PI-Mamba: Linear-Time Protein Backbone Generation via Spectrally Initialized Flow Matching

arXiv:2603.26705 · q-bio.BM, cs.AI, cs.LG · Submitted 2026-03-17 · Read on arXiv

q-bio.BM, cs.AI, cs.LG

Submitted: 2026-03-17

Updated: 2026-03-17

Journal ref: Bioinformatics (2026)

DOI: 10.1093/bioinformatics/btag370

License: http://creativecommons.org/licenses/by/4.0/

The gist: Motivation: Generative models for protein backbone design have to simultaneously ensure geometric validity, sampling efficiency, and scalability to long sequences.

Terminology

Abstract

Motivation: Generative models for protein backbone design have to simultaneously ensure geometric validity, sampling efficiency, and scalability to long sequences. However, most existing approaches rely on iterative refinement, quadratic attention mechanisms, or post-hoc geometry correction, leading to a persistent trade-off between computational efficiency and structural fidelity. Results: We present Physics-Informed Mamba (PI-Mamba), a generative model that enforces exact local covalent geometry by construction while enabling linear-time inference. PI-Mamba integrates a differentiable constraint-enforcement operator into a flow-matching framework and couples it with a Mamba-based state-space architecture. To improve optimisation stability and backbone realism, we introduce a spectral initialization derived from the Rouse polymer model and an auxiliary cis-proline awareness head. Across benchmark tasks, PI-Mamba achieves 0.0% local geometry violations and high designability (scTM = 0.91 plus or minus 0.03, n = 100), while scaling to proteins exceeding 2,000 residues on a single A5000 GPU (24 GB).

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