ymoslem/acl-abstracts huggingface dataset:
Classifying the reported ability in clinical mobility descriptions (2019)

Assessing how individuals perform different activities is key information for modeling health states of individuals and populations. Descriptions of activity performance in clinical free text are complex, including syntactic negation and similarities to textual entailment tasks. We explore a variety of methods for the novel task of classifying four types of assertions about activity performance: Able, Unable, Unclear, and None (no information). We find that ensembling an SVM trained with lexical features and a CNN achieves 77.9{\%} macro F1 score on our task, and yields nearly 80{\%} recall on the rare Unclear and Unable samples. Finally, we highlight several challenges in classifying performance assertions, including capturing information about sources of assistance, incorporating syntactic structure and negation scope, and handling new modalities at test time. Our findings establish a strong baseline for this novel task, and identify intriguing areas for further research.
Learning from the Experience of Doctors: Automated Diagnosis of Appendicitis Based on Clinical Notes (2019)

The objective of this work is to develop an automated diagnosis system that is able to predict the probability of appendicitis given a free-text emergency department (ED) note and additional structured information (e.g., lab test results). Our clinical corpus consists of about 180,000 ED notes based on ten years of patient visits to the Accident and Emergency (A{\&}E) Department of the National University Hospital (NUH), Singapore. We propose a novel neural network approach that learns to diagnose acute appendicitis based on doctors' free-text ED notes without any feature engineering. On a test set of 2,000 ED notes with equal number of appendicitis (positive) and non-appendicitis (negative) diagnosis and in which all the negative ED notes only consist of abdominal-related diagnosis, our model is able to achieve a promising F{\_}0.5-score of 0.895 while ED doctors achieve F{\_}0.5-score of 0.900. Visualization shows that our model is able to learn important features, signs, and symptoms of patients from unstructured free-text ED notes, which will help doctors to make better diagnosis.
A Paraphrase Generation System for EHR Question Answering (2019)

This paper proposes a dataset and method for automatically generating paraphrases for clinical questions relating to patient-specific information in electronic health records (EHRs). Crowdsourcing is used to collect 10,578 unique questions across 946 semantically distinct paraphrase clusters. This corpus is then used with a deep learning-based question paraphrasing method utilizing variational autoencoder and LSTM encoder/decoder. The ultimate use of such a method is to improve the performance of automatic question answering methods for EHRs.
REflex: Flexible Framework for Relation Extraction in Multiple Domains (2019)

Systematic comparison of methods for relation extraction (RE) is difficult because many experiments in the field are not described precisely enough to be completely reproducible and many papers fail to report ablation studies that would highlight the relative contributions of their various combined techniques. In this work, we build a unifying framework for RE, applying this on three highly used datasets (from the general, biomedical and clinical domains) with the ability to be extendable to new datasets. By performing a systematic exploration of modeling, pre-processing and training methodologies, we find that choices of preprocessing are a large contributor performance and that omission of such information can further hinder fair comparison. Other insights from our exploration allow us to provide recommendations for future research in this area.
Analysing Representations of Memory Impairment in a Clinical Notes Classification Model (2019)

Despite recent advances in the application of deep neural networks to various kinds of medical data, extracting information from unstructured textual sources remains a challenging task. The challenges of training and interpreting document classification models are amplified when dealing with small and highly technical datasets, as are common in the clinical domain. Using a dataset of de-identified clinical letters gathered at a memory clinic, we construct several recurrent neural network models for letter classification, and evaluate them on their ability to build meaningful representations of the documents and predict patients' diagnoses. Additionally, we probe sentence embedding models in order to build a human-interpretable representation of the neural network`s features, using a simple and intuitive technique based on perturbative approaches to sentence importance. In addition to showing which sentences in a document are most informative about the patient`s condition, this method reveals the types of sentences that lead the model to make incorrect diagnoses. Furthermore, we identify clusters of sentences in the embedding space that correlate strongly with importance scores for each clinical diagnosis class.
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets (2019)

Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language representations in the biomedicine domain. The benchmark consists of five tasks with ten datasets that cover both biomedical and clinical texts with different dataset sizes and difficulties. We also evaluate several baselines based on BERT and ELMo and find that the BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieves the best results. We make the datasets, pre-trained models, and codes publicly available at \url{https://github.com/ncbi-nlp/BLUE_Benchmark}.
Combining Structured and Free-text Electronic Medical Record Data for Real-time Clinical Decision Support (2019)

The goal of this work is to utilize Electronic Medical Record (EMR) data for real-time Clinical Decision Support (CDS). We present a deep learning approach to combining in real time available diagnosis codes (ICD codes) and free-text notes: Patient Context Vectors. Patient Context Vectors are created by averaging ICD code embeddings, and by predicting the same from free-text notes via a Convolutional Neural Network. The Patient Context Vectors were then simply appended to available structured data (vital signs and lab results) to build prediction models for a specific condition. Experiments on predicting ARDS, a rare and complex condition, demonstrate the utility of Patient Context Vectors as a means of summarizing the patient history and overall condition, and improve significantly the prediction model results.
MoNERo: a Biomedical Gold Standard Corpus for the Romanian Language (2019)

In an era when large amounts of data are generated daily in various fields, the biomedical field among others, linguistic resources can be exploited for various tasks of Natural Language Processing. Moreover, increasing number of biomedical documents are available in languages other than English. To be able to extract information from natural language free text resources, methods and tools are needed for a variety of languages. This paper presents the creation of the MoNERo corpus, a gold standard biomedical corpus for Romanian, annotated with both part of speech tags and named entities. MoNERo comprises 154,825 morphologically annotated tokens and 23,188 entity annotations belonging to four entity semantic groups corresponding to UMLS Semantic Groups.
Domain Adaptation of SRL Systems for Biological Processes (2019)

Domain adaptation remains one of the most challenging aspects in the wide-spread use of Semantic Role Labeling (SRL) systems. Current state-of-the-art methods are typically trained on large-scale datasets, but their performances do not directly transfer to low-resource domain-specific settings. In this paper, we propose two approaches for domain adaptation in the biological domain that involves pre-training LSTM-CRF based on existing large-scale datasets and adapting it for a low-resource corpus of biological processes. Our first approach defines a mapping between the source labels and the target labels, and the other approach modifies the final CRF layer in sequence-labeling neural network architecture. We perform our experiments on ProcessBank dataset which contains less than 200 paragraphs on biological processes. We improve over the previous state-of-the-art system on this dataset by 21 F1 points. We also show that, by incorporating event-event relationship in ProcessBank, we are able to achieve an additional 2.6 F1 gain, giving us possible insights into how to improve SRL systems for biological process using richer annotations.
Deep Contextualized Biomedical Abbreviation Expansion (2019)

Automatic identification and expansion of ambiguous abbreviations are essential for biomedical natural language processing applications, such as information retrieval and question answering systems. In this paper, we present DEep Contextualized Biomedical Abbreviation Expansion (DECBAE) model. DECBAE automatically collects substantial and relatively clean annotated contexts for 950 ambiguous abbreviations from PubMed abstracts using a simple heuristic. Then it utilizes BioELMo to extract the contextualized features of words, and feed those features to abbreviation-specific bidirectional LSTMs, where the hidden states of the ambiguous abbreviations are used to assign the exact definitions. Our DECBAE model outperforms other baselines by large margins, achieving average accuracy of 0.961 and macro-F1 of 0.917 on the dataset. It also surpasses human performance for expanding a sample abbreviation, and remains robust in imbalanced, low-resources and clinical settings.
RNN Embeddings for Identifying Difficult to Understand Medical Words (2019)

Patients and their families often require a better understanding of medical information provided by doctors. We currently address this issue by improving the identification of difficult to understand medical words. We introduce novel embeddings received from RNN - FrnnMUTE (French RNN Medical Understandability Text Embeddings) which allow to reach up to 87.0 F1 score in identification of difficult words. We also note that adding pre-trained FastText word embeddings to the feature set substantially improves the performance of the model which classifies words according to their difficulty. We study the generalizability of different models through three cross-validation scenarios which allow testing classifiers in real-world conditions: understanding of medical words by new users, and classification of new unseen words by the automatic models. The RNN - FrnnMUTE embeddings and the categorization code are being made available for the research.
A distantly supervised dataset for automated data extraction from diagnostic studies (2019)

Systematic reviews are important in evidence based medicine, but are expensive to produce. Automating or semi-automating the data extraction of index test, target condition, and reference standard from articles has the potential to decrease the cost of conducting systematic reviews of diagnostic test accuracy, but relevant training data is not available. We create a distantly supervised dataset of approximately 90,000 sentences, and let two experts manually annotate a small subset of around 1,000 sentences for evaluation. We evaluate the performance of BioBERT and logistic regression for ranking the sentences, and compare the performance for distant and direct supervision. Our results suggest that distant supervision can work as well as, or better than direct supervision on this problem, and that distantly trained models can perform as well as, or better than human annotators.
Query selection methods for automated corpora construction with a use case in food-drug interactions (2019)

In this paper, we address the problem of automatically constructing a relevant corpus of scientific articles about food-drug interactions. There is a growing number of scientific publications that describe food-drug interactions but currently building a high-coverage corpus that can be used for information extraction purposes is not trivial. We investigate several methods for automating the query selection process using an expert-curated corpus of food-drug interactions. Our experiments show that index term features along with a decision tree classifier are the best approach for this task and that feature selection approaches and in particular gain ratio outperform frequency-based methods for query selection.
Enhancing biomedical word embeddings by retrofitting to verb clusters (2019)

Verbs play a fundamental role in many biomed-ical tasks and applications such as relation and event extraction. We hypothesize that performance on many downstream tasks can be improved by aligning the input pretrained embeddings according to semantic verb classes. In this work, we show that by using semantic clusters for verbs, a large lexicon of verbclasses derived from biomedical literature, weare able to improve the performance of common pretrained embeddings in downstream tasks by retrofitting them to verb classes. We present a simple and computationally efficient approach using a widely-available {\textquotedblleft}off-the-shelf{\textquotedblright} retrofitting algorithm to align pretrained embeddings according to semantic verb clusters. We achieve state-of-the-art results on text classification and relation extraction tasks.
A Comparison of Word-based and Context-based Representations for Classification Problems in Health Informatics (2019)

Distributed representations of text can be used as features when training a statistical classifier. These representations may be created as a composition of word vectors or as context-based sentence vectors. We compare the two kinds of representations (word versus context) for three classification problems: influenza infection classification, drug usage classification and personal health mention classification. For statistical classifiers trained for each of these problems, context-based representations based on ELMo, Universal Sentence Encoder, Neural-Net Language Model and FLAIR are better than Word2Vec, GloVe and the two adapted using the MESH ontology. There is an improvement of 2-4{\%} in the accuracy when these context-based representations are used instead of word-based representations.
Constructing large scale biomedical knowledge bases from scratch with rapid annotation of interpretable patterns (2019)

Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is therapeutic target for disease Y) severely limits a domain expert`s ability to create a usable knowledge base, either directly or by training a relation extraction model. In this paper, we present a simple and effective method of extracting new facts with a pre-specified binary relationship type from the biomedical literature, without requiring any training data or hand-crafted rules. Our system discovers, ranks and presents the most salient patterns to domain experts in an interpretable form. By marking patterns as compatible with the desired relationship type, experts indirectly batch-annotate candidate pairs whose relationship is expressed with such patterns in the literature. Even with a complete absence of seed data, experts are able to discover thousands of high-quality pairs with the desired relationship within minutes. When a small number of relevant pairs do exist - even when their relationship is more general (e.g. gene X is biologically associated with disease Y) than the relationship of interest - our system leverages them in order to i) learn a better ranking of the patterns to be annotated or ii) generate weakly labelled pairs in a fully automated manner. We evaluate our method both intrinsically and via a downstream knowledge base completion task, and show that it is an effective way of constructing knowledge bases when few or no relevant facts are already available.
First Steps towards Building a Medical Lexicon for Spanish with Linguistic and Semantic Information (2019)

We report the work-in-progress of collecting MedLexSp, an unified medical lexicon for the Spanish language, featuring terms and inflected word forms mapped to Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs), semantic types and groups. First, we leveraged a list of term lemmas and forms from a previous project, and mapped them to UMLS terms and CUIs. To enrich the lexicon, we used both domain-corpora (e.g. Summaries of Product Characteristics and MedlinePlus) and natural language processing techniques such as string distance methods or generation of syntactic variants of multi-word terms. We also added term variants by mapping their CUIs to missing items available in the Spanish versions of standard thesauri (e.g. Medical Subject Headings and World Health Organization Adverse Drug Reactions terminology). We enhanced the vocabulary coverage by gathering missing terms from resources such as the Anatomical Therapeutical Classification, the National Cancer Institute (NCI) Dictionary of Cancer Terms, OrphaData, or the Nomencl{\'a}tor de Prescripci{\'o}n for drug names. Part-of-Speech information is being included in the lexicon, and the current version amounts up to 76 454 lemmas and 203 043 inflected forms (including conjugated verbs, number and gender variants), corresponding to 30 647 UMLS CUIs. MedLexSp is distributed freely for research purposes.
Incorporating Figure Captions and Descriptive Text in MeSH Term Indexing (2019)

The goal of text classification is to automatically assign categories to documents. Deep learning automatically learns effective features from data instead of adopting human-designed features. In this paper, we focus specifically on biomedical document classification using a deep learning approach. We present a novel multichannel TextCNN model for MeSH term indexing. Beyond the normal use of the text from the abstract and title for model training, we also consider figure and table captions, as well as paragraphs associated with the figures and tables. We demonstrate that these latter text sources are important feature sources for our method. A new dataset consisting of these text segments curated from 257,590 full text articles together with the articles' MEDLINE/PubMed MeSH terms is publicly available.
BioRelEx 1.0: Biological Relation Extraction Benchmark (2019)

Automatic extraction of relations and interactions between biological entities from scientific literature remains an extremely challenging problem in biomedical information extraction and natural language processing in general. One of the reasons for slow progress is the relative scarcity of standardized and publicly available benchmarks. In this paper we introduce BioRelEx, a new dataset of fully annotated sentences from biomedical literature that capture \textit{binding} interactions between proteins and/or biomolecules. To foster reproducible research on the interaction extraction task, we define a precise and transparent evaluation process, tools for error analysis and significance tests. Finally, we conduct extensive experiments to evaluate several baselines, including SciIE, a recently introduced neural multi-task architecture that has demonstrated state-of-the-art performance on several tasks.
Extraction of Lactation Frames from Drug Labels and LactMed (2019)

This paper describes a natural language processing (NLP) approach to extracting lactation-specific drug information from two sources: FDA-mandated drug labels and the NLM Drugs and Lactation Database (LactMed). A frame semantic approach is utilized, and the paper describes the selected frames, their annotation on a set of 900 sections from drug labels and LactMed articles, and the NLP system to extract such frame instances automatically. The ultimate goal of the project is to use such a system to identify discrepancies in lactation-related drug information between these resources.
Annotating Temporal Information in Clinical Notes for Timeline Reconstruction: Towards the Definition of Calendar Expressions (2019)

To automatically analyse complex trajectory information enclosed in clinical text (e.g. timing of symptoms, duration of treatment), it is important to understand the related temporal aspects, anchoring each event on an absolute point in time. In the clinical domain, few temporally annotated corpora are currently available. Moreover, underlying annotation schemas - which mainly rely on the TimeML standard - are not necessarily easily applicable for applications such as patient timeline reconstruction. In this work, we investigated how temporal information is documented in clinical text by annotating a corpus of medical reports with time expressions (TIMEXes), based on TimeML. The developed corpus is available to the NLP community. Starting from our annotations, we analysed the suitability of the TimeML TIMEX schema for capturing timeline information, identifying challenges and possible solutions. As a result, we propose a novel annotation schema that could be useful for timeline reconstruction: CALendar EXpression (CALEX).
Leveraging Sublanguage Features for the Semantic Categorization of Clinical Terms (2019)

The automatic processing of clinical documents, such as Electronic Health Records (EHRs), could benefit substantially from the enrichment of medical terminologies with terms encountered in clinical practice. To integrate such terms into existing knowledge sources, they must be linked to corresponding concepts. We present a method for the semantic categorization of clinical terms based on their surface form. We find that features based on sublanguage properties can provide valuable cues for the classification of term variants.
Enhancing PIO Element Detection in Medical Text Using Contextualized Embedding (2019)

In this paper, we presented an improved methodology to extract PIO elements, from abstracts of medical papers, that reduces ambiguity. The proposed technique was used to build a dataset of PIO elements that we call PICONET. We further proposed a model of PIO elements classification using state of the art BERT embedding. In addition, we investigated a contextualized embedding, BioBERT, trained on medical corpora. It has been found that using the BioBERT embedding improved the classification accuracy, outperforming the BERT-based model. This result reinforces the idea of the importance of embedding contextualization in subsequent classification tasks in this specific context. Furthermore, to enhance the accuracy of the model, we have investigated an ensemble method based on the LGBM algorithm. We trained the LGBM model, with the above models as base learners, to learn a linear combination of the predicted probabilities for the 3 classes with the TF-IDF score and the QIEF that optimizes the classification. The results indicate that these text features were good features to consider in order to boost the deeply contextualized classification model. We compared the performance of the classifier when using the features with one of the base learners and the case where we combine the base learners along with the features. We obtained the highest score in terms of AUC when we combine the base learners. The present work resulted in the creation of a PIO element dataset, PICONET, and a classification tool. These constitute and important component of our system of automatic mining of medical abstracts. We intend to extend the dataset to full medical articles. The model will be modified to take into account the higher complexity of full text data and more efficient features for model boosting will be investigated.