AIMC Topic: Genes
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Semi-supervised Learning for the BioNLP Gene Regulation Network.
BMC bioinformatics
Jul 13, 2015
BACKGROUND: The BioNLP Gene Regulation Task has attracted a diverse collection of submissions showcasing state-of-the-art systems. However, a principal challenge remains in obtaining a significant amount of recall. We argue that this is an important ...
Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task.
BMC bioinformatics
Jul 13, 2015
BACKGROUND: The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating system...
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013.
BMC bioinformatics
Jul 13, 2015
BACKGROUND: Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we pre...
Adaptable, high recall, event extraction system with minimal configuration.
BMC bioinformatics
Jul 13, 2015
BACKGROUND: Biomedical event extraction has been a major focus of biomedical natural language processing (BioNLP) research since the first BioNLP shared task was held in 2009. Accordingly, a large number of event extraction systems have been develope...
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.
PloS one
Feb 9, 2015
BACKGROUND: Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the con...
HyDRA: gene prioritization via hybrid distance-score rank aggregation.
Bioinformatics (Oxford, England)
Nov 18, 2014
UNLABELLED: Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the traini...
Harnessing the Power of Large Language Models (LLMs) to Unravel the Influence of Genes and Medications on Biological Processes of Wound Healing.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Jan 1, 2024
Recent advancements in Large Language Models (LLMs) have ushered in a new era for knowledge extraction in the domains of biological and clinical natural language processing (NLP). In this research, we present a novel approach to understanding the reg...
Machine learning-based chemical binding similarity using evolutionary relationships of target genes.
Nucleic acids research
Nov 18, 2019
Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to functional ac...
Doc2Hpo: a web application for efficient and accurate HPO concept curation.
Nucleic acids research
Jul 2, 2019
We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts aut...
ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine.
Nucleic acids research
Mar 18, 2019
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
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