AIMC Topic: PubMed

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Improving precision in concept normalization.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2018
Most natural language processing applications exhibit a trade-off between precision and recall. In some use cases for natural language processing, there are reasons to prefer to tilt that trade-off toward high precision. Relying on the Zipfian distri...
Computational Biology Natural Language Processing Electronic Health Records Humans Reproducibility of Results Precision Medicine Biological Ontologies PubMed False Positive Reactions Data Mining
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nala: text mining natural language mutation mentions.

Bioinformatics (Oxford, England) Jun 15, 2017
MOTIVATION: The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. 'E6V'), leaving relevant mentions natural language (NL) largely untapped (e.g. 'glu...
Humans Software PubMed Data Mining Natural Language Processing Unsupervised Machine Learning Mutation
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PubMedReco: A Real-Time Recommender System for PubMed Citations.

Studies in health technology and informatics Jan 1, 2017
We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous co...
Internet PubMed Information Storage and Retrieval Medical Subject Headings Humans Databases, Factual User-Computer Interface
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A Case Study on Sepsis Using PubMed and Deep Learning for Ontology Learning.

Studies in health technology and informatics Jan 1, 2017
We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora. Term extraction is used as the first step of an ontology learning process that aims to (semi-)aut...
Natural Language Processing PubMed Sepsis Information Storage and Retrieval Semantics Humans Machine Learning
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Probability Statements Extraction with Constrained Conditional Random Fields.

Studies in health technology and informatics Jan 1, 2016
This paper investigates how to extract probability statements from academic medical papers. In previous work we have explored traditional classification methods which led to numerous false negatives. This current work focuses on constraining classifi...
Probability Information Storage and Retrieval Natural Language Processing PubMed Breast Neoplasms Humans Algorithms Female
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Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer.

IET systems biology Aug 1, 2015
Constructing interaction network from biomedical texts is a very important and interesting work. The authors take advantage of text mining and reinforcement learning approaches to establish protein interaction network. Considering the high computatio...
Signal Transduction Neoplasm Proteins Machine Learning Protein Interaction Mapping Natural Language Processing Male Humans PubMed Prostatic Neoplasms Periodicals as Topic Data Mining
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Identifying Clinical Study Types from PubMed Metadata: The Active (Machine) Learning Approach.

Studies in health technology and informatics Jan 1, 2015
We examined a process for automating the classification of articles in MEDLINE aimed at minimising manual effort without sacrificing accuracy. From 22,808 articles pertaining to 19 antidepressants, 1000 were randomly selected and manually labelled ac...
Machine Learning Randomized Controlled Trials as Topic Humans Abstracting and Indexing PubMed MEDLINE Clinical Studies as Topic
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