Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems

Learning Models of Sequential Decision-Making without Complete State Specification using Bayesian Nonparametric Inference and Active Querying

Learning models of decision-making behavior during sequential tasks is useful across a variety of applications, including human-machine interaction. In this paper, we present an approach to learning such models within Markovian domains based on observing and querying a decision-making agent. In contrast to classical approaches to behavior learning, we do not assume complete knowledge of the state features that impact an agent's decisions. Using tools from Bayesian nonparametric inference and time series of agents decisions, we first provide an inference algorithm to identify the presence of any unmodeled state features that impact decision making, as well as likely candidate models. In order to identify the best model among these candidates, we next provide an active querying approach that resolves model ambiguity by querying the decision maker. Results from our evaluations demonstrate that, using the proposed algorithms, an observer can identify the presence of latent state features, recover their dynamics, and estimate their impact on decisions during sequential tasks

Bounded Situation Calculus Action Theories

In this paper, we investigate bounded action theories in the situation calculus. A bounded action theory is one which entails that, in every situation, the number of object tuples in the extension of fluents is bounded by a given constant, although such extensions are in general different across the infinitely many situations. We argue that such theories are common in applications, either because facts do not persist indefinitely or because the agent eventually forgets some facts, as new ones are learnt. We discuss various classes of bounded action theories. Then we show that verification of a powerful first-order variant of the mu-calculus is decidable for such theories. Notably, this variant supports a controlled form of quantification across situations. We also show that through verification, we can actually check whether an arbitrary action theory maintains boundedness.Comment: 51 page

Dagstuhl News January - December 2000

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

AI Methods in Algorithmic Composition: A Comprehensive Survey

Algorithmic composition is the partial or total automation of the process of music composition by using computers. Since the 1950s, different computational techniques related to Artificial Intelligence have been used for algorithmic composition, including grammatical representations, probabilistic methods, neural networks, symbolic rule-based systems, constraint programming and evolutionary algorithms. This survey aims to be a comprehensive account of research on algorithmic composition, presenting a thorough view of the field for researchers in Artificial Intelligence.This study was partially supported by a grant for the MELOMICS project (IPT-300000-2010-010) from the Spanish Ministerio de Ciencia e Innovación, and a grant for the CAUCE project (TSI-090302-2011-8) from the Spanish Ministerio de Industria, Turismo y Comercio. The first author was supported by a grant for the GENEX project (P09-TIC- 5123) from the Consejería de Innovación y Ciencia de Andalucía