Add JAX-based hyperedge network preprocessing design document

[bibymaths]

Motivation

• Provide a concrete, developer-oriented blueprint for an independent, optional pure-JAX preprocessing module that discovers/prunes kinase–site–substrate hyperedges, detects 3-node motifs, builds a sparse theta tensor, and runs identifiability preprocessing prior to JAXopt fitting without changing existing default workflows.

Description

• Add a single new design doc docs/jax_hyperedge_network_preprocessing.md that contains a repository scan summary, proposed module layout and public API, detailed JAX implementation plan (JIT/vmap/scan/batching boundaries and dtype guidance), algorithms for hyperedge discovery/pruning/motif detection/sparse-tensor construction/identifiability, integration points with networkmodel, output and plotting specifications, failure-mode safeguards, testing guidance, and a staged roadmap.

Testing

• Performed automated repository scans to locate relevant integration points and ran git diff --check -- docs/jax_hyperedge_network_preprocessing.md to validate the new file format; the check completed without errors.

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Codex Task