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FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

BIOINFORMATICS 2013年第9期29卷 1218-1219页

作者： Grove, Laurie E. Hall, David R. Beglov, Dmitri Vajda, Sandor Kozakov, Dima Wentworth Inst Technol Dept Sci Boston MA 01746 USA Acpharis Inc Holliston MA 01746 USA Boston Univ Dept Biomed Engn Boston MA 02215 USA

Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted.

关键词： DRUG design computer algorithms LIGANDS (Biochemistry) BIOINFORMATICS COMPUTATIONAL biology GENE mapping BINDING sites (Biochemistry)

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Probabilistic gait modelling and recognition

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IET computer VISION 2013年第1期7卷 56-70页

作者： Hong, Sungjun Lee, Heesung Kim, Euntai Yonsei Univ Sch Elect & Elect Engn Seoul 120749 South Korea

Biometric researchers have recently found considerable applicability of gait recognition in visual surveillance systems. This study proposes a probabilistic framework for gait modelling that is applied to gait recognition. The basic idea of this framework is to consider the silhouette shape as a multivariate random variable and model it in a full probabilistic framework. The Bernoulli mixture model is employed to model silhouette distribution and recursive algorithms are provided for silhouette image and sequence classification. Finally, the proposed probabilistic method is applied to benchmark databases and its validity is demonstrated through experiments.

关键词： PATTERN recognition systems BIOMETRIC identification SURVEILLANCE detection IMAGE analysis computer algorithms

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Fast error-tolerant quartet phylogeny algorithms

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THEORETICAL computer SCIENCE 2013年 483卷 104-114页

作者： Brown, Daniel G. Truszkowski, Jakub Univ Waterloo David R Cheriton Sch Comp Sci Waterloo ON N2L 3G1 Canada

We present a quartet-based phylogeny algorithm that returns the correct topology for n taxa in O(n log n) time with high probability, assuming that each quartet is inconsistent with the true tree topology with constant probability, independent of other quartets. Our incremental algorithm relies upon a search tree structure for the phylogeny that is balanced, with high probability, no matter the true topology. In experiments, our prototype was as fast as the fastest heuristics, but because real data do not typically satisfy our probabilistic assumptions, its overall performance is not as good as our theoretical results predict. (C) 2012 Elsevier B.V. All rights reserved.

关键词： DEBUGGING in computer science PHYLOGENY computer algorithms TOPOLOGY PROBABILITY theory DATA analysis

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Trust-aware peer sampling: Performance and privacy tradeoffs

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THEORETICAL computer SCIENCE 2013年 512卷 67-83页

作者： Frey, Davide Jegou, Arnaud Kermarrec, Anne-Marie Raynal, Michel Stainer, Julien INRIA Rennes Bretagne Atlantique Rennes France Univ Rennes IRISA F-35042 Rennes France Ecole Polytech Fed Lausanne Lausanne Switzerland

The ability to identify people that share one's own interests is one of the most interesting promises of the Web 2.0 driving user-centric applications such as recommendation systems or collaborative marketplaces. To be truly useful, however, information about other users also needs to be associated with some notion of trust. Consider a user wishing to sell a concert ticket. Not only must she find someone who is interested in the concert, but she must also make sure she can trust this person to pay for it. This paper addresses the need for trust in user-centric applications by proposing two novel distributed protocols that combine interest-based connections between users with explicit links obtained from social networks a-la Facebook. Both protocols build trusted multi-hop paths between users in an explicit social network supporting the creation of semantic overlays backed up by social trust. The first protocol, TAPS2, extends our previous work on TAPS (Trust-Aware Peer Sampling), by improving the ability to locate trusted nodes. Yet, it remains vulnerable to attackers wishing to learn about trust values between arbitrary pairs of users. The second protocol, PTAPS (Private TAPS), improves TAPS2 with provable privacy guarantees by preventing users from revealing their friendship links to users that are more than two hops away in the social network. In addition to proving this privacy property, we evaluate the performance of our protocols through event-based simulations, showing significant improvements over the state of the art. (C) 2013 Elsevier B.V. All rights reserved.

关键词： CONJOINT analysis (Marketing) APPLICATION software MARKETPLACES DISTRIBUTED network protocols computer networks INFORMATION theory computer algorithms

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Estimation of backlog and delay in OFDM/TDMA systems with traffic policing using Network Calculus

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computerS & ELECTRICAL ENGINEERING 2013年第8期39卷 2507-2520页

作者： Vieira, F. H. T. Santos, J. A., Jr. Cardoso, A. A. Fed Univ Goias UFG Sch Elect Mech & Comp Engn EMC Goiania Go Brazil

Achieving quality of service (QoS) in OFDM based networks depends, among other factors, on mechanisms for traffic policing or control. Aggregate traffic in high speed networks can present multifractal characteristics such as bursts over a wide range of time scales, heavy tailed inter-arrival time densities, self-similarity and long-range dependence. These properties are followed by a degradation of quality of service for the traffic flows. In this paper, we firstly propose a policing algorithm based on multifractal traffic modeling, evaluating its performance in comparison to other algorithms. We present a more precise in general envelope modeling process in order to efficiently police the input traffic to the system. Further, we present an approach based on Network Calculus for estimating quality of service parameters, such as mean queue length (backlog) and delay. We analyze these two parameters for an OFDM/TDMA based simplified WiMAX system with and without the application of traffic modeling based policing algorithms. In other words, we propose an approach for evaluating some QoS parameters of an OFDM/TDMA system where the traffic is policed. We also evaluate the performance of the proposed algorithm in policing the traffic in an OFDM/TDMA system. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： ORTHOGONAL frequency division multiplexing TIME division multiple access QUALITY of service IEEE 802.11 (Standard) computer algorithms ESTIMATION theory TRAFFIC police

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A Self-Organized Neural Comparator

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NEURAL COMPUTATION 2013年第4期25卷 1006-1028页

作者： Luduena, Guillermo A. Gros, Claudius Goethe Univ Frankfurt Inst Theoret Phys D-60438 Frankfurt Hessen Germany

Learning algorithms need generally the ability to compare several streams of information. Neural learning architectures hence need a unit, a comparator, able to compare several inputs encoding either internal or external information, for instance, predictions and sensory readings. Without the possibility of comparing the values of predictions to actual sensory inputs, reward evaluation and supervised learning would not be possible. Comparators are usually not implemented explicitly. Necessary comparisons are commonly performed by directly comparing the respective activities one-to-one. This implies that the characteristics of the two input streams (like size and encoding) must be provided at the time of designing the system. It is, however, plausible that biological comparators emerge from self-organizing, genetically encoded principles, which allow the system to adapt to the changes in the input and the organism. We propose an unsupervised neural circuitry, where the function of input comparison emerges via self-organization only from the interaction of the system with the respective inputs, without external influence or supervision. The proposed neural comparator adapts in an unsupervised form according to the correlations present in the input streams. The system consists of a multilayer feedforward neural network, which follows a local output minimization (anti-Hebbian) rule for adaptation of the synaptic weights. The local output minimization allows the circuit to autonomously acquire the capability of comparing the neural activities received from different neural populations, which may differ in population size and the neural encoding used. The comparator is able to compare objects never encountered before in the sensory input streams and evaluate a measure of their similarity even when differently encoded.

关键词： COMPARATOR circuits NEURAL networks (computer science) computer algorithms MACHINE learning COMPARATIVE studies PREDICTION theory NEURAL circuitry

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Representing Objects, Relations, and Sequences

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NEURAL COMPUTATION 2013年第8期25卷 2038-2078页

作者： Gallant, Stephen I. Okaywe, T. Wendy Pitney Bowes & MultiModel Res Cambridge MA 02138 USA Multimodel Res Cambridge MA 02138 USA

Vector symbolic architectures (VSAs) are high-dimensional vector representations of objects (e.g., words, image parts), relations (e.g., sentence structures), and sequences for use with machine learning algorithms. They consist of a vector addition operator for representing a collection of unordered objects, a binding operator for associating groups of objects, and a methodology for encoding complex structures. We first develop constraints that machine learning imposes on VSAs;for example, similar structures must be represented by similar vectors. The constraints suggest that current VSAs should represent phrases ("The smart Brazilian girl") by binding sums of terms, in addition to simply binding the terms directly. We show that matrix multiplication can be used as the binding operator for a VSA, and that matrix elements can be chosen at random. A consequence for living systems is that binding is mathematically possible without the need to specify, in advance, precise neuron-to-neuron connection properties for large numbers of synapses. A VSA that incorporates these ideas, Matrix Binding of Additive Terms (MBAT), is described that satisfies all constraints. With respect to machine learning, for some types of problems appropriate VSA representations permit us to prove learnability rather than relying on simulations. We also propose dividing machine (and neural) learning and representation into three stages, with differing roles for learning in each stage. For neural modeling, we give representational reasons for nervous systems to have many recurrent connections, as well as for the importance of phrases in language processing. Sizing simulations and analyses suggest that VSAs in general, and MBAT in particular, are ready for real-world applications.

关键词： SEQUENCES (Mathematics) MACHINE learning computer algorithms VECTOR analysis OPERATOR theory MATHEMATICAL analysis

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Space lower bounds for online pattern matching

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THEORETICAL computer SCIENCE 2013年 483卷 68-74页

作者： Clifford, Raphael Jalsenius, Markus Porat, Ely Sach, Benjamin Univ Bristol Dept Comp Sci Bristol Avon England Bar Ilan Univ Dept Comp Sci Ramat Gan Israel Univ Warwick Dept Comp Sci Coventry CV4 7AL W Midlands England

We present space lower bounds for online pattern matching under a number of different distance measures. Given a pattern of length m and a text that arrives one character at a time, the online pattern matching problem is to report the distance between the pattern and a sliding window of the text as soon as the new character arrives. We require that the correct answer is given at each position with constant probability. We give Omega(m) bit space lower bounds for L-1, L-2, L-infinity, Hamming, edit and swap distances as well as for any algorithm that computes the cross-correlation/convolution. We then show a dichotomy between distance functions that have wildcard-like properties and those that do not. In the former case which includes, as an example, pattern matching with character classes, we give Omega(m) bit space lower bounds. For other distance functions, we show that there exist space bounds of Omega (log m) and O(log(2) m) bits. Finally we discuss space lower bounds for non-binary inputs and show how in some cases they can be improved. (C) 2012 Elsevier B.V. All rights reserved.

关键词： TEXT files PROBABILITY theory computer algorithms CROSS correlation (Mathematics) BOUNDS (Mathematics)

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Simple real-time constant-space string matching

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THEORETICAL computer SCIENCE 2013年 483卷 2-9页

作者： Breslauer, Dany Grossi, Roberto Mignosi, Filippo Univ Haifa Caesarea Rothschild Inst Interdisciplinary Applic IL-31999 Haifa Israel Univ Pisa Dipartimento Informat Pisa Italy Univ Aquila Dipartimento Informat I-67100 Laquila Italy Univ Palermo I-90133 Palermo Italy

String matching is the classical problem of finding all occurrences of a pattern in a text. A real-time string matching algorithm takes worst-case constant-time to check if a pattern occurrence ends at each text location. We derive a real-time variation of the elegant Crochemore-Perrin constant-space string matching algorithm that has a simple and efficient control structure. We use observations about the locations of critical factorizations to deploy two tightly-coupled simplified real-time instances of the Crochemore-Perrin algorithm that search for complementary parts of the pattern whose simultaneous occurrence indicates an occurrence of the complete pattern. (C) 2012 Elsevier B.V. All rights reserved.

关键词： REAL-time computing computer algorithms TEXT processing (computer science) FACTORIZATION (Mathematics) computer simulation computer systems

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Adaptive Dynamic Programming for Control: algorithms and Stability 1

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丛书名： Communications and Control Engineering

2013年

作者： Huaguang Zhang, Derong Liu, Yanhong Luo, Ding Wang (auth.)

ISBN: (数字)9781447147572

ISBN: (纸本)9781447147565;9781447147572

There are many methods of stable controller design for nonlinear systems. In seeking to go beyond the minimum requirement of stability, Adaptive Dynamic Programming in Discrete Time approaches the challenging topic of optimal control for nonlinear systems using the tools of adaptive dynamic programming (ADP). The range of systems treated is extensive; affine, switched, singularly perturbed and time-delay nonlinear systems are discussed as are the uses of neural networks and techniques of value and policy iteration. The text features three main aspects of ADP in which the methods proposed for stabilization and for tracking and games benefit from the incorporation of optimal control methods: infinite-horizon control for which the difficulty of solving partial differential HamiltonJacobiBellman equations directly is overcome, and proof provided that the iterative value function updating sequence converges to the infimum of all the value functions obtained by admissible control law sequences; finite-horizon control, implemented in discrete-time nonlinear systems showing the reader how to obtain suboptimal control solutions within a fixed number of control steps and with results more easily applied in real systems than those usually gained from infinite-horizon control; nonlinear games for which a pair of mixed optimal policies are derived for solving games both when the saddle point does not exist, and, when it does, avoiding the existence conditions of the saddle point. Non-zero-sum games are studied in the context of a single network scheme in which policies are obtained guaranteeing system stability and minimizing the individual performance function yielding a Nash equilibrium. In order to make the coverage suitable for the student as well as for the expert reader, Adaptive Dynamic Programming in Discrete Time: establishes the fundamental theory involved clearly with each chapter devoted to a clearly identifiable control paradigm; demonstrates convergence proofs of t

关键词： Dynamic programming. Adaptive control systems. computer algorithms

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