ymoslem/acl-abstracts huggingface dataset:
Towards Automatic Generation of Shareable Synthetic Clinical Notes Using Neural Language Models (2019)

Large-scale clinical data is invaluable to driving many computational scientific advances today. However, understandable concerns regarding patient privacy hinder the open dissemination of such data and give rise to suboptimal siloed research. De-identification methods attempt to address these concerns but were shown to be susceptible to adversarial attacks. In this work, we focus on the vast amounts of unstructured natural language data stored in clinical notes and propose to automatically generate synthetic clinical notes that are more amenable to sharing using generative models trained on real de-identified records. To evaluate the merit of such notes, we measure both their privacy preservation properties as well as utility in training clinical NLP models. Experiments using neural language models yield notes whose utility is close to that of the real ones in some clinical NLP tasks, yet leave ample room for future improvements.
A Novel System for Extractive Clinical Note Summarization using EHR Data (2019)

While much data within a patient`s electronic health record (EHR) is coded, crucial information concerning the patient`s care and management remain buried in unstructured clinical notes, making it difficult and time-consuming for physicians to review during their usual clinical workflow. In this paper, we present our clinical note processing pipeline, which extends beyond basic medical natural language processing (NLP) with concept recognition and relation detection to also include components specific to EHR data, such as structured data associated with the encounter, sentence-level clinical aspects, and structures of the clinical notes. We report on the use of this pipeline in a disease-specific extractive text summarization task on clinical notes, focusing primarily on progress notes by physicians and nurse practitioners. We show how the addition of EHR-specific components to the pipeline resulted in an improvement in our overall system performance and discuss the potential impact of EHR-specific components on other higher-level clinical NLP tasks.
Study of lexical aspect in the French medical language. Development of a lexical resource (2019)

This paper details the development of a linguistic resource designed to improve temporal information extraction systems and to integrate aspectual values. After a brief review of recent works in temporal information extraction for the medical area, we discuss the linguistic notion of aspect and how it got a place in the NLP field. Then, we present our clinical data and describe the five-step approach adopted in this study. Finally, we represent the linguistic resource itself and explain how we elaborated it and which properties were selected for the creation of the tables.
A BERT-based Universal Model for Both Within- and Cross-sentence Clinical Temporal Relation Extraction (2019)

Classic methods for clinical temporal relation extraction focus on relational candidates within a sentence. On the other hand, break-through Bidirectional Encoder Representations from Transformers (BERT) are trained on large quantities of arbitrary spans of contiguous text instead of sentences. In this study, we aim to build a sentence-agnostic framework for the task of CONTAINS temporal relation extraction. We establish a new state-of-the-art result for the task, 0.684F for in-domain (0.055-point improvement) and 0.565F for cross-domain (0.018-point improvement), by fine-tuning BERT and pre-training domain-specific BERT models on sentence-agnostic temporal relation instances with WordPiece-compatible encodings, and augmenting the labeled data with automatically generated {\textquotedblleft}silver{\textquotedblright} instances.
Publicly Available Clinical BERT Embeddings (2019)

Contextual word embedding models such as ELMo and BERT have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such as clinical text; moreover, in the clinical domain, no publicly-available pre-trained BERT models yet exist. In this work, we address this need by exploring and releasing BERT models for clinical text: one for generic clinical text and another for discharge summaries specifically. We demonstrate that using a domain-specific model yields performance improvements on 3/5 clinical NLP tasks, establishing a new state-of-the-art on the MedNLI dataset. We find that these domain-specific models are not as performant on 2 clinical de-identification tasks, and argue that this is a natural consequence of the differences between de-identified source text and synthetically non de-identified task text.
A General-Purpose Annotation Model for Knowledge Discovery: Case Study in Spanish Clinical Text (2019)

Knowledge discovery from text in natural language is a task usually aided by the manual construction of annotated corpora. Specifically in the clinical domain, several annotation models are used depending on the characteristics of the task to solve (e.g., named entity recognition, relation extraction, etc.). However, few general-purpose annotation models exist, that can support a broad range of knowledge extraction tasks. This paper presents an annotation model designed to capture a large portion of the semantics of natural language text. The structure of the annotation model is presented, with examples of annotated sentences and a brief description of each semantic role and relation defined. This research focuses on an application to clinical texts in the Spanish language. Nevertheless, the presented annotation model is extensible to other domains and languages. An example of annotated sentences, guidelines, and suitable configuration files for an annotation tool are also provided for the research community.
Predicting ICU transfers using text messages between nurses and doctors (2019)

We explore the use of real-time clinical information, i.e., text messages sent between nurses and doctors regarding patient conditions in order to predict transfer to the intensive care unit(ICU). Preliminary results, in data from five hospitals, indicate that, despite being short and full of noise, text messages can augment other visit information to improve the performance of ICU transfer prediction.
Medical Entity Linking using Triplet Network (2019)

Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also be used for merging different medical and clinical ontologies. In this paper, we center around the problem of disease linking or normalization. This task is executed in two phases: candidate generation and candidate scoring. In this paper, we present an approach to rank the candidate Knowledge Base entries based on their similarity with disease mention. We make use of the Triplet Network for candidate ranking. While the existing methods have used carefully generated sieves and external resources for candidate generation, we introduce a robust and portable candidate generation scheme that does not make use of the hand-crafted rules. Experimental results on the standard benchmark NCBI disease dataset demonstrate that our system outperforms the prior methods by a significant margin.
Annotating and Characterizing Clinical Sentences with Explicit Why-QA Cues (2019)

Many clinical information needs can be stated as why-questions. The answers to them represent important clinical reasoning and justification. Clinical notes are a rich source for such why-question answering (why-QA). However, there are few dedicated corpora, and little is known about the characteristics of clinical why-QA narratives. To address this gap, the study performed manual annotation of 277 sentences containing explicit why-QA cues and summarized their quantitative and qualitative properties. The contributions are: 1) sharing a seed corpus that can be used for various QA-related training purposes, 2) adding to our knowledge about the diversity and distribution of clinical why-QA contents.
Extracting Factual Min/Max Age Information from Clinical Trial Studies (2019)

Population age information is an essential characteristic of clinical trials. In this paper, we focus on extracting minimum and maximum (min/max) age values for the study samples from clinical research articles. Specifically, we investigate the use of a neural network model for question answering to address this information extraction task. The min/max age QA model is trained on the massive structured clinical study records from ClinicalTrials.gov. For each article, based on multiple min and max age values extracted from the QA model, we predict both actual min/max age values for the study samples and filter out non-factual age expressions. Our system improves the results over (i) a passage retrieval based IE system and (ii) a CRF-based system by a large margin when evaluated on an annotated dataset consisting of 50 research papers on smoking cessation.
Distinguishing Clinical Sentiment: The Importance of Domain Adaptation in Psychiatric Patient Health Records (2019)

Recently natural language processing (NLP) tools have been developed to identify and extract salient risk indicators in electronic health records (EHRs). Sentiment analysis, although widely used in non-medical areas for improving decision making, has been studied minimally in the clinical setting. In this study, we undertook, to our knowledge, the first domain adaptation of sentiment analysis to psychiatric EHRs by defining psychiatric clinical sentiment, performing an annotation project, and evaluating multiple sentence-level sentiment machine learning (ML) models. Results indicate that off-the-shelf sentiment analysis tools fail in identifying clinically positive or negative polarity, and that the definition of clinical sentiment that we provide is learnable with relatively small amounts of training data. This project is an initial step towards further refining sentiment analysis methods for clinical use. Our long-term objective is to incorporate the results of this project as part of a machine learning model that predicts inpatient readmission risk. We hope that this work will initiate a discussion concerning domain adaptation of sentiment analysis to the clinical setting.
Medical Word Embeddings for Spanish: Development and Evaluation (2019)

Word embeddings are representations of words in a dense vector space. Although they are not recent phenomena in Natural Language Processing (NLP), they have gained momentum after the recent developments of neural methods and Word2Vec. Regarding their applications in medical and clinical NLP, they are invaluable resources when training in-domain named entity recognition systems, classifiers or taggers, for instance. Thus, the development of tailored word embeddings for medical NLP is of great interest. However, we identified a gap in the literature which we aim to fill in this paper: the availability of embeddings for medical NLP in Spanish, as well as a standardized form of intrinsic evaluation. Since most work has been done for English, some established datasets for intrinsic evaluation are already available. In this paper, we show the steps we employed to adapt such datasets for the first time to Spanish, of particular relevance due to the considerable volume of EHRs in this language, as well as the creation of in-domain medical word embeddings for the Spanish using the state-of-the-art FastText model. We performed intrinsic evaluation with our adapted datasets, as well as extrinsic evaluation with a named entity recognition systems using a baseline embedding of general-domain. Both experiments proved that our embeddings are suitable for use in medical NLP in the Spanish language, and are more accurate than general-domain ones.
Attention Neural Model for Temporal Relation Extraction (2019)

Neural network models have shown promise in the temporal relation extraction task. In this paper, we present the attention based neural network model to extract the containment relations within sentences from clinical narratives. The attention mechanism used on top of GRU model outperforms the existing state-of-the-art neural network models on THYME corpus in intra-sentence temporal relation extraction.
Automatically Generating Psychiatric Case Notes From Digital Transcripts of Doctor-Patient Conversations (2019)

Electronic health records (EHRs) are notorious for reducing the face-to-face time with patients while increasing the screen-time for clinicians leading to burnout. This is especially problematic for psychiatry care in which maintaining consistent eye-contact and non-verbal cues are just as important as the spoken words. In this ongoing work, we explore the feasibility of automatically generating psychiatric EHR case notes from digital transcripts of doctor-patient conversation using a two-step approach: (1) predicting semantic topics for segments of transcripts using supervised machine learning, and (2) generating formal text of those segments using natural language processing. Through a series of preliminary experimental results obtained through a collection of synthetic and real-life transcripts, we demonstrate the viability of this approach.
Clinical Data Classification using Conditional Random Fields and Neural Parsing for Morphologically Rich Languages (2019)

Past prescriptions constitute a central element in patient records. These are often written in an unstructured and brief form. Extracting information from such prescriptions enables the development of automated processes in the medical data mining field. This paper presents a Conditional Random Fields (CRFs) based approach to extract relevant information from prescriptions. We focus on Finnish language prescriptions and make use of Finnish language specific features. Our labeling accuracy is 95{\%}, which compares favorably to the current state-of-the-art in English language prescriptions. This, to the best of our knowledge, is the first such work for the Finnish language.
Neural Vector Conceptualization for Word Vector Space Interpretation (2019)

Distributed word vector spaces are considered hard to interpret which hinders the understanding of natural language processing (NLP) models. In this work, we introduce a new method to interpret arbitrary samples from a word vector space. To this end, we train a neural model to conceptualize word vectors, which means that it activates higher order concepts it recognizes in a given vector. Contrary to prior approaches, our model operates in the original vector space and is capable of learning non-linear relations between word vectors and concepts. Furthermore, we show that it produces considerably less entropic concept activation profiles than the popular cosine similarity.
Characterizing the Impact of Geometric Properties of Word Embeddings on Task Performance (2019)

Analysis of word embedding properties to inform their use in downstream NLP tasks has largely been studied by assessing nearest neighbors. However, geometric properties of the continuous feature space contribute directly to the use of embedding features in downstream models, and are largely unexplored. We consider four properties of word embedding geometry, namely: position relative to the origin, distribution of features in the vector space, global pairwise distances, and local pairwise distances. We define a sequence of transformations to generate new embeddings that expose subsets of these properties to downstream models and evaluate change in task performance to understand the contribution of each property to NLP models. We transform publicly available pretrained embeddings from three popular toolkits (word2vec, GloVe, and FastText) and evaluate on a variety of intrinsic tasks, which model linguistic information in the vector space, and extrinsic tasks, which use vectors as input to machine learning models. We find that intrinsic evaluations are highly sensitive to absolute position, while extrinsic tasks rely primarily on local similarity. Our findings suggest that future embedding models and post-processing techniques should focus primarily on similarity to nearby points in vector space.
The Influence of Down-Sampling Strategies on SVD Word Embedding Stability (2019)

The stability of word embedding algorithms, i.e., the consistency of the word representations they reveal when trained repeatedly on the same data set, has recently raised concerns. We here compare word embedding algorithms on three corpora of different sizes, and evaluate both their stability and accuracy. We find strong evidence that down-sampling strategies (used as part of their training procedures) are particularly influential for the stability of SVD-PPMI-type embeddings. This finding seems to explain diverging reports on their stability and lead us to a simple modification which provides superior stability as well as accuracy on par with skip-gram embedding
How Well Do Embedding Models Capture Non-compositionality? A View from Multiword Expressions (2019)

In this paper, we apply various embedding methods on multiword expressions to study how well they capture the nuances of non-compositional data. Our results from a pool of word-, character-, and document-level embbedings suggest that Word2vec performs the best, followed by FastText and Infersent. Moreover, we find that recently-proposed contextualised embedding models such as Bert and ELMo are not adept at handling non-compositionality in multiword expressions.
Measuring Semantic Abstraction of Multilingual NMT with Paraphrase Recognition and Generation Tasks (2019)

In this paper, we investigate whether multilingual neural translation models learn stronger semantic abstractions of sentences than bilingual ones. We test this hypotheses by measuring the perplexity of such models when applied to paraphrases of the source language. The intuition is that an encoder produces better representations if a decoder is capable of recognizing synonymous sentences in the same language even though the model is never trained for that task. In our setup, we add 16 different auxiliary languages to a bidirectional bilingual baseline model (English-French) and test it with in-domain and out-of-domain paraphrases in English. The results show that the perplexity is significantly reduced in each of the cases, indicating that meaning can be grounded in translation. This is further supported by a study on paraphrase generation that we also include at the end of the paper.
SWOW-8500: Word Association task for Intrinsic Evaluation of Word Embeddings (2019)

Downstream evaluation of pretrained word embeddings is expensive, more so for tasks where current state of the art models are very large architectures. Intrinsic evaluation using word similarity or analogy datasets, on the other hand, suffers from several disadvantages. We propose a novel intrinsic evaluation task employing large word association datasets (particularly the Small World of Words dataset). We observe correlations not just between performances on SWOW-8500 and previously proposed intrinsic tasks of word similarity prediction, but also with downstream tasks (eg. Text Classification and Natural Language Inference). Most importantly, we report better confidence intervals for scores on our word association task, with no fall in correlation with downstream performance.
Classification of Semantic Paraphasias: Optimization of a Word Embedding Model (2019)

In clinical assessment of people with aphasia, impairment in the ability to recall and produce words for objects (anomia) is assessed using a confrontation naming task, where a target stimulus is viewed and a corresponding label is spoken by the participant. Vector space word embedding models have had inital results in assessing semantic similarity of target-production pairs in order to automate scoring of this task; however, the resulting models are also highly dependent upon training parameters. To select an optimal family of models, we fit a beta regression model to the distribution of performance metrics on a set of 2,880 grid search models and evaluate the resultant first- and second-order effects to explore how parameterization affects model performance. Comparing to SimLex-999, we show that clinical data can be used in an evaluation task with comparable optimal parameter settings as standard NLP evaluation datasets.
CODAH: An Adversarially-Authored Question Answering Dataset for Common Sense (2019)

Commonsense reasoning is a critical AI capability, but it is difficult to construct challenging datasets that test common sense. Recent neural question answering systems, based on large pre-trained models of language, have already achieved near-human-level performance on commonsense knowledge benchmarks. These systems do not possess human-level common sense, but are able to exploit limitations of the datasets to achieve human-level scores. We introduce the CODAH dataset, an adversarially-constructed evaluation dataset for testing common sense. CODAH forms a challenging extension to the recently-proposed SWAG dataset, which tests commonsense knowledge using sentence-completion questions that describe situations observed in video. To produce a more difficult dataset, we introduce a novel procedure for question acquisition in which workers author questions designed to target weaknesses of state-of-the-art neural question answering systems. Workers are rewarded for submissions that models fail to answer correctly both before and after fine-tuning (in cross-validation). We create 2.8k questions via this procedure and evaluate the performance of multiple state-of-the-art question answering systems on our dataset. We observe a significant gap between human performance, which is 95.3{\%}, and the performance of the best baseline accuracy of 65.3{\%} by the OpenAI GPT model.
Syntactic Interchangeability in Word Embedding Models (2019)

Nearest neighbors in word embedding models are commonly observed to be semantically similar, but the relations between them can vary greatly. We investigate the extent to which word embedding models preserve syntactic interchangeability, as reflected by distances between word vectors, and the effect of hyper-parameters{---}context window size in particular. We use part of speech (POS) as a proxy for syntactic interchangeability, as generally speaking, words with the same POS are syntactically valid in the same contexts. We also investigate the relationship between interchangeability and similarity as judged by commonly-used word similarity benchmarks, and correlate the result with the performance of word embedding models on these benchmarks. Our results will inform future research and applications in the selection of word embedding model, suggesting a principle for an appropriate selection of the context window size parameter depending on the use-case.
Evaluation of Morphological Embeddings for English and Russian Languages (2019)

This paper evaluates morphology-based embeddings for English and Russian languages. Despite the interest and introduction of several morphology based word embedding models in the past and acclaimed performance improvements on word similarity and language modeling tasks, in our experiments, we did not observe any stable preference over two of our baseline models - SkipGram and FastText. The performance exhibited by morphological embeddings is the average of the two baselines mentioned above.