A Method to Identify and Analyze Biological Programs through Automated Reasoning.

Predictive biology is elusive because rigorous, data-constrained, mechanistic models of complex biological systems are difficult to derive and validate. Current approaches tend to construct and examine static interaction network models, which are descriptively rich but often lack explanatory and predictive power, or dynamic models that can be simulated to reproduce known behavior. However, in such approaches implicit assumptions are introduced as typically only one mechanism is considered, and exhaustively investigating all scenarios is impractical using simulation. To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations. We test hypotheses against all candidate models, and remove the need for simulation by characterizing and simultaneously analyzing all mechanistic explanations of observed behavior. Our methodology transforms knowledge of complex biological processes from sets of possible interactions and experimental observations to precise, predictive biological programs governing cell function

Optimisation of Mobile Communication Networks - OMCO NET

The mini conference “Optimisation of Mobile Communication Networks” focuses on advanced methods for search and optimisation applied to wireless communication networks. It is sponsored by Research & Enterprise Fund Southampton Solent University. The conference strives to widen knowledge on advanced search methods capable of optimisation of wireless communications networks. The aim is to provide a forum for exchange of recent knowledge, new ideas and trends in this progressive and challenging area. The conference will popularise new successful approaches on resolving hard tasks such as minimisation of transmit power, cooperative and optimal routing

A New Basis for Sparse PCA

The statistical and computational performance of sparse principal component analysis (PCA) can be dramatically improved when the principal components are allowed to be sparse in a rotated eigenbasis. For this, we propose a new method for sparse PCA. In the simplest version of the algorithm, the component scores and loadings are initialized with a low-rank singular value decomposition. Then, the singular vectors are rotated with orthogonal rotations to make them approximately sparse. Finally, soft-thresholding is applied to the rotated singular vectors. This approach differs from prior approaches because it uses an orthogonal rotation to approximate a sparse basis. Our sparse PCA framework is versatile; for example, it extends naturally to the two-way analysis of a data matrix for simultaneous dimensionality reduction of rows and columns. We identify the close relationship between sparse PCA and independent component analysis for separating sparse signals. We provide empirical evidence showing that for the same level of sparsity, the proposed sparse PCA method is more stable and can explain more variance compared to alternative methods. Through three applications---sparse coding of images, analysis of transcriptome sequencing data, and large-scale clustering of Twitter accounts, we demonstrate the usefulness of sparse PCA in exploring modern multivariate data.Comment: 33 pages, 8 figure

Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications (Extended Version)

Although the ``scale-free'' literature is large and growing, it gives neither a precise definition of scale-free graphs nor rigorous proofs of many of their claimed properties. In fact, it is easily shown that the existing theory has many inherent contradictions and verifiably false claims. In this paper, we propose a new, mathematically precise, and structural definition of the extent to which a graph is scale-free, and prove a series of results that recover many of the claimed properties while suggesting the potential for a rich and interesting theory. With this definition, scale-free (or its opposite, scale-rich) is closely related to other structural graph properties such as various notions of self-similarity (or respectively, self-dissimilarity). Scale-free graphs are also shown to be the likely outcome of random construction processes, consistent with the heuristic definitions implicit in existing random graph approaches. Our approach clarifies much of the confusion surrounding the sensational qualitative claims in the scale-free literature, and offers rigorous and quantitative alternatives.Comment: 44 pages, 16 figures. The primary version is to appear in Internet Mathematics (2005

Users guide Advanced Reactive Electronic Simulation (ARES) version 1.12

This Users Guide is for the Advanced Reactive Electronic Warfare Simulation (ARES) Version 1.12, created at the Naval Research Laboratory (NRL) under a project sponsored by the Office of Naval Research (ONR) titled Distributed and Networked C2W Technology (FY98-FYOO). The simulation is used to determine the optimum distributed C2W/EA configuration of assets including placement of sensors and system selection (jammer or receiver or both) for important mission scenarios leading to a better understanding of the minimum requirements for suppression of enemy air defense operations. ARES is a pulse level simulation that models the complex interaction of multiple radar systems being acted upon by multiple AEA aircraft, considering target aircraft radar cross section (RCS) and altitude, terrain masking effects, both standoff jamming and self protection jamming effects, and network connection effect. Its features include an object%-oriented scenario workbook allowing the users to build a battlefield scenario and a search procedure based on a genetic algorithm (GA) for optimizing configurations of what the core and peripheral components of the AEA architecture should be. ARES is available in two forms: Graphical User Interface (GUI) and parallel. ARES' GUI runs on a personal computer (PC) and its primary application is for setting up scenarios and post processing. ARES' parallel version runs over a cluster of Intel based Linux machines with Message- Passing Interface (MPI) and provides capability to execute multipleThis report was sponsored by the Applied Physics Laboratory, Johns Hopkins University