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Evidence accumulation clustering using combinations of features.

ABSTRACT: Evidence accumulation clustering (EAC) is an ensemble clustering algorithm that can cluster data for arbitrary shapes and numbers of clusters. Here, we present a variant of EAC in which we aimed to better cluster data with a large number of features, many of which may be uninformative. Our new method builds on the existing EAC algorithm by populating the clustering ensemble with clusterings based on combinations of fewer features than the original dataset at a time. Our method also calls for prewhitening the recombined data and weighting the influence of each individual clustering by an estimate of its informativeness. We provide code of an example implementation of the algorithm in Matlab and demonstrate its effectiveness compared to ordinary evidence accumulation clustering with synthetic data.•The clustering ensemble is made by clustering on subset combinations of features from the data•The recombined data may be prewhitened•Evidence accumulation can be improved by weighting the evidence with a goodness-of-clustering measure.

SUBMITTER: Wong W

PROVIDER: S-EPMC7251952 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Evidence accumulation clustering using combinations of features.

Wong William W Tsuchiya Naotsugu N

MethodsX 20200514

Evidence accumulation clustering (EAC) is an ensemble clustering algorithm that can cluster data for arbitrary shapes and numbers of clusters. Here, we present a variant of EAC in which we aimed to better cluster data with a large number of features, many of which may be uninformative. Our new method builds on the existing EAC algorithm by populating the clustering ensemble with clusterings based on combinations of fewer features than the original dataset at a time. Our method also calls for pre ...[more]

PMID: 32477894

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Project description:Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill biologically relevant information from MD trajectories, especially for docking purposes.

Dataset Information

Evidence accumulation clustering using combinations of features.

Publications

Evidence accumulation clustering using combinations of features.

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