Software

• OpenMendel project

  • I have maintained over 20 packages in the project, including:
  • SnpArrays.jl, for accelerated computation on PLINK 1 BED-formated genotype files
  • TrajGWAS.jl, for GWAS of trajectory and longitudinal measurements
  • OpenADMIXTURE.jl, performance-enhanced Julia reimplementation of the famous ADMIXTURE program

• SparseKmeansFeatureRanking.jl: Efficient implementation of Sparse K-means clustering with feature ranking used underneath OpenADMIXTURE.jl.

• near-circulant-splitting

  • Splitting with Near-Circulant Linear Systems: Applications to Total Variation CT and PET

• ParProx.jl

  • Julia package for penalized logistic regression and Cox proportional hazard regression using the proximal gradient method developed for omics studies. Supports plain lasso and group lasso penalties (groups may overlap).

• DistStat.jl

  • Julia package for distributed computation supporting distributed matrix data structure and operations.

• dist_stat

  • Python package distributed computation based on the distributed submodule of PyTorch. Supports distributed matrix data structure (distmat) and operations.

• dist-primal-dual

  • Python package for optimally accelerated primal-dual algorithms for convex composite optimization. Multi-GPU parallelization enabled