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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

A survey on deep learning in medical image analysis

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

\emph{Over-fitting} and \emph{over-smoothing} are two main obstacles of developing deep Graph Convolutional Networks (GCNs) for node classification. In particular, over-fitting weakens the generalization ability on small dataset, while over-smoothing impedes model training by isolating output representations from the input features with the increase in network depth. This paper proposes DropEdge, a novel and flexible technique to alleviate both issues. At its core, DropEdge randomly removes a certain number of edges from the input graph at each training epoch, acting like a data augmenter and also a message passing reducer. Furthermore, we theoretically demonstrate that DropEdge either reduces the convergence speed of over-smoothing or relieves the information loss caused by it. More importantly, our DropEdge is a general skill that can be equipped with many other backbone models (e.g. GCN, ResGCN, GraphSAGE, and JKNet) for enhanced performance. Extensive experiments on several benchmarks verify that DropEdge consistently improves the performance on a variety of both shallow and deep GCNs. The effect of DropEdge on preventing over-smoothing is empirically visualized and validated as well. Codes are released on~\url{this https URL}.

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification.

This paper develops a theory for group Lasso using a concept called strong group sparsity. Our result shows that group Lasso is superior to standard Lasso for strongly group-sparse signals. This provides a convincing theoretical justification for using group sparse regularization when the underlying group structure is consistent with the data. Moreover, the theory predicts some limitations of the group Lasso formulation that are confirmed by simulation studies.

/pdf/the-benefit-of-group-sparsity-43rxrb0q00.pdf

The Benefit of Group Sparsity

Online learned tracking is widely used for it's adaptive ability to handle appearance changes. However, it introduces potential drifting problems due to the accumulation of errors during the self-updating, especially for occluded scenarios. The recent literature demonstrates that appropriate combinations of trackers can help balance stability and flexibility requirements. We have developed a robust tracking algorithm using a local sparse appearance model (SPT). A static sparse dictionary and a dynamically online updated basis distribution model the target appearance. A novel sparse representation-based voting map and sparse constraint regularized mean-shift support the robust object tracking. Besides these contributions, we also introduce a new dictionary learning algorithm with a locally constrained sparse representation, called K-Selection. Based on a set of comprehensive experiments, our algorithm has demonstrated better performance than alternatives reported in the recent literature.

Robust tracking using local sparse appearance model and K-selection

Most state-of-the-art action localization systems process each action proposal individually, without explicitly exploiting their relations during learning. However, the relations between proposals actually play an important role in action localization, since a meaningful action always consists of multiple proposals in a video. In this paper, we propose to exploit the proposal-proposal relations using GraphConvolutional Networks (GCNs). First, we construct an action proposal graph, where each proposal is represented as a node and their relations between two proposals as an edge. Here, we use two types of relations, one for capturing the context information for each proposal and the other one for characterizing the correlations between distinct actions. Then we apply the GCNs over the graph to model the relations among different proposals and learn powerful representations for the action classification and localization. Experimental results show that our approach significantly outperforms the state-of-the-art on THUMOS14(49.1% versus 42.8%). Moreover, augmentation experiments on ActivityNet also verify the efficacy of modeling action proposal relationships.

/pdf/graph-convolutional-networks-for-temporal-action-4g93tuammc.pdf

Graph Convolutional Networks for Temporal Action Localization

This paper investigates a new learning formulation called structured sparsity, which is a natural extension of the standard sparsity concept in statistical learning and compressive sensing. By allowing arbitrary structures on the feature set, this concept generalizes the group sparsity idea that has become popular in recent years. A general theory is developed for learning with structured sparsity, based on the notion of coding complexity associated with the structure. It is shown that if the coding complexity of the target signal is small, then one can achieve improved performance by using coding complexity regularization methods, which generalize the standard sparse regularization. Moreover, a structured greedy algorithm is proposed to efficiently solve the structured sparsity problem. It is shown that the greedy algorithm approximately solves the coding complexity optimization problem under appropriate conditions. Experiments are included to demonstrate the advantage of structured sparsity over standard sparsity on some real applications.

Junzhou Huang

Papers

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification.

The Benefit of Group Sparsity

Robust tracking using local sparse appearance model and K-selection

Graph Convolutional Networks for Temporal Action Localization

Learning with Structured Sparsity