Perspectives for proof unwinding by programming languages techniques

In this chapter, we propose some future directions of work, potentially beneficial to Mathematics and its foundations, based on the recent import of methodology from the theory of programming languages into proof theory. This scientific essay, written for the audience of proof theorists as well as the working mathematician, is not a survey of the field, but rather a personal view of the author who hopes that it may inspire future and fellow researchers

On the enumeration of closures and environments with an application to random generation

Environments and closures are two of the main ingredients of evaluation in lambda-calculus. A closure is a pair consisting of a lambda-term and an environment, whereas an environment is a list of lambda-terms assigned to free variables. In this paper we investigate some dynamic aspects of evaluation in lambda-calculus considering the quantitative, combinatorial properties of environments and closures. Focusing on two classes of environments and closures, namely the so-called plain and closed ones, we consider the problem of their asymptotic counting and effective random generation. We provide an asymptotic approximation of the number of both plain environments and closures of size $n$. Using the associated generating functions, we construct effective samplers for both classes of combinatorial structures. Finally, we discuss the related problem of asymptotic counting and random generation of closed environemnts and closures

Predicting Genetic Regulatory Response Using Classification

We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular experiment based on (1) the presence of binding site subsequences (``motifs'') in the gene's regulatory region and (2) the expression levels of regulators such as transcription factors in the experiment (``parents''). Thus our learning task integrates two qualitatively different data sources: genome-wide cDNA microarray data across multiple perturbation and mutant experiments along with motif profile data from regulatory sequences. We convert the regression task of predicting real-valued gene expression measurement to a classification task of predicting +1 and -1 labels, corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. The learning algorithm employed is boosting with a margin-based generalization of decision trees, alternating decision trees. This large-margin classifier is sufficiently flexible to allow complex logical functions, yet sufficiently simple to give insight into the combinatorial mechanisms of gene regulation. We observe encouraging prediction accuracy on experiments based on the Gasch S. cerevisiae dataset, and we show that we can accurately predict up- and down-regulation on held-out experiments. Our method thus provides predictive hypotheses, suggests biological experiments, and provides interpretable insight into the structure of genetic regulatory networks.Comment: 8 pages, 4 figures, presented at Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB 2004), supplemental website: http://www.cs.columbia.edu/compbio/geneclas

Symmetry-breaking Answer Set Solving

In the context of Answer Set Programming, this paper investigates symmetry-breaking to eliminate symmetric parts of the search space and, thereby, simplify the solution process. We propose a reduction of disjunctive logic programs to a coloured digraph such that permutational symmetries can be constructed from graph automorphisms. Symmetries are then broken by introducing symmetry-breaking constraints. For this purpose, we formulate a preprocessor that integrates a graph automorphism system. Experiments demonstrate its computational impact.Comment: Proceedings of ICLP'10 Workshop on Answer Set Programming and Other Computing Paradig

Automatic Generation of Cognitive Theories using Genetic Programming

Cognitive neuroscience is the branch of neuroscience that studies the neural mechanisms underpinning cognition and develops theories explaining them. Within cognitive neuroscience, computational neuroscience focuses on modeling behavior, using theories expressed as computer programs. Up to now, computational theories have been formulated by neuroscientists. In this paper, we present a new approach to theory development in neuroscience: the automatic generation and testing of cognitive theories using genetic programming. Our approach evolves from experimental data cognitive theories that explain “the mental program” that subjects use to solve a specific task. As an example, we have focused on a typical neuroscience experiment, the delayed-match-to-sample (DMTS) task. The main goal of our approach is to develop a tool that neuroscientists can use to develop better cognitive theories