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ACCELERATING SPARSE CANONICAL CORRELATION ANALYSIS FOR LARGE BRAIN IMAGING GENETICS DATA Jingwen Yan, Hui Zhang, Lei Du, Eric Wernert, Andew J. Saykin,

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Presentation on theme: "ACCELERATING SPARSE CANONICAL CORRELATION ANALYSIS FOR LARGE BRAIN IMAGING GENETICS DATA Jingwen Yan, Hui Zhang, Lei Du, Eric Wernert, Andew J. Saykin,"— Presentation transcript:

1 ACCELERATING SPARSE CANONICAL CORRELATION ANALYSIS FOR LARGE BRAIN IMAGING GENETICS DATA Jingwen Yan, Hui Zhang, Lei Du, Eric Wernert, Andew J. Saykin, Li Shen

2 OUTLINE Imaging Genetics Sparse Canonical Correlation Analysis (SCCA) Computational Challenges and Methods Data Simulation Experimental Results

3 IMAGING GENETICS CellsSystems Behavior: Disorders, Complex interactions, phenomena, diseases. Genes UCI, S. Potkin et al.

4 Underlying Biological Pathway and Mechanism IMAGING GENETICS

5 Risacher et al 2010 Sloan et al 2010 Potkin et al 2009; Saykin et al 2010 Risacher et al 2013 AV45 ROIs & APOE Swaminathan et al 2012 PiB ROIs & amyloid pathway Potkin et al 2009 Mol Psych schizophrenia study Ho et al 2010 FTO; Reiman et al PNAS 2009 Chiang et al 2012 SNP/Gene networks & WM integrity Shen et al 2010 ROIs; Stein et al 2010 voxels Single ROI Circuit Whole Brain Candidate Gene/SNP Biological Pathway Genome-wide IMAGING GENETICS

6 OUTLINE Imaging Genetics Sparse Canonical Correlation Analysis (SCCA) Computational Challenges and Methods Data Simulation Experimental Results

7 X1 X2 X3 Xn Y1 Y2 Y3 Yn X1 X2 X3 Xn Y1 Y2 Y3 W’X Yn X1 X2 X3 Xn Y1 Y2 Y3 Xu Yn Yv Massive Univariate Analysis Multivariate Multiple Regression Canonical Correlation Analysis SCCA

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10 OUTLINE Imaging Genetics Sparse Canonical Correlation Analysis (SCCA) Computational Challenges and Methods Data Simulation Experimental Results

11 COMPUTATIONAL CHALLENGES Example SCCA run at a small scale Participants: 1000 Genotype: 3,200 SNPs Phenotype: 10,000 voxels Permutation: 10,000 permutation tests Running time: more than 12,000 hours Scale up Genotype (array): 6M SNPs Genotype (NGS): 40M variants Phenotype: 200K voxels, imaging, cognitive and biomarker Permutation: 10M permutation to reach p=10 -7 Parameter tuning via cross-validation 10-fold cross-validation coupled with an 11-by-11 grid search SCCA runs: 10×11×11 = 1,210

12 ACCELERATION WITH MKL Intel Math Kernel Library (MKL) accelerate application performance and reduce development time highly vectorized and threaded linear algebra, fast fourier transforms (FFT), vector math and statistics functions MKL has been optimized to utilize multiple processing cores wider vector units more varied architectures available in a high end system MKL can provide parallelism transparently and speed up programs with supported math routines without changing code. Compiling R with MKL

13 ACCELERATION WITH OFFLOAD MODEL Xeon Phi SE10P Coprocessor 60 cores with 8GB GDDR5 Intel x86 instruction set Usage of familiar programming models, software, and tools Pros The host system can offload computing workload partially to the Xeon Phi Independently run a compatible program

14 Texas Advanced Computing Center Stampede cluster MKL + offload Each computing node Two Intel Xeon E processors each with eight 32GB DDR3 memory The Xeon Phi SE10P Coprocessor has 61 cores with 8GB GDDR5 The NVIDIA K20 GPUs on each node have 5GB of on-board GDDR5 Software CentOS 6.3. Stock R 3.01 package compiled with the Intel compilers (v.13) and built with MKL v.11. COMPUTATIONAL PLATFORM

15 OUTLINE Imaging Genetics Sparse Canonical Correlation Analysis (SCCA) Computational Challenges and Methods Data Simulation Experimental Results

16 FREGENE genome simulator Simulate sequence-like data over large genomic regions in large diploid populations Simulated data N=1,000 diploid individuals over 20,000 generations 1 0 Mb genome with the average mutation rate as 2.5e-8 /site/generation 3,274 SNPs with minor allele frequency (MAF) greater than 0.05 included Four SNP data sets (i.e., g500, g1000, g2000, and g3274) by taking the first 500, 1,000, 2,000, and 3,274 SNPs from the entire data, respectively. SYNTHETIC DATA (GENETICS)

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18 SYNTHETIC DATA (IMAGING)

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20 OUTLINE Imaging Genetics Sparse Canonical Correlation Analysis (SCCA) Computational Challenges and Methods Data Simulation Experimental Results

21 R snowfall package (sfLapply) with MKL and offload model RESULTS Baseline Parallel (MKL+ offload)

22 RESULTS Accelerated SCCA implementations yielded the same results These correlation coefficients are close to the ground truth value of 1 Correlation coefficient between the first pair of canonical components

23 RESULTS

24 CONCLUSION Initial steps to accelerate the SCCA implementation for brain imaging genetics applications. Parallelism achieved in system implementation level to accelerate linear algebra computation using math kernel library (MKL) and partial offloading computing workload. The 2-fold speedup, although encouraging, is still insufficient to handle extremely large-scale neuroimaging genetics data millions of image voxels and millions of SNPs. Future work Big data analytic strategies at the parallel computing model level Parallelization of multiplicative algorithms using MapReduce and CUDA. Application to accelerate enhanced SCCA models as well as other bi- multivariate statistical models for analyzing brain imaging genetics data.

25 ACKNOWLEDGEMENT This research was supported by NIH R01 LM NIH U01 AG NIH RC2 AG NIH R01 AG19771 NIH P30 AG10133 NSF IIS

26 Thank you


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