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arXiv · 2609.38690

GATE-ST: Gene-Aware Text-image Encoder for Spatial Transcriptomics

Lucas Ni·Jian Luo·Wentao Huang·Chao Chen
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Abstract

Spatial transcriptomics enables spatially resolved gene expression analysis from slide-level images while preserving morphological features, providing valuable information for studying disease mechanisms and developing treatments. However, spatial gene expression profiling typically requires expensive and time-consuming tests. While existing image-based prediction optimizations mostly revolve around including positional embeddings and further image-based changes, text-based optimizations remain relatively unexplored. We present GATE-ST, which incorporates text-based inputs into image-based spatial gene expression predictions. With this approach, generated text descriptions of genes are utilized to better spatial transcriptomics prediction results. Gene summaries are put through a text encoder, generating embeddings that integrate with image embeddings through cross-attention layers to align with morphological features. We demonstrate the effectiveness of such text inputs by benchmarking performance against random gene embeddings and multiple other image-text fusion architectures, and show that GATE-ST outperforms these alternatives. Our results demonstrate the effectiveness of GATE-ST in pathology imaging, which may greatly reduce the time and cost of accurate spatial transcriptomic predictions, proving the potential of text-guided spatial gene expression prediction.

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Lucas Ni, Jian Luo, Wentao Huang, Chao Chen. 2026-09-30. GATE-ST: Gene-Aware Text-image Encoder for Spatial Transcriptomics. https://arxiv.org/abs/2609.38690

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