Issues

• Refactor existing prediction to do one timepoint to the next

  li-lab-mcgill/scTimeBench#127 · Filter by author ehuan2 opened on Jun 3, 2026

• Cell-MNN is failing tests

  li-lab-mcgill/scTimeBench#122 · Filter by author ehuan2 opened on May 31, 2026
  3

• Dataset preprocessors have _parameters, though kwargs solves this issue

  li-lab-mcgill/scTimeBench#119 · Filter by author ehuan2 opened on May 27, 2026

• Running the BaseMetric solely does not work properly

  li-lab-mcgill/scTimeBench#114 · Filter by author ehuan2 opened on May 11, 2026

• Change --to_csv, --csv_dir to be more user friendly

  li-lab-mcgill/scTimeBench#112 · Filter by author ehuan2 opened on Apr 16, 2026
  6

• Update docs to be more beginner friendly

  li-lab-mcgill/scTimeBench#111 · Filter by author ehuan2 opened on Apr 16, 2026

• Change metrics' supported datasets to be read from yaml config file directly instead

  li-lab-mcgill/scTimeBench#101 · Filter by author ehuan2 opened on Mar 23, 2026
  

• Design of "cell_lineages" folder placement

  li-lab-mcgill/scTimeBench#96 · Filter by author ehuan2 opened on Mar 18, 2026

• Generalizing Database csv export functions for future convenience

  li-lab-mcgill/scTimeBench#84 · Filter by author aosakwe opened on Feb 27, 2026

• Problem with the parameter encoding in GraphSimMetric

  li-lab-mcgill/scTimeBench#82 · Filter by author ehuan2 opened on Feb 26, 2026

• Improve next tp generation for scNODE

  li-lab-mcgill/scTimeBench#80 · Filter by author ehuan2 opened on Feb 25, 2026

• Caching for OT loss metrics

  li-lab-mcgill/scTimeBench#74 · Filter by author ehuan2 opened on Feb 21, 2026
  1

  

• Subgraph Analysis

  low-priority
  li-lab-mcgill/scTimeBench#73 · Filter by author ehuan2 opened on Feb 21, 2026

• Use scVI in pseudotime

  li-lab-mcgill/scTimeBench#72 · Filter by author ehuan2 opened on Feb 21, 2026

• QOL for better analysis

  li-lab-mcgill/scTimeBench#71 · Filter by author ehuan2 opened on Feb 19, 2026
  

• [Enhancement] Tweak main to evaluate all metrics one dataset at a time

  li-lab-mcgill/scTimeBench#70 · Filter by author aosakwe opened on Feb 19, 2026
  

• Include timepoint sorting of cells in anndata loading

  enhancement
  li-lab-mcgill/scTimeBench#67 · Filter by author aosakwe opened on Feb 18, 2026

• Shift role of compatible dataset

  enhancement
  li-lab-mcgill/scTimeBench#63 · Filter by author aosakwe opened on Feb 17, 2026

• Put the model runner into a try catch block to delete any created model outputs in case it failed

  li-lab-mcgill/scTimeBench#45 · Filter by author ehuan2 opened on Feb 3, 2026
  

• Refactor of Dataset Initialization Logic

  li-lab-mcgill/scTimeBench#40 · Filter by author ehuan2 opened on Jan 27, 2026
  

• Extend existing cell ontology trajectory inference module for time-dependent trajectories

  cell-ontologylow-priority
  li-lab-mcgill/scTimeBench#24 · Filter by author ehuan2 opened on Jan 21, 2026
  

• Gut the project for just its general framework for benchmarking

  low-priority
  li-lab-mcgill/scTimeBench#10 · Filter by author ehuan2 opened on Jan 13, 2026

• Accounting for Model-specific indexing of time

  li-lab-mcgill/scTimeBench#4 · Filter by author aosakwe opened on Jan 12, 2026