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  - Gebser, Martin
A1  - Kaminski, Roland
A1  - Kaufmann, Benjamin
A1  - Lühne, Patrick
A1  - Obermeier, Philipp
A1  - Ostrowski, Max
A1  - Romero Davila, Javier
A1  - Schaub, Torsten H.
A1  - Schellhorn, Sebastian
A1  - Wanko, Philipp
T1  - The Potsdam Answer Set Solving Collection 5.0
JF  - Künstliche Intelligenz
N2  - The Potsdam answer set solving collection, or Potassco for short, bundles various tools implementing and/or applying answer set programming. The article at hand succeeds an earlier description of the Potassco project published in Gebser et al. (AI Commun 24(2):107-124, 2011). Hence, we concentrate in what follows on the major features of the most recent, fifth generation of the ASP system clingo and highlight some recent resulting application systems.
Y1  - 2018
U6  - https://doi.org/10.1007/s13218-018-0528-x
SN  - 0933-1875
SN  - 1610-1987
VL  - 32
IS  - 2-3
SP  - 181
EP  - 182
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Haubelt, Christian
A1  - Neubauer, Kai
A1  - Schaub, Torsten H.
A1  - Wanko, Philipp
T1  - Design space exploration with answer set programming
JF  - Künstliche Intelligenz
N2  - The aim of our project design space exploration with answer set programming is to develop a general framework based on Answer Set Programming (ASP) that finds valid solutions to the system design problem and simultaneously performs Design Space Exploration (DSE) to find the most favorable alternatives. We leverage recent developments in ASP solving that allow for tight integration of background theories to create a holistic framework for effective DSE.
Y1  - 2018
U6  - https://doi.org/10.1007/s13218-018-0530-3
SN  - 0933-1875
SN  - 1610-1987
VL  - 32
IS  - 2-3
SP  - 205
EP  - 206
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - GEN
A1  - Neubauer, Kai
A1  - Haubelt, Christian
A1  - Wanko, Philipp
A1  - Schaub, Torsten H.
T1  - Utilizing quad-trees for efficient design space exploration with partial assignment evaluation
T2  - 2018 23rd Asia and South Pacific Design Automation Conference (ASP-DAC)
N2  - Recently, it has been shown that constraint-based symbolic solving techniques offer an efficient way for deciding binding and routing options in order to obtain a feasible system level implementation. In combination with various background theories, a feasibility analysis of the resulting system may already be performed on partial solutions. That is, infeasible subsets of mapping and routing options can be pruned early in the decision process, which fastens the solving accordingly. However, allowing a proper design space exploration including multi-objective optimization also requires an efficient structure for storing and managing non-dominated solutions. In this work, we propose and study the usage of the Quad-Tree data structure in the context of partial assignment evaluation during system synthesis. Out experiments show that unnecessary dominance checks can be avoided, which indicates a preference of Quad-Trees over a commonly used list-based implementation for large combinatorial optimization problems.
Y1  - 2018
SN  - 978-1-5090-0602-1
U6  - https://doi.org/10.1109/ASPDAC.2018.8297362
SN  - 2153-6961
SP  - 434
EP  - 439
PB  - IEEE
CY  - New York
ER  - 
TY  - GEN
A1  - Neubauer, Kai
A1  - Wanko, Philipp
A1  - Schaub, Torsten H.
A1  - Haubelt, Christian
T1  - Exact multi-objective design space exploration using ASPmT
T2  - Proceedings of the 2018 Design, Automation & Test in Europe Conference & Exhibition (DATE)
N2  - An efficient Design Space Exploration (DSE) is imperative for the design of modern, highly complex embedded systems in order to steer the development towards optimal design points. The early evaluation of design decisions at system-level abstraction layer helps to find promising regions for subsequent development steps in lower abstraction levels by diminishing the complexity of the search problem. In recent works, symbolic techniques, especially Answer Set Programming (ASP) modulo Theories (ASPmT), have been shown to find feasible solutions of highly complex system-level synthesis problems with non-linear constraints very efficiently. In this paper, we present a novel approach to a holistic system-level DSE based on ASPmT. To this end, we include additional background theories that concurrently guarantee compliance with hard constraints and perform the simultaneous optimization of several design objectives. We implement and compare our approach with a state-of-the-art preference handling framework for ASP. Experimental results indicate that our proposed method produces better solutions with respect to both diversity and convergence to the true Pareto front.
Y1  - 2018
SN  - 978-3-9819-2630-9
U6  - https://doi.org/10.23919/DATE.2018.8342014
SN  - 1530-1591
SN  - 1558-1101
SP  - 257
EP  - 260
PB  - IEEE
CY  - New York
ER  - 
TY  - JOUR
A1  - Banbara, Mutsunori
A1  - Inoue, Katsumi
A1  - Kaufmann, Benjamin
A1  - Okimoto, Tenda
A1  - Schaub, Torsten H.
A1  - Soh, Takehide
A1  - Tamura, Naoyuki
A1  - Wanko, Philipp
T1  - teaspoon
BT  - solving the curriculum-based course timetabling problems with answer set programming
JF  - Annals of operation research
N2  - Answer Set Programming (ASP) is an approach to declarative problem solving, combining a rich yet simple modeling language with high performance solving capacities. We here develop an ASP-based approach to curriculum-based course timetabling (CB-CTT), one of the most widely studied course timetabling problems. The resulting teaspoon system reads a CB-CTT instance of a standard input format and converts it into a set of ASP facts. In turn, these facts are combined with a first-order encoding for CB-CTT solving, which can subsequently be solved by any off-the-shelf ASP systems. We establish the competitiveness of our approach by empirically contrasting it to the best known bounds obtained so far via dedicated implementations. Furthermore, we extend the teaspoon system to multi-objective course timetabling and consider minimal perturbation problems.
KW  - Educational timetabling
KW  - Course timetabling
KW  - Answer set programming
KW  - Multi-objective optimization
KW  - Minimal perturbation problems
Y1  - 2018
U6  - https://doi.org/10.1007/s10479-018-2757-7
SN  - 0254-5330
SN  - 1572-9338
VL  - 275
IS  - 1
SP  - 3
EP  - 37
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Janhunen, Tomi
A1  - Kaminski, Roland
A1  - Ostrowski, Max
A1  - Schellhorn, Sebastian
A1  - Wanko, Philipp
A1  - Schaub, Torsten H.
T1  - Clingo goes linear constraints over reals and integers
JF  - Theory and practice of logic programming
N2  - The recent series 5 of the Answer Set Programming (ASP) system clingo provides generic means to enhance basic ASP with theory reasoning capabilities. We instantiate this framework with different forms of linear constraints and elaborate upon its formal properties. Given this, we discuss the respective implementations, and present techniques for using these constraints in a reactive context. More precisely, we introduce extensions to clingo with difference and linear constraints over integers and reals, respectively, and realize them in complementary ways. Finally, we empirically evaluate the resulting clingo derivatives clingo[dl] and clingo[lp] on common language fragments and contrast them to related ASP systems.
KW  - Constraint Answer Set Programming (CASP)
KW  - Answer Set Programming (ASP)
KW  - Constraint Processing (CP)
KW  - Theory Solving
Y1  - 2017
U6  - https://doi.org/10.1017/S1471068417000242
SN  - 1471-0684
SN  - 1475-3081
VL  - 17
SP  - 872
EP  - 888
PB  - Cambridge Univ. Press
CY  - New York
ER  - 
TY  - GEN
A1  - Neubauer, Kai
A1  - Wanko, Philipp
A1  - Schaub, Torsten H.
A1  - Haubelt, Christian
T1  - Enhancing symbolic system synthesis through ASPmT with partial assignment evaluation
T2  - Proceedings of the Design, Automation & Test in Europe Conference & Exhibition (DATE), 2017
N2  - The design of embedded systems is becoming continuously more complex such that efficient system-level design methods are becoming crucial. Recently, combined Answer Set Programming (ASP) and Quantifier Free Integer Difference Logic (QF-IDL) solving has been shown to be a promising approach in system synthesis. However, this approach still has several restrictions limiting its applicability. In the paper at hand, we propose a novel ASP modulo Theories (ASPmT) system synthesis approach, which (i) supports more sophisticated system models, (ii) tightly integrates the QF-IDL solving into the ASP solving, and (iii) makes use of partial assignment checking. As a result, more realistic systems are considered and an early exclusion of infeasible solutions improves the entire system synthesis.
Y1  - 2017
SN  - 978-3-9815370-9-3
U6  - https://doi.org/10.23919/DATE.2017.7927005
SN  - 1530-1591
SP  - 306
EP  - 309
PB  - IEEE
CY  - New York
ER  -