TiMSA Engine - BioZig

TiMSA Engine TOPOLOGY-INSPIRED MULTIPLE SEQUENCE ALIGNMENT

TiMSA is the first topological multiple sequence alignment (MSA) geometry engine, developed as a core module in BioZig. It fundamentally changes how sequences are aligned by projecting them onto mathematical manifolds to identify true structural and functional conservation, transcending standard affine gap scoring.

TiMSA is biologically coupled with ATLAZ to compute structural ablation, 1-Wasserstein optimal transport, and H1 recombination loops.

Topological State Machine MODES OF OPERATION

TiMSA Rigidity (Ablation)

Employs an Ablation Gradient (ΔWp). TiMSA systematically isolates active site sentinels by mathematically stripping columns and measuring the structural deformation. The distance matrix is strictly patched using an O(1) incremental update model (O(L * N^2) total complexity).

TiMSA Recomb (H1 Cycles)

Harnesses H1 Persistent Homology. It implements a bitwise sparse accumulator over GF(2) to rapidly detect H1 cycles (loops in the distance graph), directly identifying and outputting structural recombination breakpoints without combinatorial explosion.

Multi-Core Scaling Architecture SRFSCHEDULER

Strict Memory Boundaries

TiMSA operates strictly within the defined memory_budget_bytes utilizing chunked dynamic programming via SRFScheduler. By chunking sequences into K = sqrt(N) blocks, it dynamically drops and recomputes intermediate matrices to explicitly bound memory at O(L).

Parallel H1 Sentinel Fusion

Features a dedicated C++ fusion kernel (fuse_network.cpp) that derives the final structural epistasis edge weight natively via: Weight = MI * (|Rigidity_i| + |Rigidity_j|), explicitly bridging statistical covariance with topological rigidity floats.