TMEformer.

A virtual perturbation platform for spatial transcriptomics.
Run in silico perturbation predictions and analyses to identify potential key regulators.

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ISP Submit

Submit a new perturbation prediction task — gene OE/KD or TME adjustment across three ISP types.

Submit task →
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ISP Query

Query all completed perturbation tasks and jump directly to statistical analysis.

Query results →
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ISP Stat

Run statistical analysis on computed perturbation results — significance testing, volcano plots, and CSV export.

Run analysis →
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Task Tracking

Monitor GPU inference task progress in real time — view logs and manage running jobs.

View tasks →
Tumor microenvironment concept

(Concept) The tumor microenvironment — a network of interdependent cells where neighboring cell states influence tumor response to perturbation.

ISP system pipeline overview

(Pipeline) End-to-end ISP workflow — Submit a perturbation task, compute on GPU, query results, and run statistical analysis.

TMEformer modeling structure

(a) TMEformer modeling structure — High-resolution spatial transcriptome to TME-aware single-cell transformer.

TMEformer in silico perturbation framework

(b) Perturbation framework — Target-Rank, TME-Composition, TME-Rank → Prediction → Discovery.