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

From the Publisher:
This is the first comprehensive treatment of feed-forward neural networks from the perspective of statistical pattern recognition. After introducing the basic concepts, the book examines techniques for modelling probability density functions and the properties and merits of the multi-layer perceptron and radial basis function network models. Also covered are various forms of error functions, principal algorithms for error function minimalization, learning and generalization in neural networks, and Bayesian techniques and their applications. Designed as a text, with over 100 exercises, this fully up-to-date work will benefit anyone involved in the fields of neural computation and pattern recognition.

/pdf/neural-networks-for-pattern-recognition-34puigiau1.pdf

Neural networks for pattern recognition

https://ai.stanford.edu/~ronnyk/wrappersPrint.pdf

Wrappers for feature subset selection

The primary goal of pattern recognition is supervised or unsupervised classification. Among the various frameworks in which pattern recognition has been traditionally formulated, the statistical approach has been most intensively studied and used in practice. More recently, neural network techniques and methods imported from statistical learning theory have been receiving increasing attention. The design of a recognition system requires careful attention to the following issues: definition of pattern classes, sensing environment, pattern representation, feature extraction and selection, cluster analysis, classifier design and learning, selection of training and test samples, and performance evaluation. In spite of almost 50 years of research and development in this field, the general problem of recognizing complex patterns with arbitrary orientation, location, and scale remains unsolved. New and emerging applications, such as data mining, web searching, retrieval of multimedia data, face recognition, and cursive handwriting recognition, require robust and efficient pattern recognition techniques. The objective of this review paper is to summarize and compare some of the well-known methods used in various stages of a pattern recognition system and identify research topics and applications which are at the forefront of this exciting and challenging field.

/pdf/statistical-pattern-recognition-a-review-1kz1b0tte4.pdf

Statistical pattern recognition: a review

From the Publisher:
Pattern recognition has long been studied in relation to many different (and mainly unrelated) applications, such as remote sensing, computer vision, space research, and medical imaging. In this book Professor Ripley brings together two crucial ideas in pattern recognition; statistical methods and machine learning via neural networks. Unifying principles are brought to the fore, and the author gives an overview of the state of the subject. Many examples are included to illustrate real problems in pattern recognition and how to overcome them.This is a self-contained account, ideal both as an introduction for non-specialists readers, and also as a handbook for the more expert reader.

Pattern recognition and neural networks

: This paper presents a general theoretical framework for ensemble methods of constructing significantly improved regression estimates. Given a population of regression estimators, the authors construct a hybrid estimator that is as good or better in the mean square error sense than any estimator in the population. They argue that the ensemble method presented has several properties: (1) it efficiently uses all the networks of a population -- none of the networks need to be discarded; (2) it efficiently uses all of the available data for training without over-fitting; (3) it inherently performs regularization by smoothing in functional space, which helps to avoid over-fitting; (4) it utilizes local minima to construct improved estimates whereas other neural network algorithms are hindered by local minima; (5) it is ideally suited for parallel computation; (6) it leads to a very useful and natural measure of the number of distinct estimators in a population; and (7) the optimal parameters of the ensemble estimator are given in closed form. Experimental results show that the ensemble method dramatically improves neural network performance on difficult real-world optical character recognition tasks.

/pdf/when-networks-disagree-ensemble-methods-for-hybrid-neural-2zhi0m1pfg.pdf

When Networks Disagree: Ensemble Methods for Hybrid Neural Networks

Multicore designs promise various power-performance and area-performance benefits. But inadequate design of the on-chip communication network can deprive applications of these benefits. To illuminate this important point in multicore processor design, the authors analyze the cell processor's communication network, using a series of benchmarks involving various DMA traffic patterns and synchronization protocols

Cell Multiprocessor Communication Network: Built for Speed

A general theoretical framework for Monte Carlo averaging methods of improving regression estimates is presented with application to neural network classification and time series prediction Given a population of regression estimators, it is shown how to construct a hybrid estimator which is as good as or better than, in the MSE sense, any estimator in the population
It is argued that the ensemble method presented has several properties: It efficiently uses all the regressors of a population--none need be discarded It efficiently uses all the available data for training without over-fitting It inherently performs regularization by smoothing in functional space which helps to avoid over-fitting It utilizes local minima to construct improved estimates whereas other regression algorithms are hindered by local minima It is ideally suited for parallel computation It leads to a very useful and natural measure of the number of distinct estimators in a population The optimal parameters of the ensemble estimator are given in closed form
It is shown that this result derives from the notion of convexity and can be applied to a wide variety of optimization algorithms including: Mean Square Error, a general class of $L\sb{p}$-norm cost functions, Maximum Likelihood Estimation, Maximum Entropy, Maximum Mutual Information, the Kullback-Leibler Information (Cross Entropy), Penalized Maximum Likelihood Estimation and Smoothing Splines
The connection to Bayesian Inference is discussed
Experimental results on the NIST OCR database, the Turk and Pentland human face database and sunspot time series prediction are presented which demonstrate that the ensemble method dramatically improves regression performance on real-world classification tasks

Improving regression estimation: Averaging methods for variance reduction with extensions to general convex measure optimization

The Cell Broadband Engine (BE) processor provides the potential to achieve an impressive level of performance for scientific applications. This level of performance can be reached by exploiting several dimensions of parallelism, such as thread-level parallelism using several synergistic processing elements, data streaming parallelism, vector parallelism in the form of 128-bit SIMD operations, and pipeline parallelism by issuing multiple instructions in the same clock cycle. In our exploration to achieve the optimum level of performance for Sweep3D, we have enjoyed many pleasant surprises, such as a very high floating point performance, reaching 64% of the theoretical peak in double precision, and an over all performance speedup ranging from 4.5 times when compared with "heavy iron" processors, up to over 20 times with conventional processors.

/pdf/multicore-surprises-lessons-learned-from-optimizing-sweep3d-9davg11o2j.pdf

Multicore Surprises: Lessons Learned from Optimizing Sweep3D on the Cell Broadband Engine

In order to improve the readability and the automatic recognition of handwritten document images, preprocessing steps are imperative. These steps in addition to conventional steps of noise removal and filtering include text normalization such as baseline correction, slant normalization and skew correction. These steps make the feature extraction process more reliable and effective. Recently Arabic handwriting recognition has received some attention from the research community. Due to the unique nature of the script, the conventional methods do not prove to be effective. In our work, we describe an orientation independent technique for baseline detection of Arabic words. In addition to that we describe, in the rest of the paper, our techniques for slant normalization, slope correction, line and word separation in handwritten Arabic documents. We show how the baseline can be exploited for slope and skew correction before proceeding with the steps of line and word separation.

Michael P. Perrone

Papers

When Networks Disagree: Ensemble Methods for Hybrid Neural Networks

Cell Multiprocessor Communication Network: Built for Speed

Improving regression estimation: Averaging methods for variance reduction with extensions to general convex measure optimization

Multicore Surprises: Lessons Learned from Optimizing Sweep3D on the Cell Broadband Engine

Pre-processing methods for handwritten Arabic documents