Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining

Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri net’s architecture. We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony. We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual “perfect” Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction

Ms Pac-Man versus Ghost Team CEC 2011 competition

Games provide an ideal test bed for computational intelligence and significant progress has been made in recent years, most notably in games such as Go, where the level of play is now competitive with expert human play on smaller boards. Recently, a significantly more complex class of games has received increasing attention: real-time video games. These games pose many new challenges, including strict time constraints, simultaneous moves and open-endedness. Unlike in traditional board games, computational play is generally unable to compete with human players. One driving force in improving the overall performance of artificial intelligence players are game competitions where practitioners may evaluate and compare their methods against those submitted by others and possibly human players as well. In this paper we introduce a new competition based on the popular arcade video game Ms Pac-Man: Ms Pac-Man versus Ghost Team. The competition, to be held at the Congress on Evolutionary Computation 2011 for the first time, allows participants to develop controllers for either the Ms Pac-Man agent or for the Ghost Team and unlike previous Ms Pac-Man competitions that relied on screen capture, the players now interface directly with the game engine. In this paper we introduce the competition, including a review of previous work as well as a discussion of several aspects regarding the setting up of the game competition itself. © 2011 IEEE

Modeling and Analysis of Scholar Mobility on Scientific Landscape

Scientific literature till date can be thought of as a partially revealed landscape, where scholars continue to unveil hidden knowledge by exploring novel research topics. How do scholars explore the scientific landscape , i.e., choose research topics to work on? We propose an agent-based model of topic mobility behavior where scholars migrate across research topics on the space of science following different strategies, seeking different utilities. We use this model to study whether strategies widely used in current scientific community can provide a balance between individual scientific success and the efficiency and diversity of the whole academic society. Through extensive simulations, we provide insights into the roles of different strategies, such as choosing topics according to research potential or the popularity. Our model provides a conceptual framework and a computational approach to analyze scholars' behavior and its impact on scientific production. We also discuss how such an agent-based modeling approach can be integrated with big real-world scholarly data.Comment: To appear in BigScholar, WWW 201

Semantically-guided evolutionary knowledge discovery from texts

This thesis proposes a new approach for structured knowledge discovery from texts which considers both the mining process itself, the evaluation of this knowledge by the model, and the human assessment of the quality of the outcome.This is achieved by integrating Natural-Language technology and Genetic Algorithms to produce explanatory novel hypotheses. Natural-Language techniques are specifically used to extract genre-based information from text documents. Additional semantic and rhetorical information for generating training data and for feeding a semistructured Latent Semantic Analysis process is also captured.The discovery process is modeled by a semantically-guided Genetic Algorithm which uses training data to guide the search and optimization process. A number of novel criteria to evaluate the quality of the new knowledge are proposed. Consequently, new genetic operations suitable for text mining are designed, and techniques for Evolutionary Multi-Objective Optimization are adapted for the model to trade off between different criteria in the hypotheses.Domain experts were used in an experiment to assess the quality of the hypotheses produced by the model so as to establish their effectiveness in terms of novel and interesting knowledge. The assessment showed encouraging results for the discovered knowledge and for the correlation between the model and the human opinions