Effectively Solving NP-SPEC Encodings by Translation to ASP

NP-SPEC is a language for specifying problems in NP in a declarative way. Despite the fact that the semantics of the language was given by referring to Datalog with circumscription, which is very close to ASP, so far the only existing implementations are by means of ECLiPSe Prolog and via Boolean satisfiability solvers. In this paper, we present translations from NP-SPEC into ASP, and provide an experimental evaluation of existing implementations and the proposed translations to ASP using various ASP solvers. The results show that translating to ASP clearly has an edge over the existing translation into SAT, which involves an intrinsic grounding process. We also argue that it might be useful to incorporate certain language constructs of NPSPEC into mainstream ASP

Controlled Natural Language Processing as Answer Set Programming: an Experiment

Most controlled natural languages (CNLs) are processed with the help of a pipeline architecture that relies on different software components. We investigate in this paper in an experimental way how well answer set programming (ASP) is suited as a unifying framework for parsing a CNL, deriving a formal representation for the resulting syntax trees, and for reasoning with that representation. We start from a list of input tokens in ASP notation and show how this input can be transformed into a syntax tree using an ASP grammar and then into reified ASP rules in form of a set of facts. These facts are then processed by an ASP meta-interpreter that allows us to infer new knowledge

Proteus: A Hierarchical Portfolio of Solvers and Transformations

In recent years, portfolio approaches to solving SAT problems and CSPs have become increasingly common. There are also a number of different encodings for representing CSPs as SAT instances. In this paper, we leverage advances in both SAT and CSP solving to present a novel hierarchical portfolio-based approach to CSP solving, which we call Proteus, that does not rely purely on CSP solvers. Instead, it may decide that it is best to encode a CSP problem instance into SAT, selecting an appropriate encoding and a corresponding SAT solver. Our experimental evaluation used an instance of Proteus that involved four CSP solvers, three SAT encodings, and six SAT solvers, evaluated on the most challenging problem instances from the CSP solver competitions, involving global and intensional constraints. We show that significant performance improvements can be achieved by Proteus obtained by exploiting alternative view-points and solvers for combinatorial problem-solving.Comment: 11th International Conference on Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems. The final publication is available at link.springer.co

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming

A fundamental question in systems biology is the construction and training to data of mathematical models. Logic formalisms have become very popular to model signaling networks because their simplicity allows us to model large systems encompassing hundreds of proteins. An approach to train (Boolean) logic models to high-throughput phospho-proteomics data was recently introduced and solved using optimization heuristics based on stochastic methods. Here we demonstrate how this problem can be solved using Answer Set Programming (ASP), a declarative problem solving paradigm, in which a problem is encoded as a logical program such that its answer sets represent solutions to the problem. ASP has significant improvements over heuristic methods in terms of efficiency and scalability, it guarantees global optimality of solutions as well as provides a complete set of solutions. We illustrate the application of ASP with in silico cases based on realistic networks and data

Treewidth and Counting Projected Answer Sets

In this paper, we introduce novel algorithms to solve projected answer set counting (#PAs). #PAs asks to count the number of answer sets with respect to a given set of projected atoms, where multiple answer sets that are identical when restricted to the projected atoms count as only one projected answer set. Our algorithms exploit small treewidth of the primal graph of the input instance by dynamic programming (DP). We establish a new algorithm for head-cycle-free (HCF) programs and lift very recent results from projected model counting to #PAs when the input is restricted to HCF programs. Further, we show how established DP algorithms for tight, normal, and disjunctive answer set programs can be extended to solve #PAs. Our algorithms run in polynomial time while requiring double exponential time in the treewidth for tight, normal, and HCF programs, and triple exponential time for disjunctive programs. Finally, we take the exponential time hypothesis (ETH) into account and establish lower bounds of bounded treewidth algorithms for #PAs. Under ETH, one cannot significantly improve our obtained worst-case runtimes

aspcud: A Linux Package Configuration Tool Based on Answer Set Programming

We present the Linux package configuration tool aspcud based on Answer Set Programming. In particular, we detail aspcud's preprocessor turning a CUDF specification into a set of logical facts.Comment: In Proceedings LoCoCo 2011, arXiv:1108.609

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system

Hybrid ASP-based multi-objective scheduling of semiconductor manufacturing processes (Extended version)

Modern semiconductor manufacturing involves intricate production processes consisting of hundreds of operations, which can take several months from lot release to completion. The high-tech machines used in these processes are diverse, operate on individual wafers, lots, or batches in multiple stages, and necessitate product-specific setups and specialized maintenance procedures. This situation is different from traditional job-shop scheduling scenarios, which have less complex production processes and machines, and mainly focus on solving highly combinatorial but abstract scheduling problems. In this work, we address the scheduling of realistic semiconductor manufacturing processes by modeling their specific requirements using hybrid Answer Set Programming with difference logic, incorporating flexible machine processing, setup, batching and maintenance operations. Unlike existing methods that schedule semiconductor manufacturing processes locally with greedy heuristics or by independently optimizing specific machine group allocations, we examine the potentials of large-scale scheduling subject to multiple optimization objectives.Comment: 17 pages, 1 figure, 4 listings, 1 table; a short version of this paper is presented at the 18th European Conference on Logics in Artificial Intelligence (JELIA 2023

Evaluation Techniques and Systems for Answer Set Programming: a Survey

Answer set programming (ASP) is a prominent knowledge representation and reasoning paradigm that found both industrial and scientific applications. The success of ASP is due to the combination of two factors: a rich modeling language and the availability of efficient ASP implementations. In this paper we trace the history of ASP systems, describing the key evaluation techniques and their implementation in actual tools

One More Decidable Class of Finitely Ground Programs

Abstract. When a logic program is processed by an answer set solver, the first task is to generate its instantiation. In a recent paper, Calimeri et el. made the idea of efficient instantiation precise for the case of disjunctive programs with function symbols, and introduced the class of “finitely ground ” programs that can be efficiently instantiated. Since that class is undecidable, it is important to find its large decidable subsets. In this paper, we introduce such a subset—the class of argument-restricted programs. It includes, in particular, all finite domain programs, ω-restricted programs, and λ-restricted programs.