efficient, and better-performing transformer, called Zipformer. Modeling changes include: 1) a U-Net-like encoder structure where middle stacks operate at lower frame rates; 2) reorganized block structure with more modules, within which we re-use attention weights for efficiency; 3) a modified form of LayerNorm called BiasNorm allows us to retain some length information; 4) new activation functions SwooshR and SwooshL work better than Swish. We also propose a new optimizer, called ScaledAdam, which scales the update by each tensor's current scale to keep the relative change about the same, and also explictly learns the parameter scale. It achieves faster convergence and better performance than Adam. Extensive experiments on LibriSpeech, Aishell-1, and WenetSpeech datasets demonstrate the effectiveness of our proposed Zipformer over other state-of-the-art ASR models. Our code is publicly available at https://github.com/k2-fsa/icefall.

A core process in human cognition is analogical mapping: the ability to identify a similar relational structure between different situations. We introduce a novel task, Visual Analogies of Situation Recognition, adapting the classical word-analogy task into the visual domain. Given a triplet of images, the task is to select an image candidate B' that completes the analogy (A to A' is like B to what?). Unlike previous work on visual analogy that focused on simple image transformations, we tackle complex analogies requiring understanding of scenes. We leverage situation recognition annotations and the CLIP model to generate a large set of 500k candidate analogies. Crowdsourced annotations for a sample of the data indicate that humans agree with the dataset label ~80% of the time (chance level 25%). Furthermore, we use human annotations to create a gold-standard dataset of 3,820 validated analogies. Our experiments demonstrate that state-of-the-art models do well when distractors are chosen randomly (~86%), but struggle with carefully chosen distractors (~53%, compared to 90% human accuracy). We hope our dataset will encourage the development of new analogy-making models. Website: https://vasr-dataset.github.io/

Context-aware STR methods typically use internal autoregressive (AR) language models (LM). Inherent limitations of AR models motivated two-stage methods which employ an external LM. The conditional independence of the external LM on the input image may cause it to erroneously rectify correct predictions, leading to significant inefficiencies. Our method, PARSeq, learns an ensemble of internal AR LMs with shared weights using Permutation Language Modeling. It unifies context-free non-AR and context-aware AR inference, and iterative refinement using bidirectional context. Using synthetic training data, PARSeq achieves state-of-the-art (SOTA) results in STR benchmarks (91.9% accuracy) and more challenging datasets. It establishes new SOTA results (96.0% accuracy) when trained on real data. PARSeq is optimal on accuracy vs parameter count, FLOPS, and latency because of its simple, unified structure and parallel token processing. Due to its extensive use of attention, it is robust on arbitrarily-oriented text which is common in real-world images. Code, pretrained weights, and data are available at: https://github.com/baudm/parseq.

The increasing diversity of languages used on the web introduces a new level of complexity to Information Retrieval (IR) systems. We can no longer assume that textual content is written in one language or even the same language family. In this paper, we demonstrate how to build massive multilingual annotators with minimal human expertise and intervention. We describe a system that builds Named Entity Recognition (NER) annotators for 40 major languages using Wikipedia and Freebase. Our approach does not require NER human annotated datasets or language specific resources like treebanks, parallel corpora, and orthographic rules. The novelty of approach lies therein - using only language agnostic techniques, while achieving competitive performance. Our method learns distributed word representations (word embeddings) which encode semantic and syntactic features of words in each language. Then, we automatically generate datasets from Wikipedia link structure and Freebase attributes. Finally, we apply two preprocessing stages (oversampling and exact surface form matching) which do not require any linguistic expertise. Our evaluation is two fold: First, we demonstrate the system performance on human annotated datasets. Second, for languages where no gold-standard benchmarks are available, we propose a new method, distant evaluation, based on statistical machine translation.

This paper presents OmniDataComposer, an innovative approach for multimodal data fusion and unlimited data generation with an intent to refine and uncomplicate interplay among diverse data modalities. Coming to the core breakthrough, it introduces a cohesive data structure proficient in processing and merging multimodal data inputs, which include video, audio, and text. Our crafted algorithm leverages advancements across multiple operations such as video/image caption extraction, dense caption extraction, Automatic Speech Recognition (ASR), Optical Character Recognition (OCR), Recognize Anything Model(RAM), and object tracking. OmniDataComposer is capable of identifying over 6400 categories of objects, substantially broadening the spectrum of visual information. It amalgamates these diverse modalities, promoting reciprocal enhancement among modalities and facilitating cross-modal data correction. The final output metamorphoses each video input into an elaborate sequential document, virtually transmuting videos into thorough narratives, making them easier to be processed by large language models. Future prospects include optimizing datasets for each modality to encourage unlimited data generation. This robust base will offer priceless insights to models like ChatGPT, enabling them to create higher quality datasets for video captioning and easing question-answering tasks based on video content. OmniDataComposer inaugurates a new stage in multimodal learning, imparting enormous potential for augmenting AI's understanding and generation of complex, real-world data.

The Transformer architecture model, based on self-attention and multi-head attention, has achieved remarkable success in offline end-to-end Automatic Speech Recognition (ASR). However, self-attention and multi-head attention cannot be easily applied for streaming or online ASR. For self-attention in Transformer ASR, the softmax normalization function-based attention mechanism makes it impossible to highlight important speech information. For multi-head attention in Transformer ASR, it is not easy to model monotonic alignments in different heads. To overcome these two limits, we integrate sparse attention and monotonic attention into Transformer-based ASR. The sparse mechanism introduces a learned sparsity scheme to enable each self-attention structure to fit the corresponding head better. The monotonic attention deploys regularization to prune redundant heads for the multi-head attention structure. The experiments show that our method can effectively improve the attention mechanism on widely used benchmarks of speech recognition.

Scene Text Recognition (STR) is an important and challenging upstream task for building structured information databases, that involves recognizing text within images of natural scenes. Although current state-of-the-art (SOTA) models for STR exhibit high performance, they typically suffer from low inference efficiency due to their reliance on hybrid architectures comprised of visual encoders and sequence decoders. In this work, we propose a VIsion Permutable extractor for fast and efficient Scene Text Recognition (SVIPTR), which achieves an impressive balance between high performance and rapid inference speeds in the domain of STR. Specifically, SVIPTR leverages a visual-semantic extractor with a pyramid structure, characterized by the Permutation and combination of local and global self-attention layers. This design results in a lightweight and efficient model and its inference is insensitive to input length. Extensive experimental results on various standard datasets for both Chinese and English scene text recognition validate the superiority of SVIPTR. Notably, the SVIPTR-T (Tiny) variant delivers highly competitive accuracy on par with other lightweight models and achieves SOTA inference speeds. Meanwhile, the SVIPTR-L (Large) attains SOTA accuracy in single-encoder-type models, while maintaining a low parameter count and favorable inference speed. Our proposed method provides a compelling solution for the STR challenge, which greatly benefits real-world applications requiring fast and efficient STR. The code is publicly available at https://github.com/cxfyxl/VIPTR.

The Handwritten Mathematical Expression Recognition (HMER) task is a critical branch in the field of OCR. Recent studies have demonstrated that incorporating bidirectional context information significantly improves the performance of HMER models. However, existing methods fail to effectively utilize bidirectional context information during the inference stage. Furthermore, current bidirectional training methods are primarily designed for string decoders and cannot adequately generalize to tree decoders, which offer superior generalization capabilities and structural analysis capacity. In order to overcome these limitations, we propose the Mirror-Flipped Symbol Layout Tree (MF-SLT) and Bidirectional Asynchronous Training (BAT) structure. Our method extends the bidirectional training strategy to the tree decoder, allowing for more effective training by leveraging bidirectional information. Additionally, we analyze the impact of the visual and linguistic perception of the HMER model separately and introduce the Shared Language Modeling (SLM) mechanism. Through the SLM, we enhance the model's robustness and generalization when dealing with visual ambiguity, particularly in scenarios with abundant training data. Our approach has been validated through extensive experiments, demonstrating its ability to achieve new state-of-the-art results on the CROHME 2014, 2016, and 2019 datasets, as well as the HME100K dataset. The code used in our experiments will be publicly available.

Robust 3D perception under corruption has become an essential task for the realm of 3D vision. While current data augmentation techniques usually perform random transformations on all point cloud objects in an offline way and ignore the structure of the samples, resulting in over-or-under enhancement. In this work, we propose an alternative to make sample-adaptive transformations based on the structure of the sample to cope with potential corruption via an auto-augmentation framework, named as AdaptPoint. Specially, we leverage a imitator, consisting of a Deformation Controller and a Mask Controller, respectively in charge of predicting deformation parameters and producing a per-point mask, based on the intrinsic structural information of the input point cloud, and then conduct corruption simulations on top. Then a discriminator is utilized to prevent the generation of excessive corruption that deviates from the original data distribution. In addition, a perception-guidance feedback mechanism is incorporated to guide the generation of samples with appropriate difficulty level. Furthermore, to address the paucity of real-world corrupted point cloud, we also introduce a new dataset ScanObjectNN-C, that exhibits greater similarity to actual data in real-world environments, especially when contrasted with preceding CAD datasets. Experiments show that our method achieves state-of-the-art results on multiple corruption benchmarks, including ModelNet-C, our ScanObjectNN-C, and ShapeNet-C.

Due to the absence of explicit connectives, implicit discourse relation recognition (IDRR) remains a challenging task in discourse analysis. The critical step for IDRR is to learn high-quality discourse relation representations between two arguments. Recent methods tend to integrate the whole hierarchical information of senses into discourse relation representations for multi-level sense recognition. Nevertheless, they insufficiently incorporate the static hierarchical structure containing all senses (defined as global hierarchy), and ignore the hierarchical sense label sequence corresponding to each instance (defined as local hierarchy). For the purpose of sufficiently exploiting global and local hierarchies of senses to learn better discourse relation representations, we propose a novel GlObal and Local Hierarchy-aware Contrastive Framework (GOLF), to model two kinds of hierarchies with the aid of multi-task learning and contrastive learning. Experimental results on PDTB 2.0 and PDTB 3.0 datasets demonstrate that our method remarkably outperforms current state-of-the-art models at all hierarchical levels. Our code is publicly available at https://github.com/YJiangcm/GOLF_for_IDRR

Handwritten mathematical expression recognition (HMER) is a challenging task that has many potential applications. Recent methods for HMER have achieved outstanding performance with an encoder-decoder architecture. However, these methods adhere to the paradigm that the prediction is made "from one character to another", which inevitably yields prediction errors due to the complicated structures of mathematical expressions or crabbed handwritings. In this paper, we propose a simple and efficient method for HMER, which is the first to incorporate syntax information into an encoder-decoder network. Specifically, we present a set of grammar rules for converting the LaTeX markup sequence of each expression into a parsing tree; then, we model the markup sequence prediction as a tree traverse process with a deep neural network. In this way, the proposed method can effectively describe the syntax context of expressions, alleviating the structure prediction errors of HMER. Experiments on three benchmark datasets demonstrate that our method achieves better recognition performance than prior arts. To further validate the effectiveness of our method, we create a large-scale dataset consisting of 100k handwritten mathematical expression images acquired from ten thousand writers. The source code, new dataset, and pre-trained models of this work will be publicly available.

Scene text recognition (STR) is a challenging task in computer vision due to the large number of possible text appearances in natural scenes. Most STR models rely on synthetic datasets for training since there are no sufficiently big and publicly available labelled real datasets. Since STR models are evaluated using real data, the mismatch between training and testing data distributions results into poor performance of models especially on challenging text that are affected by noise, artifacts, geometry, structure, etc. In this paper, we introduce STRAug which is made of 36 image augmentation functions designed for STR. Each function mimics certain text image properties that can be found in natural scenes, caused by camera sensors, or induced by signal processing operations but poorly represented in the training dataset. When applied to strong baseline models using RandAugment, STRAug significantly increases the overall absolute accuracy of STR models across regular and irregular test datasets by as much as 2.10% on Rosetta, 1.48% on R2AM, 1.30% on CRNN, 1.35% on RARE, 1.06% on TRBA and 0.89% on GCRNN. The diversity and simplicity of API provided by STRAug functions enable easy replication and validation of existing data augmentation methods for STR. STRAug is available at https://github.com/roatienza/straug.

Deep convolutional neural networks achieve remarkable visual recognition performance, at the cost of high computational complexity. In this paper, we have a new design of efficient convolutional layers based on three schemes. The 3D convolution operation in a convolutional layer can be considered as performing spatial convolution in each channel and linear projection across channels simultaneously. By unravelling them and arranging the spatial convolution sequentially, the proposed layer is composed of a single intra-channel convolution, of which the computation is negligible, and a linear channel projection. A topological subdivisioning is adopted to reduce the connection between the input channels and output channels. Additionally, we also introduce a spatial "bottleneck" structure that utilizes a convolution-projection-deconvolution pipeline to take advantage of the correlation between adjacent pixels in the input. Our experiments demonstrate that the proposed layers remarkably outperform the standard convolutional layers with regard to accuracy/complexity ratio. Our models achieve similar accuracy to VGG, ResNet-50, ResNet-101 while requiring 42, 4.5, 6.5 times less computation respectively.

We present OpenNER 1.0, a standardized collection of openly available named entity recognition (NER) datasets. OpenNER contains 34 datasets spanning 51 languages, annotated in varying named entity ontologies. We correct annotation format issues, standardize the original datasets into a uniform representation, map entity type names to be more consistent across corpora, and provide the collection in a structure that enables research in multilingual and multi-ontology NER. We provide baseline models using three pretrained multilingual language models to compare the performance of recent models and facilitate future research in NER.

Multi-lingual speech recognition aims to distinguish linguistic expressions in different languages and integrate acoustic processing simultaneously. In contrast, current multi-lingual speech recognition research follows a language-aware paradigm, mainly targeted to improve recognition performance rather than discriminate language characteristics. In this paper, we present a multi-lingual speech recognition network named Mixture-of-Language-Expert(MoLE), which digests speech in a variety of languages. Specifically, MoLE analyzes linguistic expression from input speech in arbitrary languages, activating a language-specific expert with a lightweight language tokenizer. The tokenizer not only activates experts, but also estimates the reliability of the activation. Based on the reliability, the activated expert and the language-agnostic expert are aggregated to represent language-conditioned embedding for efficient speech recognition. Our proposed model is evaluated in 5 languages scenario, and the experimental results show that our structure is advantageous on multi-lingual recognition, especially for speech in low-resource language.

Vision-language models (VLMs) like CLIP have been cherished for their ability to perform zero-shot visual recognition on open-vocabulary concepts. This is achieved by selecting the object category whose textual representation bears the highest similarity with the query image. While successful in some domains, this method struggles with identifying fine-grained entities as well as generalizing to unseen concepts that are not captured by the training distribution. Recent works attempt to mitigate these challenges by integrating category descriptions at test time, albeit yielding modest improvements. We attribute these limited gains to a fundamental misalignment between image and description representations, which is rooted in the pretraining structure of CLIP. In this paper, we propose GRAIN, a new pretraining strategy aimed at aligning representations at both fine and coarse levels simultaneously. Our approach learns to jointly ground textual descriptions in image regions along with aligning overarching captions with global image representations. To drive this pre-training, we leverage frozen Multimodal Large Language Models (MLLMs) to derive large-scale synthetic annotations. We demonstrate the enhanced zero-shot performance of our model compared to current state-of-the art methods across 11 diverse image classification datasets. Additionally, we introduce Products-2023, a newly curated, manually labeled dataset featuring novel concepts, and showcase our model's ability to recognize these concepts by benchmarking on it. Significant improvements achieved by our model on other downstream tasks like retrieval further highlight the superior quality of representations learned by our approach. Code available at https://github.com/shaunak27/grain-clip .

The analysis of patterns of walking is an important area of research that has numerous applications in security, healthcare, sports and human-computer interaction. Lately, walking patterns have been regarded as a unique fingerprinting method for automatic person identification at a distance. In this work, we propose a novel gait recognition architecture called Gait Pyramid Transformer (GaitPT) that leverages pose estimation skeletons to capture unique walking patterns, without relying on appearance information. GaitPT adopts a hierarchical transformer architecture that effectively extracts both spatial and temporal features of movement in an anatomically consistent manner, guided by the structure of the human skeleton. Our results show that GaitPT achieves state-of-the-art performance compared to other skeleton-based gait recognition works, in both controlled and in-the-wild scenarios. GaitPT obtains 82.6% average accuracy on CASIA-B, surpassing other works by a margin of 6%. Moreover, it obtains 52.16% Rank-1 accuracy on GREW, outperforming both skeleton-based and appearance-based approaches.

Recently, most handwritten mathematical expression recognition (HMER) methods adopt the encoder-decoder networks, which directly predict the markup sequences from formula images with the attention mechanism. However, such methods may fail to accurately read formulas with complicated structure or generate long markup sequences, as the attention results are often inaccurate due to the large variance of writing styles or spatial layouts. To alleviate this problem, we propose an unconventional network for HMER named Counting-Aware Network (CAN), which jointly optimizes two tasks: HMER and symbol counting. Specifically, we design a weakly-supervised counting module that can predict the number of each symbol class without the symbol-level position annotations, and then plug it into a typical attention-based encoder-decoder model for HMER. Experiments on the benchmark datasets for HMER validate that both joint optimization and counting results are beneficial for correcting the prediction errors of encoder-decoder models, and CAN consistently outperforms the state-of-the-art methods. In particular, compared with an encoder-decoder model for HMER, the extra time cost caused by the proposed counting module is marginal. The source code is available at https://github.com/LBH1024/CAN.

The recently proposed Conformer model has become the de facto backbone model for various downstream speech tasks based on its hybrid attention-convolution architecture that captures both local and global features. However, through a series of systematic studies, we find that the Conformer architecture's design choices are not optimal. After re-examining the design choices for both the macro and micro-architecture of Conformer, we propose Squeezeformer which consistently outperforms the state-of-the-art ASR models under the same training schemes. In particular, for the macro-architecture, Squeezeformer incorporates (i) the Temporal U-Net structure which reduces the cost of the multi-head attention modules on long sequences, and (ii) a simpler block structure of multi-head attention or convolution modules followed up by feed-forward module instead of the Macaron structure proposed in Conformer. Furthermore, for the micro-architecture, Squeezeformer (i) simplifies the activations in the convolutional block, (ii) removes redundant Layer Normalization operations, and (iii) incorporates an efficient depthwise down-sampling layer to efficiently sub-sample the input signal. Squeezeformer achieves state-of-the-art results of 7.5%, 6.5%, and 6.0% word-error-rate (WER) on LibriSpeech test-other without external language models, which are 3.1%, 1.4%, and 0.6% better than Conformer-CTC with the same number of FLOPs. Our code is open-sourced and available online.

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its latent states. Its architecture attempts to address two major concerns of variational Bayes RNNs: how can latent variables learn meaningful representations and how can the inference model transfer future observations to the latent variables. PV-RNN does both by introducing adaptive vectors mirroring the training data, whose values can then be adapted differently during evaluation. Moreover, prediction errors during backpropagation, rather than external inputs during the forward computation, are used to convey information to the network about the external data. For testing, we introduce error regression for predicting unseen sequences as inspired by predictive coding that leverages those mechanisms. The model introduces a weighting parameter, the meta-prior, to balance the optimization pressure placed on two terms of a lower bound on the marginal likelihood of the sequential data. We test the model on two datasets with probabilistic structures and show that with high values of the meta-prior the network develops deterministic chaos through which the data's randomness is imitated. For low values, the model behaves as a random process. The network performs best on intermediate values, and is able to capture the latent probabilistic structure with good generalization. Analyzing the meta-prior's impact on the network allows to precisely study the theoretical value and practical benefits of incorporating stochastic dynamics in our model. We demonstrate better prediction performance on a robot imitation task with our model using error regression compared to a standard variational Bayes model lacking such a procedure.

While the Transformer architecture has become the de-facto standard for natural language processing tasks, its applications to computer vision remain limited. In vision, attention is either applied in conjunction with convolutional networks, or used to replace certain components of convolutional networks while keeping their overall structure in place. We show that this reliance on CNNs is not necessary and a pure transformer applied directly to sequences of image patches can perform very well on image classification tasks. When pre-trained on large amounts of data and transferred to multiple mid-sized or small image recognition benchmarks (ImageNet, CIFAR-100, VTAB, etc.), Vision Transformer (ViT) attains excellent results compared to state-of-the-art convolutional networks while requiring substantially fewer computational resources to train.

Understanding human behavior requires measuring behavioral actions. Due to its complexity, behavior is best mapped onto a rich, semantic structure such as language. The recent development of multi-modal large language models (MLLMs) is a promising candidate for a wide range of action understanding tasks. In this work, we focus on evaluating and then improving MLLMs to perform action recognition. We reformulate EPIC-KITCHENS-100, one of the largest and most challenging egocentric action datasets, to the form of video multiple question answering (EPIC-KITCHENS-100-MQA). We show that when we sample difficult incorrect answers as distractors, leading MLLMs struggle to recognize the correct actions. We propose a series of methods that greatly improve the MLLMs' ability to perform action recognition, achieving state-of-the-art on both the EPIC-KITCHENS-100 validation set, as well as outperforming GPT-4o by 21 points in accuracy on EPIC-KITCHENS-100-MQA. Lastly, we show improvements on other action-related video benchmarks such as EgoSchema, PerceptionTest, LongVideoBench, VideoMME and MVBench, suggesting that MLLMs are a promising path forward for complex action tasks. Code and models are available at: https://github.com/AdaptiveMotorControlLab/LLaVAction.

Tactics, Techniques and Procedures (TTPs) represent sophisticated attack patterns in the cybersecurity domain, described encyclopedically in textual knowledge bases. Identifying TTPs in cybersecurity writing, often called TTP mapping, is an important and challenging task. Conventional learning approaches often target the problem in the classical multi-class or multilabel classification setting. This setting hinders the learning ability of the model due to a large number of classes (i.e., TTPs), the inevitable skewness of the label distribution and the complex hierarchical structure of the label space. We formulate the problem in a different learning paradigm, where the assignment of a text to a TTP label is decided by the direct semantic similarity between the two, thus reducing the complexity of competing solely over the large labeling space. To that end, we propose a neural matching architecture with an effective sampling-based learn-to-compare mechanism, facilitating the learning process of the matching model despite constrained resources.

For named entity recognition (NER) in zero-resource languages, utilizing knowledge distillation methods to transfer language-independent knowledge from the rich-resource source languages to zero-resource languages is an effective means. Typically, these approaches adopt a teacher-student architecture, where the teacher network is trained in the source language, and the student network seeks to learn knowledge from the teacher network and is expected to perform well in the target language. Despite the impressive performance achieved by these methods, we argue that they have two limitations. Firstly, the teacher network fails to effectively learn language-independent knowledge shared across languages due to the differences in the feature distribution between the source and target languages. Secondly, the student network acquires all of its knowledge from the teacher network and ignores the learning of target language-specific knowledge. Undesirably, these limitations would hinder the model's performance in the target language. This paper proposes an unsupervised prototype knowledge distillation network (ProKD) to address these issues. Specifically, ProKD presents a contrastive learning-based prototype alignment method to achieve class feature alignment by adjusting the distance among prototypes in the source and target languages, boosting the teacher network's capacity to acquire language-independent knowledge. In addition, ProKD introduces a prototypical self-training method to learn the intrinsic structure of the language by retraining the student network on the target data using samples' distance information from prototypes, thereby enhancing the student network's ability to acquire language-specific knowledge. Extensive experiments on three benchmark cross-lingual NER datasets demonstrate the effectiveness of our approach.

The capability to learn latent representations plays a key role in the effectiveness of recent machine learning methods. An active frontier in representation learning is understanding representations for combinatorial structures which may not admit well-behaved local neighborhoods or distance functions. For example, for polygons, slightly perturbing vertex locations might lead to significant changes in their combinatorial structure and may even lead to invalid polygons. In this paper, we investigate representations to capture the underlying combinatorial structures of polygons. Specifically, we study the open problem of Visibility Reconstruction: Given a visibility graph G, construct a polygon P whose visibility graph is G. We introduce VisDiff, a novel diffusion-based approach to reconstruct a polygon from its given visibility graph G. Our method first estimates the signed distance function (SDF) of P from G. Afterwards, it extracts ordered vertex locations that have the pairwise visibility relationship given by the edges of G. Our main insight is that going through the SDF significantly improves learning for reconstruction. In order to train VisDiff, we make two main contributions: (1) We design novel loss components for computing the visibility in a differentiable manner and (2) create a carefully curated dataset. We use this dataset to benchmark our method and achieve 21% improvement in F1-Score over standard methods. We also demonstrate effective generalization to out-of-distribution polygon types and show that learning a generative model allows us to sample the set of polygons with a given visibility graph. Finally, we extend our method to the related combinatorial problem of reconstruction from a triangulation. We achieve 95% classification accuracy of triangulation edges and a 4% improvement in Chamfer distance compared to current architectures.

Creating machines capable of understanding the world in 3D is essential in assisting designers that build and edit 3D environments and robots navigating and interacting within a three-dimensional space. Inspired by advances in language and image modeling, we investigate the potential of autoregressive models for a new modality: structured 3D scenes. To this end, we propose a unified LLM framework that aligns language, images, and 3D scenes and provide a detailed ''cookbook'' outlining critical design choices for achieving optimal training and performance addressing key questions related to data representation, modality-specific objectives, and more. We evaluate performance across four core 3D tasks -- rendering, recognition, instruction-following, and question-answering -- and four 3D datasets, synthetic and real-world. We extend our approach to reconstruct complex 3D object shapes by enriching our 3D modality with quantized shape encodings, and show our model's effectiveness on real-world 3D object recognition tasks. Project webpage: https://glab-caltech.github.io/kyvo/

This paper announces the early release of SpokesBiz, a freely available corpus of conversational Polish developed within the CLARIN-BIZ project and comprising over 650 hours of recordings. The transcribed recordings have been diarized and manually annotated for punctuation and casing. We outline the general structure and content of the corpus, showcasing selected applications in linguistic research, evaluation and improvement of automatic speech recognition (ASR) systems

Can Transformer perform 2D object- and region-level recognition from a pure sequence-to-sequence perspective with minimal knowledge about the 2D spatial structure? To answer this question, we present You Only Look at One Sequence (YOLOS), a series of object detection models based on the vanilla Vision Transformer with the fewest possible modifications, region priors, as well as inductive biases of the target task. We find that YOLOS pre-trained on the mid-sized ImageNet-1k dataset only can already achieve quite competitive performance on the challenging COCO object detection benchmark, e.g., YOLOS-Base directly adopted from BERT-Base architecture can obtain 42.0 box AP on COCO val. We also discuss the impacts as well as limitations of current pre-train schemes and model scaling strategies for Transformer in vision through YOLOS. Code and pre-trained models are available at https://github.com/hustvl/YOLOS.

Punctuation restoration is an important task in automatic speech recognition (ASR) which aim to restore the syntactic structure of generated ASR texts to improve readability. While punctuated texts are abundant from written documents, the discrepancy between written punctuated texts and ASR texts limits the usability of written texts in training punctuation restoration systems for ASR texts. This paper proposes a reinforcement learning method to exploit in-topic written texts and recent advances in large pre-trained generative language models to bridge this gap. The experiments show that our method achieves state-of-the-art performance on the ASR test set on two benchmark datasets for punctuation restoration.

3D affordance reasoning is essential in associating human instructions with the functional regions of 3D objects, facilitating precise, task-oriented manipulations in embodied AI. However, current methods, which predominantly depend on sparse 3D point clouds, exhibit limited generalizability and robustness due to their sensitivity to coordinate variations and the inherent sparsity of the data. By contrast, 3D Gaussian Splatting (3DGS) delivers high-fidelity, real-time rendering with minimal computational overhead by representing scenes as dense, continuous distributions. This positions 3DGS as a highly effective approach for capturing fine-grained affordance details and improving recognition accuracy. Nevertheless, its full potential remains largely untapped due to the absence of large-scale, 3DGS-specific affordance datasets. To overcome these limitations, we present 3DAffordSplat, the first large-scale, multi-modal dataset tailored for 3DGS-based affordance reasoning. This dataset includes 23,677 Gaussian instances, 8,354 point cloud instances, and 6,631 manually annotated affordance labels, encompassing 21 object categories and 18 affordance types. Building upon this dataset, we introduce AffordSplatNet, a novel model specifically designed for affordance reasoning using 3DGS representations. AffordSplatNet features an innovative cross-modal structure alignment module that exploits structural consistency priors to align 3D point cloud and 3DGS representations, resulting in enhanced affordance recognition accuracy. Extensive experiments demonstrate that the 3DAffordSplat dataset significantly advances affordance learning within the 3DGS domain, while AffordSplatNet consistently outperforms existing methods across both seen and unseen settings, highlighting its robust generalization capabilities.

Although large multimodal models (LMMs) have demonstrated remarkable capabilities in visual scene interpretation and reasoning, their capacity for complex and precise 3-dimensional spatial reasoning remains uncertain. Existing benchmarks focus predominantly on 2D spatial understanding and lack a framework to comprehensively evaluate 6D spatial reasoning across varying complexities. To address this limitation, we present PulseCheck457, a scalable and unbiased synthetic dataset designed with 4 key capability for spatial reasoning: multi-object recognition, 2D location, 3D location, and 3D orientation. We develop a cascading evaluation structure, constructing 7 question types across 5 difficulty levels that range from basic single object recognition to our new proposed complex 6D spatial reasoning tasks. We evaluated various large multimodal models (LMMs) on PulseCheck457, observing a general decline in performance as task complexity increases, particularly in 3D reasoning and 6D spatial tasks. To quantify these challenges, we introduce the Relative Performance Dropping Rate (RPDR), highlighting key weaknesses in 3D reasoning capabilities. Leveraging the unbiased attribute design of our dataset, we also uncover prediction biases across different attributes, with similar patterns observed in real-world image settings.

The iMet 2020 dataset is a valuable resource in the space of fine-grained art attribution recognition, but we believe it has yet to reach its true potential. We document the unique properties of the dataset and observe that many of the attribute labels are noisy, more than is implied by the dataset description. Oftentimes, there are also semantic relationships between the labels (e.g., identical, mutual exclusion, subsumption, overlap with uncertainty) which we believe are underutilized. We propose an approach to cleaning and structuring the iMet 2020 labels, and discuss the implications and value of doing so. Further, we demonstrate the benefits of our proposed approach through several experiments. Our code and cleaned labels are available at https://github.com/sunniesuhyoung/iMet2020cleaned.

We propose a cascade of neural models that performs sentence classification, phrase recognition, and triple extraction to automatically structure the scholarly contributions of NLP publications. To identify the most important contribution sentences in a paper, we used a BERT-based classifier with positional features (Subtask 1). A BERT-CRF model was used to recognize and characterize relevant phrases in contribution sentences (Subtask 2). We categorized the triples into several types based on whether and how their elements were expressed in text, and addressed each type using separate BERT-based classifiers as well as rules (Subtask 3). Our system was officially ranked second in Phase 1 evaluation and first in both parts of Phase 2 evaluation. After fixing a submission error in Pharse 1, our approach yields the best results overall. In this paper, in addition to a system description, we also provide further analysis of our results, highlighting its strengths and limitations. We make our code publicly available at https://github.com/Liu-Hy/nlp-contrib-graph.

While understanding the knowledge boundaries of LLMs is crucial to prevent hallucination, research on knowledge boundaries of LLMs has predominantly focused on English. In this work, we present the first study to analyze how LLMs recognize knowledge boundaries across different languages by probing their internal representations when processing known and unknown questions in multiple languages. Our empirical studies reveal three key findings: 1) LLMs' perceptions of knowledge boundaries are encoded in the middle to middle-upper layers across different languages. 2) Language differences in knowledge boundary perception follow a linear structure, which motivates our proposal of a training-free alignment method that effectively transfers knowledge boundary perception ability across languages, thereby helping reduce hallucination risk in low-resource languages; 3) Fine-tuning on bilingual question pair translation further enhances LLMs' recognition of knowledge boundaries across languages. Given the absence of standard testbeds for cross-lingual knowledge boundary analysis, we construct a multilingual evaluation suite comprising three representative types of knowledge boundary data. Our code and datasets are publicly available at https://github.com/DAMO-NLP-SG/LLM-Multilingual-Knowledge-Boundaries.

With the growing adoption of Retrieval-Augmented Generation (RAG) in document processing, robust text recognition has become increasingly critical for knowledge extraction. While OCR (Optical Character Recognition) for English and other languages benefits from large datasets and well-established benchmarks, Arabic OCR faces unique challenges due to its cursive script, right-to-left text flow, and complex typographic and calligraphic features. We present KITAB-Bench, a comprehensive Arabic OCR benchmark that fills the gaps in current evaluation systems. Our benchmark comprises 8,809 samples across 9 major domains and 36 sub-domains, encompassing diverse document types including handwritten text, structured tables, and specialized coverage of 21 chart types for business intelligence. Our findings show that modern vision-language models (such as GPT-4, Gemini, and Qwen) outperform traditional OCR approaches (like EasyOCR, PaddleOCR, and Surya) by an average of 60% in Character Error Rate (CER). Furthermore, we highlight significant limitations of current Arabic OCR models, particularly in PDF-to-Markdown conversion, where the best model Gemini-2.0-Flash achieves only 65% accuracy. This underscores the challenges in accurately recognizing Arabic text, including issues with complex fonts, numeral recognition errors, word elongation, and table structure detection. This work establishes a rigorous evaluation framework that can drive improvements in Arabic document analysis methods and bridge the performance gap with English OCR technologies.

Visually-situated text parsing (VsTP) has recently seen notable advancements, driven by the growing demand for automated document understanding and the emergence of large language models capable of processing document-based questions. While various methods have been proposed to tackle the complexities of VsTP, existing solutions often rely on task-specific architectures and objectives for individual tasks. This leads to modal isolation and complex workflows due to the diversified targets and heterogeneous schemas. In this paper, we introduce OmniParser V2, a universal model that unifies VsTP typical tasks, including text spotting, key information extraction, table recognition, and layout analysis, into a unified framework. Central to our approach is the proposed Structured-Points-of-Thought (SPOT) prompting schemas, which improves model performance across diverse scenarios by leveraging a unified encoder-decoder architecture, objective, and input\&output representation. SPOT eliminates the need for task-specific architectures and loss functions, significantly simplifying the processing pipeline. Our extensive evaluations across four tasks on eight different datasets show that OmniParser V2 achieves state-of-the-art or competitive results in VsTP. Additionally, we explore the integration of SPOT within a multimodal large language model structure, further enhancing text localization and recognition capabilities, thereby confirming the generality of SPOT prompting technique. The code is available at https://github.com/AlibabaResearch/AdvancedLiterateMachinery{AdvancedLiterateMachinery}.

Humans do not acquire perceptual abilities in the way we train machines. While machine learning algorithms typically operate on large collections of randomly-chosen, explicitly-labeled examples, human acquisition relies more heavily on multimodal unsupervised learning (as infants) and active learning (as children). With this motivation, we present a learning framework for sound representation and recognition that combines (i) a self-supervised objective based on a general notion of unimodal and cross-modal coincidence, (ii) a clustering objective that reflects our need to impose categorical structure on our experiences, and (iii) a cluster-based active learning procedure that solicits targeted weak supervision to consolidate categories into relevant semantic classes. By training a combined sound embedding/clustering/classification network according to these criteria, we achieve a new state-of-the-art unsupervised audio representation and demonstrate up to a 20-fold reduction in the number of labels required to reach a desired classification performance.

Understanding the content of videos is one of the core techniques for developing various helpful applications in the real world, such as recognizing various human actions for surveillance systems or customer behavior analysis in an autonomous shop. However, understanding the content or story of the video still remains a challenging problem due to its sheer amount of data and temporal structure. In this paper, we propose a multi-channel neural network structure that adopts a two-stream network structure, which has been shown high performance in human action recognition field, and use it as a spatiotemporal video feature extractor for solving video question and answering task. We also adopt a squeeze-and-excitation structure to two-stream network structure for achieving a channel-wise attended spatiotemporal feature. For jointly modeling the spatiotemporal features from video and the textual features from the question, we design a context matching module with a level adjusting layer to remove the gap of information between visual and textual features by applying attention mechanism on joint modeling. Finally, we adopt a scoring mechanism and smoothed ranking loss objective function for selecting the correct answer from answer candidates. We evaluate our model with TVQA dataset, and our approach shows the improved result in textual only setting, but the result with visual feature shows the limitation and possibility of our approach.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

We introduce PartGlot, a neural framework and associated architectures for learning semantic part segmentation of 3D shape geometry, based solely on part referential language. We exploit the fact that linguistic descriptions of a shape can provide priors on the shape's parts -- as natural language has evolved to reflect human perception of the compositional structure of objects, essential to their recognition and use. For training, we use the paired geometry / language data collected in the ShapeGlot work for their reference game, where a speaker creates an utterance to differentiate a target shape from two distractors and the listener has to find the target based on this utterance. Our network is designed to solve this target discrimination problem, carefully incorporating a Transformer-based attention module so that the output attention can precisely highlight the semantic part or parts described in the language. Furthermore, the network operates without any direct supervision on the 3D geometry itself. Surprisingly, we further demonstrate that the learned part information is generalizable to shape classes unseen during training. Our approach opens the possibility of learning 3D shape parts from language alone, without the need for large-scale part geometry annotations, thus facilitating annotation acquisition.

Artificial neural networks typically struggle in generalizing to out-of-context examples. One reason for this limitation is caused by having datasets that incorporate only partial information regarding the potential correlational structure of the world. In this work, we propose TIDA (Targeted Image-editing Data Augmentation), a targeted data augmentation method focused on improving models' human-like abilities (e.g., gender recognition) by filling the correlational structure gap using a text-to-image generative model. More specifically, TIDA identifies specific skills in captions describing images (e.g., the presence of a specific gender in the image), changes the caption (e.g., "woman" to "man"), and then uses a text-to-image model to edit the image in order to match the novel caption (e.g., uniquely changing a woman to a man while maintaining the context identical). Based on the Flickr30K benchmark, we show that, compared with the original data set, a TIDA-enhanced dataset related to gender, color, and counting abilities induces better performance in several image captioning metrics. Furthermore, on top of relying on the classical BLEU metric, we conduct a fine-grained analysis of the improvements of our models against the baseline in different ways. We compared text-to-image generative models and found different behaviors of the image captioning models in terms of encoding visual encoding and textual decoding.

Human perception of 3D shapes goes beyond reconstructing them as a set of points or a composition of geometric primitives: we also effortlessly understand higher-level shape structure such as the repetition and reflective symmetry of object parts. In contrast, recent advances in 3D shape sensing focus more on low-level geometry but less on these higher-level relationships. In this paper, we propose 3D shape programs, integrating bottom-up recognition systems with top-down, symbolic program structure to capture both low-level geometry and high-level structural priors for 3D shapes. Because there are no annotations of shape programs for real shapes, we develop neural modules that not only learn to infer 3D shape programs from raw, unannotated shapes, but also to execute these programs for shape reconstruction. After initial bootstrapping, our end-to-end differentiable model learns 3D shape programs by reconstructing shapes in a self-supervised manner. Experiments demonstrate that our model accurately infers and executes 3D shape programs for highly complex shapes from various categories. It can also be integrated with an image-to-shape module to infer 3D shape programs directly from an RGB image, leading to 3D shape reconstructions that are both more accurate and more physically plausible.

Despite advances in Large Language Models (LLMs) and Multimodal LLMs (MLLMs) for visual document understanding (VDU), visual information extraction (VIE) from relation-rich documents remains challenging due to the layout diversity and limited training data. While existing synthetic document generators attempt to address data scarcity, they either rely on manually designed layouts and templates, or adopt rule-based approaches that limit layout diversity. Besides, current layout generation methods focus solely on topological patterns without considering textual content, making them impractical for generating documents with complex associations between the contents and layouts. In this paper, we propose a Relation-rIch visual Document GEnerator (RIDGE) that addresses these limitations through a two-stage approach: (1) Content Generation, which leverages LLMs to generate document content using a carefully designed Hierarchical Structure Text format which captures entity categories and relationships, and (2) Content-driven Layout Generation, which learns to create diverse, plausible document layouts solely from easily available Optical Character Recognition (OCR) results, requiring no human labeling or annotations efforts. Experimental results have demonstrated that our method significantly enhances the performance of document understanding models on various VIE benchmarks. The code and model will be available at https://github.com/AI-Application-and-Integration-Lab/RIDGE .

We study the problem of 3D object generation. We propose a novel framework, namely 3D Generative Adversarial Network (3D-GAN), which generates 3D objects from a probabilistic space by leveraging recent advances in volumetric convolutional networks and generative adversarial nets. The benefits of our model are three-fold: first, the use of an adversarial criterion, instead of traditional heuristic criteria, enables the generator to capture object structure implicitly and to synthesize high-quality 3D objects; second, the generator establishes a mapping from a low-dimensional probabilistic space to the space of 3D objects, so that we can sample objects without a reference image or CAD models, and explore the 3D object manifold; third, the adversarial discriminator provides a powerful 3D shape descriptor which, learned without supervision, has wide applications in 3D object recognition. Experiments demonstrate that our method generates high-quality 3D objects, and our unsupervisedly learned features achieve impressive performance on 3D object recognition, comparable with those of supervised learning methods.

Web search is an essential way for humans to obtain information, but it's still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of structural reading comprehension (SRC) on web. Given a web page and a question about it, the task is to find the answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages. Along with the QA pairs, corresponding HTML source code, screenshots, and metadata are also provided in our dataset. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available at https://x-lance.github.io/WebSRC/.

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

In this work, the human parsing task, namely decomposing a human image into semantic fashion/body regions, is formulated as an Active Template Regression (ATR) problem, where the normalized mask of each fashion/body item is expressed as the linear combination of the learned mask templates, and then morphed to a more precise mask with the active shape parameters, including position, scale and visibility of each semantic region. The mask template coefficients and the active shape parameters together can generate the human parsing results, and are thus called the structure outputs for human parsing. The deep Convolutional Neural Network (CNN) is utilized to build the end-to-end relation between the input human image and the structure outputs for human parsing. More specifically, the structure outputs are predicted by two separate networks. The first CNN network is with max-pooling, and designed to predict the template coefficients for each label mask, while the second CNN network is without max-pooling to preserve sensitivity to label mask position and accurately predict the active shape parameters. For a new image, the structure outputs of the two networks are fused to generate the probability of each label for each pixel, and super-pixel smoothing is finally used to refine the human parsing result. Comprehensive evaluations on a large dataset well demonstrate the significant superiority of the ATR framework over other state-of-the-arts for human parsing. In particular, the F1-score reaches 64.38% by our ATR framework, significantly higher than 44.76% based on the state-of-the-art algorithm.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

We propose a new method for learning the structure of convolutional neural networks (CNNs) that is more efficient than recent state-of-the-art methods based on reinforcement learning and evolutionary algorithms. Our approach uses a sequential model-based optimization (SMBO) strategy, in which we search for structures in order of increasing complexity, while simultaneously learning a surrogate model to guide the search through structure space. Direct comparison under the same search space shows that our method is up to 5 times more efficient than the RL method of Zoph et al. (2018) in terms of number of models evaluated, and 8 times faster in terms of total compute. The structures we discover in this way achieve state of the art classification accuracies on CIFAR-10 and ImageNet.

Recently, there has been growing interest in developing learning-based methods to detect and utilize salient semi-global or global structures, such as junctions, lines, planes, cuboids, smooth surfaces, and all types of symmetries, for 3D scene modeling and understanding. However, the ground truth annotations are often obtained via human labor, which is particularly challenging and inefficient for such tasks due to the large number of 3D structure instances (e.g., line segments) and other factors such as viewpoints and occlusions. In this paper, we present a new synthetic dataset, Structured3D, with the aim of providing large-scale photo-realistic images with rich 3D structure annotations for a wide spectrum of structured 3D modeling tasks. We take advantage of the availability of professional interior designs and automatically extract 3D structures from them. We generate high-quality images with an industry-leading rendering engine. We use our synthetic dataset in combination with real images to train deep networks for room layout estimation and demonstrate improved performance on benchmark datasets.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Transformers are widely used to extract semantic meanings from input tokens, yet they usually operate as black-box models. In this paper, we present a simple yet informative decomposition of hidden states (or embeddings) of trained transformers into interpretable components. For any layer, embedding vectors of input sequence samples are represented by a tensor h in R^{C times T times d}. Given embedding vector h_{c,t} in R^d at sequence position t le T in a sequence (or context) c le C, extracting the mean effects yields the decomposition \[ h_{c,t} = \mu + pos_t + ctx_c + resid_{c,t} \] where mu is the global mean vector, pos_t and ctx_c are the mean vectors across contexts and across positions respectively, and resid_{c,t} is the residual vector. For popular transformer architectures and diverse text datasets, empirically we find pervasive mathematical structure: (1) (pos_t)_{t} forms a low-dimensional, continuous, and often spiral shape across layers, (2) (ctx_c)_c shows clear cluster structure that falls into context topics, and (3) (pos_t)_{t} and (ctx_c)_c are mutually nearly orthogonal. We argue that smoothness is pervasive and beneficial to transformers trained on languages, and our decomposition leads to improved model interpretability.

Dramatic progress has been witnessed in basic vision tasks involving low-level perception, such as object recognition, detection, and tracking. Unfortunately, there is still an enormous performance gap between artificial vision systems and human intelligence in terms of higher-level vision problems, especially ones involving reasoning. Earlier attempts in equipping machines with high-level reasoning have hovered around Visual Question Answering (VQA), one typical task associating vision and language understanding. In this work, we propose a new dataset, built in the context of Raven's Progressive Matrices (RPM) and aimed at lifting machine intelligence by associating vision with structural, relational, and analogical reasoning in a hierarchical representation. Unlike previous works in measuring abstract reasoning using RPM, we establish a semantic link between vision and reasoning by providing structure representation. This addition enables a new type of abstract reasoning by jointly operating on the structure representation. Machine reasoning ability using modern computer vision is evaluated in this newly proposed dataset. Additionally, we also provide human performance as a reference. Finally, we show consistent improvement across all models by incorporating a simple neural module that combines visual understanding and structure reasoning.

The inference of topological principles is a key problem in structured reconstruction. We observe that wrongly predicted topological relationships are often incurred by the lack of holistic geometry clues in low-level features. Inspired by the fact that massive signals can be compactly described with frequency analysis, we experimentally explore the efficiency and tendency of learning structure geometry in the frequency domain. Accordingly, we propose a frequency-domain feature learning strategy (F-Learn) to fuse scattered geometric fragments holistically for topology-intact structure reasoning. Benefiting from the parsimonious design, the F-Learn strategy can be easily deployed into a deep reconstructor with a lightweight model modification. Experiments demonstrate that the F-Learn strategy can effectively introduce structure awareness into geometric primitive detection and topology inference, bringing significant performance improvement to final structured reconstruction. Code and pre-trained models are available at https://github.com/Geo-Tell/F-Learn.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

Vision and Language (VL) models have demonstrated remarkable zero-shot performance in a variety of tasks. However, some aspects of complex language understanding still remain a challenge. We introduce the collective notion of Structured Vision&Language Concepts (SVLC) which includes object attributes, relations, and states which are present in the text and visible in the image. Recent studies have shown that even the best VL models struggle with SVLC. A possible way of fixing this issue is by collecting dedicated datasets for teaching each SVLC type, yet this might be expensive and time-consuming. Instead, we propose a more elegant data-driven approach for enhancing VL models' understanding of SVLCs that makes more effective use of existing VL pre-training datasets and does not require any additional data. While automatic understanding of image structure still remains largely unsolved, language structure is much better modeled and understood, allowing for its effective utilization in teaching VL models. In this paper, we propose various techniques based on language structure understanding that can be used to manipulate the textual part of off-the-shelf paired VL datasets. VL models trained with the updated data exhibit a significant improvement of up to 15% in their SVLC understanding with only a mild degradation in their zero-shot capabilities both when training from scratch or fine-tuning a pre-trained model.

Tables organize valuable content in a concise and compact representation. This content is extremely valuable for systems such as search engines, Knowledge Graph's, etc, since they enhance their predictive capabilities. Unfortunately, tables come in a large variety of shapes and sizes. Furthermore, they can have complex column/row-header configurations, multiline rows, different variety of separation lines, missing entries, etc. As such, the correct identification of the table-structure from an image is a non-trivial task. In this paper, we present a new table-structure identification model. The latter improves the latest end-to-end deep learning model (i.e. encoder-dual-decoder from PubTabNet) in two significant ways. First, we introduce a new object detection decoder for table-cells. In this way, we can obtain the content of the table-cells from programmatic PDF's directly from the PDF source and avoid the training of the custom OCR decoders. This architectural change leads to more accurate table-content extraction and allows us to tackle non-english tables. Second, we replace the LSTM decoders with transformer based decoders. This upgrade improves significantly the previous state-of-the-art tree-editing-distance-score (TEDS) from 91% to 98.5% on simple tables and from 88.7% to 95% on complex tables.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

This paper proposes LayoutLLM, a more flexible document analysis method for understanding imaged documents. Visually Rich Document Understanding tasks, such as document image classification and information extraction, have gained significant attention due to their importance. Existing methods have been developed to enhance document comprehension by incorporating pre-training awareness of images, text, and layout structure. However, these methods require fine-tuning for each task and dataset, and the models are expensive to train and operate. To overcome this limitation, we propose a new LayoutLLM that integrates these with large-scale language models (LLMs). By leveraging the strengths of existing research in document image understanding and LLMs' superior language understanding capabilities, the proposed model, fine-tuned with multimodal instruction datasets, performs an understanding of document images in a single model. Our experiments demonstrate improvement over the baseline model in various document analysis tasks.

The growing prevalence of visually rich documents, such as webpages and scanned/digital-born documents (images, PDFs, etc.), has led to increased interest in automatic document understanding and information extraction across academia and industry. Although various document modalities, including image, text, layout, and structure, facilitate human information retrieval, the interconnected nature of these modalities presents challenges for neural networks. In this paper, we introduce WebLM, a multimodal pre-training network designed to address the limitations of solely modeling text and structure modalities of HTML in webpages. Instead of processing document images as unified natural images, WebLM integrates the hierarchical structure of document images to enhance the understanding of markup-language-based documents. Additionally, we propose several pre-training tasks to model the interaction among text, structure, and image modalities effectively. Empirical results demonstrate that the pre-trained WebLM significantly surpasses previous state-of-the-art pre-trained models across several webpage understanding tasks. The pre-trained models and code are available at https://github.com/X-LANCE/weblm.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

When reading long-form text, human cognition is complex and structurized. While large language models (LLMs) process input contexts through a causal and sequential perspective, this approach can potentially limit their ability to handle intricate and complex inputs effectively. To enhance LLM's cognition capability, this paper presents a novel concept of context structurization. Specifically, we transform the plain, unordered contextual sentences into well-ordered and hierarchically structurized elements. By doing so, LLMs can better grasp intricate and extended contexts through precise attention and information-seeking along the organized structures. Extensive evaluations are conducted across various model architectures and sizes (including a series of auto-regressive LLMs as well as BERT-like masking models) on a diverse set of NLP tasks (e.g., context-based question-answering, exhaustive hallucination evaluation, and passage-level dense retrieval). Empirical results show consistent and significant performance gains afforded by a single-round structurization. In particular, we boost the open-sourced LLaMA2-70B model to achieve comparable performance against GPT-3.5-Turbo as the hallucination evaluator. Besides, we show the feasibility of distilling advanced LLMs' language processing abilities to a smaller yet effective StruXGPT-7B to execute structurization, addressing the practicality of our approach. Code is available at https://github.com/alibaba/struxgpt.

Pre-training techniques have been verified successfully in a variety of NLP tasks in recent years. Despite the widespread use of pre-training models for NLP applications, they almost exclusively focus on text-level manipulation, while neglecting layout and style information that is vital for document image understanding. In this paper, we propose the LayoutLM to jointly model interactions between text and layout information across scanned document images, which is beneficial for a great number of real-world document image understanding tasks such as information extraction from scanned documents. Furthermore, we also leverage image features to incorporate words' visual information into LayoutLM. To the best of our knowledge, this is the first time that text and layout are jointly learned in a single framework for document-level pre-training. It achieves new state-of-the-art results in several downstream tasks, including form understanding (from 70.72 to 79.27), receipt understanding (from 94.02 to 95.24) and document image classification (from 93.07 to 94.42). The code and pre-trained LayoutLM models are publicly available at https://aka.ms/layoutlm.

Tables are widely used in documents because of their compact and structured representation of information. In particular, in scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Since the layout of tables is highly variable, it would be useful to interpret their content and classify them into categories. This could be helpful to directly extract information from scientific papers, for instance comparing performance of some models given their paper result tables. In this work, we address the classification of tables using a Graph Neural Network, exploiting the table structure for the message passing algorithm in use. We evaluate our model on a subset of the Tab2Know dataset. Since it contains few examples manually annotated, we propose data augmentation techniques directly on the table graph structures. We achieve promising preliminary results, proposing a data augmentation method suitable for graph-based table representation.

Large-scale pre-trained Vision Language Models (VLMs) have proven effective for zero-shot classification. Despite the success, most traditional VLMs-based methods are restricted by the assumption of partial source supervision or ideal vocabularies, which rarely satisfy the open-world scenario. In this paper, we aim at a more challenging setting, Realistic Zero-Shot Classification, which assumes no annotation but instead a broad vocabulary. To address this challenge, we propose the Self Structural Semantic Alignment (S^3A) framework, which extracts the structural semantic information from unlabeled data while simultaneously self-learning. Our S^3A framework adopts a unique Cluster-Vote-Prompt-Realign (CVPR) algorithm, which iteratively groups unlabeled data to derive structural semantics for pseudo-supervision. Our CVPR process includes iterative clustering on images, voting within each cluster to identify initial class candidates from the vocabulary, generating discriminative prompts with large language models to discern confusing candidates, and realigning images and the vocabulary as structural semantic alignment. Finally, we propose to self-learn the CLIP image encoder with both individual and structural semantic alignment through a teacher-student learning strategy. Our comprehensive experiments across various generic and fine-grained benchmarks demonstrate that the S^3A method offers substantial improvements over existing VLMs-based approaches, achieving a more than 15% accuracy improvement over CLIP on average. Our codes, models, and prompts are publicly released at https://github.com/sheng-eatamath/S3A.

Graphs are able to model interconnected entities in many online services, supporting a wide range of applications on the Web. This raises an important question: How can we train a graph foundational model on multiple source domains and adapt to an unseen target domain? A major obstacle is that graphs from different domains often exhibit divergent characteristics. Some studies leverage large language models to align multiple domains based on textual descriptions associated with the graphs, limiting their applicability to text-attributed graphs. For text-free graphs, a few recent works attempt to align different feature distributions across domains, while generally neglecting structural differences. In this work, we propose a novel Structure Alignment framework for text-free Multi-domain Graph Pre-Training and cross-domain adaptation (SAMGPT). It is designed to learn multi-domain knowledge from graphs originating in multiple source domains, which can then be adapted to address applications in an unseen target domain. Specifically, we introduce a set of structure tokens to harmonize structure-based aggregation across source domains during the pre-training phase. Next, for cross-domain adaptation, we design dual prompts, namely, holistic prompts and specific prompts, which adapt unified multi-domain structural knowledge and fine-grained, domain-specific information, respectively, to a target domain. Finally, we conduct comprehensive experiments on seven public datasets to evaluate and analyze the effectiveness of SAMGPT.

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

Recognizing the layout of unstructured digital documents is an important step when parsing the documents into structured machine-readable format for downstream applications. Deep neural networks that are developed for computer vision have been proven to be an effective method to analyze layout of document images. However, document layout datasets that are currently publicly available are several magnitudes smaller than established computing vision datasets. Models have to be trained by transfer learning from a base model that is pre-trained on a traditional computer vision dataset. In this paper, we develop the PubLayNet dataset for document layout analysis by automatically matching the XML representations and the content of over 1 million PDF articles that are publicly available on PubMed Central. The size of the dataset is comparable to established computer vision datasets, containing over 360 thousand document images, where typical document layout elements are annotated. The experiments demonstrate that deep neural networks trained on PubLayNet accurately recognize the layout of scientific articles. The pre-trained models are also a more effective base mode for transfer learning on a different document domain. We release the dataset (https://github.com/ibm-aur-nlp/PubLayNet) to support development and evaluation of more advanced models for document layout analysis.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Non-exemplar class-incremental learning is to recognize both the old and new classes when old class samples cannot be saved. It is a challenging task since representation optimization and feature retention can only be achieved under supervision from new classes. To address this problem, we propose a novel self-sustaining representation expansion scheme. Our scheme consists of a structure reorganization strategy that fuses main-branch expansion and side-branch updating to maintain the old features, and a main-branch distillation scheme to transfer the invariant knowledge. Furthermore, a prototype selection mechanism is proposed to enhance the discrimination between the old and new classes by selectively incorporating new samples into the distillation process. Extensive experiments on three benchmarks demonstrate significant incremental performance, outperforming the state-of-the-art methods by a margin of 3%, 3% and 6%, respectively.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

Multi-modal document retrieval is designed to identify and retrieve various forms of multi-modal content, such as figures, tables, charts, and layout information from extensive documents. Despite its significance, there is a notable lack of a robust benchmark to effectively evaluate the performance of systems in multi-modal document retrieval. To address this gap, this work introduces a new benchmark, named as MMDocIR, encompassing two distinct tasks: page-level and layout-level retrieval. The former focuses on localizing the most relevant pages within a long document, while the latter targets the detection of specific layouts, offering a more fine-grained granularity than whole-page analysis. A layout can refer to a variety of elements such as textual paragraphs, equations, figures, tables, or charts. The MMDocIR benchmark comprises a rich dataset featuring expertly annotated labels for 1,685 questions and bootstrapped labels for 173,843 questions, making it a pivotal resource for advancing multi-modal document retrieval for both training and evaluation. Through rigorous experiments, we reveal that (i) visual retrievers significantly outperform their text counterparts, (ii) MMDocIR train set can effectively benefit the training process of multi-modal document retrieval and (iii) text retrievers leveraging on VLM-text perform much better than those using OCR-text. These findings underscores the potential advantages of integrating visual elements for multi-modal document retrieval.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding ({3D GU}) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates {3D GU} tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse {3D GU} tasks within a single autoregressive framework. Extensive experiments across multiple microscopic {3D GU} tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

The CLEVR dataset has been used extensively in language grounded visual reasoning in Machine Learning (ML) and Natural Language Processing (NLP) domains. We present a graph parser library for CLEVR, that provides functionalities for object-centric attributes and relationships extraction, and construction of structural graph representations for dual modalities. Structural order-invariant representations enable geometric learning and can aid in downstream tasks like language grounding to vision, robotics, compositionality, interpretability, and computational grammar construction. We provide three extensible main components - parser, embedder, and visualizer that can be tailored to suit specific learning setups. We also provide out-of-the-box functionality for seamless integration with popular deep graph neural network (GNN) libraries. Additionally, we discuss downstream usage and applications of the library, and how it accelerates research for the NLP research community.

We propose a novel method for discovering shape regions that strongly correlate with user-prescribed tags. For example, given a collection of chairs tagged as either "has armrest" or "lacks armrest", our system correctly highlights the armrest regions as the main distinctive parts between the two chair types. To obtain point-wise predictions from shape-wise tags we develop a novel neural network architecture that is trained with tag classification loss, but is designed to rely on segmentation to predict the tag. Our network is inspired by U-Net, but we replicate shallow U structures several times with new skip connections and pooling layers, and call the resulting architecture "WU-Net". We test our method on segmentation benchmarks and show that even with weak supervision of whole shape tags, our method can infer meaningful semantic regions, without ever observing shape segmentations. Further, once trained, the model can process shapes for which the tag is entirely unknown. As a bonus, our architecture is directly operational under full supervision and performs strongly on standard benchmarks. We validate our method through experiments with many variant architectures and prior baselines, and demonstrate several applications.

Optical Character Recognition (OCR) technology is widely used to extract text from images of documents, facilitating efficient digitization and data retrieval. However, merely extracting text is insufficient when dealing with complex documents. Fully comprehending such documents requires an understanding of their structure -- including formatting, formulas, tables, and the reading order of multiple blocks and columns across multiple pages -- as well as semantic information for detecting elements like footnotes and image captions. This comprehensive understanding is crucial for downstream tasks such as retrieval, document question answering, and data curation for training Large Language Models (LLMs) and Vision Language Models (VLMs). To address this, we introduce \'Eclair, a general-purpose text-extraction tool specifically designed to process a wide range of document types. Given an image, \'Eclair is able to extract formatted text in reading order, along with bounding boxes and their corresponding semantic classes. To thoroughly evaluate these novel capabilities, we introduce our diverse human-annotated benchmark for document-level OCR and semantic classification. \'Eclair achieves state-of-the-art accuracy on this benchmark, outperforming other methods across key metrics. Additionally, we evaluate \'Eclair on established benchmarks, demonstrating its versatility and strength across several evaluation standards.

Topic segmentation is critical for obtaining structured documents and improving downstream tasks such as information retrieval. Due to its ability of automatically exploring clues of topic shift from abundant labeled data, recent supervised neural models have greatly promoted the development of long document topic segmentation, but leaving the deeper relationship between coherence and topic segmentation underexplored. Therefore, this paper enhances the ability of supervised models to capture coherence from both logical structure and semantic similarity perspectives to further improve the topic segmentation performance, proposing Topic-aware Sentence Structure Prediction (TSSP) and Contrastive Semantic Similarity Learning (CSSL). Specifically, the TSSP task is proposed to force the model to comprehend structural information by learning the original relations between adjacent sentences in a disarrayed document, which is constructed by jointly disrupting the original document at topic and sentence levels. Moreover, we utilize inter- and intra-topic information to construct contrastive samples and design the CSSL objective to ensure that the sentences representations in the same topic have higher similarity, while those in different topics are less similar. Extensive experiments show that the Longformer with our approach significantly outperforms old state-of-the-art (SOTA) methods. Our approach improve F_1 of old SOTA by 3.42 (73.74 -> 77.16) and reduces P_k by 1.11 points (15.0 -> 13.89) on WIKI-727K and achieves an average relative reduction of 4.3% on P_k on WikiSection. The average relative P_k drop of 8.38% on two out-of-domain datasets also demonstrates the robustness of our approach.

This paper introduces layout-aware graph modeling for multimodal RAG. Different from traditional RAG methods that mostly deal with flat text chunks, the proposed method takes into account the relationship of multimodalities by using a graph structure. To do that, a graph modeling structure is defined based on document layout parsing. The structure of an input document is retained with the connection of text chunks, tables, and figures. This representation allows the method to handle complex questions that require information from multimodalities. To confirm the efficiency of the graph modeling, a flexible RAG pipeline is developed using robust components. Experimental results on four benchmark test sets confirm the contribution of the layout-aware modeling for performance improvement of the RAG pipeline.

What sorts of structure might enable a learner to discover classes from unlabeled data? Traditional approaches rely on feature-space similarity and heroic assumptions on the data. In this paper, we introduce unsupervised learning under Latent Label Shift (LLS), where we have access to unlabeled data from multiple domains such that the label marginals p_d(y) can shift across domains but the class conditionals p(x|y) do not. This work instantiates a new principle for identifying classes: elements that shift together group together. For finite input spaces, we establish an isomorphism between LLS and topic modeling: inputs correspond to words, domains to documents, and labels to topics. Addressing continuous data, we prove that when each label's support contains a separable region, analogous to an anchor word, oracle access to p(d|x) suffices to identify p_d(y) and p_d(y|x) up to permutation. Thus motivated, we introduce a practical algorithm that leverages domain-discriminative models as follows: (i) push examples through domain discriminator p(d|x); (ii) discretize the data by clustering examples in p(d|x) space; (iii) perform non-negative matrix factorization on the discrete data; (iv) combine the recovered p(y|d) with the discriminator outputs p(d|x) to compute p_d(y|x) ; forall d. With semi-synthetic experiments, we show that our algorithm can leverage domain information to improve upon competitive unsupervised classification methods. We reveal a failure mode of standard unsupervised classification methods when feature-space similarity does not indicate true groupings, and show empirically that our method better handles this case. Our results establish a deep connection between distribution shift and topic modeling, opening promising lines for future work.

Documents are visually rich structures that convey information through text, as well as tables, figures, page layouts, or fonts. While modern document retrieval systems exhibit strong performance on query-to-text matching, they struggle to exploit visual cues efficiently, hindering their performance on practical document retrieval applications such as Retrieval Augmented Generation. To benchmark current systems on visually rich document retrieval, we introduce the Visual Document Retrieval Benchmark ViDoRe, composed of various page-level retrieving tasks spanning multiple domains, languages, and settings. The inherent shortcomings of modern systems motivate the introduction of a new retrieval model architecture, ColPali, which leverages the document understanding capabilities of recent Vision Language Models to produce high-quality contextualized embeddings solely from images of document pages. Combined with a late interaction matching mechanism, ColPali largely outperforms modern document retrieval pipelines while being drastically faster and end-to-end trainable.

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at [email protected] for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

Document structure analysis (aka document layout analysis) is crucial for understanding the physical layout and logical structure of documents, with applications in information retrieval, document summarization, knowledge extraction, etc. In this paper, we concentrate on Hierarchical Document Structure Analysis (HDSA) to explore hierarchical relationships within structured documents created using authoring software employing hierarchical schemas, such as LaTeX, Microsoft Word, and HTML. To comprehensively analyze hierarchical document structures, we propose a tree construction based approach that addresses multiple subtasks concurrently, including page object detection (Detect), reading order prediction of identified objects (Order), and the construction of intended hierarchical structure (Construct). We present an effective end-to-end solution based on this framework to demonstrate its performance. To assess our approach, we develop a comprehensive benchmark called Comp-HRDoc, which evaluates the above subtasks simultaneously. Our end-to-end system achieves state-of-the-art performance on two large-scale document layout analysis datasets (PubLayNet and DocLayNet), a high-quality hierarchical document structure reconstruction dataset (HRDoc), and our Comp-HRDoc benchmark. The Comp-HRDoc benchmark will be released to facilitate further research in this field.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Retrieving relevant documents from a corpus is typically based on the semantic similarity between the document content and query text. The inclusion of structural relationship between documents can benefit the retrieval mechanism by addressing semantic gaps. However, incorporating these relationships requires tractable mechanisms that balance structure with semantics and take advantage of the prevalent pre-train/fine-tune paradigm. We propose here a holistic approach to learning document representations by integrating intra-document content with inter-document relations. Our deep metric learning solution analyzes the complex neighborhood structure in the relationship network to efficiently sample similar/dissimilar document pairs and defines a novel quintuplet loss function that simultaneously encourages document pairs that are semantically relevant to be closer and structurally unrelated to be far apart in the representation space. Furthermore, the separation margins between the documents are varied flexibly to encode the heterogeneity in relationship strengths. The model is fully fine-tunable and natively supports query projection during inference. We demonstrate that it outperforms competing methods on multiple datasets for document retrieval tasks.

Zero-shot medical detection can further improve detection performance without relying on annotated medical images even upon the fine-tuned model, showing great clinical value. Recent studies leverage grounded vision-language models (GLIP) to achieve this by using detailed disease descriptions as prompts for the target disease name during the inference phase. However, these methods typically treat prompts as equivalent context to the target name, making it difficult to assign specific disease knowledge based on visual information, leading to a coarse alignment between images and target descriptions. In this paper, we propose StructuralGLIP, which introduces an auxiliary branch to encode prompts into a latent knowledge bank layer-by-layer, enabling more context-aware and fine-grained alignment. Specifically, in each layer, we select highly similar features from both the image representation and the knowledge bank, forming structural representations that capture nuanced relationships between image patches and target descriptions. These features are then fused across modalities to further enhance detection performance. Extensive experiments demonstrate that StructuralGLIP achieves a +4.1\% AP improvement over prior state-of-the-art methods across seven zero-shot medical detection benchmarks, and consistently improves fine-tuned models by +3.2\% AP on endoscopy image datasets.

Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper insights, existing TAG representation learning primarily relies on supervised methods, necessitating extensive labeled data and limiting applicability across diverse contexts. This paper introduces a new self-supervised learning framework, Text-And-Graph Multi-View Alignment (TAGA), which overcomes these constraints by integrating TAGs' structural and semantic dimensions. TAGA constructs two complementary views: Text-of-Graph view, which organizes node texts into structured documents based on graph topology, and the Graph-of-Text view, which converts textual nodes and connections into graph data. By aligning representations from both views, TAGA captures joint textual and structural information. In addition, a novel structure-preserving random walk algorithm is proposed for efficient training on large-sized TAGs. Our framework demonstrates strong performance in zero-shot and few-shot scenarios across eight real-world datasets.

Recent advances in large-scale pretraining have yielded visual foundation models with strong capabilities. Not only can recent models generalize to arbitrary images for their training task, their intermediate representations are useful for other visual tasks such as detection and segmentation. Given that such models can classify, delineate, and localize objects in 2D, we ask whether they also represent their 3D structure? In this work, we analyze the 3D awareness of visual foundation models. We posit that 3D awareness implies that representations (1) encode the 3D structure of the scene and (2) consistently represent the surface across views. We conduct a series of experiments using task-specific probes and zero-shot inference procedures on frozen features. Our experiments reveal several limitations of the current models. Our code and analysis can be found at https://github.com/mbanani/probe3d.

The ability to describe images with natural language sentences is the hallmark for image and language understanding. Such a system has wide ranging applications such as annotating images and using natural sentences to search for images.In this project we focus on the task of bidirectional image retrieval: such asystem is capable of retrieving an image based on a sentence (image search) andretrieve sentence based on an image query (image annotation). We present asystem based on a global ranking objective function which uses a combinationof convolutional neural networks (CNN) and multi layer perceptrons (MLP).It takes a pair of image and sentence and processes them in different channels,finally embedding it into a common multimodal vector space. These embeddingsencode abstract semantic information about the two inputs and can be comparedusing traditional information retrieval approaches. For each such pair, the modelreturns a score which is interpretted as a similarity metric. If this score is high,the image and sentence are likely to convey similar meaning, and if the score is low then they are likely not to. The visual input is modeled via deep convolutional neural network. On theother hand we explore three models for the textual module. The first one isbag of words with an MLP. The second one uses n-grams (bigram, trigrams,and a combination of trigram & skip-grams) with an MLP. The third is morespecialized deep network specific for modeling variable length sequences (SSE).We report comparable performance to recent work in the field, even though ouroverall model is simpler. We also show that the training time choice of how wecan generate our negative samples has a significant impact on performance, and can be used to specialize the bi-directional system in one particular task.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

Tables are widely used in several types of documents since they can bring important information in a structured way. In scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Several methods perform table analysis working on document images, losing useful information during the conversion from the PDF files since OCR tools can be prone to recognition errors, in particular for text inside tables. The main contribution of this work is to tackle the problem of table extraction, exploiting Graph Neural Networks. Node features are enriched with suitably designed representation embeddings. These representations help to better distinguish not only tables from the other parts of the paper, but also table cells from table headers. We experimentally evaluated the proposed approach on a new dataset obtained by merging the information provided in the PubLayNet and PubTables-1M datasets.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Legal case retrieval, which aims to find relevant cases for a query case, plays a core role in the intelligent legal system. Despite the success that pre-training has achieved in ad-hoc retrieval tasks, effective pre-training strategies for legal case retrieval remain to be explored. Compared with general documents, legal case documents are typically long text sequences with intrinsic logical structures. However, most existing language models have difficulty understanding the long-distance dependencies between different structures. Moreover, in contrast to the general retrieval, the relevance in the legal domain is sensitive to key legal elements. Even subtle differences in key legal elements can significantly affect the judgement of relevance. However, existing pre-trained language models designed for general purposes have not been equipped to handle legal elements. To address these issues, in this paper, we propose SAILER, a new Structure-Aware pre-traIned language model for LEgal case Retrieval. It is highlighted in the following three aspects: (1) SAILER fully utilizes the structural information contained in legal case documents and pays more attention to key legal elements, similar to how legal experts browse legal case documents. (2) SAILER employs an asymmetric encoder-decoder architecture to integrate several different pre-training objectives. In this way, rich semantic information across tasks is encoded into dense vectors. (3) SAILER has powerful discriminative ability, even without any legal annotation data. It can distinguish legal cases with different charges accurately. Extensive experiments over publicly available legal benchmarks demonstrate that our approach can significantly outperform previous state-of-the-art methods in legal case retrieval.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Foundation models are a strong trend in deep learning and computer vision. These models serve as a base for applications as they require minor or no further fine-tuning by developers to integrate into their applications. Foundation models for zero-shot object segmentation such as Segment Anything (SAM) output segmentation masks from images without any further object information. When they are followed in a pipeline by an object identification model, they can perform object detection without training. Here, we focus on training such an object identification model. A crucial practical aspect for an object identification model is to be flexible in input size. As object identification is an image retrieval problem, a suitable method should handle multi-query multi-gallery situations without constraining the number of input images (e.g. by having fixed-size aggregation layers). The key solution to train such a model is the centroid triplet loss (CTL), which aggregates image features to their centroids. CTL yields high accuracy, avoids misleading training signals and keeps the model input size flexible. In our experiments, we establish a new state of the art on the ArmBench object identification task, which shows general applicability of our model. We furthermore demonstrate an integrated unseen object detection pipeline on the challenging HOPE dataset, which requires fine-grained detection. There, our pipeline matches and surpasses related methods which have been trained on dataset-specific data.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

We develop information geometric techniques to understand the representations learned by deep networks when they are trained on different tasks using supervised, meta-, semi-supervised and contrastive learning. We shed light on the following phenomena that relate to the structure of the space of tasks: (1) the manifold of probabilistic models trained on different tasks using different representation learning methods is effectively low-dimensional; (2) supervised learning on one task results in a surprising amount of progress even on seemingly dissimilar tasks; progress on other tasks is larger if the training task has diverse classes; (3) the structure of the space of tasks indicated by our analysis is consistent with parts of the Wordnet phylogenetic tree; (4) episodic meta-learning algorithms and supervised learning traverse different trajectories during training but they fit similar models eventually; (5) contrastive and semi-supervised learning methods traverse trajectories similar to those of supervised learning. We use classification tasks constructed from the CIFAR-10 and Imagenet datasets to study these phenomena.

The ever-increasing number of materials science articles makes it hard to infer chemistry-structure-property relations from published literature. We used natural language processing (NLP) methods to automatically extract material property data from the abstracts of polymer literature. As a component of our pipeline, we trained MaterialsBERT, a language model, using 2.4 million materials science abstracts, which outperforms other baseline models in three out of five named entity recognition datasets when used as the encoder for text. Using this pipeline, we obtained ~300,000 material property records from ~130,000 abstracts in 60 hours. The extracted data was analyzed for a diverse range of applications such as fuel cells, supercapacitors, and polymer solar cells to recover non-trivial insights. The data extracted through our pipeline is made available through a web platform at https://polymerscholar.org which can be used to locate material property data recorded in abstracts conveniently. This work demonstrates the feasibility of an automatic pipeline that starts from published literature and ends with a complete set of extracted material property information.

In this paper, we propose the Hierarchical Document Transformer (HDT), a novel sparse Transformer architecture tailored for structured hierarchical documents. Such documents are extremely important in numerous domains, including science, law or medicine. However, most existing solutions are inefficient and fail to make use of the structure inherent to documents. HDT exploits document structure by introducing auxiliary anchor tokens and redesigning the attention mechanism into a sparse multi-level hierarchy. This approach facilitates information exchange between tokens at different levels while maintaining sparsity, thereby enhancing computational and memory efficiency while exploiting the document structure as an inductive bias. We address the technical challenge of implementing HDT's sample-dependent hierarchical attention pattern by developing a novel sparse attention kernel that considers the hierarchical structure of documents. As demonstrated by our experiments, utilizing structural information present in documents leads to faster convergence, higher sample efficiency and better performance on downstream tasks.

The task of composed image retrieval (CIR) aims to retrieve images based on the query image and the text describing the users' intent. Existing methods have made great progress with the advanced large vision-language (VL) model in CIR task, however, they generally suffer from two main issues: lack of labeled triplets for model training and difficulty of deployment on resource-restricted environments when deploying the large vision-language model. To tackle the above problems, we propose Image2Sentence based Asymmetric zero-shot composed image retrieval (ISA), which takes advantage of the VL model and only relies on unlabeled images for composition learning. In the framework, we propose a new adaptive token learner that maps an image to a sentence in the word embedding space of VL model. The sentence adaptively captures discriminative visual information and is further integrated with the text modifier. An asymmetric structure is devised for flexible deployment, in which the lightweight model is adopted for the query side while the large VL model is deployed on the gallery side. The global contrastive distillation and the local alignment regularization are adopted for the alignment between the light model and the VL model for CIR task. Our experiments demonstrate that the proposed ISA could better cope with the real retrieval scenarios and further improve retrieval accuracy and efficiency.

Recent advances in foundation models present new opportunities for interpretable visual recognition -- one can first query Large Language Models (LLMs) to obtain a set of attributes that describe each class, then apply vision-language models to classify images via these attributes. Pioneering work shows that querying thousands of attributes can achieve performance competitive with image features. However, our further investigation on 8 datasets reveals that LLM-generated attributes in a large quantity perform almost the same as random words. This surprising finding suggests that significant noise may be present in these attributes. We hypothesize that there exist subsets of attributes that can maintain the classification performance with much smaller sizes, and propose a novel learning-to-search method to discover those concise sets of attributes. As a result, on the CUB dataset, our method achieves performance close to that of massive LLM-generated attributes (e.g., 10k attributes for CUB), yet using only 32 attributes in total to distinguish 200 bird species. Furthermore, our new paradigm demonstrates several additional benefits: higher interpretability and interactivity for humans, and the ability to summarize knowledge for a recognition task.

Benefiting from the message passing mechanism, Graph Neural Networks (GNNs) have been successful on flourish tasks over graph data. However, recent studies have shown that attackers can catastrophically degrade the performance of GNNs by maliciously modifying the graph structure. A straightforward solution to remedy this issue is to model the edge weights by learning a metric function between pairwise representations of two end nodes, which attempts to assign low weights to adversarial edges. The existing methods use either raw features or representations learned by supervised GNNs to model the edge weights. However, both strategies are faced with some immediate problems: raw features cannot represent various properties of nodes (e.g., structure information), and representations learned by supervised GNN may suffer from the poor performance of the classifier on the poisoned graph. We need representations that carry both feature information and as mush correct structure information as possible and are insensitive to structural perturbations. To this end, we propose an unsupervised pipeline, named STABLE, to optimize the graph structure. Finally, we input the well-refined graph into a downstream classifier. For this part, we design an advanced GCN that significantly enhances the robustness of vanilla GCN without increasing the time complexity. Extensive experiments on four real-world graph benchmarks demonstrate that STABLE outperforms the state-of-the-art methods and successfully defends against various attacks.

Vision-Language Models have made significant progress on many perception-focused tasks, however, their progress on reasoning-focused tasks seem to be limited due to the lack of high-quality and diverse training data. In this work, we aim to address the scarcity issue of reasoning-focused multimodal datasets. We propose VisualWebInstruct - a novel approach that leverages search engine to create a diverse, and high-quality dataset spanning multiple disciplines like math, physics, finance, chemistry, etc. Starting with meticulously selected 30,000 seed images, we employ Google Image search to identify websites containing similar images. We collect and process the HTMLs from over 700K unique URL sources. Through a pipeline of content extraction, filtering and synthesis, we build a dataset of approximately 900K question-answer pairs, with 40% being visual QA pairs and the rest as text QA pairs. Models fine-tuned on VisualWebInstruct demonstrate significant performance gains: (1) training from Llava-OV-mid shows 10-20% absolute point gains across benchmarks, (2) training from MAmmoTH-VL shows 5% absoluate gain. Our best model MAmmoTH-VL2 shows state-of-the-art performance within the 10B parameter class on MMMU-Pro-std (40.7%), MathVerse (42.6%), and DynaMath (55.7%). These remarkable results highlight the effectiveness of our dataset in enhancing VLMs' reasoning capabilities for complex multimodal tasks.

Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. In this work, we demonstrate a set of methods for analyzing protein Transformer models through the lens of attention. We show that attention: (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We find this behavior to be consistent across three Transformer architectures (BERT, ALBERT, XLNet) and two distinct protein datasets. We also present a three-dimensional visualization of the interaction between attention and protein structure. Code for visualization and analysis is available at https://github.com/salesforce/provis.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

We present a new open-vocabulary detection approach based on detection-oriented image-text pretraining to bridge the gap between image-level pretraining and open-vocabulary object detection. At the pretraining phase, we replace the commonly used classification architecture with the detector architecture, which better serves the region-level recognition needs of detection by enabling the detector heads to learn from noisy image-text pairs. Using only standard contrastive loss and no pseudo-labeling, our approach is a simple yet effective extension of the contrastive learning method to learn emergent object-semantic cues. In addition, we propose a shifted-window learning approach upon window attention to make the backbone representation more robust, translation-invariant, and less biased by the window pattern. On the popular LVIS open-vocabulary detection benchmark, our approach sets a new state of the art of 40.4 mask AP_r using the common ViT-L backbone, significantly outperforming the best existing approach by +6.5 mask AP_r at system level. On the COCO benchmark, we achieve very competitive 40.8 novel AP without pseudo labeling or weak supervision. In addition, we evaluate our approach on the transfer detection setup, where ours outperforms the baseline significantly. Visualization reveals emerging object locality from the pretraining recipes compared to the baseline. Code and models will be publicly released.

Graph contrastive learning (GCL) has become a powerful tool for learning graph data, but its scalability remains a significant challenge. In this work, we propose a simple yet effective training framework called Structural Compression (StructComp) to address this issue. Inspired by a sparse low-rank approximation on the diffusion matrix, StructComp trains the encoder with the compressed nodes. This allows the encoder not to perform any message passing during the training stage, and significantly reduces the number of sample pairs in the contrastive loss. We theoretically prove that the original GCL loss can be approximated with the contrastive loss computed by StructComp. Moreover, StructComp can be regarded as an additional regularization term for GCL models, resulting in a more robust encoder. Empirical studies on seven benchmark datasets show that StructComp greatly reduces the time and memory consumption while improving model performance compared to the vanilla GCL models and scalable training methods.

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

Transformers generalize to novel compositions of structures and entities after being trained on a complex dataset, but easily overfit on datasets of insufficient complexity. We observe that when the training set is sufficiently complex, the model encodes sentences that have a common syntactic structure using a systematic attention pattern. Inspired by this observation, we propose SQ-Transformer (Structurally Quantized) that explicitly encourages systematicity in the embeddings and attention layers, even with a training set of low complexity. At the embedding level, we introduce Structure-oriented Vector Quantization (SoVQ) to cluster word embeddings into several classes of structurally equivalent entities. At the attention level, we devise the Systematic Attention Layer (SAL) and an alternative, Systematically Regularized Layer (SRL) that operate on the quantized word embeddings so that sentences of the same structure are encoded with invariant or similar attention patterns. Empirically, we show that SQ-Transformer achieves stronger compositional generalization than the vanilla Transformer on multiple low-complexity semantic parsing and machine translation datasets. In our analysis, we show that SoVQ indeed learns a syntactically clustered embedding space and SAL/SRL induces generalizable attention patterns, which lead to improved systematicity.

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

Recipe generation from food images and ingredients is a challenging task, which requires the interpretation of the information from another modality. Different from the image captioning task, where the captions usually have one sentence, cooking instructions contain multiple sentences and have obvious structures. To help the model capture the recipe structure and avoid missing some cooking details, we propose a novel framework: Decomposing Generation Networks (DGN) with structure prediction, to get more structured and complete recipe generation outputs. Specifically, we split each cooking instruction into several phases, and assign different sub-generators to each phase. Our approach includes two novel ideas: (i) learning the recipe structures with the global structure prediction component and (ii) producing recipe phases in the sub-generator output component based on the predicted structure. Extensive experiments on the challenging large-scale Recipe1M dataset validate the effectiveness of our proposed model, which improves the performance over the state-of-the-art results.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

We present a Neural Network based Handwritten Text Recognition (HTR) model architecture that can be trained to recognize full pages of handwritten or printed text without image segmentation. Being based on Image to Sequence architecture, it can extract text present in an image and then sequence it correctly without imposing any constraints regarding orientation, layout and size of text and non-text. Further, it can also be trained to generate auxiliary markup related to formatting, layout and content. We use character level vocabulary, thereby enabling language and terminology of any subject. The model achieves a new state-of-art in paragraph level recognition on the IAM dataset. When evaluated on scans of real world handwritten free form test answers - beset with curved and slanted lines, drawings, tables, math, chemistry and other symbols - it performs better than all commercially available HTR cloud APIs. It is deployed in production as part of a commercial web application.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Recently, the retrieval models based on dense representations have been gradually applied in the first stage of the document retrieval tasks, showing better performance than traditional sparse vector space models. To obtain high efficiency, the basic structure of these models is Bi-encoder in most cases. However, this simple structure may cause serious information loss during the encoding of documents since the queries are agnostic. To address this problem, we design a method to mimic the queries on each of the documents by an iterative clustering process and represent the documents by multiple pseudo queries (i.e., the cluster centroids). To boost the retrieval process using approximate nearest neighbor search library, we also optimize the matching function with a two-step score calculation procedure. Experimental results on several popular ranking and QA datasets show that our model can achieve state-of-the-art results.

Document layout analysis is a known problem to the documents research community and has been vastly explored yielding a multitude of solutions ranging from text mining, and recognition to graph-based representation, visual feature extraction, etc. However, most of the existing works have ignored the crucial fact regarding the scarcity of labeled data. With growing internet connectivity to personal life, an enormous amount of documents had been available in the public domain and thus making data annotation a tedious task. We address this challenge using self-supervision and unlike, the few existing self-supervised document segmentation approaches which use text mining and textual labels, we use a complete vision-based approach in pre-training without any ground-truth label or its derivative. Instead, we generate pseudo-layouts from the document images to pre-train an image encoder to learn the document object representation and localization in a self-supervised framework before fine-tuning it with an object detection model. We show that our pipeline sets a new benchmark in this context and performs at par with the existing methods and the supervised counterparts, if not outperforms. The code is made publicly available at: https://github.com/MaitySubhajit/SelfDocSeg

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

The growing complexity of legal cases has lead to an increasing interest in legal information retrieval systems that can effectively satisfy user-specific information needs. However, such downstream systems typically require documents to be properly formatted and segmented, which is often done with relatively simple pre-processing steps, disregarding topical coherence of segments. Systems generally rely on representations of individual sentences or paragraphs, which may lack crucial context, or document-level representations, which are too long for meaningful search results. To address this issue, we propose a segmentation system that can predict topical coherence of sequential text segments spanning several paragraphs, effectively segmenting a document and providing a more balanced representation for downstream applications. We build our model on top of popular transformer networks and formulate structural text segmentation as topical change detection, by performing a series of independent classifications that allow for efficient fine-tuning on task-specific data. We crawl a novel dataset consisting of roughly 74,000 online Terms-of-Service documents, including hierarchical topic annotations, which we use for training. Results show that our proposed system significantly outperforms baselines, and adapts well to structural peculiarities of legal documents. We release both data and trained models to the research community for future work.https://github.com/dennlinger/TopicalChange

Vision-language models (VLMs) such as CLIP have shown promising performance on a variety of recognition tasks using the standard zero-shot classification procedure -- computing similarity between the query image and the embedded words for each category. By only using the category name, they neglect to make use of the rich context of additional information that language affords. The procedure gives no intermediate understanding of why a category is chosen, and furthermore provides no mechanism for adjusting the criteria used towards this decision. We present an alternative framework for classification with VLMs, which we call classification by description. We ask VLMs to check for descriptive features rather than broad categories: to find a tiger, look for its stripes; its claws; and more. By basing decisions on these descriptors, we can provide additional cues that encourage using the features we want to be used. In the process, we can get a clear idea of what features the model uses to construct its decision; it gains some level of inherent explainability. We query large language models (e.g., GPT-3) for these descriptors to obtain them in a scalable way. Extensive experiments show our framework has numerous advantages past interpretability. We show improvements in accuracy on ImageNet across distribution shifts; demonstrate the ability to adapt VLMs to recognize concepts unseen during training; and illustrate how descriptors can be edited to effectively mitigate bias compared to the baseline.

Multi-task learning has the potential to improve generalization by maximizing positive transfer between tasks while reducing task interference. Fully achieving this potential is hindered by manually designed architectures that remain static throughout training. On the contrary, learning in the brain occurs through structural changes that are in tandem with changes in synaptic strength. Thus, we propose Multi-Task Structural Learning (MTSL) that simultaneously learns the multi-task architecture and its parameters. MTSL begins with an identical single-task network for each task and alternates between a task-learning phase and a structural-learning phase. In the task learning phase, each network specializes in the corresponding task. In each of the structural learning phases, starting from the earliest layer, locally similar task layers first transfer their knowledge to a newly created group layer before being removed. MTSL then uses the group layer in place of the corresponding removed task layers and moves on to the next layers. Our empirical results show that MTSL achieves competitive generalization with various baselines and improves robustness to out-of-distribution data.

Image descriptions can help visually impaired people to quickly understand the image content. While we made significant progress in automatically describing images and optical character recognition, current approaches are unable to include written text in their descriptions, although text is omnipresent in human environments and frequently critical to understand our surroundings. To study how to comprehend text in the context of an image we collect a novel dataset, TextCaps, with 145k captions for 28k images. Our dataset challenges a model to recognize text, relate it to its visual context, and decide what part of the text to copy or paraphrase, requiring spatial, semantic, and visual reasoning between multiple text tokens and visual entities, such as objects. We study baselines and adapt existing approaches to this new task, which we refer to as image captioning with reading comprehension. Our analysis with automatic and human studies shows that our new TextCaps dataset provides many new technical challenges over previous datasets.

Despite rapid advancements in the capabilities of generative models, pretrained text-to-image models still struggle in capturing the semantics conveyed by complex prompts that compound multiple objects and instance-level attributes. Consequently, we are witnessing growing interests in integrating additional structural constraints, typically in the form of coarse bounding boxes, to better guide the generation process in such challenging cases. In this work, we take the idea of structural guidance a step further by making the observation that contemporary image generation models can directly provide a plausible fine-grained structural initialization. We propose a technique that couples this image-based structural guidance with LLM-based instance-level instructions, yielding output images that adhere to all parts of the text prompt, including object counts, instance-level attributes, and spatial relations between instances.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

People say, "A picture is worth a thousand words". Then how can we get the rich information out of the image? We argue that by using visual clues to bridge large pretrained vision foundation models and language models, we can do so without any extra cross-modal training. Thanks to the strong zero-shot capability of foundation models, we start by constructing a rich semantic representation of the image (e.g., image tags, object attributes / locations, captions) as a structured textual prompt, called visual clues, using a vision foundation model. Based on visual clues, we use large language model to produce a series of comprehensive descriptions for the visual content, which is then verified by the vision model again to select the candidate that aligns best with the image. We evaluate the quality of generated descriptions by quantitative and qualitative measurement. The results demonstrate the effectiveness of such a structured semantic representation.

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein representation learning have utilized only one or two of these modalities due to the difficulty of capturing the asymmetric interrelationships between them. To account for this asymmetry, we introduce our novel asymmetric multi-modal masked autoencoder (AMMA). AMMA adopts (1) a unified multi-modal encoder to integrate all three modalities into a unified representation space and (2) asymmetric decoders to ensure that sequence latent features reflect structural and functional information. The experiments demonstrate that the proposed AMMA is highly effective in learning protein representations that exhibit well-aligned inter-modal relationships, which in turn makes it effective for various downstream protein-related tasks.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

Recent years have witnessed the rise and success of pre-training techniques in visually-rich document understanding. However, most existing methods lack the systematic mining and utilization of layout-centered knowledge, leading to sub-optimal performances. In this paper, we propose ERNIE-Layout, a novel document pre-training solution with layout knowledge enhancement in the whole workflow, to learn better representations that combine the features from text, layout, and image. Specifically, we first rearrange input sequences in the serialization stage, and then present a correlative pre-training task, reading order prediction, to learn the proper reading order of documents. To improve the layout awareness of the model, we integrate a spatial-aware disentangled attention into the multi-modal transformer and a replaced regions prediction task into the pre-training phase. Experimental results show that ERNIE-Layout achieves superior performance on various downstream tasks, setting new state-of-the-art on key information extraction, document image classification, and document question answering datasets. The code and models are publicly available at http://github.com/PaddlePaddle/PaddleNLP/tree/develop/model_zoo/ernie-layout.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

We present a simple few-shot named entity recognition (NER) system based on nearest neighbor learning and structured inference. Our system uses a supervised NER model trained on the source domain, as a feature extractor. Across several test domains, we show that a nearest neighbor classifier in this feature-space is far more effective than the standard meta-learning approaches. We further propose a cheap but effective method to capture the label dependencies between entity tags without expensive CRF training. We show that our method of combining structured decoding with nearest neighbor learning achieves state-of-the-art performance on standard few-shot NER evaluation tasks, improving F1 scores by 6% to 16% absolute points over prior meta-learning based systems.

The challenge of information extraction (IE) lies in the diversity of label schemas and the heterogeneity of structures. Traditional methods require task-specific model design and rely heavily on expensive supervision, making them difficult to generalize to new schemas. In this paper, we decouple IE into two basic abilities, structuring and conceptualizing, which are shared by different tasks and schemas. Based on this paradigm, we propose to universally model various IE tasks with Unified Semantic Matching (USM) framework, which introduces three unified token linking operations to model the abilities of structuring and conceptualizing. In this way, USM can jointly encode schema and input text, uniformly extract substructures in parallel, and controllably decode target structures on demand. Empirical evaluation on 4 IE tasks shows that the proposed method achieves state-of-the-art performance under the supervised experiments and shows strong generalization ability in zero/few-shot transfer settings.

We propose Samba ASR, the first state-of-the-art Automatic Speech Recognition (ASR) model leveraging the novel Mamba architecture as both encoder and decoder, built on the foundation of state-space models (SSMs). Unlike transformer-based ASR models, which rely on self-attention mechanisms to capture dependencies, Samba ASR effectively models both local and global temporal dependencies using efficient state-space dynamics, achieving remarkable performance gains. By addressing the limitations of transformers, such as quadratic scaling with input length and difficulty in handling long-range dependencies, Samba ASR achieves superior accuracy and efficiency. Experimental results demonstrate that Samba ASR surpasses existing open-source transformer-based ASR models across various standard benchmarks, establishing it as the new state of the art in ASR. Extensive evaluations on benchmark datasets show significant improvements in Word Error Rate (WER), with competitive performance even in low-resource scenarios. Furthermore, the computational efficiency and parameter optimization of the Mamba architecture make Samba ASR a scalable and robust solution for diverse ASR tasks. Our contributions include: A new Samba ASR architecture demonstrating the superiority of SSMs over transformer-based models for speech sequence processing. A comprehensive evaluation on public benchmarks showcasing state-of-the-art performance. An analysis of computational efficiency, robustness to noise, and sequence generalization. This work highlights the viability of Mamba SSMs as a transformer-free alternative for efficient and accurate ASR. By leveraging state-space modeling advancements, Samba ASR sets a new benchmark for ASR performance and future research.