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

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

A comprehensive and self-contained introduction to Gaussian processes, which provide a principled, practical, probabilistic approach to learning in kernel machines. Gaussian processes (GPs) provide a principled, practical, probabilistic approach to learning in kernel machines. GPs have received increased attention in the machine-learning community over the past decade, and this book provides a long-needed systematic and unified treatment of theoretical and practical aspects of GPs in machine learning. The treatment is comprehensive and self-contained, targeted at researchers and students in machine learning and applied statistics. The book deals with the supervised-learning problem for both regression and classification, and includes detailed algorithms. A wide variety of covariance (kernel) functions are presented and their properties discussed. Model selection is discussed both from a Bayesian and a classical perspective. Many connections to other well-known techniques from machine learning and statistics are discussed, including support-vector machines, neural networks, splines, regularization networks, relevance vector machines and others. Theoretical issues including learning curves and the PAC-Bayesian framework are treated, and several approximation methods for learning with large datasets are discussed. The book contains illustrative examples and exercises, and code and datasets are available on the Web. Appendixes provide mathematical background and a discussion of Gaussian Markov processes.

/pdf/gaussian-processes-for-machine-learning-40fp9c190d.pdf

Gaussian Processes for Machine Learning

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Organizing data into sensible groupings is one of the most fundamental modes of understanding and learning. As an example, a common scheme of scientific classification puts organisms into a system of ranked taxa: domain, kingdom, phylum, class, etc. Cluster analysis is the formal study of methods and algorithms for grouping, or clustering, objects according to measured or perceived intrinsic characteristics or similarity. Cluster analysis does not use category labels that tag objects with prior identifiers, i.e., class labels. The absence of category information distinguishes data clustering (unsupervised learning) from classification or discriminant analysis (supervised learning). The aim of clustering is to find structure in data and is therefore exploratory in nature. Clustering has a long and rich history in a variety of scientific fields. One of the most popular and simple clustering algorithms, K-means, was first published in 1955. In spite of the fact that K-means was proposed over 50 years ago and thousands of clustering algorithms have been published since then, K-means is still widely used. This speaks to the difficulty in designing a general purpose clustering algorithm and the ill-posed problem of clustering. We provide a brief overview of clustering, summarize well known clustering methods, discuss the major challenges and key issues in designing clustering algorithms, and point out some of the emerging and useful research directions, including semi-supervised clustering, ensemble clustering, simultaneous feature selection during data clustering, and large scale data clustering.

Data clustering: 50 years beyond K-means

This paper provides an introduction to support vector machines, kernel Fisher discriminant analysis, and kernel principal component analysis, as examples for successful kernel-based learning methods. We first give a short background about Vapnik-Chervonenkis theory and kernel feature spaces and then proceed to kernel based learning in supervised and unsupervised scenarios including practical and algorithmic considerations. We illustrate the usefulness of kernel algorithms by discussing applications such as optical character recognition and DNA analysis.

/pdf/an-introduction-to-kernel-based-learning-algorithms-4blkbqa7z6.pdf

An introduction to kernel-based learning algorithms

A new kernel function between two labeled graphs is presented. Feature vectors are defined as the counts of label paths produced by random walks on graphs. The kernel computation finally boils down to obtaining the stationary state of a discrete-time linear system, thus is efficiently performed by solving simultaneous linear equations. Our kernel is based on an infinite dimensional feature space, so it is fundamentally different from other string or tree kernels based on dynamic programming. We will present promising empirical results in classification of chemical compounds.

/pdf/marginalized-kernels-between-labeled-graphs-1lfid2nyzm.pdf

Marginalized kernels between labeled graphs

Modern machine learning techniques are proving to be extremely valuable for the analysis of data in computational biology problems. One branch of machine learning, kernel methods, lends itself particularly well to the difficult aspects of biological data, which include high dimensionality (as in microarray measurements), representation as discrete and structured data (as in DNA or amino acid sequences), and the need to combine heterogeneous sources of information. This book provides a detailed overview of current research in kernel methods and their applications to computational biology.Following three introductory chapters -- an introduction to molecular and computational biology, a short review of kernel methods that focuses on intuitive concepts rather than technical details, and a detailed survey of recent applications of kernel methods in computational biology -- the book is divided into three sections that reflect three general trends in current research. The first part presents different ideas for the design of kernel functions specifically adapted to various biological data; the second part covers different approaches to learning from heterogeneous data; and the third part offers examples of successful applications of support vector machine methods.

/pdf/kernel-methods-in-computational-biology-22zq9ss87g.pdf

Kernel Methods in Computational Biology

Compounds of low lattice thermal conductivity (LTC) are essential for seeking thermoelectric materials with high conversion efficiency. Some strategies have been used to decrease LTC. However, such trials have yielded successes only within a limited exploration space. Here, we report the virtual screening of a library containing 54,779 compounds. Our strategy is to search the library through Bayesian optimization using for the initial data the LTC obtained from first-principles anharmonic lattice-dynamics calculations for a set of 101 compounds. We discovered 221 materials with very low LTC. Two of them even have an electronic band gap <1 eV, which makes them exceptional candidates for thermoelectric applications. In addition to those newly discovered thermoelectric materials, the present strategy is believed to be powerful for many other applications in which the chemistry of materials is required to be optimized.

/pdf/prediction-of-low-thermal-conductivity-compounds-with-first-4tfjma9ybe.pdf

Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization

/pdf/a-primer-on-kernel-methods-233d3gtfg2.pdf

Koji Tsuda

Papers

An introduction to kernel-based learning algorithms

Marginalized kernels between labeled graphs

Kernel Methods in Computational Biology

Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization

A Primer on Kernel Methods