Edit this page | Blame

Implementing parallel correlation with rust

Notes

In an attempt to speed the current gn2 correlation we are doing an reimplentation in rust to support parralel computation

Tags

  • assigned:alexm
  • type: upgrade
  • priority: medium
  • status: in progress
  • keywords: correlation,rust,parralel

Tasks

  • [X] implementation of basic pearson and spearman correlation in rust
  • [X] add unittests and benchmarks
  • [X] loading datasets;format
  • [X] package the library as a guix package
  • [x] gn2 integration
  • [x] parsing input datasets
  • [x] benchmark for all datasets rust v gn2 version
  • [ ] Figure out how to tell cargo to use the declared dependencies, rather than dowloading the dependencies
  • [ ] db queries migration to gn3 or use partial correlation queries
  • [ ] add parralel computation
  • [ ] code optimization and minor fixes

Notes

You can call the lib as an external process from any language or directly call it in a rust cargo

code can be found here:

added a documentation for correlation rust

PR for integrating to genenetwork:

8 ,July 2022

worked on input data parsing and enhancements

PR for parsing datasets


(made with skribilo)