TY  - JOUR
A1  - Frioux, Clémence
A1  - Schaub, Torsten H.
A1  - Schellhorn, Sebastian
A1  - Siegel, Anne
A1  - Wanko, Philipp
T1  - Hybrid metabolic network completion
JF  - Theory and practice of logic programming
N2  - Metabolic networks play a crucial role in biology since they capture all chemical reactions in an organism. While there are networks of high quality for many model organisms, networks for less studied organisms are often of poor quality and suffer from incompleteness. To this end, we introduced in previous work an answer set programming (ASP)-based approach to metabolic network completion. Although this qualitative approach allows for restoring moderately degraded networks, it fails to restore highly degraded ones. This is because it ignores quantitative constraints capturing reaction rates. To address this problem, we propose a hybrid approach to metabolic network completion that integrates our qualitative ASP approach with quantitative means for capturing reaction rates. We begin by formally reconciling existing stoichiometric and topological approaches to network completion in a unified formalism. With it, we develop a hybrid ASP encoding and rely upon the theory reasoning capacities of the ASP system dingo for solving the resulting logic program with linear constraints over reals. We empirically evaluate our approach by means of the metabolic network of Escherichia coli. Our analysis shows that our novel approach yields greatly superior results than obtainable from purely qualitative or quantitative approaches.
KW  - answer set programming
KW  - metabolic network
KW  - gap-filling
KW  - linear programming
KW  - hybrid solving
KW  - bioinformatics
Y1  - 2018
U6  - https://doi.org/10.1017/S1471068418000455
SN  - 1471-0684
SN  - 1475-3081
VL  - 19
IS  - 1
SP  - 83
EP  - 108
PB  - Cambridge University Press
CY  - New York
ER  - 
TY  - JOUR
A1  - Dimopoulos, Yannis
A1  - Gebser, Martin
A1  - Lühne, Patrick
A1  - Romero Davila, Javier
A1  - Schaub, Torsten H.
T1  - plasp 3
BT  - Towards Effective ASP Planning
JF  - Theory and practice of logic programming
N2  - We describe the new version of the Planning Domain Definition Language (PDDL)-to-Answer Set Programming (ASP) translator plasp. First, it widens the range of accepted PDDL features. Second, it contains novel planning encodings, some inspired by Satisfiability Testing (SAT) planning and others exploiting ASP features such as well-foundedness. All of them are designed for handling multivalued fluents in order to capture both PDDL as well as SAS planning formats. Third, enabled by multishot ASP solving, it offers advanced planning algorithms also borrowed from SAT planning. As a result, plasp provides us with an ASP-based framework for studying a variety of planning techniques in a uniform setting. Finally, we demonstrate in an empirical analysis that these techniques have a significant impact on the performance of ASP planning.
KW  - knowledge representation and nonmonotonic reasoning
KW  - technical notes and rapid communications
KW  - answer set programming
KW  - automated planning
KW  - action and change
Y1  - 2019
U6  - https://doi.org/10.1017/S1471068418000583
SN  - 1471-0684
SN  - 1475-3081
VL  - 19
IS  - 3
SP  - 477
EP  - 504
PB  - Cambridge Univ. Press
CY  - New York
ER  -