Geneformer V2-316M attention edges, layer not stated (Kendiukhov 2026)
Attention edges from Geneformer V2-316M where the article does not name the layer (K562 CRISPRa, K562 propensity-matched, RPE1 confound battery).
5 evaluations · 5 results3 open disagreements between studies involve its model
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5 evaluations · 5 results. Different protocols are not a single leaderboard.
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) · Original source · Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-kendiukhov2026-config-geneformer-v2-316m-attention-layer-unstated
- areas
- single-cell; biological-networks
- contexts
- research
- method types
- foundation_model
- reported name
- attention
- foundation model eligible
- true
- representation
- Attention edges from Geneformer V2-316M where the article does not name the layer (K562 CRISPRa, K562 propensity-matched, RPE1 confound battery).
- source locator
- Page 13 'Models and data', 'Attention extraction and edge score computation', 'Model coverage by analysis family'
- training setting
- Zero-shot; pretrained weights, attention read out without fine-tuning
- checkpoint
- Geneformer V2-316M, HuggingFace ctheodoris/Geneformer subfolder Geneformer-V2-316M (18 layers, 18 heads), loaded with attn_implementation='eager'; revision not stated
- version
- Geneformer V2-316M
- access reuse
- Analysis code github.com/Biodyn-AI/biomechinterp-framework and Zenodo 10.5281/zenodo.18701417; not pinned to a commit in the article
Related records
- configuration of: Geneformer
- system: Geneformer V2-316M attention edges, layer not stated on K562 CRISPRa, 77 perturbations
- system: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations
- system: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 418 perturbations with the top 2,000 HVGs
- system: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- system: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- system: Geneformer V2-316M attention edges, layer not stated on Replogle CRISPRi K562, propensity-matched pairs
- system: Geneformer V2-316M attention edges, layer not stated on Replogle CRISPRi RPE1, propensity-matched pairs