ymoslem/acl-abstracts huggingface dataset:
BioCite: A Deep Learning-based Citation Linkage Framework for Biomedical Research Articles (2022)

Research papers reflect scientific advances. Citations are widely used in research publications to support the new findings and show their benefits, while also regulating the information flow to make the contents clearer for the audience. A citation in a research article refers to the information`s source, but not the specific text span from that source article. In biomedical research articles, this task is challenging as the same chemical or biological component can be represented in multiple ways in different papers from various domains. This paper suggests a mechanism for linking citing sentences in a publication with cited sentences in referenced sources. The framework presented here pairs the citing sentence with all of the sentences in the reference text, and then tries to retrieve the semantically equivalent pairs. These semantically related sentences from the reference paper are chosen as the cited statements. This effort involves designing a citation linkage framework utilizing sequential and tree-structured siamese deep learning models. This paper also provides a method to create a synthetic corpus for such a task.
Low Resource Causal Event Detection from Biomedical Literature (2022)

Recognizing causal precedence relations among the chemical interactions in biomedical literature is crucial to understanding the underlying biological mechanisms. However, detecting such causal relation can be hard because: (1) many times, such causal relations among events are not explicitly expressed by certain phrases but implicitly implied by very diverse expressions in the text, and (2) annotating such causal relation detection datasets requires considerable expert knowledge and effort. In this paper, we propose a strategy to address both challenges by training neural models with in-domain pre-training and knowledge distillation. We show that, by using very limited amount of labeled data, and sufficient amount of unlabeled data, the neural models outperform previous baselines on the causal precedence detection task, and are ten times faster at inference compared to the BERT base model.
Overview of the MedVidQA 2022 Shared Task on Medical Video Question-Answering (2022)

In this paper, we present an overview of the MedVidQA 2022 shared task, collocated with the 21st BioNLP workshop at ACL 2022. The shared task addressed two of the challenges faced by medical video question answering: (I) a video classification task that explores new approaches to medical video understanding (labeling), and (ii) a visual answer localization task. Visual answer localization refers to the identification of the relevant temporal segments (start and end timestamps) in the video where the answer to the medical question is being shown or illustrated. A total of thirteen teams participated in the shared task challenges, with eleven system descriptions submitted to the workshop. The descriptions present monomodal and multi-modal approaches developed for medical video classification and visual answer localization. This paper describes the tasks, the datasets, evaluation metrics, and baseline systems for both tasks. Finally, the paper summarizes the techniques and results of the evaluation of the various approaches explored by the participating teams.
Inter-annotator agreement is not the ceiling of machine learning performance: Evidence from a comprehensive set of simulations (2022)

It is commonly claimed that inter-annotator agreement (IAA) is the ceiling of machine learning (ML) performance, i.e., that the agreement between an ML system`s predictions and an annotator can not be higher than the agreement between two annotators. Although Boguslav {\&} Cohen (2017) showed that this claim is falsified by many real-world ML systems, the claim has persisted. As a complement to this real-world evidence, we conducted a comprehensive set of simulations, and show that an ML model can beat IAA even if (and especially if) annotators are noisy and differ in their underlying classification functions, as long as the ML model is reasonably well-specified. Although the latter condition has long been elusive, leading ML models to underperform IAA, we anticipate that this condition will be increasingly met in the era of big data and deep learning. Our work has implications for (1) maximizing the value of machine learning, (2) adherence to ethical standards in computing, and (3) economical use of annotated resources, which is paramount in settings where annotation is especially expensive, like biomedical natural language processing.
Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues (2022)

Conversational bots have become non-traditional methods for therapy among individuals suffering from psychological illnesses. Leveraging deep neural generative language models, we propose a deep trainable neural conversational model for therapy-oriented response generation. We leverage transfer learning methods during training on therapy and counseling based data from Reddit and AlexanderStreet. This was done to adapt existing generative models {--} GPT2 and DialoGPT {--} to the task of automated dialog generation. Through quantitative evaluation of the linguistic quality, we observe that the dialog generation model - DialoGPT (345M) with transfer learning on video data attains scores similar to a human response baseline. However, human evaluation of responses by conversational bots show mostly signs of generic advice or information sharing instead of therapeutic interaction.
BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering (2022)

Automatic extraction of event structures from text is a promising way to extract important facts from the evergrowing amount of biomedical literature. We propose BEEDS, a new approach on how to mine event structures from PubMed based on a question-answering paradigm. Using a three-step pipeline comprising a document retriever, a document reader, and an entity normalizer, BEEDS is able to fully automatically extract event triples involving a query protein or gene and to store this information directly in a knowledge base. BEEDS applies a transformer-based architecture for event extraction and uses distant supervision to augment the scarce training data in event mining. In a knowledge base population setting, it outperforms a strong baseline in finding post-translational modification events consisting of enzyme-substrate-site triples while achieving competitive results in extracting binary relations consisting of protein-protein and protein-site interactions.
Data Augmentation for Rare Symptoms in Vaccine Side-Effect Detection (2022)

We study the problem of entity detection and normalization applied to patient self-reports of symptoms that arise as side-effects of vaccines. Our application domain presents unique challenges that render traditional classification methods ineffective: the number of entity types is large; and many symptoms are rare, resulting in a long-tail distribution of training examples per entity type. We tackle these challenges with an autoregressive model that generates standardized names of symptoms. We introduce a data augmentation technique to increase the number of training examples for rare symptoms. Experiments on real-life patient vaccine symptom self-reports show that our approach outperforms strong baselines, and that additional examples improve performance on the long-tail entities.
Improving Romanian BioNER Using a Biologically Inspired System (2022)

Recognition of named entities present in text is an important step towards information extraction and natural language understanding. This work presents a named entity recognition system for the Romanian biomedical domain. The system makes use of a new and extended version of SiMoNERo corpus, that is open sourced. Also, the best system is available for direct usage in the RELATE platform.
BanglaBioMed: A Biomedical Named-Entity Annotated Corpus for Bangla (Bengali) (2022)

Recognizing biomedical entities in the text has significance in biomedical and health science research, as it benefits myriad downstream tasks, including entity linking, relation extraction, or entity resolution. While English and a few other widely used languages enjoy ample resources for automatic biomedical entity recognition, it is not the case for Bangla, a low-resource language. On that account, in this paper, we introduce BanglaBioMed, a Bangla biomedical named entity (NE) annotated dataset in standard IOB format, the first of its kind, consisting of over 12000 tokens annotated with the biomedical entities. The corpus is created by collecting Bangla text from a list of health articles and then annotated with four distinct types of entities: Anatomy (AN), Chemical and Drugs (CD), Disease and Symptom (DS), and Medical Procedure (MP). We provide the details of the entire data collection and annotation procedure and illustrate various statistics of the created corpus. Our developed corpus is a much-needed addition to the Bangla NLP resource that will facilitate biomedical NLP research in Bangla.
ICDBigBird: A Contextual Embedding Model for ICD Code Classification (2022)

The International Classification of Diseases (ICD) system is the international standard for classifying diseases and procedures during a healthcare encounter and is widely used for healthcare reporting and management purposes. Assigning correct codes for clinical procedures is important for clinical, operational and financial decision-making in healthcare. Contextual word embedding models have achieved state-of-the-art results in multiple NLP tasks. However, these models have yet to achieve state-of-the-art results in the ICD classification task since one of their main disadvantages is that they can only process documents that contain a small number of tokens which is rarely the case with real patient notes. In this paper, we introduce ICDBigBird a BigBird-based model which can integrate a Graph Convolutional Network (GCN), that takes advantage of the relations between ICD codes in order to create {\textquoteleft}enriched' representations of their embeddings, with a BigBird contextual model that can process larger documents. Our experiments on a real-world clinical dataset demonstrate the effectiveness of our BigBird-based model on the ICD classification task as it outperforms the previous state-of-the-art models.
Doctor XAvIer: Explainable Diagnosis on Physician-Patient Dialogues and XAI Evaluation (2022)

We introduce Doctor XAvIer {---} a BERT-based diagnostic system that extracts relevant clinical data from transcribed patient-doctor dialogues and explains predictions using feature attribution methods. We present a novel performance plot and evaluation metric for feature attribution methods {---} Feature Attribution Dropping (FAD) curve and its Normalized Area Under the Curve (N-AUC). FAD curve analysis shows that integrated gradients outperforms Shapley values in explaining diagnosis classification. Doctor XAvIer outperforms the baseline with 0.97 F1-score in named entity recognition and symptom pertinence classification and 0.91 F1-score in diagnosis classification.
DISTANT-CTO: A Zero Cost, Distantly Supervised Approach to Improve Low-Resource Entity Extraction Using Clinical Trials Literature (2022)

PICO recognition is an information extraction task for identifying participant, intervention, comparator, and outcome information from clinical literature. Manually identifying PICO information is the most time-consuming step for conducting systematic reviews (SR), which is already labor-intensive. A lack of diversified and large, annotated corpora restricts innovation and adoption of automated PICO recognition systems. The largest-available PICO entity/span corpus is manually annotated which is too expensive for a majority of the scientific community. To break through the bottleneck, we propose DISTANT-CTO, a novel distantly supervised PICO entity extraction approach using the clinical trials literature, to generate a massive weakly-labeled dataset with more than a million {\textquoteleft}Intervention' and {\textquoteleft}Comparator' entity annotations. We train distant NER (named-entity recognition) models using this weakly-labeled dataset and demonstrate that it outperforms even the sophisticated models trained on the manually annotated dataset with a 2{\%} F1 improvement over the Intervention entity of the PICO benchmark and more than 5{\%} improvement when combined with the manually annotated dataset. We investigate the generalizability of our approach and gain an impressive F1 score on another domain-specific PICO benchmark. The approach is not only zero-cost but is also scalable for a constant stream of PICO entity annotations.
EchoGen: Generating Conclusions from Echocardiogram Notes (2022)

Generating a summary from findings has been recently explored (Zhang et al., 2018, 2020) in note types such as radiology reports that typically have short length. In this work, we focus on echocardiogram notes that is longer and more complex compared to previous note types. We formally define the task of echocardiography conclusion generation (EchoGen) as generating a conclusion given the findings section, with emphasis on key cardiac findings. To promote the development of EchoGen methods, we present a new benchmark, which consists of two datasets collected from two hospitals. We further compare both standard and start-of-the-art methods on this new benchmark, with an emphasis on factual consistency. To accomplish this, we develop a tool to automatically extract concept-attribute tuples from the text. We then propose an evaluation metric, FactComp, to compare concept-attribute tuples between the human reference and generated conclusions. Both automatic and human evaluations show that there is still a significant gap between human-written and machine-generated conclusions on echo reports in terms of factuality and overall quality.
Quantifying Clinical Outcome Measures in Patients with Epilepsy Using the Electronic Health Record (2022)

A wealth of important clinical information lies untouched in the Electronic Health Record, often in the form of unstructured textual documents. For patients with Epilepsy, such information includes outcome measures like Seizure Frequency and Dates of Last Seizure, key parameters that guide all therapy for these patients. Transformer models have been able to extract such outcome measures from unstructured clinical note text as sentences with human-like accuracy; however, these sentences are not yet usable in a quantitative analysis for large-scale studies. In this study, we developed a pipeline to quantify these outcome measures. We used text summarization models to convert unstructured sentences into specific formats, and then employed rules-based quantifiers to calculate seizure frequencies and dates of last seizure. We demonstrated that our pipeline of models does not excessively propagate errors and we analyzed its mistakes. We anticipate that our methods can be generalized outside of epilepsy to other disorders to drive large-scale clinical research.
Comparing Encoder-Only and Encoder-Decoder Transformers for Relation Extraction from Biomedical Texts: An Empirical Study on Ten Benchmark Datasets (2022)

Biomedical relation extraction, aiming to automatically discover high-quality and semantic relations between the entities from free text, is becoming a vital step for automated knowledge discovery. Pretrained language models have achieved impressive performance on various natural language processing tasks, including relation extraction. In this paper, we perform extensive empirical comparisons of encoder-only transformers with the encoder-decoder transformer, specifically T5, on ten public biomedical relation extraction datasets. We study the relation extraction task from four major biomedical tasks, namely chemical-protein relation extraction, disease-protein relation extraction, drug-drug interaction, and protein-protein interaction. We also explore the use of multi-task fine-tuning to investigate the correlation among major biomedical relation extraction tasks. We report performance (micro F-score) using T5, BioBERT and PubMedBERT, demonstrating that T5 and multi-task learning can improve the performance of the biomedical relation extraction task.
Utility Preservation of Clinical Text After De-Identification (2022)

Electronic health records contain valuable information about symptoms, diagnosis, treatment and outcomes of the treatments of individual patients. However, the records may also contain information that can reveal the identity of the patients. Removing these identifiers - the Protected Health Information (PHI) - can protect the identity of the patient. Automatic de-identification is a process which employs machine learning techniques to detect and remove PHI. However, automatic techniques are imperfect in their precision and introduce noise into the data. This study examines the impact of this noise on the utility of Swedish de-identified clinical data by using human evaluators and by training and testing BERT models. Our results indicate that de-identification does not harm the utility for clinical NLP and that human evaluators are less sensitive to noise from de-identification than expected.
Horses to Zebras: Ontology-Guided Data Augmentation and Synthesis for ICD-9 Coding (2022)

Medical document coding is the process of assigning labels from a structured label space (ontology {--} e.g., ICD-9) to medical documents. This process is laborious, costly, and error-prone. In recent years, efforts have been made to automate this process with neural models. The label spaces are large (in the order of thousands of labels) and follow a big-head long-tail label distribution, giving rise to few-shot and zero-shot scenarios. Previous efforts tried to address these scenarios within the model, leading to improvements on rare labels, but worse results on frequent ones. We propose data augmentation and synthesis techniques in order to address these scenarios. We further introduce an analysis technique for this setting inspired by confusion matrices. This analysis technique points to the positive impact of data augmentation and synthesis, but also highlights more general issues of confusion within families of codes, and underprediction.
Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models (2022)

Antibiotic resistance has become a growing worldwide concern as new resistance mechanisms are emerging and spreading globally, and thus detecting and collecting the cause {--} Antibiotic Resistance Genes (ARGs), have been more critical than ever. In this work, we aim to automate the curation of ARGs by extracting ARG-related assertive statements from scientific papers. To support the research towards this direction, we build SciARG, a new benchmark dataset containing 2,000 manually annotated statements as the evaluation set and 12,516 silver-standard training statements that are automatically created from scientific papers by a set of rules. To set up the baseline performance on SciARG, we exploit three state-of-the-art neural architectures based on pre-trained language models and prompt tuning, and further ensemble them to attain the highest 77.0{\%} F-score. To the best of our knowledge, we are the first to leverage natural language processing techniques to curate all validated ARGs from scientific papers. Both the code and data are publicly available at \url{https://github.com/VT-NLP/SciARG}.
Model Distillation for Faithful Explanations of Medical Code Predictions (2022)

Machine learning models that offer excellent predictive performance often lack the interpretability necessary to support integrated human machine decision-making. In clinical medicine and other high-risk settings, domain experts may be unwilling to trust model predictions without explanations. Work in explainable AI must balance competing objectives along two different axes: 1) Models should ideally be both accurate and simple. 2) Explanations must balance faithfulness to the model`s decision-making with their plausibility to a domain expert. We propose to use knowledge distillation, or training a student model that mimics the behavior of a trained teacher model, as a technique to generate faithful and plausible explanations. We evaluate our approach on the task of assigning ICD codes to clinical notes to demonstrate that the student model is faithful to the teacher model`s behavior and produces quality natural language explanations.
Towards Generalizable Methods for Automating Risk Score Calculation (2022)

Clinical risk scores enable clinicians to tabulate a set of patient data into simple scores to stratify patients into risk categories. Although risk scores are widely used to inform decision-making at the point-of-care, collecting the information necessary to calculate such scores requires considerable time and effort. Previous studies have focused on specific risk scores and involved manual curation of relevant terms or codes and heuristics for each data element of a risk score. To support more generalizable methods for risk score calculation, we annotate 100 patients in MIMIC-III with elements of CHA2DS2-VASc and PERC scores, and explore using question answering (QA) and off-the-shelf tools. We show that QA models can achieve comparable or better performance for certain risk score elements as compared to heuristic-based methods, and demonstrate the potential for more scalable risk score automation without the need for expert-curated heuristics. Our annotated dataset will be released to the community to encourage efforts in generalizable methods for automating risk scores.
DoSSIER at MedVidQA 2022: Text-based Approaches to Medical Video Answer Localization Problem (2022)

This paper describes our contribution to the Answer Localization track of the MedVidQA 2022 Shared Task. We propose two answer localization approaches that use only textual information extracted from the video. In particular, our approaches exploit the text extracted from the video`s transcripts along with the text displayed in the video`s frames to create a set of features. Having created a set of features that represents a video`s textual information, we employ four different models to measure the similarity between a video`s segment and a corresponding question. Then, we employ two different methods to obtain the start and end times of the identified answer. One of them is based on a random forest regressor, whereas the other one uses an unsupervised peak detection model to detect the answer`s start time. Our findings suggest that for this task, leveraging only text-related features (transmitted either verbally or visually) and using a small amount of training data, lead to significant improvements over the benchmark Video Span Localization model that is based on deep neural networks.
Using ASR-Generated Text for Spoken Language Modeling (2022)

This papers aims at improving spoken language modeling (LM) using very large amount of automatically transcribed speech. We leverage the INA (French National Audiovisual Institute) collection and obtain 19GB of text after applying ASR on 350,000 hours of diverse TV shows. From this, spoken language models are trained either by fine-tuning an existing LM (FlauBERT) or through training a LM from scratch. The new models (FlauBERT-Oral) will be shared with the community and are evaluated not only in terms of word prediction accuracy but also for two downstream tasks : classification of TV shows and syntactic parsing of speech. Experimental results show that FlauBERT-Oral is better than its initial FlauBERT version demonstrating that, despite its inherent noisy nature, ASR-Generated text can be useful to improve spoken language modeling.