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README.md
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## Key
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**Structure
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* Efficient, context-aware causal GRN inference in a latent factor space.
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* Uses a Mixture-of-Experts (MoE) architecture so different latent experts capture distinct regulatory contexts; this enables per-cell GRN specialization without learning a full causal model per cell.
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* Outputs: per-cell directed edges with causal confidence, context assignment, and compact latent summaries.
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**Embedding
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* Learns gene and cell embeddings guided by the SFM-inferred causal structure (e.g., contrastive/cause-aware objectives).
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* Embeddings are transferable: they improve downstream supervised and unsupervised tasks (drug sensitivity, perturbation response prediction, trajectory/lineage inference).
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## Model
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The release package separates biological resources, shared tokenizer assets, and model-specific weights:
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* `resources/human_tfs.csv`
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* `resources/mouse_tfs.csv`
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<br/>
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## Key features
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**Structure foundation module (SFM)**
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* Efficient, context-aware causal GRN inference in a latent factor space.
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* Uses a Mixture-of-Experts (MoE) architecture so different latent experts capture distinct regulatory contexts; this enables per-cell GRN specialization without learning a full causal model per cell.
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* Outputs: per-cell directed edges with causal confidence, context assignment, and compact latent summaries.
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**Embedding foundation module (EFM)**
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* Learns gene and cell embeddings guided by the SFM-inferred causal structure (e.g., contrastive/cause-aware objectives).
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* Embeddings are transferable: they improve downstream supervised and unsupervised tasks (drug sensitivity, perturbation response prediction, trajectory/lineage inference).
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## Model assets
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The release package separates biological resources, shared tokenizer assets, and model-specific weights:
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* `resources/human_tfs.csv`
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* `resources/mouse_tfs.csv`
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