vcbench-geneformer-perturbation — Geneformer V2-316M fine-tuned on Norman 2019

Geneformer V2-316M fine-tuned for Norman 2019 K562 perturbation classification. The fine-tuning uses BertForSequenceClassification over 247 perturbation classes; PRR is recovered downstream by passing the predicted class probabilities through the canonical perturbation-mean predictor for the corresponding class.

This is a VCBench Dim A foundation-model checkpoint — see AppliedScientific/VCBench for the evaluation code.

Headline results (Dim A, Norman 2019 K562, GEARS test split)

Regime	PRR	DES
FT+D (fine-tuned + decoder)	0.627	0.878

Geneformer V2-316M scores VC Level 1 under VCBench v1.0 (exceeds no-change baseline 0.000 on Dim A; fails to exceed mean-prediction baseline 0.579).

Files

model.safetensors                        # Fine-tuned classifier weights (1.27 GB)
config.json                              # HF model config (BertForSequenceClassification)
training_args.bin
norman_id_class_dict.pkl                 # Perturbation ID → class index mapping
norman_labeled_train.dataset/            # Tokenized training split (123 MB, Arrow)
norman_labeled_test.dataset/             # Tokenized held-out test split (14 MB, Arrow)

Loading

from transformers import BertForSequenceClassification

model = BertForSequenceClassification.from_pretrained(
    "appliedscientific/vcbench-geneformer-perturbation",
    revision="8be3f3681718b706d351b12b19b0a0b4d76420ca",  # pin to a specific revision
    num_labels=247,
)

For the full Dim A evaluation pipeline (predicted probabilities → predicted expression → PRR), see AppliedScientific/VCBench/src/models/run_geneformer_perturbation.py.

Citation

@misc{vcbench_geneformer_norman,
  author       = {{VCBench contributors}},
  title        = {Geneformer V2-316M fine-tuned on Norman 2019 (VCBench)},
  year         = {2026},
  publisher    = {Hugging Face},
  howpublished = {\url{https://huggingface.co/appliedscientific/vcbench-geneformer-perturbation}},
  note         = {Companion Dim A artefact to VCBench v1.0 (AppliedScientific/VCBench, release tag v1.0.0)}
}

License

MIT (Geneformer V2 base checkpoint also MIT, attribution: Ying Lab).

Access

Publicly available on HuggingFace.