We propose a novel framework for learning normal logic programs from transitions of interpretations. Given a set of pairs of interpretations (I, J) such that J = T P (I), where T P is the immediate consequence operator, we infer the program P. The learning framework can be repeatedly applied for identifying Boolean networks from basins of attraction. Two algorithms have been implemented for this learning task, and are compared using examples from the biological literature. We also show how to incorporate background knowledge and inductive biases, then apply the framework to learning transition rules of cellular automata.

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In a previous work we proposed a framework for learning normal logic programs from transitions of interpretations. Given a set of pairs of interpretations (I, J) such that J = TP (I), where TP is the immediate consequence operator, we infer the program P. Here we propose a new learning approach that is more efficient in terms of output quality. This new approach relies on specialization in place of generalization. It generates hypotheses by specialization from the most general clauses until no negative transition is covered. Contrary to previous approaches, the output of this method does not depend on variables/transitions ordering. The new method guarantees that the learned rules are minimal, that is, the body of each rule constitutes a prime implicant to infer the head.

Abstract.Learning from interpretation transition (LFIT) automatically constructs a model of the dynamics of a system from the observation of its state transitions. So far, the systems that LFIT handles are restricted to synchronous deterministic dynamics, i.e., all variables update their values at the same time and, for each state of the system, there is only one possible next state. However, other dynamics exist in the field of logical modeling, in particular the asynchronous semantics which is widely used to model biological systems. In this paper, we focus on a method that learns the dynamics of the system independently of its semantics. For this purpose, we propose a modeling of multi-valued systems as logic programs in which a rule represents what can occurs rather than what will occurs. This modeling allows us to represent nondeterminism and to propose an extension of LFIT in the form of a semantics free algorithm to learn from discrete multi-valued transitions, regardless of their update schemes. We show through theoretical results that synchronous, asynchronous and general semantics are all captured by this method. Practical evaluation is performed on randomly generated systems and benchmarks from biological literature to study the scalability of this new algorithm regarding the three aforementioned semantics.Keywords: Dynamical semantics, learning from interpretation transition, dynamical systems, Inductive Logic Programming IntroductionLearning the dynamics of systems with many interactive components becomes more and more important due to many applications, e.g., multi-agent systems, robotics and bioinformatics. Knowledge of a system dynamics can be used by agents and robots for planning and scheduling. In bioinformatics, learning the dynamics of biological systems can correspond to the identification of the influence of genes and can help to understand their interactions. While building a model, the choice of a relevant semantics associated to the studied system represents a major issue with regard to the kind of dynamical properties to analyze. The differences and common features of different semantics w.r.t. properties of interest (attractors, oscillators, etc.) constitutes an area of research per itself, especially in the field of Boolean networks. In [8], the author exhibits the translation from Boolean networks into logic programs and discusses the point attractors in both synchronous and asynchronous semantics. In [6], A. Garg et al. address the differences and complementarity of synchronous and asynchronous semantics to model biological networks and identify attractors. The benefits of the synchronous model are to be computationally tractable, while classical state space exploration algorithms fail on asynchronous ones. For some applications, like the biological ones, asynchronous semantics is said to capture more realistic behaviors: at a given time, a single gene can change its expression level. This results in a potential combinatorial explosion of the number of reachable states. To illustr...

Boolean networks are widely used model to represent gene interactions and global dynamical behavior of gene regulatory networks. To understand the memory effect involved in some interactions between biological components, it is necessary to include delayed influences in the model. In this paper, we present a logical method to learn such models from sequences of gene expression data. This method analyzes each sequence one by one to iteratively construct a Boolean network that captures the dynamics of these observations. To illustrate the merits of this approach, we apply it to learning real data from bioinformatic literature. Using data from the yeast cell cycle, we give experimental results and show the scalability of the method. We show empirically that using this method we can handle millions of observations and successfully capture delayed influences of Boolean networks.

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Abstract. Many problems in multi-agent systems can be represented as a Distributed Constraint Optimization Problem (DCOP) where the goal is to find the best assignment to variables in order to minimize the cost. More complex problems including several criteria can be represented as a Multi-Objective Distributed Constraint Optimization Problem (MO-DCOP) where the goal is to optimize several criteria at the same time. However, many problems are subject to changes over time and need to be represented as dynamic problems. In this paper, we formalize the Dynamic Multi-Objective Distributed Constraint Optimization Problem (DMO-DCOP) and introduce the first algorithm called DMOBB to handle changes in the number of objectives.

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