Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Clustering is the division of data into groups of similar objects. In clustering, some details are disregarded in exchange for data simplification. Clustering can be viewed as a data modeling technique that provides for concise summaries of the data. Clustering is therefore related to many disciplines and plays an important role in a broad range of applications. The applications of clustering usually deal with large datasets and data with many attributes. Exploration of such data is a subject of data mining. This survey concentrates on clustering algorithms from a data mining perspective.

A Survey of Clustering Data Mining Techniques

In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes contain a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with Shared Information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different level of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems. This special issue aims at gathering the recent advances in learning with shared information methods and their applications in computer vision and multimedia analysis. Both state-of-the-art works, as well as literature reviews, are welcome for submission. Papers addressing interesting real-world computer vision and multimedia applications are especially encouraged. Topics of interest include, but are not limited to:  • Multi-task learning or transfer learning for large-scale computer vision and multimedia analysis • Deep learning for large-scale computer vision and multimedia analysis • Multi-modal approach for large-scale computer vision and multimedia analysis • Different sharing strategies, e.g., sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, • Real-world computer vision and multimedia applications based on learning with shared information, e.g., event detection, object recognition, object detection, action recognition, human head pose estimation, object tracking, location-based services, semantic indexing. • New datasets and metrics to evaluate the benefit of the proposed sharing ability for the specific computer vision or multimedia problem. • Survey papers regarding the topic of learning with shared information.  Authors who are unsure whether their planned submission is in scope may contact the guest editors prior to the submission deadline with an abstract, in order to receive feedback.

IEEE transactions on pattern analysis and machine intelligence

Matrix Differential Calculus with Applications in Statistics and Econometrics

Latent variable models represent the probability density of data in a space of several dimensions in terms of a smaller number of latent, or hidden, variables. A familiar example is factor analysis which is based on a linear transformations between the latent space and the data space. In this paper we introduce a form of non-linear latent variable model called the Generative Topographic Mapping, for which the parameters of the model can be determined using the EM algorithm. GTM provides a principled alternative to the widely used Self-Organizing Map (SOM) of Kohonen (1982), and overcomes most of the significant limitations of the SOM. We demonstrate the performance of the GTM algorithm on a toy problem and on simulated data from flow diagnostics for a multi-phase oil pipeline.

/pdf/gtm-the-generative-topographic-mapping-1ccaqggbwx.pdf

GTM: the generative topographic mapping

http://psystems.disco.unimib.it/download/snpasyP.pdf

Asynchronous spiking neural P systems

The increasing popularity of social networks has initiated a fertile research area in information extraction and data mining. Although such analysis can facilitate better understanding of sociological, behavioral, and other interesting phenomena, there is a growing concern about personal privacy being breached, thereby requiring effective anonymization techniques. In this paper, we consider edge weight anonymization in social graphs. Our approach builds a linear programming (LP) model which preserves properties of the graph that are expressible as linear functions of the edge weights. Such properties form the foundations of many important graph-theoretic algorithms such as shortest paths, k-nearest neighbors, minimum spanning tree, etc. Off-the-shelf LP solvers can then be used to find solutions to the resulting model where the computed solution constitutes the weights in the anonymized graph. As a proof of concept, we choose the shortest paths problem, and experimentally evaluate the proposed techniques using real social network data sets.

/pdf/anonymizing-weighted-social-network-graphs-2onyeihz93.pdf

Anonymizing weighted social network graphs

The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach was designed to reveal the highly conserved fragments by discarding poorly conserved initial and terminal segments. However, the existing notion of local similarity has a serious flaw: it does not discard poorly conserved intermediate segments. The Smith-Waterman algorithm finds the local alignment with maximal score but it is unable to find local alignment with maximum degree of similarity (e.g. maximal percent of matches). Moreover, there is still no efficient algorithm that answers the following natural question: do two sequences share a (sufficiently long) fragment with more than 70% of similarity? As a result, the local alignment sometimes produces a mosaic of well-conserved fragments artificially connected by poorly-conserved or even unrelated fragments. This may lead to problems in comparison of long genomic sequences and comparative gene prediction as recently pointed out by Zhang et al. (Bioinformatics, 15, 1012-1019, 1999). In this paper we propose a new sequence comparison algorithm (normalized local alignment ) that reports the regions with maximum degree of similarity. The algorithm is based on fractional programming and its running time is O(n2log n). In practice, normalized local alignment is only 3-5 times slower than the standard Smith-Waterman algorithm.

A new approach to sequence comparison: normalized sequence alignment.

The minimum-energy broadcasting problem in wireless networks consists of finding a transmission radius vector for all stations in such a way that the total transmission power of the whole network is least possible. The minimum-energy broadcast problem may by modeled by an edge weighted complete graph in which each vertex in the graph represents a station and the weight of the edge is distance between the two nodes it joins. This is the weighted graph version of the minimum-energy broadcast problem. Wan, Calinescu, Li and Frieder showed that for arbitrary weights, this problem is NP-hard, and also hard to approximate. In this paper we show that the weighted graph minimum-energy broadcast problem is NP-hard in metric space when transmissions are restricted to a given set of power levels by means of an upper bound d on the allowed transmission radius. This restriction is justified because it is unrealistic to expect transmissions with unbounded power which may be needed in an optimal solution for large diameter networks. We also show that our problem can be solved in polynomial time when there is an optimal solution with a fixed number of transmitter nodes.

Minimum-energy Broadcast in Simple Graphs with Limited Node Power

This paper addresses the problem of efficient maintenance of a materialized skyline view in response to skyline removals. While there has been significant progress on skyline query computation, an equally important but largely unanswered issue is on the incremental maintenance for skyline deletions. Previous work suggested the use of the so called exclusive dominance region (EDR) to achieve optimal I/O performance for deletion maintenance. However, the shape of an EDR becomes extremely complex in higher dimensions, and algorithms for its computation have not been developed. We derive a systematic way to decompose a d-dimensional EDR into a collection of hyper-rectangles. We show that the number of such hyper-rectangles is O(md), where m is the current skyline result size. We then propose a novel algorithm DeltaSky which determines whether an intermediate R-tree MBR intersects with the EDR without explicitly calculating the EDR itself. This reduces the worse case complexity of the EDR intersection check from O(md) to O(md). Thus DeltaSky helps the branch and bound skyline algorithm achieve I/O optimality for deletion maintenance by finding only the newly appeared skyline points after the deletion. We discuss implementation issues and show that DeltaSky can be efficiently implemented using one extra B-Tree. Moreover, we propose two optimization techniques which further reduce the average cost in practice. Extensive experiments demonstrate that DeltaSky achieves orders of magnitude performance gain over alternative solutions.

Ömer Eğecioğlu

Papers

Asynchronous spiking neural P systems

Anonymizing weighted social network graphs

A new approach to sequence comparison: normalized sequence alignment.

Minimum-energy Broadcast in Simple Graphs with Limited Node Power

DeltaSky: Optimal Maintenance of Skyline Deletions without Exclusive Dominance Region Generation