Modeling Biological Networks by Action Languages via Answer Set Programming

Authors:
Steve Dworschak;Susanne Grell;Victoria J. Nikiforova;Torsten Schaub;Joachim Selbig
Affiliations:
Institut für Informatik, Universität Potsdam, Potsdam, Germany 14482;Institut für Informatik, Universität Potsdam, Potsdam, Germany 14482 and Max-Planck-Institut für molekulare Pflanzenphysiologie, Potsdam, Germany 14424;Max-Planck-Institut für molekulare Pflanzenphysiologie, Potsdam, Germany 14424 and Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia 127276;Institut für Informatik, Universität Potsdam, Potsdam, Germany 14482;Institut für Informatik, Universität Potsdam, Potsdam, Germany 14482 and Max-Planck-Institut für molekulare Pflanzenphysiologie, Potsdam, Germany 14424 and Institut für Biologi ...
Venue:
Constraints
Year:
2008

Citing 26
Cited 16

Splitting a logic program

Proceedings of the eleventh international conference on Logic programming
An action language based on causal explanation: preliminary report

AAAI '98/IAAI '98 Proceedings of the fifteenth national/tenth conference on Artificial intelligence/Innovative applications of artificial intelligence
Model checking

Model checking
Extending and implementing the stable model semantics

Artificial Intelligence
Knowledge Representation, Reasoning, and Declarative Problem Solving

Knowledge Representation, Reasoning, and Declarative Problem Solving
Logic programs with stable model semantics as a constraint programming paradigm

Annals of Mathematics and Artificial Intelligence
Petri Net Representations in Metabolic Pathways

Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
A logic programming approach to knowledge-state planning, II: the DLVk system

Artificial Intelligence
A logic programming approach to knowledge-state planning: Semantics and complexity

ACM Transactions on Computational Logic (TOCL)
A multi-scale constraint programming model of alternative splicing regulation

Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
A knowledge based approach for representing and reasoning about signaling networks

Bioinformatics
Why are there so many loop formulas?

ACM Transactions on Computational Logic (TOCL)
Application of abductive ILP to learning metabolic network inhibition from temporal data

Machine Learning
Reasoning and hypothesizing about signaling networks

Reasoning and hypothesizing about signaling networks
Efficient haplotype inference with boolean satisfiability

AAAI'06 Proceedings of the 21st national conference on Artificial intelligence - Volume 1
Issues in reasoning about interaction networks in cells: necessity of event ordering knowledge

AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 2
Conflict-driven answer set solving

IJCAI'07 Proceedings of the 20th international joint conference on Artifical intelligence
Proceedings of the 9th international conference on Logic programming and nonmonotonic reasoning

LPNMR'07 Proceedings of the 9th international conference on Logic programming and nonmonotonic reasoning
Clasp: a conflict-driven answer set solver

LPNMR'07 Proceedings of the 9th international conference on Logic programming and nonmonotonic reasoning
GrinGo: a new grounder for answer set programming

LPNMR'07 Proceedings of the 9th international conference on Logic programming and nonmonotonic reasoning
Inference of gene relations from microarray data by abduction

LPNMR'05 Proceedings of the 8th international conference on Logic Programming and Nonmonotonic Reasoning
Construction of an agent-based framework for evolutionary biology: a progress report

DALT'04 Proceedings of the Second international conference on Declarative Agent Languages and Technologies
Modeling the molecular network controlling adhesion between human endothelial cells: inference and simulation using constraint logic programming

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
The biochemical abstract machine BIOCHAM

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
SAT in bioinformatics: making the case with haplotype inference

SAT'06 Proceedings of the 9th international conference on Theory and Applications of Satisfiability Testing

Here's the Beef: Answer Set Programming !

ICLP '08 Proceedings of the 24th International Conference on Logic Programming
Metabolic Network Expansion with Answer Set Programming

ICLP '09 Proceedings of the 25th International Conference on Logic Programming
Reasoning About Actions for the Management of Urban Wastewater Systems: Preliminary report

Proceedings of the 2009 conference on Artificial Intelligence Research and Development: Proceedings of the 12th International Conference of the Catalan Association for Artificial Intelligence
An investigation in parallel execution of answer set programs on distributed memory platforms: Task sharing and dynamic scheduling

Computer Languages, Systems and Structures
Reasoning About Actions for the Management of Urban Wastewater Systems: Preliminary report

Proceedings of the 2009 conference on Artificial Intelligence Research and Development: Proceedings of the 12th International Conference of the Catalan Association for Artificial Intelligence
Review:

The Knowledge Engineering Review
Coala: a compiler from action languages to ASP

JELIA'10 Proceedings of the 12th European conference on Logics in artificial intelligence
Loop-separable programs and their first-order definability

Artificial Intelligence
Supporting decision making in urban wastewater systems using a knowledge-based approach

Environmental Modelling & Software
Modelling gene and protein regulatory networks with Answer Set Programming

International Journal of Data Mining and Bioinformatics
Potassco: The Potsdam Answer Set Solving Collection

AI Communications - Answer Set Programming
Applications of answer set programming in phylogenetic systematics

Logic programming, knowledge representation, and nonmonotonic reasoning
Analyzing pathways using ASP-based approaches

ANB'10 Proceedings of the 4th international conference on Algebraic and Numeric Biology
Applications of action languages in cognitive robotics

Correct Reasoning
Modeling actions based on a situative space model for recognizing human activities

AIMSA'12 Proceedings of the 15th international conference on Artificial Intelligence: methodology, systems, and applications
Annotating answer-set programs in lana*

Theory and Practice of Logic Programming

Quantified Score

Hi-index	0.00

Visualization

Abstract

We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage.