Christina Theodoris

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New activity in ctheodoris/Geneformer 2 months ago

device="cuda" hardcoded in emb_extractor.py and perturber_utils.py, breaks CPU-only inference

3

#592 opened 2 months ago by

dlgenomics

Use dynamic CUDA check instead of hardcoded device in emb_extractor.py

1

#593 opened 2 months ago by

dlgenomics

Use dynamic CUDA check instead of hardcoded device in perturber_utils.py

#594 opened 2 months ago by

dlgenomics

Is cell-level train/validation/test splitting acceptable for Geneformer in silico perturbation?

1

#591 opened 2 months ago by

lifei116

Question about the color scale in Fig. 6b vs. plot_predictions()

1

#590 opened 2 months ago by

lishensuo

New activity in ctheodoris/Geneformer 4 months ago

Input data type for best results

1

#589 opened 4 months ago by

retract

New activity in ctheodoris/Geneformer 5 months ago

Unable to fine-tune model with n_hyperopt_trials > 0. cc.validate gets stuck

1

#587 opened 5 months ago by

Sheyiphunmi

Should n_counts reflect pre- or post–gene-symbol-to-Ensembl conversion when unmapped genes are removed?

1

#586 opened 5 months ago by

suanzaoren

New activity in ctheodoris/Geneformer 7 months ago

Update geneformer/mtl/model.py

2

#585 opened 7 months ago by

MajorasMeow

New activity in ctheodoris/Genecorpus-30M 8 months ago

Technical Dropout vs. Biological Silencing

1

#28 opened 8 months ago by

rgholami

New activity in ctheodoris/Geneformer 8 months ago

Multi task classifier, True values incorrect

2

#584 opened 8 months ago by

saranyabalachandran

Question regarding post-perturbation Cell × Embedding matrix extraction

1

#583 opened 8 months ago by

eastmancodes

New activity in ctheodoris/Geneformer 9 months ago

Setting max_layers_to_freeze overrun in MTLClassifier

5

#581 opened 9 months ago by

MajorasMeow

Update geneformer/mtl/train.py

1

#582 opened 9 months ago by

MajorasMeow

A MTLClassifier.load_and_evaluate_test_model error

➕ 1

1

#580 opened 10 months ago by

c57bl6j

New activity in ctheodoris/Geneformer 10 months ago

Issue reproducing TTN detection counts in In Silico Treatment Analysis

1

#579 opened 10 months ago by

LucasACyyy

Genecorpus 30 M annotation

1

#578 opened 10 months ago by

lorenzocampini

GPU requirements

1

#577 opened 10 months ago by

lorenzocampini

Considerations on Gene symbol and Ensembl ID mapping

1

#576 opened 10 months ago by

lorenzocampini

New activity in ctheodoris/Geneformer 11 months ago

Ensembl gene ID version used in Geneformer (ENSG)

1

#575 opened 11 months ago by

jenny143