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Jun 3

EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical Text

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

A Large Dataset of Spontaneous Speech with the Accent Spoken in São Paulo for Automatic Speech Recognition Evaluation

We present a freely available spontaneous speech corpus for the Brazilian Portuguese language and report preliminary automatic speech recognition (ASR) results, using both the Wav2Vec2-XLSR-53 and Distil-Whisper models fine-tuned and trained on our corpus. The NURC-SP Audio Corpus comprises 401 different speakers (204 females, 197 males) with a total of 239.30 hours of transcribed audio recordings. To the best of our knowledge, this is the first large Paulistano accented spontaneous speech corpus dedicated to the ASR task in Portuguese. We first present the design and development procedures of the NURC-SP Audio Corpus, and then describe four ASR experiments in detail. The experiments demonstrated promising results for the applicability of the corpus for ASR. Specifically, we fine-tuned two versions of Wav2Vec2-XLSR-53 model, trained a Distil-Whisper model using our dataset with labels determined by Whisper Large-V3 model, and fine-tuned this Distil-Whisper model with our corpus. Our best results were the Distil-Whisper fine-tuned over NURC-SP Audio Corpus with a WER of 24.22% followed by a fine-tuned versions of Wav2Vec2-XLSR-53 model with a WER of 33.73%, that is almost 10% point worse than Distil-Whisper's. To enable experiment reproducibility, we share the NURC-SP Audio Corpus dataset, pre-trained models, and training recipes in Hugging-Face and Github repositories.

Salamandra Technical Report

This work introduces Salamandra, a suite of open-source decoder-only large language models available in three different sizes: 2, 7, and 40 billion parameters. The models were trained from scratch on highly multilingual data that comprises text in 35 European languages and code. Our carefully curated corpus is made exclusively from open-access data compiled from a wide variety of sources. Along with the base models, supplementary checkpoints that were fine-tuned on public-domain instruction data are also released for chat applications. Additionally, we also share our preliminary experiments on multimodality, which serve as proof-of-concept to showcase potential applications for the Salamandra family. Our extensive evaluations on multilingual benchmarks reveal that Salamandra has strong capabilities, achieving competitive performance when compared to similarly sized open-source models. We provide comprehensive evaluation results both on standard downstream tasks as well as key aspects related to bias and safety.With this technical report, we intend to promote open science by sharing all the details behind our design choices, data curation strategy and evaluation methodology. In addition to that, we deviate from the usual practice by making our training and evaluation scripts publicly accessible. We release all models under a permissive Apache 2.0 license in order to foster future research and facilitate commercial use, thereby contributing to the open-source ecosystem of large language models.

A standardized Project Gutenberg corpus for statistical analysis of natural language and quantitative linguistics

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than 3 times 10^9 word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

A Biomedical Entity Extraction Pipeline for Oncology Health Records in Portuguese

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

ClArTTS: An Open-Source Classical Arabic Text-to-Speech Corpus

At present, Text-to-speech (TTS) systems that are trained with high-quality transcribed speech data using end-to-end neural models can generate speech that is intelligible, natural, and closely resembles human speech. These models are trained with relatively large single-speaker professionally recorded audio, typically extracted from audiobooks. Meanwhile, due to the scarcity of freely available speech corpora of this kind, a larger gap exists in Arabic TTS research and development. Most of the existing freely available Arabic speech corpora are not suitable for TTS training as they contain multi-speaker casual speech with variations in recording conditions and quality, whereas the corpus curated for speech synthesis are generally small in size and not suitable for training state-of-the-art end-to-end models. In a move towards filling this gap in resources, we present a speech corpus for Classical Arabic Text-to-Speech (ClArTTS) to support the development of end-to-end TTS systems for Arabic. The speech is extracted from a LibriVox audiobook, which is then processed, segmented, and manually transcribed and annotated. The final ClArTTS corpus contains about 12 hours of speech from a single male speaker sampled at 40100 kHz. In this paper, we describe the process of corpus creation and provide details of corpus statistics and a comparison with existing resources. Furthermore, we develop two TTS systems based on Grad-TTS and Glow-TTS and illustrate the performance of the resulting systems via subjective and objective evaluations. The corpus will be made publicly available at www.clartts.com for research purposes, along with the baseline TTS systems demo.

Wav2Small: Distilling Wav2Vec2 to 72K parameters for Low-Resource Speech emotion recognition

Speech Emotion Recognition (SER) needs high computational resources to overcome the challenge of substantial annotator disagreement. Today SER is shifting towards dimensional annotations of arousal, dominance, and valence (A/D/V). Universal metrics as the L2 distance prove unsuitable for evaluating A/D/V accuracy due to non converging consensus of annotator opinions. However, Concordance Correlation Coefficient (CCC) arose as an alternative metric for A/D/V where a model's output is evaluated to match a whole dataset's CCC rather than L2 distances of individual audios. Recent studies have shown that Wav2Vec2.0 / WavLM architectures outputing a float value for each A/D/V dimension achieve today's State-of-the-art (SOTA) CCC on A/D/V. The Wav2Vec2.0 / WavLM family has high computational footprint, but training tiny models using human annotations has been unsuccessful. In this paper we use a large Transformer SOTA A/D/V model as Teacher/Annotator to train 5 student models: 4 MobileNets and our proposed Wav2Small, using only the Teacher's A/D/V predictions instead of human annotations. We chose MobileNet-V4 / MobileNet-V3 as students, as MobileNet has been designed for fast execution times. We propose Wav2Small an architecture designed for minimal parameter number and RAM consumption. Wav2Small with an .onnx (quantized) of only 60KB is a potential solution for A/D/V on hearing aids, having only 72K parameters vs 3.12M parameters for MobileNet-V4-Small. The Teacher model we construct sets a new SOTA on the MSP Podcast Test-1 dataset with valence CCC=0.676.

Localising In-Domain Adaptation of Transformer-Based Biomedical Language Models

In the era of digital healthcare, the huge volumes of textual information generated every day in hospitals constitute an essential but underused asset that could be exploited with task-specific, fine-tuned biomedical language representation models, improving patient care and management. For such specialized domains, previous research has shown that fine-tuning models stemming from broad-coverage checkpoints can largely benefit additional training rounds over large-scale in-domain resources. However, these resources are often unreachable for less-resourced languages like Italian, preventing local medical institutions to employ in-domain adaptation. In order to reduce this gap, our work investigates two accessible approaches to derive biomedical language models in languages other than English, taking Italian as a concrete use-case: one based on neural machine translation of English resources, favoring quantity over quality; the other based on a high-grade, narrow-scoped corpus natively written in Italian, thus preferring quality over quantity. Our study shows that data quantity is a harder constraint than data quality for biomedical adaptation, but the concatenation of high-quality data can improve model performance even when dealing with relatively size-limited corpora. The models published from our investigations have the potential to unlock important research opportunities for Italian hospitals and academia. Finally, the set of lessons learned from the study constitutes valuable insights towards a solution to build biomedical language models that are generalizable to other less-resourced languages and different domain settings.

Leveraging Natural Language Processing For Public Health Screening On YouTube: A COVID-19 Case Study

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

ATCO2 corpus: A Large-Scale Dataset for Research on Automatic Speech Recognition and Natural Language Understanding of Air Traffic Control Communications

Personal assistants, automatic speech recognizers and dialogue understanding systems are becoming more critical in our interconnected digital world. A clear example is air traffic control (ATC) communications. ATC aims at guiding aircraft and controlling the airspace in a safe and optimal manner. These voice-based dialogues are carried between an air traffic controller (ATCO) and pilots via very-high frequency radio channels. In order to incorporate these novel technologies into ATC (low-resource domain), large-scale annotated datasets are required to develop the data-driven AI systems. Two examples are automatic speech recognition (ASR) and natural language understanding (NLU). In this paper, we introduce the ATCO2 corpus, a dataset that aims at fostering research on the challenging ATC field, which has lagged behind due to lack of annotated data. The ATCO2 corpus covers 1) data collection and pre-processing, 2) pseudo-annotations of speech data, and 3) extraction of ATC-related named entities. The ATCO2 corpus is split into three subsets. 1) ATCO2-test-set corpus contains 4 hours of ATC speech with manual transcripts and a subset with gold annotations for named-entity recognition (callsign, command, value). 2) The ATCO2-PL-set corpus consists of 5281 hours of unlabeled ATC data enriched with automatic transcripts from an in-domain speech recognizer, contextual information, speaker turn information, signal-to-noise ratio estimate and English language detection score per sample. Both available for purchase through ELDA at http://catalog.elra.info/en-us/repository/browse/ELRA-S0484. 3) The ATCO2-test-set-1h corpus is a one-hour subset from the original test set corpus, that we are offering for free at https://www.atco2.org/data. We expect the ATCO2 corpus will foster research on robust ASR and NLU not only in the field of ATC communications but also in the general research community.

Clinical Document Corpora and Assorted Domain Proxies: A Survey of Diversity in Corpus Design, with Focus on German Text Data

We survey clinical document corpora, with focus on German textual data. Due to rigid data privacy legislation in Germany these resources, with only few exceptions, are stored in safe clinical data spaces and locked against clinic-external researchers. This situation stands in stark contrast with established workflows in the field of natural language processing where easy accessibility and reuse of data collections are common practice. Hence, alternative corpus designs have been examined to escape from this data poverty. Besides machine translation of English clinical datasets and the generation of synthetic corpora with fictitious clinical contents, several other types of domain proxies have come up as substitutes for authentic clinical documents. Common instances of close proxies are medical journal publications, clinical therapy guidelines, drug labels, etc., more distant proxies include online encyclopedic medical articles or medical contents from social media channels. After PRISM-conformant screening of 359 hits from four bibliographic systems, 75 relevant documents were finally selected for this review and 59 distinct corpora were determined. We identified 24 real clinical corpora (from 40 publications) out of which only 5 are publicly distributable. 2 translations of real corpora and 3 synthetic ones complement the set of clinical corpora. 14 corpora were categorized as close domain proxies, 16 as distant ones. There is a clear divide between the large number of non-accessible authentic clinical German-language corpora and their publicly accessible substitutes: translated or synthetic, close or more distant proxies. So on first sight, the data bottleneck seems broken. Intuitively yet, differences in genre-specific writing style, wording and medical domain expertise in this typological space are also obvious. This raises the question how valid alternative corpus designs really are.

COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

Medical mT5: An Open-Source Multilingual Text-to-Text LLM for The Medical Domain

Research on language technology for the development of medical applications is currently a hot topic in Natural Language Understanding and Generation. Thus, a number of large language models (LLMs) have recently been adapted to the medical domain, so that they can be used as a tool for mediating in human-AI interaction. While these LLMs display competitive performance on automated medical texts benchmarks, they have been pre-trained and evaluated with a focus on a single language (English mostly). This is particularly true of text-to-text models, which typically require large amounts of domain-specific pre-training data, often not easily accessible for many languages. In this paper, we address these shortcomings by compiling, to the best of our knowledge, the largest multilingual corpus for the medical domain in four languages, namely English, French, Italian and Spanish. This new corpus has been used to train Medical mT5, the first open-source text-to-text multilingual model for the medical domain. Additionally, we present two new evaluation benchmarks for all four languages with the aim of facilitating multilingual research in this domain. A comprehensive evaluation shows that Medical mT5 outperforms both encoders and similarly sized text-to-text models for the Spanish, French, and Italian benchmarks, while being competitive with current state-of-the-art LLMs in English.

An analysis of full-size Russian complexly NER labelled corpus of Internet user reviews on the drugs based on deep learning and language neural nets

We present the full-size Russian complexly NER-labeled corpus of Internet user reviews, along with an evaluation of accuracy levels reached on this corpus by a set of advanced deep learning neural networks to extract the pharmacologically meaningful entities from Russian texts. The corpus annotation includes mentions of the following entities: Medication (33005 mentions), Adverse Drug Reaction (1778), Disease (17403), and Note (4490). Two of them - Medication and Disease - comprise a set of attributes. A part of the corpus has the coreference annotation with 1560 coreference chains in 300 documents. Special multi-label model based on a language model and the set of features is developed, appropriate for presented corpus labeling. The influence of the choice of different modifications of the models: word vector representations, types of language models pre-trained for Russian, text normalization styles, and other preliminary processing are analyzed. The sufficient size of our corpus allows to study the effects of particularities of corpus labeling and balancing entities in the corpus. As a result, the state of the art for the pharmacological entity extraction problem for Russian is established on a full-size labeled corpus. In case of the adverse drug reaction (ADR) recognition, it is 61.1 by the F1-exact metric that, as our analysis shows, is on par with the accuracy level for other language corpora with similar characteristics and the ADR representativnes. The evaluated baseline precision of coreference relation extraction on the corpus is 71, that is higher the results reached on other Russian corpora.

CORAA: a large corpus of spontaneous and prepared speech manually validated for speech recognition in Brazilian Portuguese

Automatic Speech recognition (ASR) is a complex and challenging task. In recent years, there have been significant advances in the area. In particular, for the Brazilian Portuguese (BP) language, there were about 376 hours public available for ASR task until the second half of 2020. With the release of new datasets in early 2021, this number increased to 574 hours. The existing resources, however, are composed of audios containing only read and prepared speech. There is a lack of datasets including spontaneous speech, which are essential in different ASR applications. This paper presents CORAA (Corpus of Annotated Audios) v1. with 290.77 hours, a publicly available dataset for ASR in BP containing validated pairs (audio-transcription). CORAA also contains European Portuguese audios (4.69 hours). We also present a public ASR model based on Wav2Vec 2.0 XLSR-53 and fine-tuned over CORAA. Our model achieved a Word Error Rate of 24.18% on CORAA test set and 20.08% on Common Voice test set. When measuring the Character Error Rate, we obtained 11.02% and 6.34% for CORAA and Common Voice, respectively. CORAA corpora were assembled to both improve ASR models in BP with phenomena from spontaneous speech and motivate young researchers to start their studies on ASR for Portuguese. All the corpora are publicly available at https://github.com/nilc-nlp/CORAA under the CC BY-NC-ND 4.0 license.

WenetSpeech: A 10000+ Hours Multi-domain Mandarin Corpus for Speech Recognition

In this paper, we present WenetSpeech, a multi-domain Mandarin corpus consisting of 10000+ hours high-quality labeled speech, 2400+ hours weakly labeled speech, and about 10000 hours unlabeled speech, with 22400+ hours in total. We collect the data from YouTube and Podcast, which covers a variety of speaking styles, scenarios, domains, topics, and noisy conditions. An optical character recognition (OCR) based method is introduced to generate the audio/text segmentation candidates for the YouTube data on its corresponding video captions, while a high-quality ASR transcription system is used to generate audio/text pair candidates for the Podcast data. Then we propose a novel end-to-end label error detection approach to further validate and filter the candidates. We also provide three manually labelled high-quality test sets along with WenetSpeech for evaluation -- Dev for cross-validation purpose in training, Test_Net, collected from Internet for matched test, and Test\_Meeting, recorded from real meetings for more challenging mismatched test. Baseline systems trained with WenetSpeech are provided for three popular speech recognition toolkits, namely Kaldi, ESPnet, and WeNet, and recognition results on the three test sets are also provided as benchmarks. To the best of our knowledge, WenetSpeech is the current largest open-sourced Mandarin speech corpus with transcriptions, which benefits research on production-level speech recognition.

SIB-200: A Simple, Inclusive, and Big Evaluation Dataset for Topic Classification in 200+ Languages and Dialects

Despite the progress we have recorded in the last few years in multilingual natural language processing, evaluation is typically limited to a small set of languages with available datasets which excludes a large number of low-resource languages. In this paper, we created SIB-200 -- a large-scale open-sourced benchmark dataset for topic classification in 200 languages and dialects to address the lack of evaluation dataset for Natural Language Understanding (NLU). For many of the languages covered in SIB-200, this is the first publicly available evaluation dataset for NLU. The dataset is based on Flores-200 machine translation corpus. We annotated the English portion of the dataset and extended the sentence-level annotation to the remaining 203 languages covered in the corpus. Despite the simplicity of this task, our evaluation in full-supervised setting, cross-lingual transfer setting and prompting of large language model setting show that there is still a large gap between the performance of high-resource and low-resource languages when multilingual evaluation is scaled to numerous world languages. We found that languages unseen during the pre-training of multilingual language models, under-represented language families (like Nilotic and Altantic-Congo), and languages from the regions of Africa, Americas, Oceania and South East Asia, often have the lowest performance on our topic classification dataset. We hope our dataset will encourage a more inclusive evaluation of multilingual language models on a more diverse set of languages. https://github.com/dadelani/sib-200

Am I eligible? Natural Language Inference for Clinical Trial Patient Recruitment: the Patient's Point of View

Recruiting patients to participate in clinical trials can be challenging and time-consuming. Usually, participation in a clinical trial is initiated by a healthcare professional and proposed to the patient. Promoting clinical trials directly to patients via online recruitment might help to reach them more efficiently. In this study, we address the case where a patient is initiating their own recruitment process and wants to determine whether they are eligible for a given clinical trial, using their own language to describe their medical profile. To study whether this creates difficulties in the patient trial matching process, we design a new dataset and task, Natural Language Inference for Patient Recruitment (NLI4PR), in which patient language profiles must be matched to clinical trials. We create it by adapting the TREC 2022 Clinical Trial Track dataset, which provides patients' medical profiles, and rephrasing them manually using patient language. We also use the associated clinical trial reports where the patients are either eligible or excluded. We prompt several open-source Large Language Models on our task and achieve from 56.5 to 71.8 of F1 score using patient language, against 64.7 to 73.1 for the same task using medical language. When using patient language, we observe only a small loss in performance for the best model, suggesting that having the patient as a starting point could be adopted to help recruit patients for clinical trials. The corpus and code bases are all freely available on our Github and HuggingFace repositories.

Fine-grained Contract NER using instruction based model

Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream tasks. Despite these advancements, the performance of Large Language Models (LLMs) in information extraction tasks like Named Entity Recognition (NER), using prompts or instructions, still falls short of supervised baselines. The reason for this performance gap can be attributed to the fundamental disparity between NER and LLMs. NER is inherently a sequence labeling task, where the model must assign entity-type labels to individual tokens within a sentence. In contrast, LLMs are designed as a text generation task. This distinction between semantic labeling and text generation leads to subpar performance. In this paper, we transform the NER task into a text-generation task that can be readily adapted by LLMs. This involves enhancing source sentences with task-specific instructions and answer choices, allowing for the identification of entities and their types within natural language. We harness the strength of LLMs by integrating supervised learning within them. The goal of this combined strategy is to boost the performance of LLMs in extraction tasks like NER while simultaneously addressing hallucination issues often observed in LLM-generated content. A novel corpus Contract NER comprising seven frequently observed contract categories, encompassing named entities associated with 18 distinct legal entity types is released along with our baseline models. Our models and dataset are available to the community for future research * .

Application of Deep Learning in Generating Structured Radiology Reports: A Transformer-Based Technique

Since radiology reports needed for clinical practice and research are written and stored in free-text narrations, extraction of relative information for further analysis is difficult. In these circumstances, natural language processing (NLP) techniques can facilitate automatic information extraction and transformation of free-text formats to structured data. In recent years, deep learning (DL)-based models have been adapted for NLP experiments with promising results. Despite the significant potential of DL models based on artificial neural networks (ANN) and convolutional neural networks (CNN), the models face some limitations to implement in clinical practice. Transformers, another new DL architecture, have been increasingly applied to improve the process. Therefore, in this study, we propose a transformer-based fine-grained named entity recognition (NER) architecture for clinical information extraction. We collected 88 abdominopelvic sonography reports in free-text formats and annotated them based on our developed information schema. The text-to-text transfer transformer model (T5) and Scifive, a pre-trained domain-specific adaptation of the T5 model, were applied for fine-tuning to extract entities and relations and transform the input into a structured format. Our transformer-based model in this study outperformed previously applied approaches such as ANN and CNN models based on ROUGE-1, ROUGE-2, ROUGE-L, and BLEU scores of 0.816, 0.668, 0.528, and 0.743, respectively, while providing an interpretable structured report.

ScanBank: A Benchmark Dataset for Figure Extraction from Scanned Electronic Theses and Dissertations

We focus on electronic theses and dissertations (ETDs), aiming to improve access and expand their utility, since more than 6 million are publicly available, and they constitute an important corpus to aid research and education across disciplines. The corpus is growing as new born-digital documents are included, and since millions of older theses and dissertations have been converted to digital form to be disseminated electronically in institutional repositories. In ETDs, as with other scholarly works, figures and tables can communicate a large amount of information in a concise way. Although methods have been proposed for extracting figures and tables from born-digital PDFs, they do not work well with scanned ETDs. Considering this problem, our assessment of state-of-the-art figure extraction systems is that the reason they do not function well on scanned PDFs is that they have only been trained on born-digital documents. To address this limitation, we present ScanBank, a new dataset containing 10 thousand scanned page images, manually labeled by humans as to the presence of the 3.3 thousand figures or tables found therein. We use this dataset to train a deep neural network model based on YOLOv5 to accurately extract figures and tables from scanned ETDs. We pose and answer important research questions aimed at finding better methods for figure extraction from scanned documents. One of those concerns the value for training, of data augmentation techniques applied to born-digital documents which are used to train models better suited for figure extraction from scanned documents. To the best of our knowledge, ScanBank is the first manually annotated dataset for figure and table extraction for scanned ETDs. A YOLOv5-based model, trained on ScanBank, outperforms existing comparable open-source and freely available baseline methods by a considerable margin.

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

The Edinburgh International Accents of English Corpus: Towards the Democratization of English ASR

English is the most widely spoken language in the world, used daily by millions of people as a first or second language in many different contexts. As a result, there are many varieties of English. Although the great many advances in English automatic speech recognition (ASR) over the past decades, results are usually reported based on test datasets which fail to represent the diversity of English as spoken today around the globe. We present the first release of The Edinburgh International Accents of English Corpus (EdAcc). This dataset attempts to better represent the wide diversity of English, encompassing almost 40 hours of dyadic video call conversations between friends. Unlike other datasets, EdAcc includes a wide range of first and second-language varieties of English and a linguistic background profile of each speaker. Results on latest public, and commercial models show that EdAcc highlights shortcomings of current English ASR models. The best performing model, trained on 680 thousand hours of transcribed data, obtains an average of 19.7% word error rate (WER) -- in contrast to the 2.7% WER obtained when evaluated on US English clean read speech. Across all models, we observe a drop in performance on Indian, Jamaican, and Nigerian English speakers. Recordings, linguistic backgrounds, data statement, and evaluation scripts are released on our website (https://groups.inf.ed.ac.uk/edacc/) under CC-BY-SA license.

Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing

Motivation: A perennial challenge for biomedical researchers and clinical practitioners is to stay abreast with the rapid growth of publications and medical notes. Natural language processing (NLP) has emerged as a promising direction for taming information overload. In particular, large neural language models facilitate transfer learning by pretraining on unlabeled text, as exemplified by the successes of BERT models in various NLP applications. However, fine-tuning such models for an end task remains challenging, especially with small labeled datasets, which are common in biomedical NLP. Results: We conduct a systematic study on fine-tuning stability in biomedical NLP. We show that finetuning performance may be sensitive to pretraining settings, especially in low-resource domains. Large models have potential to attain better performance, but increasing model size also exacerbates finetuning instability. We thus conduct a comprehensive exploration of techniques for addressing fine-tuning instability. We show that these techniques can substantially improve fine-tuning performance for lowresource biomedical NLP applications. Specifically, freezing lower layers is helpful for standard BERT-BASE models, while layerwise decay is more effective for BERT-LARGE and ELECTRA models. For low-resource text similarity tasks such as BIOSSES, reinitializing the top layer is the optimal strategy. Overall, domainspecific vocabulary and pretraining facilitate more robust models for fine-tuning. Based on these findings, we establish new state of the art on a wide range of biomedical NLP applications. Availability and implementation: To facilitate progress in biomedical NLP, we release our state-of-the-art pretrained and fine-tuned models: https://aka.ms/BLURB.

Meaning at the Planck scale? Contextualized word embeddings for doing history, philosophy, and sociology of science

This paper explores the potential of contextualized word embeddings (CWEs) as a new tool in the history, philosophy, and sociology of science (HPSS) for studying contextual and evolving meanings of scientific concepts. Using the term "Planck" as a test case, I evaluate five BERT-based models with varying degrees of domain-specific pretraining, including my custom model Astro-HEP-BERT, trained on the Astro-HEP Corpus, a dataset containing 21.84 million paragraphs from 600,000 articles in astrophysics and high-energy physics. For this analysis, I compiled two labeled datasets: (1) the Astro-HEP-Planck Corpus, consisting of 2,900 labeled occurrences of "Planck" sampled from 1,500 paragraphs in the Astro-HEP Corpus, and (2) a physics-related Wikipedia dataset comprising 1,186 labeled occurrences of "Planck" across 885 paragraphs. Results demonstrate that the domain-adapted models outperform the general-purpose ones in disambiguating the target term, predicting its known meanings, and generating high-quality sense clusters, as measured by a novel purity indicator I developed. Additionally, this approach reveals semantic shifts in the target term over three decades in the unlabeled Astro-HEP Corpus, highlighting the emergence of the Planck space mission as a dominant sense. The study underscores the importance of domain-specific pretraining for analyzing scientific language and demonstrates the cost-effectiveness of adapting pretrained models for HPSS research. By offering a scalable and transferable method for modeling the meanings of scientific concepts, CWEs open up new avenues for investigating the socio-historical dynamics of scientific discourses.

Using multiple ASR hypotheses to boost i18n NLU performance

Current voice assistants typically use the best hypothesis yielded by their Automatic Speech Recognition (ASR) module as input to their Natural Language Understanding (NLU) module, thereby losing helpful information that might be stored in lower-ranked ASR hypotheses. We explore the change in performance of NLU associated tasks when utilizing five-best ASR hypotheses when compared to status quo for two language datasets, German and Portuguese. To harvest information from the ASR five-best, we leverage extractive summarization and joint extractive-abstractive summarization models for Domain Classification (DC) experiments while using a sequence-to-sequence model with a pointer generator network for Intent Classification (IC) and Named Entity Recognition (NER) multi-task experiments. For the DC full test set, we observe significant improvements of up to 7.2% and 15.5% in micro-averaged F1 scores, for German and Portuguese, respectively. In cases where the best ASR hypothesis was not an exact match to the transcribed utterance (mismatched test set), we see improvements of up to 6.7% and 8.8% micro-averaged F1 scores, for German and Portuguese, respectively. For IC and NER multi-task experiments, when evaluating on the mismatched test set, we see improvements across all domains in German and in 17 out of 19 domains in Portuguese (improvements based on change in SeMER scores). Our results suggest that the use of multiple ASR hypotheses, as opposed to one, can lead to significant performance improvements in the DC task for these non-English datasets. In addition, it could lead to significant improvement in the performance of IC and NER tasks in cases where the ASR model makes mistakes.

Pretraining Language Models for Diachronic Linguistic Change Discovery

Large language models (LLMs) have shown potential as tools for scientific discovery. This has engendered growing interest in their use in humanistic disciplines, such as historical linguistics and literary studies. These fields often construct arguments on the basis of delineations like genre, or more inflexibly, time period. Although efforts have been made to restrict inference to specific domains via fine-tuning or model editing, we posit that the only true guarantee is domain-restricted pretraining -- typically, a data- and compute-expensive proposition. We show that efficient pretraining techniques can produce useful models over corpora too large for easy manual inspection but too small for "typical" LLM approaches. We employ a novel date-attribution pipeline in order to obtain a temporally-segmented dataset of five 10-million-word slices. We train two corresponding five-model batteries over these corpus segments, efficient pretraining and Llama3-8B parameter efficiently finetuned. We find that the pretrained models are faster to train than the finetuned baselines and that they better respect the historical divisions of our corpus. Emphasizing speed and precision over a-historical comprehensiveness enables a number of novel approaches to hypothesis discovery and testing in our target fields. Taking up diachronic linguistics as a testbed, we show that our method enables the detection of a diverse set of phenomena, including en masse lexical change, non-lexical (grammatical and morphological) change, and word sense introduction/obsolescence. We provide a ready-to-use pipeline that allows extension of our approach to other target fields with only minimal adaptation.

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for better language representations. Interestingly, in the absence of enough clinical data to train a model from scratch, we applied mixed-domain pretraining and cross-domain transfer approaches to generate a performant bio-clinical model suitable for real-world clinical data. We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports. When compared against the competitive mBERT and BETO models, we outperform them in all NER tasks by a significant margin. Finally, we studied the impact of the model's vocabulary on the NER performances by offering an interesting vocabulary-centric analysis. The results confirm that domain-specific pretraining is fundamental to achieving higher performances in downstream NER tasks, even within a mid-resource scenario. To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine. Our best models are freely available in the HuggingFace hub: https://huggingface.co/BSC-TeMU.

Datasets for Large Language Models: A Comprehensive Survey

This paper embarks on an exploration into the Large Language Model (LLM) datasets, which play a crucial role in the remarkable advancements of LLMs. The datasets serve as the foundational infrastructure analogous to a root system that sustains and nurtures the development of LLMs. Consequently, examination of these datasets emerges as a critical topic in research. In order to address the current lack of a comprehensive overview and thorough analysis of LLM datasets, and to gain insights into their current status and future trends, this survey consolidates and categorizes the fundamental aspects of LLM datasets from five perspectives: (1) Pre-training Corpora; (2) Instruction Fine-tuning Datasets; (3) Preference Datasets; (4) Evaluation Datasets; (5) Traditional Natural Language Processing (NLP) Datasets. The survey sheds light on the prevailing challenges and points out potential avenues for future investigation. Additionally, a comprehensive review of the existing available dataset resources is also provided, including statistics from 444 datasets, covering 8 language categories and spanning 32 domains. Information from 20 dimensions is incorporated into the dataset statistics. The total data size surveyed surpasses 774.5 TB for pre-training corpora and 700M instances for other datasets. We aim to present the entire landscape of LLM text datasets, serving as a comprehensive reference for researchers in this field and contributing to future studies. Related resources are available at: https://github.com/lmmlzn/Awesome-LLMs-Datasets.

Dolma: an Open Corpus of Three Trillion Tokens for Language Model Pretraining Research

Language models have become a critical technology to tackling a wide range of natural language processing tasks, yet many details about how the best-performing language models were developed are not reported. In particular, information about their pretraining corpora is seldom discussed: commercial language models rarely provide any information about their data; even open models rarely release datasets they are trained on, or an exact recipe to reproduce them. As a result, it is challenging to conduct certain threads of language modeling research, such as understanding how training data impacts model capabilities and shapes their limitations. To facilitate open research on language model pretraining, we release Dolma, a three trillion tokens English corpus, built from a diverse mixture of web content, scientific papers, code, public-domain books, social media, and encyclopedic materials. In addition, we open source our data curation toolkit to enable further experimentation and reproduction of our work. In this report, we document Dolma, including its design principles, details about its construction, and a summary of its contents. We interleave this report with analyses and experimental results from training language models on intermediate states of Dolma to share what we have learned about important data curation practices, including the role of content or quality filters, deduplication, and multi-source mixing. Dolma has been used to train OLMo, a state-of-the-art, open language model and framework designed to build and study the science of language modeling.

BhashaVerse : Translation Ecosystem for Indian Subcontinent Languages

This paper focuses on developing translation models and related applications for 36 Indian languages, including Assamese, Awadhi, Bengali, Bhojpuri, Braj, Bodo, Dogri, English, Konkani, Gondi, Gujarati, Hindi, Hinglish, Ho, Kannada, Kangri, Kashmiri (Arabic and Devanagari), Khasi, Mizo, Magahi, Maithili, Malayalam, Marathi, Manipuri (Bengali and Meitei), Nepali, Oriya, Punjabi, Sanskrit, Santali, Sinhala, Sindhi (Arabic and Devanagari), Tamil, Tulu, Telugu, and Urdu. Achieving this requires parallel and other types of corpora for all 36 * 36 language pairs, addressing challenges like script variations, phonetic differences, and syntactic diversity. For instance, languages like Kashmiri and Sindhi, which use multiple scripts, demand script normalization for alignment, while low-resource languages such as Khasi and Santali require synthetic data augmentation to ensure sufficient coverage and quality. To address these challenges, this work proposes strategies for corpus creation by leveraging existing resources, developing parallel datasets, generating domain-specific corpora, and utilizing synthetic data techniques. Additionally, it evaluates machine translation across various dimensions, including standard and discourse-level translation, domain-specific translation, reference-based and reference-free evaluation, error analysis, and automatic post-editing. By integrating these elements, the study establishes a comprehensive framework to improve machine translation quality and enable better cross-lingual communication in India's linguistically diverse ecosystem.

ChrEn: Cherokee-English Machine Translation for Endangered Language Revitalization

Cherokee is a highly endangered Native American language spoken by the Cherokee people. The Cherokee culture is deeply embedded in its language. However, there are approximately only 2,000 fluent first language Cherokee speakers remaining in the world, and the number is declining every year. To help save this endangered language, we introduce ChrEn, a Cherokee-English parallel dataset, to facilitate machine translation research between Cherokee and English. Compared to some popular machine translation language pairs, ChrEn is extremely low-resource, only containing 14k sentence pairs in total. We split our parallel data in ways that facilitate both in-domain and out-of-domain evaluation. We also collect 5k Cherokee monolingual data to enable semi-supervised learning. Besides these datasets, we propose several Cherokee-English and English-Cherokee machine translation systems. We compare SMT (phrase-based) versus NMT (RNN-based and Transformer-based) systems; supervised versus semi-supervised (via language model, back-translation, and BERT/Multilingual-BERT) methods; as well as transfer learning versus multilingual joint training with 4 other languages. Our best results are 15.8/12.7 BLEU for in-domain and 6.5/5.0 BLEU for out-of-domain Chr-En/EnChr translations, respectively, and we hope that our dataset and systems will encourage future work by the community for Cherokee language revitalization. Our data, code, and demo will be publicly available at https://github.com/ZhangShiyue/ChrEn

ERNIE-Gram: Pre-Training with Explicitly N-Gram Masked Language Modeling for Natural Language Understanding

Coarse-grained linguistic information, such as named entities or phrases, facilitates adequately representation learning in pre-training. Previous works mainly focus on extending the objective of BERT's Masked Language Modeling (MLM) from masking individual tokens to contiguous sequences of n tokens. We argue that such contiguously masking method neglects to model the intra-dependencies and inter-relation of coarse-grained linguistic information. As an alternative, we propose ERNIE-Gram, an explicitly n-gram masking method to enhance the integration of coarse-grained information into pre-training. In ERNIE-Gram, n-grams are masked and predicted directly using explicit n-gram identities rather than contiguous sequences of n tokens. Furthermore, ERNIE-Gram employs a generator model to sample plausible n-gram identities as optional n-gram masks and predict them in both coarse-grained and fine-grained manners to enable comprehensive n-gram prediction and relation modeling. We pre-train ERNIE-Gram on English and Chinese text corpora and fine-tune on 19 downstream tasks. Experimental results show that ERNIE-Gram outperforms previous pre-training models like XLNet and RoBERTa by a large margin, and achieves comparable results with state-of-the-art methods. The source codes and pre-trained models have been released at https://github.com/PaddlePaddle/ERNIE.

CoVERT: A Corpus of Fact-checked Biomedical COVID-19 Tweets

Over the course of the COVID-19 pandemic, large volumes of biomedical information concerning this new disease have been published on social media. Some of this information can pose a real danger to people's health, particularly when false information is shared, for instance recommendations on how to treat diseases without professional medical advice. Therefore, automatic fact-checking resources and systems developed specifically for the medical domain are crucial. While existing fact-checking resources cover COVID-19-related information in news or quantify the amount of misinformation in tweets, there is no dataset providing fact-checked COVID-19-related Twitter posts with detailed annotations for biomedical entities, relations and relevant evidence. We contribute CoVERT, a fact-checked corpus of tweets with a focus on the domain of biomedicine and COVID-19-related (mis)information. The corpus consists of 300 tweets, each annotated with medical named entities and relations. We employ a novel crowdsourcing methodology to annotate all tweets with fact-checking labels and supporting evidence, which crowdworkers search for online. This methodology results in moderate inter-annotator agreement. Furthermore, we use the retrieved evidence extracts as part of a fact-checking pipeline, finding that the real-world evidence is more useful than the knowledge indirectly available in pretrained language models.

How far is Language Model from 100% Few-shot Named Entity Recognition in Medical Domain

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such as name entity recognition (NER) in the general domain. (We define SLMs as pre-trained models with fewer parameters compared to models like GPT-3/3.5/4, such as T5, BERT, and others.) Nevertheless, their efficacy in the medical section remains uncertain and the performance of medical NER always needs high accuracy because of the particularity of the field. This paper aims to provide a thorough investigation to compare the performance of LMs in medical few-shot NER and answer How far is LMs from 100\% Few-shot NER in Medical Domain, and moreover to explore an effective entity recognizer to help improve the NER performance. Based on our extensive experiments conducted on 16 NER models spanning from 2018 to 2023, our findings clearly indicate that LLMs outperform SLMs in few-shot medical NER tasks, given the presence of suitable examples and appropriate logical frameworks. Despite the overall superiority of LLMs in few-shot medical NER tasks, it is important to note that they still encounter some challenges, such as misidentification, wrong template prediction, etc. Building on previous findings, we introduce a simple and effective method called RT (Retrieving and Thinking), which serves as retrievers, finding relevant examples, and as thinkers, employing a step-by-step reasoning process. Experimental results show that our proposed RT framework significantly outperforms the strong open baselines on the two open medical benchmark datasets

Selecting Influential Samples for Long Context Alignment via Homologous Models' Guidance and Contextual Awareness Measurement

The expansion of large language models to effectively handle instructions with extremely long contexts has yet to be fully investigated. The primary obstacle lies in constructing a high-quality long instruction-following dataset devised for long context alignment. Existing studies have attempted to scale up the available data volume by synthesizing long instruction-following samples. However, indiscriminately increasing the quantity of data without a well-defined strategy for ensuring data quality may introduce low-quality samples and restrict the final performance. To bridge this gap, we aim to address the unique challenge of long-context alignment, i.e., modeling the long-range dependencies for handling instructions and lengthy input contexts. We propose GATEAU, a novel framework designed to identify the influential and high-quality samples enriched with long-range dependency relations by utilizing crafted Homologous Models' Guidance (HMG) and Contextual Awareness Measurement (CAM). Specifically, HMG attempts to measure the difficulty of generating corresponding responses due to the long-range dependencies, using the perplexity scores of the response from two homologous models with different context windows. Also, the role of CAM is to measure the difficulty of understanding the long input contexts due to long-range dependencies by evaluating whether the model's attention is focused on important segments. Built upon both proposed methods, we select the most challenging samples as the influential data to effectively frame the long-range dependencies, thereby achieving better performance of LLMs. Comprehensive experiments indicate that GATEAU effectively identifies samples enriched with long-range dependency relations and the model trained on these selected samples exhibits better instruction-following and long-context understanding capabilities.