ymoslem/acl-abstracts huggingface dataset:
Characterization of Divergence in Impaired Speech of ALS Patients (2017)

Approximately 80{\%} to 95{\%} of patients with Amyotrophic Lateral Sclerosis (ALS) eventually develop speech impairments, such as defective articulation, slow laborious speech and hypernasality. The relationship between impaired speech and asymptomatic speech may be seen as a divergence from a baseline. This relationship can be characterized in terms of measurable combinations of phonological characteristics that are indicative of the degree to which the two diverge. We demonstrate that divergence measurements based on phonological characteristics of speech correlate with physiological assessments of ALS. Speech-based assessments offer benefits over commonly-used physiological assessments in that they are inexpensive, non-intrusive, and do not require trained clinical personnel for administering and interpreting the results.
Deep Learning for Punctuation Restoration in Medical Reports (2017)

In clinical dictation, speakers try to be as concise as possible to save time, often resulting in utterances without explicit punctuation commands. Since the end product of a dictated report, e.g. an out-patient letter, does require correct orthography, including exact punctuation, the latter need to be restored, preferably by automated means. This paper describes a method for punctuation restoration based on a state-of-the-art stack of NLP and machine learning techniques including B-RNNs with an attention mechanism and late fusion, as well as a feature extraction technique tailored to the processing of medical terminology using a novel vocabulary reduction model. To the best of our knowledge, the resulting performance is superior to that reported in prior art on similar tasks.
Unsupervised Domain Adaptation for Clinical Negation Detection (2017)

Detecting negated concepts in clinical texts is an important part of NLP information extraction systems. However, generalizability of negation systems is lacking, as cross-domain experiments suffer dramatic performance losses. We examine the performance of multiple unsupervised domain adaptation algorithms on clinical negation detection, finding only modest gains that fall well short of in-domain performance.
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations (2017)

The Precision Medicine Track in BioCre-ative VI aims to bring together the Bi-oNLP community for a novel challenge focused on mining the biomedical litera-ture in search of mutations and protein-protein interactions (PPI). In order to support this track with an effective train-ing dataset with limited curator time, the track organizers carefully reviewed Pub-Med articles from two different sources: curated public PPI databases, and the re-sults of state-of-the-art public text mining tools. We detail here the data collection, manual review and annotation process and describe this training corpus charac-teristics. We also describe a corpus per-formance baseline. This analysis will provide useful information to developers and researchers for comparing and devel-oping innovative text mining approaches for the BioCreative VI challenge and other Precision Medicine related applica-tions.
Painless Relation Extraction with Kindred (2017)

Relation extraction methods are essential for creating robust text mining tools to help researchers find useful knowledge in the vast published literature. Easy-to-use and generalizable methods are needed to encourage an ecosystem in which researchers can easily use shared resources and build upon each others' methods. We present the Kindred Python package for relation extraction. It builds upon methods from the most successful tools in the recent BioNLP Shared Task to predict high-quality predictions with low computational cost. It also integrates with PubAnnotation, PubTator, and BioNLP Shared Task data in order to allow easy development and application of relation extraction models.
Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction (2017)

Distant supervision has been applied to automatically generate labeled data for biomedical relation extraction. Noise exists in both positively and negatively-labeled data and affects the performance of supervised machine learning methods. In this paper, we propose three novel heuristics based on the notion of proximity, trigger word and confidence of patterns to leverage lexical and syntactic information to reduce the level of noise in the distantly labeled data. Experiments on three different tasks, extraction of protein-protein-interaction, miRNA-gene regulation relation and protein-localization event, show that the proposed methods can improve the F-score over the baseline by 6, 10 and 14 points for the three tasks, respectively. We also show that when the models are configured to output high-confidence results, high precisions can be obtained using the proposed methods, making them promising for facilitating manual curation for databases.
Role-Preserving Redaction of Medical Records to Enable Ontology-Driven Processing (2017)

Electronic medical records (EMR) have largely replaced hand-written patient files in healthcare. The growing pool of EMR data presents a significant resource in medical research, but the U.S. Health Insurance Portability and Accountability Act (HIPAA) mandates redacting medical records before performing any analysis on the same. This process complicates obtaining medical data and can remove much useful information from the record. As part of a larger project involving ontology-driven medical processing, we employ a method of recognizing protected health information (PHI) that maps to ontological terms. We then use the relationships defined in the ontology to redact medical texts so that roles and semantics of terms are retained without compromising anonymity. The method is evaluated by clinical experts on several hundred medical documents, achieving up to a 98.8{\%} f-score, and has already shown promise for retaining semantic information in later processing.
Annotation of pain and anesthesia events for surgery-related processes and outcomes extraction (2017)

Pain and anesthesia information are crucial elements to identifying surgery-related processes and outcomes. However pain is not consistently recorded in the electronic medical record. Even when recorded, the rich complex granularity of the pain experience may be lost. Similarly, anesthesia information is recorded using local electronic collection systems; though the accuracy and completeness of the information is unknown. We propose an annotation schema to capture pain, pain management, and anesthesia event information.
Identifying Comparative Structures in Biomedical Text (2017)

Comparison sentences are very commonly used by authors in biomedical literature to report results of experiments. In such comparisons, authors typically make observations under two different scenarios. In this paper, we present a system to automatically identify such comparative sentences and their components i.e. the compared entities, the scale of the comparison and the aspect on which the entities are being compared. Our methodology is based on dependencies obtained by applying a parser to extract a wide range of comparison structures. We evaluated our system for its effectiveness in identifying comparisons and their components. The system achieved a F-score of 0.87 for comparison sentence identification and 0.77-0.81 for identifying its components.
Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models (2017)

In this paper we present a solution for tagging funding bodies and grants in scientific articles using a combination of trained sequential learning models, namely conditional random fields (CRF), hidden markov models (HMM) and maximum entropy models (MaxEnt), on a benchmark set created in-house. We apply the trained models to address the BioASQ challenge 5c, which is a newly introduced task that aims to solve the problem of funding information extraction from scientific articles. Results in the dry-run data set of BioASQ task 5c show that the suggested approach can achieve a micro-recall of more than 85{\%} in tagging both funding bodies and grants.
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs (2017)

We describe a Deep Learning approach to modeling the relevance of a document`s text to a query, applied to biomedical literature. Instead of mapping each document and query to a common semantic space, we compute a variable-length difference vector between the query and document which is then passed through a deep convolution stage followed by a deep regression network to produce the estimated probability of the document`s relevance to the query. Despite the small amount of training data, this approach produces a more robust predictor than computing similarities between semantic vector representations of the query and document, and also results in significant improvements over traditional IR text factors. In the future, we plan to explore its application in improving PubMed search.
Detecting Dementia through Retrospective Analysis of Routine Blog Posts by Bloggers with Dementia (2017)

We investigate if writers with dementia can be automatically distinguished from those without by analyzing linguistic markers in written text, in the form of blog posts. We have built a corpus of several thousand blog posts, some by people with dementia and others by people with loved ones with dementia. We use this dataset to train and test several machine learning methods, and achieve prediction performance at a level far above the baseline.
Protein Word Detection using Text Segmentation Techniques (2017)

Literature in Molecular Biology is abundant with linguistic metaphors. There have been works in the past that attempt to draw parallels between linguistics and biology, driven by the fundamental premise that proteins have a language of their own. Since word detection is crucial to the decipherment of any unknown language, we attempt to establish a problem mapping from natural language text to protein sequences at the level of words. Towards this end, we explore the use of an unsupervised text segmentation algorithm to the task of extracting {\textquotedblleft}biological words{\textquotedblright} from protein sequences. In particular, we demonstrate the effectiveness of using domain knowledge to complement data driven approaches in the text segmentation task, as well as in its biological counterpart. We also propose a novel extrinsic evaluation measure for protein words through protein family classification.
External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway (2017)

This paper evaluates the impact of various event extraction systems on automatic pathway curation using the popular mTOR pathway. We quantify the impact of training data sets as well as different machine learning classifiers and show that some improve the quality of automatically extracted pathways.
Toward Automated Early Sepsis Alerting: Identifying Infection Patients from Nursing Notes (2017)

Severe sepsis and septic shock are conditions that affect millions of patients and have close to 50{\%} mortality rate. Early identification of at-risk patients significantly improves outcomes. Electronic surveillance tools have been developed to monitor structured Electronic Medical Records and automatically recognize early signs of sepsis. However, many sepsis risk factors (e.g. symptoms and signs of infection) are often captured only in free text clinical notes. In this study, we developed a method for automatic monitoring of nursing notes for signs and symptoms of infection. We utilized a creative approach to automatically generate an annotated dataset. The dataset was used to create a Machine Learning model that achieved an F1-score ranging from 79 to 96{\%}.
Enhancing Automatic ICD-9-CM Code Assignment for Medical Texts with PubMed (2017)

Assigning a standard ICD-9-CM code to disease symptoms in medical texts is an important task in the medical domain. Automating this process could greatly reduce the costs. However, the effectiveness of an automatic ICD-9-CM code classifier faces a serious problem, which can be triggered by unbalanced training data. Frequent diseases often have more training data, which helps its classification to perform better than that of an infrequent disease. However, a disease`s frequency does not necessarily reflect its importance. To resolve this training data shortage problem, we propose to strategically draw data from PubMed to enrich the training data when there is such need. We validate our method on the CMC dataset, and the evaluation results indicate that our method can significantly improve the code assignment classifiers' performance at the macro-averaging level.
Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation (2017)

In this paper, we present an analysis of feature extraction methods via dimensionality reduction for the task of biomedical Word Sense Disambiguation (WSD). We modify the vector representations in the 2-MRD WSD algorithm, and evaluate four dimensionality reduction methods: Word Embeddings using Continuous Bag of Words and Skip Gram, Singular Value Decomposition (SVD), and Principal Component Analysis (PCA). We also evaluate the effects of vector size on the performance of each of these methods. Results are evaluated on five standard evaluation datasets (Abbrev.100, Abbrev.200, Abbrev.300, NLM-WSD, and MSH-WSD). We find that vector sizes of 100 are sufficient for all techniques except SVD, for which a vector size of 1500 is referred. We also show that SVD performs on par with Word Embeddings for all but one dataset.
Investigating the Documentation of Electronic Cigarette Use in the Veteran Affairs Electronic Health Record: A Pilot Study (2017)

In this paper, we present pilot work on characterising the documentation of electronic cigarettes (e-cigarettes) in the United States Veterans Administration Electronic Health Record. The Veterans Health Administration is the largest health care system in the United States with 1,233 health care facilities nationwide, serving 8.9 million veterans per year. We identified a random sample of 2000 Veterans Administration patients, coded as current tobacco users, from 2008 to 2014. Using simple keyword matching techniques combined with qualitative analysis, we investigated the prevalence and distribution of e-cigarette terms in these clinical notes, discovering that for current smokers, 11.9{\%} of patient records contain an e-cigarette related term.
Automated Preamble Detection in Dictated Medical Reports (2017)

Dictated medical reports very often feature a preamble containing metainformation about the report such as patient and physician names, location and name of the clinic, date of procedure, and so on. In the medical transcription process, the preamble is usually omitted from the final report, as it contains information already available in the electronic medical record. We present a method which is able to automatically identify preambles in medical dictations. The method makes use of state-of-the-art NLP techniques including word embeddings and Bi-LSTMs and achieves preamble detection performance superior to humans.
A Biomedical Question Answering System in BioASQ 2017 (2017)

Question answering, the identification of short accurate answers to users questions, is a longstanding challenge widely studied over the last decades in the open domain. However, it still requires further efforts in the biomedical domain. In this paper, we describe our participation in phase B of task 5b in the 2017 BioASQ challenge using our biomedical question answering system. Our system, dealing with four types of questions (i.e., yes/no, factoid, list, and summary), is based on (1) a dictionary-based approach for generating the exact answers of yes/no questions, (2) UMLS metathesaurus and term frequency metric for extracting the exact answers of factoid and list questions, and (3) the BM25 model and UMLS concepts for retrieving the ideal answers (i.e., paragraph-sized summaries). Preliminary results show that our system achieves good and competitive results in both exact and ideal answers extraction tasks as compared with the participating systems.
Adapting Pre-trained Word Embeddings For Use In Medical Coding (2017)

Word embeddings are a crucial component in modern NLP. Pre-trained embeddings released by different groups have been a major reason for their popularity. However, they are trained on generic corpora, which limits their direct use for domain specific tasks. In this paper, we propose a method to add task specific information to pre-trained word embeddings. Such information can improve their utility. We add information from medical coding data, as well as the first level from the hierarchy of ICD-10 medical code set to different pre-trained word embeddings. We adapt CBOW algorithm from the word2vec package for our purpose. We evaluated our approach on five different pre-trained word embeddings. Both the original word embeddings, and their modified versions (the ones with added information) were used for automated review of medical coding. The modified word embeddings give an improvement in f-score by 1{\%} on the 5-fold evaluation on a private medical claims dataset. Our results show that adding extra information is possible and beneficial for the task at hand.
Initializing neural networks for hierarchical multi-label text classification (2017)

Many tasks in the biomedical domain require the assignment of one or more predefined labels to input text, where the labels are a part of a hierarchical structure (such as a taxonomy). The conventional approach is to use a one-vs.-rest (OVR) classification setup, where a binary classifier is trained for each label in the taxonomy or ontology where all instances not belonging to the class are considered negative examples. The main drawbacks to this approach are that dependencies between classes are not leveraged in the training and classification process, and the additional computational cost of training parallel classifiers. In this paper, we apply a new method for hierarchical multi-label text classification that initializes a neural network model final hidden layer such that it leverages label co-occurrence relations such as hypernymy. This approach elegantly lends itself to hierarchical classification. We evaluated this approach using two hierarchical multi-label text classification tasks in the biomedical domain using both sentence- and document-level classification. Our evaluation shows promising results for this approach.
Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models (2017)

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.
Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks (2017)

Token sequences are often used as the input for Convolutional Neural Networks (CNNs) in natural language processing. However, they might not be an ideal representation for time expressions, which are long, highly varied, and semantically complex. We describe a method for representing time expressions with single pseudo-tokens for CNNs. With this method, we establish a new state-of-the-art result for a clinical temporal relation extraction task.
Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods (2017)

Diagnosis autocoding services and research intend to both improve the productivity of clinical coders and the accuracy of the coding. It is an important step in data analysis for funding and reimbursement, as well as health services planning and resource allocation. We investigate the applicability of deep learning at autocoding of radiology reports using International Classification of Diseases (ICD). Deep learning methods are known to require large training data. Our goal is to explore how to use these methods when the training data is sparse, skewed and relatively small, and how their effectiveness compares to conventional methods. We identify optimal parameters that could be used in setting up a convolutional neural network for autocoding with comparable results to that of conventional methods.
Automatic classification of doctor-patient questions for a virtual patient record query task (2017)

We present the work-in-progress of automating the classification of doctor-patient questions in the context of a simulated consultation with a virtual patient. We classify questions according to the computational strategy (rule-based or other) needed for looking up data in the clinical record. We compare {\textquoteleft}traditional' machine learning methods (Gaussian and Multinomial Naive Bayes, and Support Vector Machines) and a neural network classifier (FastText). We obtained the best results with the SVM using semantic annotations, whereas the neural classifier achieved promising results without it.
Assessing the performance of Olelo, a real-time biomedical question answering application (2017)

Question answering (QA) can support physicians and biomedical researchers to find answers to their questions in the scientific literature. Such systems process large collections of documents in real time and include many natural language processing (NLP) procedures. We recently developed Olelo, a QA system for biomedicine which includes various NLP components, such as question processing, document and passage retrieval, answer processing and multi-document summarization. In this work, we present an evaluation of our system on the the fifth BioASQ challenge. We participated with the current state of the application and with an extension based on semantic role labeling that we are currently investigating. In addition to the BioASQ evaluation, we compared our system to other on-line biomedical QA systems in terms of the response time and the quality of the answers.
Clinical Event Detection with Hybrid Neural Architecture (2017)

Event detection from clinical notes has been traditionally solved with rule based and statistical natural language processing (NLP) approaches that require extensive domain knowledge and feature engineering. In this paper, we have explored the feasibility of approaching this task with recurrent neural networks, clinical word embeddings and introduced a hybrid architecture to improve detection for entities with smaller representation in the dataset. A comparative analysis is also done which reveals the complementary behavior of neural networks and conditional random fields in clinical entity detection.