In this paper, the early design of our self-organized agent-based simulation model for exploration of synaptic connections that faithfully generates what is observed in natural situation is given. While we take inspiration from neuroscience, our intent is not to create a veridical model of processes in neurodevelopmental biology, nor to represent a real biological system. Instead, our goal is to design a simulation model that learns acting in the same way of human nervous system by using findings on human subjects using reflex methodologies in order to estimate unknown connections.

Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to analyze these huge amounts of data. Such methods require to recognize common patterns to analyze data. As biological networks can be modeled by graphs, the problem of common patterns recognition is equivalent with frequent sub graph mining in a set of graphs. In this paper, at first the challenges of frequent subgrpahs mining in biological networks are introduced and the existing approaches are classified for each challenge.

Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization - Random Forests (BBO - RF) and BBO - SVM (Support Vector Machines) with gene ranking as a heuristic, for microarray gene expression analysis. This heuristic is obtained from information gain filter ranking procedure. The BBO algorithm generates a population of candidate subset of genes, as part of an ecosystem of habitats, and employs the migration and mutation processes across multiple generations of the population to improve the classification accuracy. The fitness of each gene subset is assessed by the classifiers - SVM and Random Forests. The performances of these hybrid techniques are evaluated on three cancer gene expression datasets retrieved from the Kent Ridge Biomedical datasets collection and the libSVM data repository. Our results demonstrate that genes selected by the proposed techniques yield classification accuracies comparable to previously reported algorithms.

We intro duce the author-topic mo del, a generative mo del for do cuments that extends Latent Dirichlet Allo cation (LDA; Blei, Ng, & Jordan, 2003) to include authorship information. Each author is asso ciated with a multinomial distribution over topics and each topic is asso ciated with a multinomial distribution over words. A do cument with multiple authors is mo deled as a distribution over topics that is a mixture of the distributions asso ci-ated with the authors. We apply the mo del to a collection of 1,700 NIPS conference pap ers and 160,000 CiteSeer abstracts. Exact inference is intractable for these datasets and we use Gibbs sampling to estimate the topic and author distributions. We compare the p erformance with two other generative mo d-els for do cuments, which are sp ecial cases of the author-topic mo del: LDA (a topic mo del) and a simple author mo del in which each author is asso ciated with a distribution over words rather than a distribution over topics. We show topics recovered by the author-topic mo del, and demonstrate applications to computing similarity b etween authors and entropy of author output.

Exponential models of distributions are widely used in machine learning for classiffication and modelling. It is well known that they can be interpreted as maximum entropy models under empirical expectation constraints. In this work, we argue that for classiffication tasks, mutual information is a more suitable information theoretic measure to be optimized. We show how the principle of minimum mutual information generalizes that of maximum entropy, and provides a comprehensive framework for building discriminative classiffiers. A game theoretic interpretation of our approach is then given, and several generalization bounds provided. We present iterative algorithms for solving the minimum information problem and its convex dual, and demonstrate their performance on various classiffication tasks. The results show that minimum information classiffiers outperform the corresponding maximum entropy models.

This paper proposes a grey interval relation TOPSIS for the decision making in which all of the attribute weights and attribute values are given by the interval grey numbers. The feature of our method different from other grey relation decision-making is that all of the subjective and objective weights are obtained by interval grey number and that decision-making is performed based on the relative approach degree of grey TOPSIS, the relative approach degree of grey incidence and the relative membership degree of grey incidence using 2-dimensional Euclidean distance. The weighted Borda method is used for combining the results of three methods. An example shows the applicability of the proposed approach.

We consider the challenge of preference elicitation in systems that help users discover the most desirable item(s) within a given database. Past work on preference elicitation focused on structured models that provide a factored representation of users' preferences. Such models require less information to construct and support efficient reasoning algorithms. This paper makes two substantial contributions to this area: (1) Strong representation theorems for factored value functions. (2) A methodology that utilizes our representation results to address the problem of optimal item selection.

In this paper, we discuss the implementation of a rule based expert system for diagnosing neuromuscular diseases. The proposed system is implemented as a rule based expert system in JESS for the diagnosis of Cerebral Palsy, Multiple Sclerosis, Muscular Dystrophy and Parkinson's disease. In the system, the user is presented with a list of questionnaires about the symptoms of the patients based on which the disease of the patient is diagnosed and possible treatment is suggested. The system can aid and support the patients suffering from neuromuscular diseases to get an idea of their disease and possible treatment for the disease.

The multiple attribute mixed type decision making is performed by four methods, that is, the relative approach degree of grey TOPSIS method, the relative approach degree of grey incidence, the relative membership degree of grey incidence and the grey relation relative approach degree method using the maximum entropy estimation, respectively. In these decision making methods, the grey incidence degree in four-dimensional Euclidean space is used. The final arrangement result is obtained by weighted Borda method. An example illustrates the applicability of the proposed approach.

The restricted Boltzmann machine (RBM) is a flexible tool for modeling complex data, however there have been significant computational difficulties in using RBMs to model high-dimensional multinomial observations. In natural language processing applications, words are naturally modeled by K-ary discrete distributions, where K is determined by the vocabulary size and can easily be in the hundreds of thousands. The conventional approach to training RBMs on word observations is limited because it requires sampling the states of K-way softmax visible units during block Gibbs updates, an operation that takes time linear in K. In this work, we address this issue by employing a more general class of Markov chain Monte Carlo operators on the visible units, yielding updates with computational complexity independent of K. We demonstrate the success of our approach by training RBMs on hundreds of millions of word n-grams using larger vocabularies than previously feasible and using the learned features to improve performance on chunking and sentiment classification tasks, achieving state-of-the-art results on the latter.