Clustering gene expression data analysis using an improved EM algorithm based on multivariate elliptical contoured mixture models

Clustering gene expression data is an important research topic in bioinformatics because knowing which genes act similarly can lead to the discovery of important biological information. Many clustering algorithms have been used in the field of gene clustering. The multivariate Gaussian mixture distribution function was frequently used as the component of the finite mixture model for clustering, however the clustering cannot be restricted to the normal distribution in the real dataset. In order to make the cluster algorithm strong adaptability, this paper proposes a new scheme for clustering gene expression data based on the multivariate elliptical contoured mixture models (MECMMs). To solve the problem of over-reliance on the initialization, we propose an improved expectation maximization (EM) algorithm by adding and deleting initial value for the classical EM algorithm, and the number of clusters can be treated as a known parameter and inferred with the QAIC criterion. The improved EM algorithm based on the MECMMs is tested and compared with some other clustering algorithms, the performance of our clustering algorithm has been extensively compared over several simulated and real gene expression datasets. Our results indicated that improved EM clustering algorithm is superior to the classical EM algorithm and the support vector machines (SVMs) algorithm, and can be widely used for gene clustering.     

Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs(BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics(MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

Personalized PageRank Clustering: A graph clustering algorithm based on random walks

Graph clustering has been an essential part in many methods and thus its accuracy has a significant effect on many applications. In addition, exponential growth of real-world graphs such as social networks, biological networks and electrical circuits demands clustering algorithms with nearly-linear time and space complexity. In this paper we propose Personalized PageRank Clustering (PPC) that employs the inherent cluster exploratory property of random walks to reveal the clusters of a given graph. We combine random walks and modularity to precisely and efficiently reveal the clusters of a graph. PPC is a top-down algorithm so it can reveal inherent clusters of a graph more accurately than other nearly-linear approaches that are mainly bottom-up. It also gives a hierarchy of clusters that is useful in many applications. PPC has a linear time and space complexity and has been superior to most of the available clustering algorithms on many datasets. Furthermore, its top-down approach makes it a flexible solution for clustering problems with different requirements.     

Verification of the inverted temperature gradient condition via molecular dynamics simulation

We perform molecular dynamics simulations to verify the critical condition for the existence of an inverted temperature profile in the vapor between two liquid slabs at slightly different temperatures. Reasonable agreement is found between the kinetic theory based condition and simulations. The deviation from theory can be explained by deviation from ideal gas behavior on which the kinetic condition is based and by deviation in the MD from diffuse boundary conditions, which are used in deriving the kinetic condition.     

Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins

Functional modules can be predicted using genome-wide protein–protein interactions (PPIs) from a systematic perspective. Various graph clustering algorithms have been applied to PPI networks for this task. In particular, the detection of overlapping clusters is necessary because a protein is involved in multiple functions under different conditions. graph entropy (GE) is a novel metric to assess the quality of clusters in a large, complex network. In this study, the unweighted and weighted GE algorithm is evaluated to prove the validity of predicting function modules. To measure clustering accuracy, the clustering results are compared to protein complexes and Gene Ontology (GO) annotations as references. We demonstrate that the GE algorithm is more accurate in overlapping clusters than the other competitive methods. Moreover, we confirm the biological feasibility of the proteins that occur most frequently in the set of identified clusters. Finally, novel proteins for the additional annotation of GO terms are revealed.     

导热系数的分子动力学模拟研究及相关问题的探讨

对于采用分子动力学方法研究导热系数的背景、研究现状及存在的问题进行了综述和分析。总结了通过分子动力学模拟方法求得导热系数的物理模型和基本算法。讨论了目前在微尺度导热问题的研究中引入分子动力学模拟方法需要考察的影响因素和几个重要问题。     

Performance Analysis and Architecture of a Clustering Hybrid Algorithm Called FA+GA-DBSCAN Using Artificial Datasets

Density-Based Spatial Clustering of Applications with Noise (DBSCAN) is a widely used algorithm for exploratory clustering applications. Despite the DBSCAN algorithm being considered an unsupervised pattern recognition method, it has two parameters that must be tuned prior to the clustering process in order to reduce uncertainties, the minimum number of points in a clustering segmentation MinPts, and the radii around selected points from a specific dataset Eps. This article presents the performance of a clustering hybrid algorithm for automatically grouping datasets into a two-dimensional space using the well-known algorithm DBSCAN. Here, the function nearest neighbor and a genetic algorithm were used for the automation of parameters MinPts and Eps. Furthermore, the Factor Analysis (FA) method was defined for pre-processing through a dimensionality reduction of high-dimensional datasets with dimensions greater than two. Finally, the performance of the clustering algorithm called FA+GA-DBSCAN was evaluated using artificial datasets. In addition, the precision and Entropy of the clustering hybrid algorithm were measured, which showed there was less probability of error in clustering the most condensed datasets.     

The sputtering properties of artificial polymorphic AB binary compound crystals

Molecular dynamics (MD) simulations of the sputtering of artificial 1:1 binary compound targets, AB, are reported. The simulations explore the sensitivity of monomer and dimer sputter yields to AB target structure and interatomic potentials. The targets have the sphalerite, wurtzite and sodium chloride lattice structures, and their atomic and material properties resemble those of ZnS polymorphs. Two different sets of interatomic potentials were used for the simulations. In the symmetric model, all bonding interactions are equivalent, while in the asymmetric model, the A-B interactions are strengthened at the expense of the A-A and B-B interactions. Both models predict similar material properties for a given target. No systematic variations of sputter yields for individual targets can be discerned between the predictions based on the symmetric and asymmetric interaction models. The relative sputter yields of monomer species A and B are independent of target structure when the A and B atoms occupy surface sites of equivalent symmetry. The relative yields of the AA and BB dimer species are similarly insensitive to the target structure, but target-dependent variations of the relative yields of AB dimers are observed. Sputtering properties other than relative yields (e.g. clustering range, depth of origin) do show structure-dependent variations. In agreement with previous MD studies of sputtering from metals, the nearest-neighbour contribution to AB clusters is found to be typically ∼50%, and may be as low as 30%.