arXiv subjects

Katsumi Inoue

Publications and source records attributed to Katsumi Inoue.

43 records · Page 3Linked to original sources

arXiv2015

Modeling of Resilience Properties in Oscillatory Biological Systems using Parametric Time Petri Nets, Supplementary Information

Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the dynamic behavior of biological oscillatory systems. In particular, we focus on the resilience properties of such systems. This notion is crucial to understand the behavior of biological systems (e.g. the mammalian circadian rhythm) that are reactive and adaptive enough to endorse major changes in their environment (e.g. jet-lags, day-night alternating work-time). We formalize these properties through parametric TCTL and demonstrate how changes of the environmental conditions can be tackled to guarantee the resilience of living organisms. In particular, we are able to discuss the influence of various perturbations, e.g. artificial jet-lag or components knock-out, with regard to quantitative delays. This analysis is crucial when it comes to model elicitation for dynamic biological systems. We demonstrate the applicability of this technique using a simplified model of circadian clock.

cs.LO↗

arXiv2013

Aspartame: Solving Constraint Satisfaction Problems with Answer Set Programming

Encoding finite linear CSPs as Boolean formulas and solving them by using modern SAT solvers has proven to be highly effective, as exemplified by the award-winning sugar system. We here develop an alternative approach based on ASP. This allows us to use first-order encodings providing us with a high degree of flexibility for easy experimentation with different implementations. The resulting system aspartame re-uses parts of sugar for parsing and normalizing CSPs. The obtained set of facts is then combined with an ASP encoding that can be grounded and solved by off-the-shelf ASP systems. We establish the competitiveness of our approach by empirically contrasting aspartame and sugar.

cs.AI↗

arXiv2013

Post-Proceedings of the First International Workshop on Learning and Nonmonotonic Reasoning

Knowledge Representation and Reasoning and Machine Learning are two important fields in AI. Nonmonotonic logic programming (NMLP) and Answer Set Programming (ASP) provide formal languages for representing and reasoning with commonsense knowledge and realize declarative problem solving in AI. On the other side, Inductive Logic Programming (ILP) realizes Machine Learning in logic programming, which provides a formal background to inductive learning and the techniques have been applied to the fields of relational learning and data mining. Generally speaking, NMLP and ASP realize nonmonotonic reasoning while lack the ability of learning. By contrast, ILP realizes inductive learning while most techniques have been developed under the classical monotonic logic. With this background, some researchers attempt to combine techniques in the context of nonmonotonic ILP. Such combination will introduce a learning mechanism to programs and would exploit new applications on the NMLP side, while on the ILP side it will extend the representation language and enable us to use existing solvers. Cross-fertilization between learning and nonmonotonic reasoning can also occur in such as the use of answer set solvers for ILP, speed-up learning while running answer set solvers, learning action theories, learning transition rules in dynamical systems, abductive learning, learning biological networks with inhibition, and applications involving default and negation. This workshop is the first attempt to provide an open forum for the identification of problems and discussion of possible collaborations among researchers with complementary expertise. The workshop was held on September 15th of 2013 in Corunna, Spain. This post-proceedings contains five technical papers (out of six accepted papers) and the abstract of the invited talk by Luc De Raedt.

cs.AI↗

arXiv2013

Encoding Petri Nets in Answer Set Programming for Simulation Based Reasoning

One of our long term research goals is to develop systems to answer realistic questions (e.g., some mentioned in textbooks) about biological pathways that a biologist may ask. To answer such questions we need formalisms that can model pathways, simulate their execution, model intervention to those pathways, and compare simulations under different circumstances. We found Petri Nets to be the starting point of a suitable formalism for the modeling and simulation needs. However, we need to make extensions to the Petri Net model and also reason with multiple simulation runs and parallel state evolutions. Towards that end Answer Set Programming (ASP) implementation of Petri Nets would allow us to do both. In this paper we show how ASP can be used to encode basic Petri Nets in an intuitive manner. We then show how we can modify this encoding to model several Petri Net extensions by making small changes. We then highlight some of the reasoning capabilities that we will use to accomplish our ultimate research goal.

cs.AI↗

arXiv2013

Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs.

cs.AI↗

arXiv2011

Confidentiality-Preserving Data Publishing for Credulous Users by Extended Abduction

Publishing private data on external servers incurs the problem of how to avoid unwanted disclosure of confidential data. We study a problem of confidentiality in extended disjunctive logic programs and show how it can be solved by extended abduction. In particular, we analyze how credulous non-monotonic reasoning affects confidentiality.

cs.AI↗

arXiv2004

An Abductive Framework For Computing Knowledge Base Updates

This paper introduces an abductive framework for updating knowledge bases represented by extended disjunctive programs. We first provide a simple transformation from abductive programs to update programs which are logic programs specifying changes on abductive hypotheses. Then, extended abduction, which was introduced by the same authors as a generalization of traditional abduction, is computed by the answer sets of update programs. Next, different types of updates, view updates and theory updates are characterized by abductive programs and computed by update programs. The task of consistency restoration is also realized as special cases of these updates. Each update problem is comparatively assessed from the computational complexity viewpoint. The result of this paper provides a uniform framework for different types of knowledge base updates, and each update is computed using existing procedures of logic programming.

cs.DB↗