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Jun 9

FNSPID: A Comprehensive Financial News Dataset in Time Series

Financial market predictions utilize historical data to anticipate future stock prices and market trends. Traditionally, these predictions have focused on the statistical analysis of quantitative factors, such as stock prices, trading volumes, inflation rates, and changes in industrial production. Recent advancements in large language models motivate the integrated financial analysis of both sentiment data, particularly market news, and numerical factors. Nonetheless, this methodology frequently encounters constraints due to the paucity of extensive datasets that amalgamate both quantitative and qualitative sentiment analyses. To address this challenge, we introduce a large-scale financial dataset, namely, Financial News and Stock Price Integration Dataset (FNSPID). It comprises 29.7 million stock prices and 15.7 million time-aligned financial news records for 4,775 S&P500 companies, covering the period from 1999 to 2023, sourced from 4 stock market news websites. We demonstrate that FNSPID excels existing stock market datasets in scale and diversity while uniquely incorporating sentiment information. Through financial analysis experiments on FNSPID, we propose: (1) the dataset's size and quality significantly boost market prediction accuracy; (2) adding sentiment scores modestly enhances performance on the transformer-based model; (3) a reproducible procedure that can update the dataset. Completed work, code, documentation, and examples are available at github.com/Zdong104/FNSPID. FNSPID offers unprecedented opportunities for the financial research community to advance predictive modeling and analysis.

  • 3 authors
·
Feb 8, 2024

Few-Shot Learning for Clinical Natural Language Processing Using Siamese Neural Networks

Clinical Natural Language Processing (NLP) has become an emerging technology in healthcare that leverages a large amount of free-text data in electronic health records (EHRs) to improve patient care, support clinical decisions, and facilitate clinical and translational science research. Recently, deep learning has achieved state-of-the-art performance in many clinical NLP tasks. However, training deep learning models usually requires large annotated datasets, which are normally not publicly available and can be time-consuming to build in clinical domains. Working with smaller annotated datasets is typical in clinical NLP and therefore, ensuring that deep learning models perform well is crucial for the models to be used in real-world applications. A widely adopted approach is fine-tuning existing Pre-trained Language Models (PLMs), but these attempts fall short when the training dataset contains only a few annotated samples. Few-Shot Learning (FSL) has recently been investigated to tackle this problem. Siamese Neural Network (SNN) has been widely utilized as an FSL approach in computer vision, but has not been studied well in NLP. Furthermore, the literature on its applications in clinical domains is scarce. In this paper, we propose two SNN-based FSL approaches for clinical NLP, including Pre-Trained SNN (PT-SNN) and SNN with Second-Order Embeddings (SOE-SNN). We evaluated the proposed approaches on two clinical tasks, namely clinical text classification and clinical named entity recognition. We tested three few-shot settings including 4-shot, 8-shot, and 16-shot learning. Both clinical NLP tasks were benchmarked using three PLMs, including BERT,BioBERT, and BioClinicalBERT. The experimental results verified the effectiveness of the proposed SNN-based FSL approaches in both NLP tasks.

  • 3 authors
·
Aug 31, 2022

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.

  • 9 authors
·
Apr 30, 2021

Adposition and Case Supersenses v2.6: Guidelines for English

This document offers a detailed linguistic description of SNACS (Semantic Network of Adposition and Case Supersenses; Schneider et al., 2018), an inventory of 52 semantic labels ("supersenses") that characterize the use of adpositions and case markers at a somewhat coarse level of granularity, as demonstrated in the STREUSLE corpus (https://github.com/nert-nlp/streusle/ ; version 4.5 tracks guidelines version 2.6). Though the SNACS inventory aspires to be universal, this document is specific to English; documentation for other languages will be published separately. Version 2 is a revision of the supersense inventory proposed for English by Schneider et al. (2015, 2016) (henceforth "v1"), which in turn was based on previous schemes. The present inventory was developed after extensive review of the v1 corpus annotations for English, plus previously unanalyzed genitive case possessives (Blodgett and Schneider, 2018), as well as consideration of adposition and case phenomena in Hebrew, Hindi, Korean, and German. Hwang et al. (2017) present the theoretical underpinnings of the v2 scheme. Schneider et al. (2018) summarize the scheme, its application to English corpus data, and an automatic disambiguation task. Liu et al. (2021) offer an English Lexical Semantic Recognition tagger that includes SNACS labels in its output. This documentation can also be browsed alongside corpus data on the Xposition website (Gessler et al., 2022): http://www.xposition.org/

  • 11 authors
·
Apr 7, 2017

PIIBench: A Unified Multi-Source Benchmark Corpus for Personally Identifiable Information Detection

We present PIIBench, a unified benchmark corpus for Personally Identifiable Information (PII) detection in natural language text. Existing resources for PII detection are fragmented across domain-specific corpora with mutually incompatible annotation schemes, preventing systematic comparison of detection systems. We consolidate ten publicly available datasets spanning synthetic PII corpora, multilingual Named Entity Recognition (NER) benchmarks, and financial domain annotated text, yielding a corpus of 2,369,883 annotated sequences and 3.35 million entity mentions across 48 canonical PII entity types. We develop a principled normalization pipeline that maps 80+ source-specific label variants to a standardized BIO tagging scheme, applies frequency-based suppression of near absent entity types, and produces stratified 80/10/10 train/validation/test splits preserving source distribution. To establish baseline difficulty, we evaluate eight published systems spanning rule-based engines (Microsoft Presidio), general purpose NER models (spaCy, BERT-base NER, XLM-RoBERTa NER, SpanMarker mBERT, SpanMarker BERT), a PII-specific model (Piiranha DeBERTa), and a financial NER specialist (XtremeDistil FiNER). All systems achieve span-level F1 below 0.14, with the best system (Presidio, F1=0.1385) still producing zero recall on most entity types. These results directly quantify the domain-silo problem and demonstrate that PIIBench presents a substantially harder and more comprehensive evaluation challenge than any existing single source PII dataset. The dataset construction pipeline and benchmark evaluation code are publicly available at https://github.com/pritesh-2711/pii-bench.

  • 1 authors
·
Apr 16

A New Data Representation Based on Training Data Characteristics to Extract Drug Named-Entity in Medical Text

One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text is special and has unique characteristics. In addition, the medical text mining poses more challenges, e.g., more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug. The mining is even more challenging due to the lack of labeled dataset sources and external knowledge, as well as multiple token representations for a single drug name that is more common in the real application setting. Although many approaches have been proposed to overwhelm the task, some problems remained with poor F-score performance (less than 0.75). This paper presents a new treatment in data representation techniques to overcome some of those challenges. We propose three data representation techniques based on the characteristics of word distribution and word similarities as a result of word embedding training. The first technique is evaluated with the standard NN model, i.e., MLP (Multi-Layer Perceptrons). The second technique involves two deep network classifiers, i.e., DBN (Deep Belief Networks), and SAE (Stacked Denoising Encoders). The third technique represents the sentence as a sequence that is evaluated with a recurrent NN model, i.e., LSTM (Long Short Term Memory). In extracting the drug name entities, the third technique gives the best F-score performance compared to the state of the art, with its average F-score being 0.8645.

  • 3 authors
·
Oct 6, 2016

SemEval-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

  • 6 authors
·
May 4, 2023

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

  • 8 authors
·
Sep 14, 2023

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.

  • 5 authors
·
Apr 18, 2023

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.

  • 2 authors
·
Dec 19, 2018

FluoroSAM: A Language-promptable Foundation Model for Flexible X-ray Image Segmentation

Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) -- machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability -- have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM's performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

  • 8 authors
·
Mar 12, 2024

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.

  • 11 authors
·
Apr 16, 2023

PPI2Text: Captioning Protein-Protein Interactions with Coordinate-Aligned Pair-Map Decoding

Protein-protein interaction (PPI) modeling has been widely studied as a binary or multi-label classification task. While emerging multimodal large language models (LLMs) can now describe single proteins, they remain unable to generate free-form descriptions of interactions between protein pairs. Moving beyond controlled vocabulary annotations, we propose to model PPI using free-text description, enabling richer expressiveness, improved interpretability, and better integration with literature knowledge base. We present PPI2Text, a multimodal LLM for free-form PPI captioning from amino acid sequences, that encodes each protein using ESM3 encoder, constructs a pair map from the two representations to capture interactions across all residue pairs, and autoregressively generates descriptions using a Qwen3 language decoder. We further introduce PaCo-RoPE, a coordinate-aligned positional encoding that aligns each axis of the pair grid with the residue positions of the corresponding protein. In addition, we release PPI2Text-Dataset, a 351k-pair corpus of free-form PPI descriptions aggregated from ten curated biological databases and further synthesized with Gemini under evidence-tiered prompting. PPI2Text consistently outperforms strong baselines across multiple ablation settings and evaluation protocols. It not only achieves higher scores on linguistic metrics against synthesized references, but also excels on factuality metrics, where an LLM-based judge evaluates outputs against raw biological evidence.

  • 7 authors
·
May 8

Diagnosing FP4 inference: a layer-wise and block-wise sensitivity analysis of NVFP4 and MXFP4

Quantization addresses the high resource demand for large language models (LLMs) by alleviating memory pressure and bandwidth congestion and providing significantly scaled compute power with a tolerable impact on accuracy. Four-bit floating point (FP4), the lowest-precision format that preserves essential numerical properties such as exponent and sign, has begun to be adopted in cutting-edge architectures, including Blackwell and AMD CDNA, to support LLM quantization and reduce deployment costs. Although aggressive quantization can yield efficiency gains, the quantization sensitivity of within-transformer layers and whether these sensitivities generalize across existing FP4 formats and model scales remain underexplored. To elucidate quantization sensitivity, this study conducts a systematic analysis of two FP4 formats, MXFP4 and NVFP4, across three Qwen2.5 model scales (0.5B, 7B, and 14B), using controlled component-wise and block-wise isolation methodologies. We observe that MLP up- and down-projection layers consistently dominate in terms of sensitivity, while gate and attention projections are moderately and substantially less sensitive to FP4 quantization, respectively. We further find that sensitivity does not universally localize to the final blocks, but early blocks can be highly sensitive, particularly under MXFP4. Our results provide a diagnostic characterization of the inference behavior of FP4 across components, depths, and FP4 formats.

  • 3 authors
·
Mar 4

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.

  • 1 authors
·
Nov 29, 2024

MedPT: A Massive Medical Question Answering Dataset for Brazilian-Portuguese Speakers

While large language models (LLMs) show transformative potential in healthcare, their development remains focused on high-resource languages, creating a critical barrier for others as simple translation fails to capture unique clinical and cultural nuances, such as endemic diseases. To address this, we introduce MedPT, the first large-scale, real-world corpus for Brazilian Portuguese, comprising 384,095 authentic question-answer pairs from patient-doctor interactions. The dataset underwent a meticulous multi-stage curation protocol, using a hybrid quantitative-qualitative analysis to filter noise and contextually enrich thousands of ambiguous queries. We further augmented the corpus via LLM-driven annotation, classifying questions into seven semantic types to capture user intent. Our analysis reveals its thematic breadth (3,200 topics) and unique linguistic properties, like the natural asymmetry in patient-doctor communication. To validate its utility, we benchmark a medical specialty routing task: fine-tuning a 1.7B parameter model achieves an outstanding 94\% F1-score on a 20-class setup. Furthermore, our qualitative error analysis shows misclassifications are not random but reflect genuine clinical ambiguities (e.g., between comorbid conditions), proving the dataset's deep semantic richness. We publicly release MedPT to foster the development of more equitable, accurate, and culturally-aware medical technologies for the Portuguese-speaking world.

  • 6 authors
·
Nov 14, 2025

Segment as You Wish -- Free-Form Language-Based Segmentation for Medical Images

Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.

  • 7 authors
·
Oct 2, 2024

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.

  • 3 authors
·
Mar 19, 2025

Finding Duplicates in 1.1M BDD Steps: cukereuse, a Paraphrase-Robust Static Detector for Cucumber and Gherkin

Behaviour-Driven Development (BDD) suites accumulate step-text duplication whose maintenance cost is established in prior work. Existing detection techniques require running the tests (Binamungu et al., 2018-2023) or are confined to a single organisation (Irshad et al., 2020-2022), leaving a gap: a purely static, paraphrase-robust, step-level detector usable on any repository. We fill the gap with cukereuse, an open-source Python CLI combining exact hashing, Levenshtein ratio, and sentence-transformer embeddings in a layered pipeline, released alongside an empirical corpus of 347 public GitHub repositories, 23,667 parsed .feature files, and 1,113,616 Gherkin steps. The step-weighted exact-duplicate rate is 80.2 %; the median-repository rate is 58.6 % (Spearman rho = 0.51 with size). The top hybrid cluster groups 20.7k occurrences across 2.2k files. Against 1,020 pairs manually labelled by the three authors under a released rubric (inter-annotator Fleiss' kappa = 0.84 on a 60-pair overlap), we report precision, recall, and F1 with bootstrap 95 % CIs under two protocols: the primary rubric and a score-free second-pass relabelling. The strongest honest pair-level number is near-exact at F1 = 0.822 on score-free labels; the primary-rubric semantic F1 = 0.906 is inflated by a stratification artefact that pins recall at 1.000. Lexical baselines (SourcererCC-style, NiCad-style) reach primary F1 = 0.761 and 0.799. The paper also presents a CDN-structured critique of Gherkin (Cognitive Dimensions of Notations); eight of fourteen dimensions are rated problematic or unsupported. The tool, corpus, labelled pairs, rubric, and pipeline are released under permissive licences.

  • 3 authors
·
Apr 21 1

SpiroLLM: Finetuning Pretrained LLMs to Understand Spirogram Time Series with Clinical Validation in COPD Reporting

Chronic Obstructive Pulmonary Disease (COPD), a major chronic respiratory disease with persistent airflow limitation, is a leading global cause of disability and mortality. Respiratory spirogram time series, routinely collected during pulmonary function tests (PFTs), play a critical role in the early detection of repsiratory diseases and in monitoring lung function over time. However, most current AI models for COPD diagnosis are limited to outputting classification results without providing a rationale for their diagnostic process, while current Large Language Models (LLMs) cannot understand spirograms yet, which severely limits their clinical trust and adoption. To tackle this challenge, we leverage a cohort of 234,028 individuals from the UK Biobank (UKB) to propose SpiroLLM, the first multimodal large language model that can understand spirogram. The model extracts morphological features from respiratory curves via a SpiroEncoder and aligns them with PFT numerical values in a unified latent space using a SpiroProjector, ultimately empowering a large language model to generate a comprehensive diagnostic report. Experimental results confirm that SpiroLLM achieved a diagnostic AUROC of 0.8980 (95% CI: 0.8820-0.9132). In a robustness test with missing core data, it maintained a 100% valid response rate, far surpassing the 13.4% of a text-only model and showcasing the superiority of its multimodal design. This work demonstrates the substantial potential of deeply fusing physiological signals with large language models, establishing a new paradigm for the next generation of interpretable and reliable clinical decision support tools.

  • 8 authors
·
Jul 21, 2025

DepNeCTI: Dependency-based Nested Compound Type Identification for Sanskrit

Multi-component compounding is a prevalent phenomenon in Sanskrit, and understanding the implicit structure of a compound's components is crucial for deciphering its meaning. Earlier approaches in Sanskrit have focused on binary compounds and neglected the multi-component compound setting. This work introduces the novel task of nested compound type identification (NeCTI), which aims to identify nested spans of a multi-component compound and decode the implicit semantic relations between them. To the best of our knowledge, this is the first attempt in the field of lexical semantics to propose this task. We present 2 newly annotated datasets including an out-of-domain dataset for this task. We also benchmark these datasets by exploring the efficacy of the standard problem formulations such as nested named entity recognition, constituency parsing and seq2seq, etc. We present a novel framework named DepNeCTI: Dependency-based Nested Compound Type Identifier that surpasses the performance of the best baseline with an average absolute improvement of 13.1 points F1-score in terms of Labeled Span Score (LSS) and a 5-fold enhancement in inference efficiency. In line with the previous findings in the binary Sanskrit compound identification task, context provides benefits for the NeCTI task. The codebase and datasets are publicly available at: https://github.com/yaswanth-iitkgp/DepNeCTI

  • 7 authors
·
Oct 14, 2023

MLLM-HWSI: A Multimodal Large Language Model for Hierarchical Whole Slide Image Understanding

Whole Slide Images (WSIs) exhibit hierarchical structure, where diagnostic information emerges from cellular morphology, regional tissue organization, and global context. Existing Computational Pathology (CPath) Multimodal Large Language Models (MLLMs) typically compress an entire WSI into a single embedding, which hinders fine-grained grounding and ignores how pathologists synthesize evidence across different scales. We introduce MLLM-HWSI, a Hierarchical WSI-level MLLM that aligns visual features with pathology language at four distinct scales, cell as word, patch as phrase, region as sentence, and WSI as paragraph to support interpretable evidence-grounded reasoning. MLLM-HWSI decomposes each WSI into multi-scale embeddings with scale-specific projectors and jointly enforces (i) a hierarchical contrastive objective and (ii) a cross-scale consistency loss, preserving semantic coherence from cells to the WSI. We compute diagnostically relevant patches and aggregate segmented cell embeddings into a compact cellular token per-patch using a lightweight Cell-Cell Attention Fusion (CCAF) transformer. The projected multi-scale tokens are fused with text tokens and fed to an instruction-tuned LLM for open-ended reasoning, VQA, report, and caption generation tasks. Trained in three stages, MLLM-HWSI achieves new SOTA results on 13 WSI-level benchmarks across six CPath tasks. By aligning language with multi-scale visual evidence, MLLM-HWSI provides accurate, interpretable outputs that mirror diagnostic workflows and advance holistic WSI understanding. Code is available at: https://github.com/BasitAlawode/HWSI-MLLM{GitHub}.

  • 9 authors
·
Mar 24

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.

  • 4 authors
·
Sep 10, 2024

What Does This Acronym Mean? Introducing a New Dataset for Acronym Identification and Disambiguation

Acronyms are the short forms of phrases that facilitate conveying lengthy sentences in documents and serve as one of the mainstays of writing. Due to their importance, identifying acronyms and corresponding phrases (i.e., acronym identification (AI)) and finding the correct meaning of each acronym (i.e., acronym disambiguation (AD)) are crucial for text understanding. Despite the recent progress on this task, there are some limitations in the existing datasets which hinder further improvement. More specifically, limited size of manually annotated AI datasets or noises in the automatically created acronym identification datasets obstruct designing advanced high-performing acronym identification models. Moreover, the existing datasets are mostly limited to the medical domain and ignore other domains. In order to address these two limitations, we first create a manually annotated large AI dataset for scientific domain. This dataset contains 17,506 sentences which is substantially larger than previous scientific AI datasets. Next, we prepare an AD dataset for scientific domain with 62,441 samples which is significantly larger than the previous scientific AD dataset. Our experiments show that the existing state-of-the-art models fall far behind human-level performance on both datasets proposed by this work. In addition, we propose a new deep learning model that utilizes the syntactical structure of the sentence to expand an ambiguous acronym in a sentence. The proposed model outperforms the state-of-the-art models on the new AD dataset, providing a strong baseline for future research on this dataset.

  • 4 authors
·
Oct 27, 2020

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.

  • 23 authors
·
Feb 12, 2025 1

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.

  • 5 authors
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Feb 27, 2024 1

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

  • 4 authors
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Feb 28, 2022

CsFEVER and CTKFacts: Acquiring Czech data for fact verification

In this paper, we examine several methods of acquiring Czech data for automated fact-checking, which is a task commonly modeled as a classification of textual claim veracity w.r.t. a corpus of trusted ground truths. We attempt to collect sets of data in form of a factual claim, evidence within the ground truth corpus, and its veracity label (supported, refuted or not enough info). As a first attempt, we generate a Czech version of the large-scale FEVER dataset built on top of Wikipedia corpus. We take a hybrid approach of machine translation and document alignment; the approach and the tools we provide can be easily applied to other languages. We discuss its weaknesses and inaccuracies, propose a future approach for their cleaning and publish the 127k resulting translations, as well as a version of such dataset reliably applicable for the Natural Language Inference task - the CsFEVER-NLI. Furthermore, we collect a novel dataset of 3,097 claims, which is annotated using the corpus of 2.2M articles of Czech News Agency. We present its extended annotation methodology based on the FEVER approach, and, as the underlying corpus is kept a trade secret, we also publish a standalone version of the dataset for the task of Natural Language Inference we call CTKFactsNLI. We analyze both acquired datasets for spurious cues - annotation patterns leading to model overfitting. CTKFacts is further examined for inter-annotator agreement, thoroughly cleaned, and a typology of common annotator errors is extracted. Finally, we provide baseline models for all stages of the fact-checking pipeline and publish the NLI datasets, as well as our annotation platform and other experimental data.

  • 5 authors
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Jan 26, 2022

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.

  • 13 authors
·
Apr 11, 2024

Improving Clinical Document Understanding on COVID-19 Research with Spark NLP

Following the global COVID-19 pandemic, the number of scientific papers studying the virus has grown massively, leading to increased interest in automated literate review. We present a clinical text mining system that improves on previous efforts in three ways. First, it can recognize over 100 different entity types including social determinants of health, anatomy, risk factors, and adverse events in addition to other commonly used clinical and biomedical entities. Second, the text processing pipeline includes assertion status detection, to distinguish between clinical facts that are present, absent, conditional, or about someone other than the patient. Third, the deep learning models used are more accurate than previously available, leveraging an integrated pipeline of state-of-the-art pretrained named entity recognition models, and improving on the previous best performing benchmarks for assertion status detection. We illustrate extracting trends and insights, e.g. most frequent disorders and symptoms, and most common vital signs and EKG findings, from the COVID-19 Open Research Dataset (CORD-19). The system is built using the Spark NLP library which natively supports scaling to use distributed clusters, leveraging GPUs, configurable and reusable NLP pipelines, healthcare specific embeddings, and the ability to train models to support new entity types or human languages with no code changes.

  • 2 authors
·
Dec 6, 2020

Evaluating the Symbol Binding Ability of Large Language Models for Multiple-Choice Questions in Vietnamese General Education

In this paper, we evaluate the ability of large language models (LLMs) to perform multiple choice symbol binding (MCSB) for multiple choice question answering (MCQA) tasks in zero-shot, one-shot, and few-shot settings. We focus on Vietnamese, with fewer challenging MCQA datasets than in English. The two existing datasets, ViMMRC 1.0 and ViMMRC 2.0, focus on literature. Recent research in Vietnamese natural language processing (NLP) has focused on the Vietnamese National High School Graduation Examination (VNHSGE) from 2019 to 2023 to evaluate ChatGPT. However, these studies have mainly focused on how ChatGPT solves the VNHSGE step by step. We aim to create a novel and high-quality dataset by providing structured guidelines for typing LaTeX formulas for mathematics, physics, chemistry, and biology. This dataset can be used to evaluate the MCSB ability of LLMs and smaller language models (LMs) because it is typed in a strict LaTeX style. We focus on predicting the character (A, B, C, or D) that is the most likely answer to a question, given the context of the question. Our evaluation of six well-known LLMs, namely BLOOMZ-7.1B-MT, LLaMA-2-7B, LLaMA-2-70B, GPT-3, GPT-3.5, and GPT-4.0, on the ViMMRC 1.0 and ViMMRC 2.0 benchmarks and our proposed dataset shows promising results on the MCSB ability of LLMs for Vietnamese. The dataset is available for research purposes only.

  • 2 authors
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Oct 18, 2023

Noise reduction in BERT NER models for clinical entity extraction

Precision is of utmost importance in the realm of clinical entity extraction from clinical notes and reports. Encoder Models fine-tuned for Named Entity Recognition (NER) are an efficient choice for this purpose, as they don't hallucinate. We pre-trained an in-house BERT over clinical data and then fine-tuned it for NER. These models performed well on recall but could not close upon the high precision range, needed for clinical models. To address this challenge, we developed a Noise Removal model that refines the output of NER. The NER model assigns token-level entity tags along with probability scores for each token. Our Noise Removal (NR) model then analyzes these probability sequences and classifies predictions as either weak or strong. A naïve approach might involve filtering predictions based on low probability values; however, this method is unreliable. Owing to the characteristics of the SoftMax function, Transformer based architectures often assign disproportionately high confidence scores even to uncertain or weak predictions, making simple thresholding ineffective. To address this issue, we adopted a supervised modeling strategy in which the NR model leverages advanced features such as the Probability Density Map (PDM). The PDM captures the Semantic-Pull effect observed within Transformer embeddings, an effect that manifests in the probability distributions of NER class predictions across token sequences. This approach enables the model to classify predictions as weak or strong with significantly improved accuracy. With these NR models we were able to reduce False Positives across various clinical NER models by 50\% to 90\%.

  • 3 authors
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Feb 3

The SourceData-NLP dataset: integrating curation into scientific publishing for training large language models

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

  • 4 authors
·
Oct 31, 2023

PVminerLLM: Structured Extraction of Patient Voice from Patient-Generated Text using Large Language Models

Motivation: Patient-generated text contains critical information about patients' lived experiences, social circumstances, and engagement in care, including factors that strongly influence adherence, care coordination, and health equity. However, these patient voice signals are rarely available in structured form, limiting their use in patient-centered outcomes research and clinical quality improvement. Reliable extraction of such information is therefore essential for understanding and addressing non-clinical drivers of health outcomes at scale. Results: We introduce PVminer, a benchmark for structured extraction of patient voice, and propose PVminerLLM, a supervised fine-tuned large language model tailored to this task. Across multiple datasets and model sizes, PVminerLLM substantially outperforms prompt-based baselines, achieving up to 83.82% F1 for Code prediction, 80.74% F1 for Sub-code prediction, and 87.03% F1 for evidence Span extraction. Notably, strong performance is achieved even with smaller models, demonstrating that reliable patient voice extraction is feasible without extreme model scale. These results enable scalable analysis of social and experiential signals embedded in patient-generated text. Availability and Implementation: Code, evaluation scripts, and trained LLMs will be released publicly. Annotated datasets will be made available upon request for research use. Keywords: Large Language Models, Supervised Fine-Tuning, Medical Annotation, Patient-Generated Text, Clinical NLP

  • 8 authors
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Mar 5

GLiNER-biomed: A Suite of Efficient Models for Open Biomedical Named Entity Recognition

Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and human annotations, struggle to generalize beyond predefined entity types or efficiently adapt to emerging concepts. To address these issues, we introduce GLiNER-biomed, a domain-adapted suite of Generalist and Lightweight Model for NER (GLiNER) models specifically tailored for biomedical NER. In contrast to conventional approaches, GLiNER uses natural language descriptions to infer arbitrary entity types, enabling zero-shot recognition. Our approach first distills the annotation capabilities of large language models (LLMs) into a smaller, more efficient model, enabling the generation of high-coverage synthetic biomedical NER data. We subsequently train two GLiNER architectures, uni- and bi-encoder, at multiple scales to balance computational efficiency and recognition performance. Evaluations on several biomedical datasets demonstrate that GLiNER-biomed outperforms state-of-the-art GLiNER models in both zero- and few-shot scenarios, achieving 5.96% improvement in F1-score over the strongest baseline. Ablation studies highlight the effectiveness of our synthetic data generation strategy and emphasize the complementary benefits of synthetic biomedical pre-training combined with fine-tuning on high-quality general-domain annotations. All datasets, models, and training pipelines are publicly available at https://github.com/ds4dh/GLiNER-biomed.

  • 3 authors
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Apr 1, 2025

NapSS: Paragraph-level Medical Text Simplification via Narrative Prompting and Sentence-matching Summarization

Accessing medical literature is difficult for laypeople as the content is written for specialists and contains medical jargon. Automated text simplification methods offer a potential means to address this issue. In this work, we propose a summarize-then-simplify two-stage strategy, which we call NapSS, identifying the relevant content to simplify while ensuring that the original narrative flow is preserved. In this approach, we first generate reference summaries via sentence matching between the original and the simplified abstracts. These summaries are then used to train an extractive summarizer, learning the most relevant content to be simplified. Then, to ensure the narrative consistency of the simplified text, we synthesize auxiliary narrative prompts combining key phrases derived from the syntactical analyses of the original text. Our model achieves results significantly better than the seq2seq baseline on an English medical corpus, yielding 3%~4% absolute improvements in terms of lexical similarity, and providing a further 1.1% improvement of SARI score when combined with the baseline. We also highlight shortcomings of existing evaluation methods, and introduce new metrics that take into account both lexical and high-level semantic similarity. A human evaluation conducted on a random sample of the test set further establishes the effectiveness of the proposed approach. Codes and models are released here: https://github.com/LuJunru/NapSS.

  • 5 authors
·
Feb 10, 2023

Exploring the Effectiveness of Instruction Tuning in Biomedical Language Processing

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

  • 3 authors
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Dec 31, 2023

A Systematic Literature Review of Automated ICD Coding and Classification Systems using Discharge Summaries

Codification of free-text clinical narratives have long been recognised to be beneficial for secondary uses such as funding, insurance claim processing and research. The current scenario of assigning codes is a manual process which is very expensive, time-consuming and error prone. In recent years, many researchers have studied the use of Natural Language Processing (NLP), related Machine Learning (ML) and Deep Learning (DL) methods and techniques to resolve the problem of manual coding of clinical narratives and to assist human coders to assign clinical codes more accurately and efficiently. This systematic literature review provides a comprehensive overview of automated clinical coding systems that utilises appropriate NLP, ML and DL methods and techniques to assign ICD codes to discharge summaries. We have followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA) guidelines and conducted a comprehensive search of publications from January, 2010 to December 2020 in four academic databases- PubMed, ScienceDirect, Association for Computing Machinery(ACM) Digital Library, and the Association for Computational Linguistics(ACL) Anthology. We reviewed 7,556 publications; 38 met the inclusion criteria. This review identified: datasets having discharge summaries; NLP techniques along with some other data extraction processes, different feature extraction and embedding techniques. To measure the performance of classification methods, different evaluation metrics are used. Lastly, future research directions are provided to scholars who are interested in automated ICD code assignment. Efforts are still required to improve ICD code prediction accuracy, availability of large-scale de-identified clinical corpora with the latest version of the classification system. This can be a platform to guide and share knowledge with the less experienced coders and researchers.

  • 3 authors
·
Jul 11, 2021