Mapping the topology of gene regulatory networks is a central problem in systems biology. The regulatory architecture controlling gene expression also controls consequent cellular behavior such as development, differentiation, homeostasis and response to stimuli, while deregulation of these networks has been implicated in oncogenesis and tumor progression (Pe'er and Hacohen, 2011). Experimental methods based e.g. on chromatin immunoprecepitation, DNaseI hypersensitivity or protein-binding assays are capable of determining the nature of gene regulation in a given system, but are time-consuming, expensive and require antibodies for each transcription factor (Elnitski et al., 2006). Accurate computational methods to infer gene regulatory networks, particularly methods that leverage genome-scale experimental data, are urgently required not only to supplement empirical approaches but also, if possible, to explore these data in new, moreintegrative ways. Many computational methods have been developed to infer regulatory networks from gene expression data, predominately employing unsupervised techniques. Several comparisons have been made of network inference methods, but a comprehensive evaluation that covers unsupervised, semi-supervised and supervised methods is lacking, and many questions remain open.

It has recently been observed that certain extremely simple feature encoding techniques are able to achieve state of the art performance on several standard image classification benchmarks including deep belief networks, convolutional nets, factored RBMs, mcRBMs, convolutional RBMs, sparse autoencoders and several others. Moreover, these "triangle" or "soft threshold" encodings are ex- tremely efficient to compute. Several intuitive arguments have been put forward to explain this remarkable performance, yet no mathematical justification has been offered. The main result of this report is to show that these features are realized as an approximate solution to the a non-negative sparse coding problem. Using this connection we describe several variants of the soft threshold features and demonstrate their effectiveness on two image classification benchmark tasks.

Sparsity-constrained optimization has wide applicability in machine learning, statistics, and signal processing problems such as feature selection and compressive Sensing. A vast body of work has studied the sparsity-constrained optimization from theoretical, algorithmic, and application aspects in the context of sparse estimation in linear models where the fidelity of the estimate is measured by the squared error. In contrast, relatively less effort has been made in the study of sparsity-constrained optimization in cases where nonlinear models are involved or the cost function is not quadratic. In this paper we propose a greedy algorithm, Gradient Support Pursuit (GraSP), to approximate sparse minima of cost functions of arbitrary form. Should a cost function have a Stable Restricted Hessian (SRH) or a Stable Restricted Linearization (SRL), both of which are introduced in this paper, our algorithm is guaranteed to produce a sparse vector within a bounded distance from the true sparse optimum. Our approach generalizes known results for quadratic cost functions that arise in sparse linear regression and Compressive Sensing. We also evaluate the performance of GraSP through numerical simulations on synthetic data, where the algorithm is employed for sparse logistic regression with and without $\ell_2$-regularization.

This work introduces a novel nonparametric density index defined on graphs, the Sum-over-Forests (SoF) density index. It is based on a clear and intuitive idea: high-density regions in a graph are characterized by the fact that they contain a large amount of low-cost trees with high outdegrees while low-density regions contain few ones. Therefore, a Boltzmann probability distribution on the countable set of forests in the graph is defined so that large (high-cost) forests occur with a low probability while short (low-cost) forests occur with a high probability. Then, the SoF density index of a node is defined as the expected outdegree of this node in a non-trivial tree of the forest, thus providing a measure of density around that node. Following the matrix-forest theorem, and a statistical physics framework, it is shown that the SoF density index can be easily computed in closed form through a simple matrix inversion. Experiments on artificial and real data sets show that the proposed index performs well on finding dense regions, for graphs of various origins.

Role mining tackles the problem of finding a role-based access control (RBAC) configuration, given an access-control matrix assigning users to access permissions as input. Most role mining approaches work by constructing a large set of candidate roles and use a greedy selection strategy to iteratively pick a small subset such that the differences between the resulting RBAC configuration and the access control matrix are minimized. In this paper, we advocate an alternative approach that recasts role mining as an inference problem rather than a lossy compression problem. Instead of using combinatorial algorithms to minimize the number of roles needed to represent the access-control matrix, we derive probabilistic models to learn the RBAC configuration that most likely underlies the given matrix. Our models are generative in that they reflect the way that permissions are assigned to users in a given RBAC configuration. We additionally model how user-permission assignments that conflict with an RBAC configuration emerge and we investigate the influence of constraints on role hierarchies and on the number of assignments. In experiments with access-control matrices from real-world enterprises, we compare our proposed models with other role mining methods. Our results show that our probabilistic models infer roles that generalize well to new system users for a wide variety of data, while other models' generalization abilities depend on the dataset given.

Many businesses are using recommender systems for marketing outreach. Recommendation algorithms can be either based on content or driven by collaborative filtering. We study different ways to incorporate content information directly into the matrix factorization approach of collaborative filtering. These content-boosted matrix factorization algorithms not only improve recommendation accuracy, but also provide useful insights about the contents, as well as make recommendations more easily interpretable.

ABSTRACT A new geometrically-motivated algorithm for nonnegative matrix factorization is developed and applied to the discovery of latent "topics" for text and image "document" corpora. The algorithm is based on robustly finding and clustering extreme-points of empirical cross-document wordfrequencies that correspond to novel "words" unique to each topic. In contrast to related approaches that are based on solving non-convex optimization problems using suboptimal approximations, locally-optimal methods, or heuristics, the new algorithm is convex, has polynomial complexity, and has competitive qualitative and quantitative performance compared to the current state-of-the-art approaches on synthetic and real-world datasets. Index Terms-- Topic modeling, nonnegative matrix factorization (NMF), extreme points, subspace clustering. 1. INTRODUCTION Topic modeling is a statistical tool for the automatic discovery and comprehension of latent thematic structure or topics, assumed to pervade a corpus of documents. Suppose that we have a corpus of M documents composed of words from a vocabulary of W distinct words indexed byw 1,...,W.

It has been conceived that children learn new objects through their affordances, that is, the actions that can be taken on them. We suggest that web pages also have affordances defined in terms of the users' information need they meet. An assumption of the proposed approach is that different parts of a text may not be equally important / relevant to a given query. Judgment on the relevance of a web document requires, therefore, a thorough look into its parts, rather than treating it as a monolithic content. We propose a method to extract and assign affordances to texts and then use these affordances to retrieve the corresponding web pages. The overall approach presented in the paper relies on case-based representations that bridge the queries to the affordances of web documents. We tested our method on the tourism domain and the results are promising.

In this paper Knowledge Discovery System (KDS) is proposed and implemented for the extraction of knowledge-mean stiffness of a polymer composite material in which when fibers are placed at different orientations. Cosine amplitude method is implemented for retrieving compatible polymer matrix and reinforcement fiber which is coming under predicted fiber class, from the polymer and reinforcement database respectively, based on the design requirements. Fuzzy classification rules to classify fibers into short, medium and long fiber classes are derived based on the fiber length and the computed or derive critical length of fiber. Longitudinal and Transverse module of Polymer Matrix Composite consisting of seven layers with different fiber volume fractions and different fibers orientations at 0,15,30,45,60,75 and 90 degrees are analyzed through Rule-of Mixture material design model. The analysis results are represented in different graphical steps and have been measured with statistical parameters. This data mining application implemented here has focused the mechanical problems of material design and analysis. Therefore, this system is an expert decision support system for optimizing the materials performance for designing light-weight and strong, and cost effective polymer composite materials.

Travel sharing, i.e., the problem of finding parts of routes which can be shared by several travellers with different points of departure and destinations, is a complex multiagent problem that requires taking into account individual agents' preferences to come up with mutually acceptable joint plans. In this paper, we apply state-of-the-art planning techniques to real-world public transportation data to evaluate the feasibility of multiagent planning techniques in this domain. The potential application value of improving travel sharing technology has great application value due to its ability to reduce the environmental impact of travelling while providing benefits to travellers at the same time. We propose a three-phase algorithm that utilises performant single-agent planners to find individual plans in a simplified domain first, then merges them using a best-response planner which ensures resulting solutions are individually rational, and then maps the resulting plan onto the full temporal planning domain to schedule actual journeys. The evaluation of our algorithm on real-world, multi-modal public transportation data for the United Kingdom shows linear scalability both in the scenario size and in the number of agents, where trade-offs have to be made between total cost improvement, the percentage of feasible timetables identified for journeys, and the prolongation of these journeys. Our system constitutes the first implementation of strategic multiagent planning algorithms in large-scale domains and provides insights into the engineering process of translating general domain-independent multiagent planning algorithms to real-world applications.