Information-based clustering.
Ontology highlight
ABSTRACT:
SUBMITTER: Slonim N
PROVIDER: S-EPMC1317937 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The purposes are to evaluate the Distributed Clustering Algorithm (DCA) applicability in the power system's big data processing and find the information economic dispatch strategy suitable for new energy consumption in power systems. A two-layer DCA algorithm is proposed based on K-Means Clustering (KMC) and Affinity Propagation (AP) clustering algorithms. Then the incentive Demand Response (DR) is introduced, and the DR flexibility of the user side is analyzed. Finally, the day-ahead dispatch and real-time dispatch schemes are combined, and a multi-period information economic dispatch model is constructed. The algorithm performance is analyzed according to case analyses of new energy consumption. Results demonstrate that the two-layer DCA's calculation time is 5.23s only, the number of iterations is small, and the classification accuracy rate reaches 0.991. Case 2 corresponding to the proposed model can consume the new energy, and the income of the aggregator can be maximized. In short, the multi-period information economic dispatch model can consume the new energy and meet the DR of the user side.
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Project description:BackgroundTime-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. 1 proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data.ResultsWe propose a computationally efficient information criterion-based clustering algorithm, called ORICC, that also takes account of the ordering in time-course microarray experiments by embedding the order-restricted inference into a model selection framework. Genes are assigned to the profile which they best match determined by a newly proposed information criterion for order-restricted inference. In addition, we also developed a bootstrap procedure to assess ORICC's clustering reliability for every gene. Simulation studies show that the ORICC method is robust, always gives better clustering accuracy than Peddada's method and saves hundreds of times computational time. Under some scenarios, its accuracy is also better than some other existing clustering methods for short time-course microarray data, such as STEM 2 and Wang et al. 3. It is also computationally much faster than Wang et al. 3.ConclusionOur ORICC algorithm, which takes advantage of the temporal ordering in time-course microarray experiments, provides good clustering accuracy and is meanwhile much faster than Peddada's method. Moreover, the clustering reliability for each gene can also be assessed, which is unavailable in Peddada's method. In a real data example, the ORICC algorithm identifies new and interesting genes that previous analyses failed to reveal.
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Project description:BackgroundA pharmacophore model consists of a group of chemical features arranged in three-dimensional space that can be used to represent the biological activities of the described molecules. Clustering of molecular interactions of ligands on the basis of their pharmacophore similarity provides an approach for investigating how diverse ligands can bind to a specific receptor site or different receptor sites with similar or dissimilar binding affinities. However, efficient clustering of pharmacophore models in three-dimensional space is currently a challenge.ResultsWe have developed a pharmacophore-assisted Iterative Closest Point (ICP) method that is able to group pharmacophores in a manner relevant to their biochemical properties, such as binding specificity etc. The implementation of the method takes pharmacophore files as input and produces distance matrices. The method integrates both alignment-dependent and alignment-independent concepts.ConclusionsWe apply our three-dimensional pharmacophore clustering method to two sets of experimental data, including 31 globulin-binding steroids and 4 groups of selected antibody-antigen complexes. Results are translated from distance matrices to Newick format and visualised using dendrograms. For the steroid dataset, the resulting classification of ligands shows good correspondence with existing classifications. For the antigen-antibody datasets, the classification of antigens reflects both antigen type and binding antibody. Overall the method runs quickly and accurately for classifying the data based on their binding affinities or antigens.
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Project description:BACKGROUND: Genetic polymorphisms in the gene encoding the ?-adrenergic receptors (?-AR) have a pivotal role in the functions of the autonomic nervous system. Using heart rate variability (HRV) as an indicator of autonomic function, we present a bottom-up genotype-phenotype analysis to investigate the association between ?-AR gene polymorphisms and heart rate dynamics. METHODS: A total of 221 healthy Han Chinese adults (59 males and 162 females, aged 33.6 ± 10.8 years, range 19 to 63 years) were recruited and genotyped for three common ?-AR polymorphisms: ?(1)-AR Ser49Gly, ?(2)-AR Arg16Gly and ?(2)-AR Gln27Glu. Each subject underwent two hours of electrocardiogram monitoring at rest. We applied an information-based similarity (IBS) index to measure the pairwise dissimilarity of heart rate dynamics among study subjects. RESULTS: With the aid of agglomerative hierarchical cluster analysis, we categorized subjects into major clusters, which were found to have significantly different distributions of ?(2)-AR Arg16Gly genotype. Furthermore, the non-randomness index, a nonlinear HRV measure derived from the IBS method, was significantly lower in Arg16 homozygotes than in Gly16 carriers. The non-randomness index was negatively correlated with parasympathetic-related HRV variables and positively correlated with those HRV indices reflecting a sympathovagal shift toward sympathetic activity. CONCLUSIONS: We demonstrate a bottom-up categorization approach combining the IBS method and hierarchical cluster analysis to detect subgroups of subjects with HRV phenotypes associated with ?-AR polymorphisms. Our results provide evidence that ?(2)-AR polymorphisms are significantly associated with the acceleration/deceleration pattern of heart rate oscillation, reflecting the underlying mode of autonomic nervous system control.
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