@article{GebserKaminskiKaufmannetal.2018, author = {Gebser, Martin and Kaminski, Roland and Kaufmann, Benjamin and Schaub, Torsten}, title = {Multi-shot ASP solving with clingo}, series = {Theory and practice of logic programming}, volume = {19}, journal = {Theory and practice of logic programming}, number = {1}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068418000054}, pages = {27 -- 82}, year = {2018}, abstract = {We introduce a new flexible paradigm of grounding and solving in Answer Set Programming (ASP), which we refer to as multi-shot ASP solving, and present its implementation in the ASP system clingo. Multi-shot ASP solving features grounding and solving processes that deal with continuously changing logic programs. In doing so, they remain operative and accommodate changes in a seamless way. For instance, such processes allow for advanced forms of search, as in optimization or theory solving, or interaction with an environment, as in robotics or query answering. Common to them is that the problem specification evolves during the reasoning process, either because data or constraints are added, deleted, or replaced. This evolutionary aspect adds another dimension to ASP since it brings about state changing operations. We address this issue by providing an operational semantics that characterizes grounding and solving processes in multi-shot ASP solving. This characterization provides a semantic account of grounder and solver states along with the operations manipulating them. The operative nature of multi-shot solving avoids redundancies in relaunching grounder and solver programs and benefits from the solver's learning capacities. clingo accomplishes this by complementing ASP's declarative input language with control capacities. On the declarative side, a new directive allows for structuring logic programs into named and parameterizable subprograms. The grounding and integration of these subprograms into the solving process is completely modular and fully controllable from the procedural side. To this end, clingo offers a new application programming interface that is conveniently accessible via scripting languages. By strictly separating logic and control, clingo also abolishes the need for dedicated systems for incremental and reactive reasoning, like iclingo and oclingo, respectively, and its flexibility goes well beyond the advanced yet still rigid solving processes of the latter.}, language = {en} } @article{FriouxSchaubSchellhornetal.2019, author = {Frioux, Cl{\´e}mence and Schaub, Torsten and Schellhorn, Sebastian and Siegel, Anne and Wanko, Philipp}, title = {Hybrid metabolic network completion}, series = {Theory and practice of logic programming}, volume = {19}, journal = {Theory and practice of logic programming}, number = {1}, publisher = {Cambridge University Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068418000455}, pages = {83 -- 108}, year = {2019}, abstract = {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.}, language = {en} } @misc{CabalarFandinoSchaubetal.2019, author = {Cabalar, Pedro and Fandi{\~n}o, Jorge and Schaub, Torsten and Schellhorn, Sebastian}, title = {Lower Bound Founded Logic of Here-and-There}, series = {Logics in Artificial Intelligence}, volume = {11468}, journal = {Logics in Artificial Intelligence}, publisher = {Springer}, address = {Cham}, isbn = {978-3-030-19570-0}, issn = {0302-9743}, doi = {10.1007/978-3-030-19570-0_34}, pages = {509 -- 525}, year = {2019}, abstract = {A distinguishing feature of Answer Set Programming is that all atoms belonging to a stable model must be founded. That is, an atom must not only be true but provably true. This can be made precise by means of the constructive logic of Here-and-There, whose equilibrium models correspond to stable models. One way of looking at foundedness is to regard Boolean truth values as ordered by letting true be greater than false. Then, each Boolean variable takes the smallest truth value that can be proven for it. This idea was generalized by Aziz to ordered domains and applied to constraint satisfaction problems. As before, the idea is that a, say integer, variable gets only assigned to the smallest integer that can be justified. In this paper, we present a logical reconstruction of Aziz' idea in the setting of the logic of Here-and-There. More precisely, we start by defining the logic of Here-and-There with lower bound founded variables along with its equilibrium models and elaborate upon its formal properties. Finally, we compare our approach with related ones and sketch future work.}, language = {en} }