Max Ostrowski

Potassco: The Potsdam Answer Set Solving Collection

This paper gives an overview of the open source project Potassco, the Potsdam Answer Set Solving Collection, bundling tools for Answer Set Programming developed at the University of Potsdam.

Engineering an Incremental ASP Solver

Many real-world applications, like planning or model checking, comprise a parameter reflecting the size of a solution. In a propositional formalism like Answer Set Programming (ASP), such problems can only be dealt with in a bounded way, considering one problem instance after another by gradually increasing the bound on the solution size. We thus propose an incremental approach to both grounding and solving in ASP. Our goal is to avoid redundancy by gradually processing the extensions to a problem rather than repeatedly re-processing the entire (extended) problem. We start by furnishing a formal framework capturing our incremental approach in terms of module theory. In turn, we take advantage of this framework for guiding the successive treatment of program slices during grounding and solving. Finally, we describe the first integrated incremental ASP system, iclingo , and provide an experimental evaluation.

Constraint Answer Set Solving

We present a new approach to integrating Constraint Processing (CP) techniques into Answer Set Programming (ASP). Based on an alternative semantic approach, we develop an algorithmic framework for conflict-driven ASP solving that exploits CP solving capacities. A significant technical issue concerns the combination of conflict information from different solver types. We have implemented our approach, combining ASP solver clingo with the generic CP solver gecode , and we empirically investigate its computational impact.

Asp modulo csp: The clingcon system

We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of Constraint Programming (CP). The new clingcon system features an extended syntax supporting global constraints and optimize statements for constraint variables. The major technical innovation improves the interaction between ASP and CP solver through elaborated learning techniques based on irreducible inconsistent sets. A broad empirical evaluation shows that these techniques yield a performance improvement of an order of magnitude.

On the Input Language of ASP Grounder Gringo

We report on recent advancements in the development of grounder Gringo for logic programs under answer set semantics. Like its relatives, DLV and Lparse , Gringo has in the meantime reached maturity and offers a rich modeling language to program developers. The attractiveness of Gringo is fostered by the fact that it significantly extends the input language of Lparse while supporting a compatible output format, recognized by many state-of-the-art ASP solvers.

Theory Solving Made Easy with Clingo 5.

Answer Set Programming (ASP) is a model, ground, and solve paradigm. The integration of application- or theory-specific reasoning into ASP systems thus impacts on many if not all elements of its workflow, viz. input language, grounding, intermediate language, solving, and output format. We address this challenge with the fifth generation of the ASP system clingo and its grounding and solving components by equipping them with well-defined generic interfaces facilitating the manifold integration efforts. On the grounders side, we introduce a generic way of specifying language extensions and propose an intermediate format accommodating their ground representation. At the solver end, this is accompanied by high-level interfaces easing the integration of theory propagators dealing with these extensions.

Automatic network reconstruction using ASP

Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.

Clingcon: The next generation

We present the third generation of the constraint answer set system clingcon, combining Answer Set Programming (ASP) with finite domain constraint processing (CP). While its predecessors rely on a black-box approach to hybrid solving by integrating the CP solver gecode, the new clingcon system pursues a lazy approach using dedicated constraint propagators to extend propagation in the underlying ASP solver clasp. No extension is needed for parsing and grounding clingcons hybrid modeling language since both can be accommodated by the new generic theory handling capabilities of the ASP grounder gringo. As a whole, clingcon 3 is thus an extension of the ASP system clingo 5, which itself relies on the grounder gringo and the solver clasp. The new approach of clingcon offers a seamless integration of CP propagation into ASP solving that benefits from the whole spectrum of clasps reasoning modes, including for instance multi-shot solving and advanced optimization techniques. This is accomplished by a lazy approach that unfolds the representation of constraints and adds it to that of the logic program only when needed. Although the unfolding is usually dictated by the constraint propagators during solving, it can already be partially (or even totally) done during preprocessing. Moreover, clingcons constraint preprocessing and propagation incorporate several well established CP techniques that greatly improve its performance. We demonstrate this via an extensive empirical evaluation contrasting, first, the various techniques in the context of CSP solving and, second, the new clingcon system with other hybrid ASP systems. Under consideration in Theory and Practice of Logic Programming (TPLP)

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming

Boolean networks (and more general logic models) are useful frameworks to study signal transduction across multiple pathways. Logic models can be learned from a prior knowledge network structure and multiplex phosphoproteomics data. However, most efficient and scalable training methods focus on the comparison of two time-points and assume that the system has reached an early steady state. In this paper, we generalize such a learning procedure to take into account the time series traces of phosphoproteomics data in order to discriminate Boolean networks according to their transient dynamics. To that end, we identify a necessary condition that must be satisfied by the dynamics of a Boolean network to be consistent with a discretized time series trace. Based on this condition, we use Answer Set Programming to compute an over-approximation of the set of Boolean networks which fit best with experimental data and provide the corresponding encodings. Combined with model-checking approaches, we end up with a global learning algorithm. Our approach is able to learn logic models with a true positive rate higher than 78% in two case studies of mammalian signaling networks; for a larger case study, our method provides optimal answers after 7min of computation. We quantified the gain in our method predictions precision compared to learning approaches based on static data. Finally, as an application, our method proposes erroneous time-points in the time series data with respect to the optimal learned logic models.

Clingo goes linear constraints over reals and integers

The recent series 5 of the ASP system clingo provides generic means to enhance basic Answer Set Programming (ASP) with theory reasoning capabilities. We instantiate this framework with different forms of linear constraints, discuss the respective implementations, and present techniques of how to use 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 fragments and contrast them to related ASP systems. This paper is under consideration for acceptance in TPLP.