Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal

• URL: http://arxiv.org/abs/2602.17532v1
• Date: Thu, 19 Feb 2026 16:43:12 GMT
• Title: Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal
• Authors: Ihor Kendiukhov,
• Abstract summary: We present a framework for assessing mechanistic interpretability in single-cell foundation models.<n>Applying this framework to scGPT and Geneformer, we find that attention patterns encode structured biological information with layer-specific organisation.
• Score: 0.0
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: We present a systematic evaluation framework - thirty-seven analyses, 153 statistical tests, four cell types, two perturbation modalities - for assessing mechanistic interpretability in single-cell foundation models. Applying this framework to scGPT and Geneformer, we find that attention patterns encode structured biological information with layer-specific organisation - protein-protein interactions in early layers, transcriptional regulation in late layers - but this structure provides no incremental value for perturbation prediction: trivial gene-level baselines outperform both attention and correlation edges (AUROC 0.81-0.88 versus 0.70), pairwise edge scores add zero predictive contribution, and causal ablation of regulatory heads produces no degradation. These findings generalise from K562 to RPE1 cells; the attention-correlation relationship is context-dependent, but gene-level dominance is universal. Cell-State Stratified Interpretability (CSSI) addresses an attention-specific scaling failure, improving GRN recovery up to 1.85x. The framework establishes reusable quality-control standards for the field.

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