Generating explanations for biomedical queries

DOI10.1017/S1471068413000598MaRDI QIDQ4592972zbMATH OpenOpenAlexFDO

Authors Esra Erdem, Umut Oztok

Publication date 9 November 2017

Published in Theory and Practice of Logic Programming (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1309.6297

zbMATH Keywords

answer set programmingquery answeringexplanation generationbiomedical queries

Mathematics Subject Classification ID

Medical applications (general) (92C50) Knowledge representation (68T30) Theory of languages and software systems (knowledge-based systems, expert systems, etc.) for artificial intelligence (68T35) Logic programming (68N17)

Abstract: We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PHARMGKB, DRUGBANK, BIOGRID, CTD, SIDER, DISEASE ONTOLOGY and ORPHADATA. To appear in Theory and Practice of Logic Programming (TPLP).

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Cites work

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Cited in

(11)

• The External Interface for Extending WASP
• Explanation generation for multi-modal multi-agent path finding with optimal resource utilization using answer set programming
• Pruning external minimality checking for answer set programs using semantic dependencies
• Specifying and verbalising answer set programs in controlled natural language
• Justifying answer sets using argumentation
• Debugging non-ground ASP programs: technique and graphical tools
• Contrastive explanations for answer-set programs
• Partial compilation of ASP programs
• Witnesses for Answer Sets of Logic Programs
• Answering the ``why in answer set programming -- a survey of explanation approaches
• Combining answer set programming and domain heuristics for solving hard industrial problems (application paper)

Describes a project that uses

Uses Software

• Gringo
• clasp
• BioGRID
• DrugBank

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