Allen's Interval Algebra Makes the Difference

Allen's Interval Algebra constitutes a framework for reasoning about temporal information in a qualitative manner. In particular, it uses intervals, i.e., pairs of endpoints, on the timeline to represent entities corresponding to actions, events, or tasks, and binary relations such as precedes and overlaps to encode the possible configurations between those entities. Allen's calculus has found its way in many academic and industrial applications that involve, most commonly, planning and scheduling, temporal databases, and healthcare. In this paper, we present a novel encoding of Interval Algebra using answer-set programming (ASP) extended by difference constraints, i.e., the fragment abbreviated as ASP(DL), and demonstrate its performance via a preliminary experimental evaluation. Although our ASP encoding is presented in the case of Allen's calculus for the sake of clarity, we suggest that analogous encodings can be devised for other point-based calculi, too.Comment: Part of DECLARE 19 proceeding

On the semantics of hybrid ASP systems based on Clingo

[Abstract]: Over the last decades, the development of Answer Set Programming (ASP) has brought about an expressive modeling language powered by highly performant systems. At the same time, it gets more and more difficult to provide semantic underpinnings capturing the resulting constructs and inferences. This is even more severe when it comes to hybrid ASP languages and systems that are often needed to handle real-world applications. We address this challenge and introduce the concept of abstract and structured theories that allow us to formally elaborate upon their integration with ASP. We then use this concept to make the semantic characterization of clingo’s theory-reasoning framework precise. This provides us with a formal framework in which we can elaborate upon the formal properties of existing hybridizations of clingo, such as clingcon, clingo[dl], and clingo[lp].This work was supported by DFG grant SCHA 550/11, Germany, by grant PID2020-116201GB-I00 funded by MCIN/AEI/ 10.13039/501100011033, Spain, by Xunta de Galicia and the European Union, GPC ED431B 2022/33, by European COST action CA17124 DigForASP, EU, and by the National Science Foundation (NSF 95-3101-0060-402), USA.Xunta de Galicia; ED431B 2022/33Deutsche Forschungsgemeinschaft; SCHA 550/11United States. National Science Foundation; NSF 95-3101-0060-40

Inductive logic programming as satisfiability modulo theories

At the intersection of machine learning, program synthesis and automated reasoning lies the field of Inductive Logic Programming (ILP). The aim of ILP is to automatically learn relational programs from input/output examples, typically through logic-based techniques. Inspired by Karl Popper’s falsification perspective on science, this dissertation sets out a new approach to ILP: Learning From Failures (LFF). In science, starting from a huge set of a priori viable hypotheses, we select a hypothesis to test. This hypothesis typically gets falsified due to failing in some specific way. By examining the failure we learn that an entire space of related hypotheses is now ruled out. Having thus reduced our set of viable hypotheses, we subsequently select from just those that remain. LFF applies this methodology to program induction, codifying it as a three-stage loop. The generate stage maintains a formula whose satisfying assignments correspond to the set of viable hypotheses. The test stage takes a satisfying assignment, interprets it as a logic program and tests it against training examples – imperfect fit is considered a failure. The constrain stage turns a failure into constraints to add to the generate stage’s formula, thereby eliminating a class of hypotheses which will fail for the same reason. The thesis of this dissertation is three-fold. The first claim is that LFF frames the ILP problem as one of Satisfiability Modulo Theories (SMT). With the search for viable hypotheses handed-off to a SAT-solver, the test stage can be regarded as a theory solver collaborating with the SAT-solver, effectively making ILP’s notion of background knowledge into a (Horn) background theory. The second claim is that LFF’s three-stage loop is an effective basis for falsification-based program induction. Chapter 4 develops the above correspondence into a feature-rich and flexible three-stage ILP system. Experimental evidence is provided for this system going beyond the state-of-the-art in ILP, e.g., by supporting large hypothesis spaces and large domains. The third claim is that the LFF-as-SMT-perspective helps apply satisfiability solving techniques to ILP, in particular to reduce hypothesis space exploration. In Chapter 5, we show that SMT-based techniques for explaining conflicts have a natural analog in terms of explaining which parts of a hypothesis are responsible for its failure. In Chapter 6, we incorporate other theory solvers alongside the test stage to reason about the (satisfiability of) over-approximating properties of hypotheses. We show that both of these techniques can significantly reduce the number of iterations of the three-stage loop

Étude de la coopération hôte-microbiote par des problèmes d'optimisation basés sur la complétion de réseaux métaboliques

Systems biology relies on computational biology to integrate knowledge and data, for a better understanding of organisms’ physiology. Challenges reside in the applicability of methods and tools to non-model organisms, for instance in marine biology. Sequencing advances and the growing importance of elucidating microbiotas’ roles, have led to an increased interest into these organisms. This thesis focuses on the modeling of the metabolism through networks, and of its functionality using graphs and constraints semantics. In particular, a first part presents work on gap-filling metabolic networks in the context of non-model organisms. A graph-based method is benchmarked and validated and a hybrid one is developed using Answer Set Programming (ASP) and linear programming. Such gap-filling is applied on algae and extended to decipher putative interactions between Ectocarpus siliculosus and a symbiotic bacterium. In this direction, the second part of the thesis aims at proposing formalisms and implementation of a tool for selecting and screening communities of interest within microbiotas. It enables to scale to large microbiotas and, with a two-step approach, to suggest symbionts that fit the desired objective. The modeling supports the computation of exchanges, and solving can cover the whole solution space. Applications are presented on the human gut microbiota and the selection of bacterial communities for a brown alga. Altogether, this thesis proposes modeling, software and biological applications using graph-based semantics to support the elaboration of hypotheses for elucidating the metabolism of organisms.La biologie des systèmes intègre données et connaissances par des méthodes bioinformatiques, afin de mieux appréhender la physiologie des organismes. Une problématique est l’applicabilité de ces techniques aux organismes non modèles, au centre de plus en plus d’études, grâce aux avancées de séquençage et à l’intérêt croissant de la recherche sur les microbiotes. Cette thèse s’intéresse à la modélisation du métabolisme par des réseaux, et de sa fonctionnalité par diverses sémantiques basées sur les graphes et les contraintes stoechiométriques. Une première partie présente des travaux sur la complétion de réseaux métaboliques pour les organismes non modèles. Une méthode basée sur les graphes est validée, et une seconde, hybride, est développée, en programmation par ensembles réponses (ASP). Ces complétions sont appliquées à des réseaux métaboliques d’algues en biologie marine, et étendues à la recherche de complémentarité métabolique entre Ectocarpus siliculosus et une bactérie symbiotique. En s’appuyant sur les méthodes de complétion, la seconde partie de la thèse vise à proposer et implémenter une sélection de communautés à l’échelle de grands microbiotes. Une approche en deux étapes permet de suggérer des symbiotes pour l’optimisation d’un objectif donné. Elle supporte la modélisation des échanges et couvre tout l’espace des solutions. Des applications sur le microbiote intestinal humain et la sélection de bactéries pour une algue brune sont présentées. Dans l’ensemble, cette thèse propose de modéliser, développer et appliquer des méthodes reposant sur des sémantiques de graphe pour élaborer des hypothèses sur le métabolisme des organismes