scverse / scverse/rapids-singlecell

[FEA] Dask-array based statistics on single cell data

Open
#412 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

enhancement
Dominant language
Python
Stars
394
Forks
52
Avg merge
22h 5m
Merged PRs (30d)
20

Description

Is your feature request related to a problem? Please describe.
This may be a tall ask, but it would be great to have GPU-acceleration for single cell modeling. The current standard for highly accurate modeling on large complex human datasets is the MAST program (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0844-5), or simply pseudobuling. Wilcoxons, t-test, and others have significant statistical flaws that undermine the accuracy of their results when applied to biological questions (like disease vs healthy and whatnot).

Even at sub-million cell sizes, MAST was slow. At 1+ million cells, it becomes unbearably slow. Being able to run MAST-like analysis in a Dask array-based AnnData would truly unlock complex statistical analysis of large scale scRNAseq analysis

Describe the solution you'd like
Dask-array based statistical modeling of scRNAseq, based on the known principles/variables that have been figured out by the MAST authors.

Dask-array based linear modeling has been implemented here:
https://ml.dask.org/modules/generated/dask_ml.linear_model.LinearRegression.html

Is there a CPU based implementation
A link to an implementation or paper with the suggested functionality

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the MAST paper linked in the issue and the Dask-ML LinearRegression documentation to identify the required statistical model and array operations. Then inspect the repository's existing single-cell analysis entry points; done should include a defined Dask-array implementation for MAST-like modeling, with documented behavior and validation against an appropriate CPU-based reference.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.