Generating explanations for biomedical queries

DOI10.1017/S1471068413000598zbMATH Open1379.68059arXiv1309.6297OpenAlexW3106329485MaRDI QIDQ4592972FDOQ4592972

Umut Oztok, Esra Erdem

Publication date: 9 November 2017

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

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).

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

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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)

Cites Work

• Extending and implementing the stable model semantics
• Title not available (Why is that?)
• The well-founded semantics for general logic programs
• Knowledge Representation, Reasoning and Declarative Problem Solving
• Weight constraints as nested expressions
• Answer set programming and plan generation
• Logic programs with stable model semantics as a constraint programming paradigm
• Title not available (Why is that?)
• Logic programming and negation: A survey
• Catching the Ouroboros: On debugging non-ground answer-set programs
• Team-building with answer set programming in the Gioia-Tauro seaport
• Logic programming and nonmonotonic reasoning. 11th international conference, LPNMR 2011, Vancouver, Canada, May 16--19, 2011. Proceedings
• Logic programming and nonmonotonic reasoning. 9th international conference, LPNMR 2007, Tempe, AZ, USA, May 15--17, 2007. Proceedings
• Justifications for logic programs under answer set semantics

Cited In (11)

• Combining Answer Set Programming and domain heuristics for solving hard industrial problems (Application Paper)
• Specifying and Verbalising Answer Set Programs in Controlled Natural Language
• Partial Compilation of ASP Programs
• Debugging Non-ground ASP Programs: Technique and Graphical Tools
• Answering the “why” in answer set programming – A survey of explanation approaches
• Justifying answer sets using argumentation
• Explanation Generation for Multi-Modal Multi-Agent Path Finding with Optimal Resource Utilization using Answer Set Programming
• Witnesses for Answer Sets of Logic Programs
• Pruning external minimality checking for answer set programs using semantic dependencies
• The External Interface for Extending WASP
• Contrastive explanations for answer-set programs

Uses Software

• Gringo
• clasp
• BioGRID
• DrugBank

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