Our aim is to build a set of rules, such that reasoning over temporal dependencies within gene regulatory networks is possible. The underlying transitions may be obtained by discretizing observed time series, or they are generated based on existing knowledge, e.g. by Boolean networks or their nondeterministic generalization. We use the mathematical discipline of formal concept analysis (FCA), which has been applied successfully in domains as knowledge representation, data mining or software engineering. By the attribute exploration algorithm, an expert or a supporting computer program is enabled to decide about the validity of a minimal set of implications and thus to construct a sound and complete knowledge base. From this all valid implications are derivable that relate to the selected properties of a set of genes. We present results of our method for the initiation of sporulation in Bacillus subtilis. However the formal structures are exhibited in a most general manner. Therefore the approach may be adapted to signal transduction or metabolic networks, as well as to discrete temporal transitions in many biological and nonbiological areas.

This paper provides the reader with a very brief introduction to some of the theory and methods of text data mining. The intent of this article is to introduce the reader to some of the current methodologies that are employed within this discipline area while at the same time making the reader aware of some of the interesting challenges that remain to be solved within the area. Finally, the articles serves as a very rudimentary tutorial on some of techniques while also providing the reader with a list of references for additional study.

The peer-review process is the most widely accepted certification mechanism for officially accepting the written results of researchers within the scientific community. An essential component of peer-review is the identification of competent referees to review a submitted manuscript. This article presents an algorithm to automatically determine the most appropriate reviewers for a manuscript by way of a co-authorship network data structure and a relative-rank particle-swarm algorithm. This approach is novel in that it is not limited to a pre-selected set of referees, is computationally efficient, requires no human-intervention, and, in some instances, can automatically identify conflict of interest situations. A useful application of this algorithm would be to open commentary peer-review systems because it provides a weighting for each referee with respects to their expertise in the domain of a manuscript. The algorithm is validated using referee bid data from the 2005 Joint Conference on Digital Libraries.

This paper studies how to verify the conformity of a program with its specification and proposes a novel constraint-programming framework for bounded program verification (CPBPV). The CPBPV framework uses constraint stores to represent the specification and the program and explores execution paths nondeterministically. The input program is partially correct if each constraint store so produced implies the post-condition. CPBPV does not explore spurious execution paths as it incrementally prunes execution paths early by detecting that the constraint store is not consistent. CPBPV uses the rich language of constraint programming to express the constraint store. Finally, CPBPV is parametrized with a list of solvers which are tried in sequence, starting with the least expensive and less general. Experimental results often produce orders of magnitude improvements over earlier approaches, running times being often independent of the variable domains. Moreover, CPBPV was able to detect subtle errors in some programs while other frameworks based on model checking have failed.

The practical applications based on recurrent spiking neurons are limited due to their non-trivial learning algorithms. The temporal nature of spiking neurons is more favorable for hardware implementation where signals can be represented in binary form and communication can be done through the use of spikes. This work investigates the potential of recurrent spiking neurons implementations on reconfigurable platforms and their applicability in temporal based applications. A theoretical framework of reservoir computing is investigated for hardware/software implementation. In this framework, only readout neurons are trained which overcomes the burden of training at the network level. These recurrent neural networks are termed as microcircuits which are viewed as basic computational units in cortical computation. This paper investigates the potential of recurrent neural reservoirs and presents a novel hardware/software strategy for their implementation on FPGAs. The design is implemented and the functionality is tested in the context of speech recognition application.

Gaussian processes retain the linear model either as a special case, or in the limit. We show how this relationship can be exploited when the data are at least partially linear. However from the perspective of the Bayesian posterior, the Gaussian processes which encode the linear model either have probability of nearly zero or are otherwise unattainable without the explicit construction of a prior with the limiting linear model in mind. We develop such a prior, and show that its practical benefits extend well beyond the computational and conceptual simplicity of the linear model. For example, linearity can be extracted on a per-dimension basis, or can be combined with treed partition models to yield a highly efficient nonstationary model. Our approach is demonstrated on synthetic and real datasets of varying linearity and dimensionality.

Algorithm selection is typically based on models of algorithm performance, learned during a separate offline training sequence, which can be prohibitively expensive. In recent work, we adopted an online approach, in which a performance model is iteratively updated and used to guide selection on a sequence of problem instances. The resulting exploration-exploitation trade-off was represented as a bandit problem with expert advice, using an existing solver for this game, but this required the setting of an arbitrary bound on algorithm runtimes, thus invalidating the optimal regret of the solver. In this paper, we propose a simpler framework for representing algorithm selection as a bandit problem, with partial information, and an unknown bound on losses. We adapt an existing solver to this game, proving a bound on its expected regret, which holds also for the resulting algorithm selection technique. We present preliminary experiments with a set of SAT solvers on a mixed SAT-UNSAT benchmark.

Representations are at the heart of artificial intelligence (AI). This book is devoted to the problem of representation discovery: how can an intelligent system construct representations from its experience? Representation discovery re-parameterizes the state space - prior to the application of information retrieval, machine learning, or optimization techniques - facilitating later inference processes by constructing new task-specific bases adapted to the state space geometry. This book presents a general approach to representation discovery using the framework of harmonic analysis, in particular Fourier and wavelet analysis. Biometric compression methods, the compact disc, the computerized axial tomography (CAT) scanner in medicine, JPEG compression, and spectral analysis of time-series data are among the many applications of classical Fourier and wavelet analysis.

Artificial systems that think and behave intelligently are one of the most exciting and challenging goals of Artificial Intelligence. Action Programming is the art and science of devising high-level control strategies for autonomous systems which employ a mental model of their environment and which reason about their actions as a means to achieve their goals. Applications of this programming paradigm include autonomous software agents, mobile robots with high-level reasoning capabilities, and General Game Playing. These lecture notes give an in-depth introduction to the current state-of-the-art in action programming. The main topics are knowledge representation for actions, procedural action programming, planning, agent logic programs, and reactive, behavior-based agents.

Bayesian model averaging, model selection and its approximations such as BIC are generally statistically consistent, but sometimes achieve slower rates og convergence than other methods such as AIC and leave-one-out cross-validation. On the other hand, these other methods can br inconsistent. We identify the "catch-up phenomenon" as a novel explanation for the slow convergence of Bayesian methods. Based on this analysis we define the switch distribution, a modification of the Bayesian marginal distribution. We show that, under broad conditions,model selection and prediction based on the switch distribution is both consistent and achieves optimal convergence rates, thereby resolving the AIC-BIC dilemma. The method is practical; we give an efficient implementation. The switch distribution has a data compression interpretation, and can thus be viewed as a "prequential" or MDL method; yet it is different from the MDL methods that are usually considered in the literature. We compare the switch distribution to Bayes factor model selection and leave-one-out cross-validation.