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27 changes: 20 additions & 7 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,26 @@ cff-version: 1.2.0
message: "If you use DeepSpot-M, please cite the following."
title: "DeepSpot-M: a multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology"
abstract: >-
DeepSpot-M is a multimodal foundation model that maps a histology image tile to
spatial gene expression. It tokenises a 224x224 H&E tile with a LoRA-adapted
pathology foundation backbone and lets each gene query attend to the patch tokens
through a cross-attention gene decoder, so one model predicts transcriptome-wide
expression and genes it never saw during training. The code is released under
PolyForm Noncommercial 1.0.0; the model weights carry a separate CC-BY-NC-SA-4.0
license. Research use only, not for clinical or diagnostic use.
Spatial transcriptomics remains costly and low-throughput, limiting it to a small
fraction of routine histology and leaving the molecular state of disease unmeasured
in most patients. Predicting spatial expression from histology could address this
gap, but existing methods are restricted to predefined genes and small cohorts. We
present DeepSpot-M, a multimodal foundation model that predicts spatial expression
by representing genes with embeddings from foundation models spanning DNA, RNA,
proteins, single cells and biomedical text. By reformulating prediction as a query
over genes, DeepSpot-M spans the protein-coding transcriptome and predicts genes
unseen during training. Trained on a large pan-cancer dataset, it transfers to
held-out cancers, outperforming specialised models trained on them, and adapts to
new cohorts and single-cell assays from one slide via test-time adaptation. Applied
to TCGA, it generates a virtual atlas of 28,664 slides across 32 cancers, recovering
a pan-cancer map of malignancy from histology. The same query interface further
enables transcriptome restoration, cross-species non-coding RNA inference, in silico
variant-effect mapping and natural-language querying. We anticipate DeepSpot-M will
provide a scalable foundation for virtual spatial transcriptomics and biomarker
discovery.
Software note: the code is released under PolyForm Noncommercial 1.0.0; the model
weights carry a separate CC-BY-NC-SA-4.0 license. Research use only, not for
clinical or diagnostic use.
authors:
- family-names: Nonchev
given-names: Kalin
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