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German Cancer Consortium

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Representative Papers

Concept-based explanation of gene expression prediction from H&E images

Aug 17, 2026

This study addresses the limitation of existing Vision Transformer interpretability methods in elucidating how morphological concepts contribute to spatial transcriptomics predictions. We propose a concept graph framework integrating Layer-wise Relevance Propagation with Top-K Sparse Autoencoders to enable global morphology-molecular association analysis from H&E images to gene expression, overcoming the constraints of local heatmaps. Experimental results demonstrate that the model achieves an F1 score of 0.872 in iCMS classification, effectively stratifies patient prognosis, and exhibits robust cross-dataset generalizability. Consequently, this work establishes a novel interpretable paradigm for understanding the intrinsic mechanisms linking tissue morphology to transcriptional programs, providing critical insights into the molecular underpinnings of histopathological features.

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Latest Papers

Concept-based explanation of gene expression prediction from H&E images

Aug 17, 2026

This study addresses the limitation of existing Vision Transformer interpretability methods in elucidating how morphological concepts contribute to spatial transcriptomics predictions. We propose a concept graph framework integrating Layer-wise Relevance Propagation with Top-K Sparse Autoencoders to enable global morphology-molecular association analysis from H&E images to gene expression, overcoming the constraints of local heatmaps. Experimental results demonstrate that the model achieves an F1 score of 0.872 in iCMS classification, effectively stratifies patient prognosis, and exhibits robust cross-dataset generalizability. Consequently, this work establishes a novel interpretable paradigm for understanding the intrinsic mechanisms linking tissue morphology to transcriptional programs, providing critical insights into the molecular underpinnings of histopathological features.

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