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Biology subjects

Climer, S.

Publications and source records attributed to Climer, S..

2 recordsLinked to original sources

Clustering the Planet: An Exascale Approach to Determining Global Climatype Zones

We present an exascale approach for producing global scale, high resolution, longitudinally based geoclimate classifications. Using a GPU implementation of the DUO Similarity Metric on the Summit supercomputer, we calculated the pairwise environmental similarity of 156,384,190 vectors of 414,640 encoded elements derived from 71 environmental variables over a 50-year time span at 1km2 resolution. GPU matrix-matrix (GEMM) kernels were optimized for the GPU architecture and their outputs were managed through aggressive concurrent MPI rank CPU communication, calculations, and transfers. Using vector transformation and highly optimized operations of generalized distributed dense linear algebra, calculation of all-vector-pairs similarity resulted in 5.07 x 1021 element comparisons and reached a peak performance of 2.31 exaflops. We demonstrated this method using existing and synthesized climate layers to show how geography can be parsed using high-performance computing. Geoclimate zones are important tools for understanding how environmental variables impact natural systems, particularly for agriculture and conservation with relevance to climate change. Historically, classification systems have been low resolution, based on limited variables, or subjective. To identify climate classes, we clustered DUO outputs at varying stringency, producing 69, 133, 340, and 717 global geoclimate zones. Our approach produced global scale, high resolution, longitudinally informed climate classifications that can be used in precision agriculture, cultivar breeding efforts, and conservation programs.

bioinformatics↗

Synchronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis

It is becoming increasingly evident that the efficacy of single-gene computational analyses for complex traits is nearly exhausted and future advances hinge on unraveling the intricate combinatorial interactions among multiple genes. However, the discovery of modules of genes working in concert to manifest a complex trait has been crippled by combinatorial complexity, genetic heterogeneity, and validation biases. We introduce Maestro, a novel network approach that employs a multifaceted correlation measure, which captures heterogeneity, and a rigorous validation method. Maestros utilization for Alzheimers disease (AD) reveals an expression pattern that has virtually zero probability of simultaneous expression by an individual, assuming independence. Yet this pattern is exhibited by 19.0% of AD cases and 7.3% of controls, establishing an unprecedented pattern of synchronized genetic activities in the human brain. This pattern is significantly associated with AD, with an odds ratio of 3.0. This study substantiates Maestros power for discovery of orchestrated genetic activities underlying complex traits. More generally, Maestro can be applied in diverse domains in which heterogeneity exists. HighlightsO_LISynchronized genetic activities associated with Alzheimers disease C_LIO_LINovel vector-based correlation measure that captures genetic heterogeneity C_LIO_LIEnhanced network model for revealing combinatorial genetic interactions C_LIO_LIPro-survival genetic activities associated with Alzheimers disease C_LIO_LIGeneral approach for revealing patterns in data subject to heterogeneity C_LI

bioinformatics↗