AIMC Topic: Natural Language Processing

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Drug drug interaction extraction from the literature using a recursive neural network.

PloS one
Detecting drug-drug interactions (DDI) is important because information on DDIs can help prevent adverse effects from drug combinations. Since there are many new DDI-related papers published in the biomedical domain, manually extracting DDI informati...

Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition.

Journal of chemical information and modeling
Inspired by natural language processing techniques, we here introduce Mol2vec, which is an unsupervised machine learning approach to learn vector representations of molecular substructures. Like the Word2vec models, where vectors of closely related w...

CUILESS2016: a clinical corpus applying compositional normalization of text mentions.

Journal of biomedical semantics
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated ...

Harnessing electronic medical records to advance research on multiple sclerosis.

Multiple sclerosis (Houndmills, Basingstoke, England)
BACKGROUND: Electronic medical records (EMR) data are increasingly used in research, but no studies have yet evaluated similarity between EMR and research-quality data and between characteristics of an EMR multiple sclerosis (MS) population and known...

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.

Database : the journal of biological databases and curation
Precision medicine aims to provide personalized treatments based on individual patient profiles. One critical step towards precision medicine is leveraging knowledge derived from biomedical publications-a tremendous literature resource presenting the...

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.

Database : the journal of biological databases and curation
Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenoty...

How Confounder Strength Can Affect Allocation of Resources in Electronic Health Records.

Perspectives in health information management
When electronic health record (EHR) data are used, multiple approaches may be available for measuring the same variable, introducing potentially confounding factors. While additional information may be gleaned and residual confounding reduced through...

Natural language processing of clinical notes for identification of critical limb ischemia.

International journal of medical informatics
BACKGROUND: Critical limb ischemia (CLI) is a complication of advanced peripheral artery disease (PAD) with diagnosis based on the presence of clinical signs and symptoms. However, automated identification of cases from electronic health records (EHR...

Framework for Infectious Disease Analysis: A comprehensive and integrative multi-modeling approach to disease prediction and management.

Health informatics journal
The impact of infectious disease on human populations is a function of many factors including environmental conditions, vector dynamics, transmission mechanics, social and cultural behaviors, and public policy. A comprehensive framework for disease m...

Information extraction from Italian medical reports: An ontology-driven approach.

International journal of medical informatics
OBJECTIVE: In this work, we propose an ontology-driven approach to identify events and their attributes from episodes of care included in medical reports written in Italian. For this language, shared resources for clinical information extraction are ...