Highly Multivariate Large-scale Spatial Stochastic Processes -- A Cross-Markov Random Field Approach

This repo contains the code for the manuscript, entitled "Highly Multivariate Large-scale Spatial Stochastic Processes -- A Cross-Markov Random Field Approach", by Xiaoqing Chen, Peter Diggle, James.V.Zideck, Gavin Shaddick.

We propose a cross-MRF model class, consisting of a mixed spatial graphical model framework and a cross-MRF theory to address various challenges of highly multivariate large-scale spatial data collectively within one unified framework.

The core contribution of the cross-MRF theory is that it realises doubly conditional independence (CI) among both p variates and n spatial locations, see here.

We achieved:

• utmost sparsity in the joint precision matrix
• lowest generation order of the joint precision matrix
• asymmetric cross-correlation in the joint covariance matrix
• scientific interpretability

[Comparative study results] [Models comparison] [Asymmetry and sparsity]

Scripts Contents

• GPU folder: auto-correlation matrix and cross-correlation matrix plots

• Figure folder: Sigma, Sigma_inv plots, p = 10, CI among p only; CAMS denoising plot
  
  

• 032c: Tst9c, 1D SG and SG_inv construction, Matern, CI among p only (non-cross-MRF), SpN + Reg, thres = 1e-3, reg_num = 1e-9 (Test construction joint Sigma and Sigma_inv; p = 6, n = 40; p = 10, n = 400, 600, 800; exact zero percentage CI among p only)

• 032d: 1D simulation plots functions for non-cross-MRF, C.I. among p only; (Plot joint Sigma and Sigma_inv; p = 6, n = 40)

• 032e: 1D SG, SG_inv construction, CI among p only (p = 10, n = 40, 400, 600, 800; elapsed system wall time, CI among p only)

• 032f: SG, SG_inv plots (p = 10)
  
  

• 034b: SG_inv construction, sparse percentage comparison among cross-MRF and non-cross-MRF for Tri-Wave and Wendland; (Percentage of exact-zero entries; elapsed system wall time cross-MRF)

• 034c: Tst10c, 1D SG_inv construction, cross-MRF, with SpNorm + Reg for b function, b can be chosen; (Joint Sigma_inv plots, p = 6)

• 034e: CI among n only, Mardia 1988; p =10, n = 400, 600, 800, 1000 (Exact-zero percentage; fully-connected graph reach memory limit)
  
  

• 037: 100 randomly evaluated Sigma_inv generation microbenchmark; (Sigma and Sigma_inv generation time)
  
  

• 046b: generate 1D true processes and noisy data, Tri-Wave and Wendland

• 046c: generate 2D true processes and noisy data, Tri-Wave and Wendland - consistent relationship between sparsity in uni-SG_inv and joint SG_inv
  
  

• 047b: optimization, Tri-Wave, Tst10c (cross-MRF)

• 047c: optimization, Wendland, Tst10c (cross-MRF)
  
  

• 048b: co-krig, Tri-Wave, 1 fold C.V. results

• 048d: co-krig, Wendland, 1 fold C.V. results
  
  

• 049: neg_logL function of non-cross-MRF, TST9d

• 049b: optimization using 049, Tri-Wave, Wendland
  
  

• 055: 2D inference (neg_logL_2D, optim) for 6 fields in Fig12, Tri-Wave (converged), Wendland (converged)
  
  

• 056: 2D cokrig (pure denoising)
  
  

• 057: Data processing, generate df_Res_log_16_sorted, sorted by Lon (asc), then by Lat (desc); 4 Lon strips
  
  

• 059: TST12 GPU version
  
  

• 060: GPU parallel + optim on 1 CPU
  
  

• 061: GPU parallel + optim on 4 CPUs
  
  

• 062: pure optim parallel on 51 CPUs, no GPU parallelisation
  
  

• 063: CAMS data processing
  
  

• 064a: CAMS data with 060, GPU parallel + optim on 1 CPU, Lon_Strip_1

• 064b: CAMS data with 060, GPU parallel + optim on 1 CPU, Lon_Strip_4
  
  

• 065a: CAMS one complete construction time for SG, and SG_inv, with GPU off-loading, df_Lon_Strip_1_Sort_new.rds;(real-world data illustration)

• 065b: CAMS data denoising

• 065c: Plot of CAMS 5

• 066a: CAMS one complete construction time for SG, and SG_inv, solo CPU, df_Lon_Strip_1_Sort_new.rds;(real-world data illustration)
  
  

Acknowledgements

• Iain Steison recommended using optimParallel() for parallel L-BFGS-B optimization on the CPU.
• David Llewellyn-Jones helped set up the HPC resource and answered lots of elementary questions regarding Baskerville HPC.
• Ryan Chan reminded XC that traditional R code will not automatically utilize GPU resources even when run on HPC.