Institut für Informatik und Computational Science
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Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge network and the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in silico numerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A-B. (C) 2014 Elsevier B.V. All rights reserved.
We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.
We introduce formal proof systems based on tableau methods for analyzing computations in Answer Set Programming (ASP). Our approach furnishes fine-grained instruments for characterizing operations as well as strategies of ASP solvers. The granularity is detailed enough to capture a variety of propagation and choice methods of algorithms used for ASP solving, also incorporating SAT-based and conflict-driven learning approaches to some extent. This provides us with a uniform setting for identifying and comparing fundamental properties of ASP solving approaches. In particular, we investigate their proof complexities and show that the run-times of best-case computations can vary exponentially between different existing ASP solvers. Apart from providing a framework for comparing ASP solving approaches, our characterizations also contribute to their understanding by pinning down the constitutive atomic operations. Furthermore, our framework is flexible enough to integrate new inference patterns, and so to study their relation to existing ones. To this end, we generalize our approach and provide an extensible basis aiming at a modular incorporation of additional language constructs. This is exemplified by augmenting our basic tableau methods with cardinality constraints and disjunctions.
We address the problem of Finite Model Computation (FMC) of first-order theories and show that FMC can efficiently and transparently be solved by taking advantage of a recent extension of Answer Set Programming (ASP), called incremental Answer Set Programming (iASP). The idea is to use the incremental parameter in iASP programs to account for the domain size of a model. The FMC problem is then successively addressed for increasing domain sizes until an answer set, representing a finite model of the original first-order theory, is found. We implemented a system based on the iASP solver iClingo and demonstrate its competitiveness by showing that it slightly outperforms the winner of the FNT division of CADE's 2009 Automated Theorem Proving (ATP) competition on the respective benchmark collection.
Automated storage and retrieval systems are principal components of modern production and warehouse facilities. In particular, automated guided vehicles nowadays substitute human-operated pallet trucks in transporting production materials between storage locations and assembly stations. While low-level control systems take care of navigating such driverless vehicles along programmed routes and avoid collisions even under unforeseen circumstances, in the common case of multiple vehicles sharing the same operation area, the problem remains how to set up routes such that a collection of transport tasks is accomplished most effectively. We address this prevalent problem in the context of car assembly at Mercedes-Benz Ludwigsfelde GmbH, a large-scale producer of commercial vehicles, where routes for automated guided vehicles used in the production process have traditionally been hand-coded by human engineers. Such adhoc methods may suffice as long as a running production process remains in place, while any change in the factory layout or production targets necessitates tedious manual reconfiguration, not to mention the missing portability between different production plants. Unlike this, we propose a declarative approach based on Answer Set Programming to optimize the routes taken by automated guided vehicles for accomplishing transport tasks. The advantages include a transparent and executable problem formalization, provable optimality of routes relative to objective criteria, as well as elaboration tolerance towards particular factory layouts and production targets. Moreover, we demonstrate that our approach is efficient enough to deal with the transport tasks evolving in realistic production processes at the car factory of Mercedes-Benz Ludwigsfelde GmbH.
Answer Set Programming (ASP) is a prominent knowledge representation language with roots in logic programming and non-monotonic reasoning. Biennial ASP competitions are organized in order to furnish challenging benchmark collections and assess the advancement of the state of the art in ASP solving. In this paper, we report on the design and results of the Seventh ASP Competition, jointly organized by the University of Calabria (Italy), the University of Genova (Italy), and the University of Potsdam (Germany), in affiliation with the 14th International Conference on Logic Programming and Non-Monotonic Reasoning (LPNMR 2017).
Answer Set Programming (ASP) is a well-known paradigm of declarative programming with roots in logic programming and non-monotonic reasoning. Similar to other closely related problemsolving technologies, such as SAT/SMT, QBF, Planning and Scheduling, advancements in ASP solving are assessed in competition events. In this paper, we report about the design and results of the Sixth ASP Competition, which was jointly organized by the University of Calabria (Italy), Aalto University (Finland), and the University of Genoa (Italy), in affiliation with the 13th International Conference on Logic Programming and Non-Monotonic Reasoning. This edition maintained some of the design decisions introduced in 2014, e.g., the conception of sub-tracks, the scoring scheme,and the adherence to a fixed modeling language in order to push the adoption of the ASP-Core-2 standard. On the other hand, it featured also some novelties, like a benchmark selection stage classifying instances according to their empirical hardness, and a “Marathon” track where the topperforming systems are given more time for solving hard benchmarks.