Issues

• Request: ordered 2000-HVG gene name list for ST-HVG-* releases (obsm['X_hvg'] is positionally consumed by tx infer)

  ArcInstitute/state#279 · Filter by author 793891645 opened on Sep 12, 2026

• Verification on how STATE is run

  ArcInstitute/state#278 · Filter by author jetrz opened on Aug 24, 2026

• Question about state tx infer output

  ArcInstitute/state#277 · Filter by author zlsys3 opened on Aug 7, 2026

• state tx predict clips AnnData.X before cell-eval scale detection and normalization

  ArcInstitute/state#276 · Filter by author AlphaSpire8 opened on Aug 3, 2026

• Do the preprint split tomls correspond to the released ST-SE-Replogle checkpoints?

  ArcInstitute/state#275 · Filter by author nikolakr7 opened on Aug 2, 2026

• True zero-shot capability of STATE (for predictions across unseen perturbations and cellular contexts)

  ArcInstitute/state#270 · Filter by author tnnandi opened on May 14, 2026
  1

• Which SE checkpoint was used to generate X_state for ST-SE-Tahoe?

  ArcInstitute/state#269 · Filter by author carloruggeri opened on May 14, 2026

• Where can I find the exact 2000 HVG gene list for ST-HVG-Tahoe?

  ArcInstitute/state#268 · Filter by author Shoichi-eisei opened on May 11, 2026
  2

• Question about perturbation direction encoding and interpretation of infer outputs

  ArcInstitute/state#263 · Filter by author rogercasalsfr opened on Apr 20, 2026

• Question about config

  ArcInstitute/state#255 · Filter by author jetrz opened on Feb 19, 2026

• Script for reproducing the results of a thesis

  ArcInstitute/state#254 · Filter by author whd1125 opened on Feb 8, 2026

• Replogle-Nadig datasets - mix of raw and normalized

  ArcInstitute/state#253 · Filter by author carmenfilarsky-rx opened on Feb 2, 2026

• How about not give validation set?

  ArcInstitute/state#248 · Filter by author Leafaeolian opened on Jan 15, 2026

• SE RUN

  ArcInstitute/state#240 · Filter by author bieyl opened on Nov 14, 2025
  1

• How to accelerate the training of the state model?

  ArcInstitute/state#234 · Filter by author Yan-Jack-jie opened on Oct 17, 2025
  1

• state tx infer doesn't output predicted .X when using embed-key

  ArcInstitute/state#230 · Filter by author asalimih opened on Oct 4, 2025
  5

• Questions about fine-tuning and combinatorial perturbation prediction.

  ArcInstitute/state#188 · Filter by author yyLIU12138 opened on Sep 1, 2025
  2

• renaming output_space for hvgs to hvg

  ArcInstitute/state#180 · Filter by author r-sayar opened on Aug 15, 2025

• _infer.py --output option

  enhancementgood first issue
  ArcInstitute/state#179 · Filter by author r-sayar opened on Aug 14, 2025

• Difference between infer and predict

  ArcInstitute/state#173 · Filter by author asalimih opened on Aug 10, 2025
  1

• Difficulty reproducing Parse-PBMC results (Figure 2) with pretrained model

  ArcInstitute/state#167 · Filter by author Jonyyqn opened on Aug 6, 2025
  1

• update preprocess command to optionally use the cell load filtering

  ArcInstitute/state#165 · Filter by author abhinadduri opened on Aug 5, 2025

• Some questions about the infer function

  ArcInstitute/state#164 · Filter by author Jonyyqn opened on Aug 5, 2025

• Typo in the paper

  ArcInstitute/state#157 · Filter by author psl-schaefer opened on Jul 27, 2025

• Total compute?

  ArcInstitute/state#154 · Filter by author samuelstevens opened on Jul 23, 2025