ymoslem/acl-abstracts huggingface dataset:
Leveraging Non-Specialists for Accurate and Time Efficient AMR Annotation (2020)

Abstract Meaning Representations (AMRs), a syntax-free representation of phrase semantics are useful for capturing the meaning of a phrase and reflecting the relationship between concepts that are referred to. However, annotating AMRs are time consuming and expensive. The existing annotation process requires expertly trained workers who have knowledge of an extensive set of guidelines for parsing phrases. In this paper, we propose a cost-saving two-step process for the creation of a corpus of AMR-phrase pairs for spatial referring expressions. The first step uses non-specialists to perform simple annotations that can be leveraged in the second step to accelerate the annotation performed by the experts. We hypothesize that our process will decrease the cost per annotation and improve consistency across annotators. Few corpora of spatial referring expressions exist and the resulting language resource will be valuable for referring expression comprehension and generation modeling.
The INCOMSLAV Platform: Experimental Website with Integrated Methods for Measuring Linguistic Distances and Asymmetries in Receptive Multilingualism (2020)

We report on a web-based resource for conducting intercomprehension experiments with native speakers of Slavic languages and present our methods for measuring linguistic distances and asymmetries in receptive multilingualism. Through a website which serves as a platform for online testing, a large number of participants with different linguistic backgrounds can be targeted. A statistical language model is used to measure information density and to gauge how language users master various degrees of (un)intelligibilty. The key idea is that intercomprehension should be better when the model adapted for understanding the unknown language exhibits relatively low average distance and surprisal. All obtained intelligibility scores together with distance and asymmetry measures for the different language pairs and processing directions are made available as an integrated online resource in the form of a Slavic intercomprehension matrix (SlavMatrix).
Identifications of Speaker Ethnicity in South-East England: Multicultural London English as a Divisible Perceptual Variety (2020)

This study uses crowdsourcing through LanguageARC to collect data on levels of accuracy in the identification of speakers' ethnicities. Ten participants (5 US; 5 South-East England) classified lexically identical speech stimuli from a corpus of 227 speakers aged 18-33yrs from South-East England into the main {\textquotedblleft}ethnic{\textquotedblright} groups in Britain: White British, Black British and Asian British. Firstly, the data reveals that there is no significant geographic proximity effect on performance between US and British participants. Secondly, results contribute to recent work suggesting that despite the varying heritages of young, ethnic minority speakers in London, they speak an innovative and emerging variety: Multicultural London English (MLE) (e.g. Cheshire et al., 2011). Countering this, participants found perceptual linguistic differences between speakers of all 3 ethnicities (80.7{\%} accuracy). The highest rate of accuracy (96{\%}) was when identifying the ethnicity of Black British speakers from London whose speech seems to form a distinct, perceptual category. Participants also perform substantially better than chance at identifying Black British and Asian British speakers who are not from London (80{\%} and 60{\%} respectively). This suggests that MLE is not a single, homogeneous variety but instead, there are perceptual linguistic differences by ethnicity which transcend the borders of London.
LanguageARC - a tutorial (2020)

LanguageARC is a portal that offers citizen linguists opportunities to contribute to language related research. It also provides researchers with infrastructure for easily creating data collection and annotation tasks on the portal and potentially connecting with contributors. This document describes LanguageARC`s main features and operation for researchers interested in creating new projects and or using the resulting data.
Various Approaches for Predicting Stroke Prognosis using Magnetic Resonance Imaging Text Records (2020)

Stroke is one of the leading causes of death and disability worldwide. Stroke is treatable, but it is prone to disability after treatment and must be prevented. To grasp the degree of disability caused by stroke, we use magnetic resonance imaging text records to predict stroke and measure the performance according to the document-level and sentence-level representation. As a result of the experiment, the document-level representation shows better performance.
Multiple Sclerosis Severity Classification From Clinical Text (2020)

Multiple Sclerosis (MS) is a chronic, inflammatory and degenerative neurological disease, which is monitored by a specialist using the Expanded Disability Status Scale (EDSS) and recorded in unstructured text in the form of a neurology consult note. An EDSS measurement contains an overall {\textquoteleft}EDSS' score and several functional subscores. Typically, expert knowledge is required to interpret consult notes and generate these scores. Previous approaches used limited context length Word2Vec embeddings and keyword searches to predict scores given a consult note, but often failed when scores were not explicitly stated. In this work, we present MS-BERT, the first publicly available transformer model trained on real clinical data other than MIMIC. Next, we present MSBC, a classifier that applies MS-BERT to generate embeddings and predict EDSS and functional subscores. Lastly, we explore combining MSBC with other models through the use of Snorkel to generate scores for unlabelled consult notes. MSBC achieves state-of-the-art performance on all metrics and prediction tasks and outperforms the models generated from the Snorkel ensemble. We improve Macro-F1 by 0.12 (to 0.88) for predicting EDSS and on average by 0.29 (to 0.63) for predicting functional subscores over previous Word2Vec CNN and rule-based approaches.
BERT-XML: Large Scale Automated ICD Coding Using BERT Pretraining (2020)

ICD coding is the task of classifying and cod-ing all diagnoses, symptoms and proceduresassociated with a patient`s visit. The process isoften manual, extremely time-consuming andexpensive for hospitals as clinical interactionsare usually recorded in free text medical notes. In this paper, we propose a machine learningmodel, BERT-XML, for large scale automatedICD coding of EHR notes, utilizing recentlydeveloped unsupervised pretraining that haveachieved state of the art performance on a va-riety of NLP tasks. We train a BERT modelfrom scratch on EHR notes, learning with vo-cabulary better suited for EHR tasks and thusoutperform off-the-shelf models. We furtheradapt the BERT architecture for ICD codingwith multi-label attention. We demonstratethe effectiveness of BERT-based models on thelarge scale ICD code classification task usingmillions of EHR notes to predict thousands ofunique codes.
Incorporating Risk Factor Embeddings in Pre-trained Transformers Improves Sentiment Prediction in Psychiatric Discharge Summaries (2020)

Reducing rates of early hospital readmission has been recognized and identified as a key to improve quality of care and reduce costs. There are a number of risk factors that have been hypothesized to be important for understanding re-admission risk, including such factors as problems with substance abuse, ability to maintain work, relations with family. In this work, we develop Roberta-based models to predict the sentiment of sentences describing readmission risk factors in discharge summaries of patients with psychosis. We improve substantially on previous results by a scheme that shares information across risk factors while also allowing the model to learn risk factor-specific information.
Information Extraction from Swedish Medical Prescriptions with Sig-Transformer Encoder (2020)

Relying on large pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) for encoding and adding a simple prediction layer has led to impressive performance in many clinical natural language processing (NLP) tasks. In this work, we present a novel extension to the Transformer architecture, by incorporating signature transform with the self-attention model. This architecture is added between embedding and prediction layers. Experiments on a new Swedish prescription data show the proposed architecture to be superior in two of the three information extraction tasks, comparing to baseline models. Finally, we evaluate two different embedding approaches between applying Multilingual BERT and translating the Swedish text to English then encode with a BERT model pretrained on clinical notes.
Evaluation of Transfer Learning for Adverse Drug Event (ADE) and Medication Entity Extraction (2020)

We evaluate several biomedical contextual embeddings (based on BERT, ELMo, and Flair) for the detection of medication entities such as Drugs and Adverse Drug Events (ADE) from Electronic Health Records (EHR) using the 2018 ADE and Medication Extraction (Track 2) n2c2 data-set. We identify best practices for transfer learning, such as language-model fine-tuning and scalar mix. Our transfer learning models achieve strong performance in the overall task (F1=92.91{\%}) as well as in ADE identification (F1=53.08{\%}). Flair-based embeddings out-perform in the identification of context-dependent entities such as ADE. BERT-based embeddings out-perform in recognizing clinical terminology such as Drug and Form entities. ELMo-based embeddings deliver competitive performance in all entities. We develop a sentence-augmentation method for enhanced ADE identification benefiting BERT-based and ELMo-based models by up to 3.13{\%} in F1 gains. Finally, we show that a simple ensemble of these models out-paces most current methods in ADE extraction (F1=55.77{\%}).
BioBERTpt - A Portuguese Neural Language Model for Clinical Named Entity Recognition (2020)

With the growing number of electronic health record data, clinical NLP tasks have become increasingly relevant to unlock valuable information from unstructured clinical text. Although the performance of downstream NLP tasks, such as named-entity recognition (NER), in English corpus has recently improved by contextualised language models, less research is available for clinical texts in low resource languages. Our goal is to assess a deep contextual embedding model for Portuguese, so called BioBERTpt, to support clinical and biomedical NER. We transfer learned information encoded in a multilingual-BERT model to a corpora of clinical narratives and biomedical-scientific papers in Brazilian Portuguese. To evaluate the performance of BioBERTpt, we ran NER experiments on two annotated corpora containing clinical narratives and compared the results with existing BERT models. Our in-domain model outperformed the baseline model in F1-score by 2.72{\%}, achieving higher performance in 11 out of 13 assessed entities. We demonstrate that enriching contextual embedding models with domain literature can play an important role in improving performance for specific NLP tasks. The transfer learning process enhanced the Portuguese biomedical NER model by reducing the necessity of labeled data and the demand for retraining a whole new model.
Dilated Convolutional Attention Network for Medical Code Assignment from Clinical Text (2020)

Medical code assignment, which predicts medical codes from clinical texts, is a fundamental task of intelligent medical information systems. The emergence of deep models in natural language processing has boosted the development of automatic assignment methods. However, recent advanced neural architectures with flat convolutions or multi-channel feature concatenation ignore the sequential causal constraint within a text sequence and may not learn meaningful clinical text representations, especially for lengthy clinical notes with long-term sequential dependency. This paper proposes a Dilated Convolutional Attention Network (DCAN), integrating dilated convolutions, residual connections, and label attention, for medical code assignment. It adopts dilated convolutions to capture complex medical patterns with a receptive field which increases exponentially with dilation size. Experiments on a real-world clinical dataset empirically show that our model improves the state of the art.
Classification of Syncope Cases in Norwegian Medical Records (2020)

Loss of consciousness, so-called syncope, is a commonly occurring symptom associated with worse prognosis for a number of heart-related diseases. We present a comparison of methods for a diagnosis classification task in Norwegian clinical notes, targeting syncope, i.e. fainting cases. We find that an often neglected baseline with keyword matching constitutes a rather strong basis, but more advanced methods do offer some improvement in classification performance, especially a convolutional neural network model. The developed pipeline is planned to be used for quantifying unregistered syncope cases in Norway.
Comparison of Machine Learning Methods for Multi-label Classification of Nursing Education and Licensure Exam Questions (2020)

In this paper, we evaluate several machine learning methods for multi-label classification of text questions. Every nursing student in the United States must pass the National Council Licensure Examination (NCLEX) to begin professional practice. NCLEX defines a number of competencies on which students are evaluated. By labeling test questions with NCLEX competencies, we can score students according to their performance in each competency. This information helps instructors measure how prepared students are for the NCLEX, as well as which competencies they may need help with. A key challenge is that questions may be related to more than one competency. Labeling questions with NCLEX competencies, therefore, equates to a multi-label, text classification problem where each competency is a label. Here we present an evaluation of several methods to support this use case along with a proposed approach. While our work is grounded in the nursing education domain, the methods described here can be used for any multi-label, text classification use case.
Clinical XLNet: Modeling Sequential Clinical Notes and Predicting Prolonged Mechanical Ventilation (2020)

Clinical notes contain rich information, which is relatively unexploited in predictive modeling compared to structured data. In this work, we developed a new clinical text representation Clinical XLNet that leverages the temporal information of the sequence of the notes. We evaluated our models on prolonged mechanical ventilation prediction problem and our experiments demonstrated that Clinical XLNet outperforms the best baselines consistently. The models and scripts are made publicly available.
Automatic recognition of abdominal lymph nodes from clinical text (2020)

Lymph node status plays a pivotal role in the treatment of cancer. The extraction of lymph nodes from radiology text reports enables large-scale training of lymph node detection on MRI. In this work, we first propose an ontology of 41 types of abdominal lymph nodes with a hierarchical relationship. We then introduce an end-to-end approach based on the combination of rules and transformer-based methods to detect these abdominal lymph node mentions and classify their types from the MRI radiology reports. We demonstrate the superior performance of a model fine-tuned on MRI reports using BlueBERT, called MriBERT. We find that MriBERT outperforms the rule-based labeler (0.957 vs 0.644 in micro weighted F1-score) as well as other BERT-based variations (0.913 - 0.928). We make the code and MriBERT publicly available at \url{https://github.com/ncbi-nlp/bluebert}, with the hope that this method can facilitate the development of medical report annotators to produce labels from scratch at scale.
How You Ask Matters: The Effect of Paraphrastic Questions to BERT Performance on a Clinical SQuAD Dataset (2020)

Reading comprehension style question-answering (QA) based on patient-specific documents represents a growing area in clinical NLP with plentiful applications. Bidirectional Encoder Representations from Transformers (BERT) and its derivatives lead the state-of-the-art accuracy on the task, but most evaluation has treated the data as a pre-mixture without systematically looking into the potential effect of imperfect train/test questions. The current study seeks to address this gap by experimenting with full versus partial train/test data consisting of paraphrastic questions. Our key findings include 1) training with all pooled question variants yielded best accuracy, 2) the accuracy varied widely, from 0.74 to 0.80, when trained with each single question variant, and 3) questions of similar lexical/syntactic structure tended to induce identical answers. The results suggest that how you ask questions matters in BERT-based QA, especially at the training stage.
Relative and Incomplete Time Expression Anchoring for Clinical Text (2020)

Extracting and modeling temporal information in clinical text is an important element for developing timelines and disease trajectories. Time information in written text varies in preciseness and explicitness, posing challenges for NLP approaches that aim to accurately anchor temporal information on a timeline. Relative and incomplete time expressions (RI-Timexes) are expressions that require additional information for their temporal anchor to be resolved, but few studies have addressed this challenge specifically. In this study, we aimed to reproduce and verify a classification approach for identifying anchor dates and relations in clinical text, and propose a novel relation classification approach for this task.
MeDAL: Medical Abbreviation Disambiguation Dataset for Natural Language Understanding Pretraining (2020)

One of the biggest challenges that prohibit the use of many current NLP methods in clinical settings is the availability of public datasets. In this work, we present MeDAL, a large medical text dataset curated for abbreviation disambiguation, designed for natural language understanding pre-training in the medical domain. We pre-trained several models of common architectures on this dataset and empirically showed that such pre-training leads to improved performance and convergence speed when fine-tuning on downstream medical tasks.
Knowledge Grounded Conversational Symptom Detection with Graph Memory Networks (2020)

In this work, we propose a novel goal-oriented dialog task, automatic symptom detection. We build a system that can interact with patients through dialog to detect and collect clinical symptoms automatically, which can save a doctor`s time interviewing the patient. Given a set of explicit symptoms provided by the patient to initiate a dialog for diagnosing, the system is trained to collect implicit symptoms by asking questions, in order to collect more information for making an accurate diagnosis. After getting the reply from the patient for each question, the system also decides whether current information is enough for a human doctor to make a diagnosis. To achieve this goal, we propose two neural models and a training pipeline for the multi-step reasoning task. We also build a knowledge graph as additional inputs to further improve model performance. Experiments show that our model significantly outperforms the baseline by 4{\%}, discovering 67{\%} of implicit symptoms on average with a limited number of questions.
Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-Art (2020)

A large array of pretrained models are available to the biomedical NLP (BioNLP) community. Finding the best model for a particular task can be difficult and time-consuming. For many applications in the biomedical and clinical domains, it is crucial that models can be built quickly and are highly accurate. We present a large-scale study across 18 established biomedical and clinical NLP tasks to determine which of several popular open-source biomedical and clinical NLP models work well in different settings. Furthermore, we apply recent advances in pretraining to train new biomedical language models, and carefully investigate the effect of various design choices on downstream performance. Our best models perform well in all of our benchmarks, and set new State-of-the-Art in 9 tasks. We release these models in the hope that they can help the community to speed up and increase the accuracy of BioNLP and text mining applications.
Assessment of DistilBERT performance on Named Entity Recognition task for the detection of Protected Health Information and medical concepts (2020)

Bidirectional Encoder Representations from Transformers (BERT) models achieve state-of-the-art performance on a number of Natural Language Processing tasks. However, their model size on disk often exceeds 1 GB and the process of fine-tuning them and using them to run inference consumes significant hardware resources and runtime. This makes them hard to deploy to production environments. This paper fine-tunes DistilBERT, a lightweight deep learning model, on medical text for the named entity recognition task of Protected Health Information (PHI) and medical concepts. This work provides a full assessment of the performance of DistilBERT in comparison with BERT models that were pre-trained on medical text. For Named Entity Recognition task of PHI, DistilBERT achieved almost the same results as medical versions of BERT in terms of F1 score at almost half the runtime and consuming approximately half the disk space. On the other hand, for the detection of medical concepts, DistilBERT`s F1 score was lower by 4 points on average than medical BERT variants.
Distinguishing between Dementia with Lewy bodies (DLB) and Alzheimer`s Disease (AD) using Mental Health Records: a Classification Approach (2020)

While Dementia with Lewy Bodies (DLB) is the second most common type of neurodegenerative dementia following Alzheimer`s Disease (AD), it is difficult to distinguish from AD. We propose a method for DLB detection by using mental health record (MHR) documents from a (3-month) period before a patient has been diagnosed with DLB or AD. Our objective is to develop a model that could be clinically useful to differentiate between DLB and AD across datasets from different healthcare institutions. We cast this as a classification task using Convolutional Neural Network (CNN), an efficient neural model for text classification. We experiment with different representation models, and explore the features that contribute to model performances. In addition, we apply temperature scaling, a simple but efficient model calibration method, to produce more reliable predictions. We believe the proposed method has important potential for clinical applications using routine healthcare records, and for generalising to other relevant clinical record datasets. To the best of our knowledge, this is the first attempt to distinguish DLB from AD using mental health records, and to improve the reliability of DLB predictions.