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Dylan Gration

dblp:358/3462 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2024
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › knowledge representation in biology
biomedical ontology
0.812024
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology · Bioinform. 2024
Bioinformatics and computational biology
biomedical text mining
0.812024
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology · Bioinform. 2024
Bioinformatics and computational biology › biomedical text mining
concept recognition
0.812024
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology · Bioinform. 2024
Bioinformatics and computational biology › biomedical text mining › concept recognition
phenotype concept recognition
0.812024
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology · Bioinform. 2024

Methods — techniques the papers use, named apart from their topics

token clustering · 0.8dictionary-based matching · 0.8
YearPublicationVenuePosition
2024 FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology
abstract
MOTIVATION: Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing adoption of large language models (LLMs) for natural language understanding has led to several LLM-based solutions, we argue that their intrinsic resource-intensive nature is not suitable for realistic management of the phenotype CR lifecycle. Consequently, we propose to go back to the basics and adopt a dictionary-based approach that enables both an immediate refresh of the ontological concepts as well as efficient re-analysis of past data. RESULTS: We developed a dictionary-based approach using a pre-built large collection of clusters of morphologically equivalent tokens-to address lexical variability and a more effective CR step by reducing the entity boundary detection strictly to candidates consisting of tokens belonging to ontology concepts. Our method achieves state-of-the-art results (0.76 F1 on the GSC+ corpus) and a processing efficiency of 10 000 publication abstracts in 5 s. AVAILABILITY AND IMPLEMENTATION: FastHPOCR is available as a Python package installable via pip. The source code is available at https://github.com/tudorgroza/fast_hpo_cr. A Java implementation of FastHPOCR will be made available as part of the Fenominal Java library available at https://github.com/monarch-initiative/fenominal. The up-to-date GCS-2024 corpus is available at https://github.com/tudorgroza/code-for-papers/tree/main/gsc-2024.
Tudor Groza, Dylan Gration, Gareth Baynam, Peter N. Robinson
Bioinform.2