Claude
d7efab34c5
feat(rvdna): add npm biomarker engine with risk scoring, streaming, and benchmarks
...
ADR-015: Pure-JS biomarker engine mirroring Rust biomarker.rs and
biomarker_stream.rs exactly. Includes:
- src/biomarker.js: 20-SNP composite risk scoring, 6 gene-gene
interactions, 64-dim L2-normalized profile vectors, synthetic
population generation with Mulberry32 PRNG
- src/stream.js: RingBuffer, StreamProcessor with Welford online
stats, CUSUM changepoint detection, z-score anomaly detection,
linear regression trend analysis, batch reading generation
- tests/test-biomarker.js: 35 tests + 5 benchmarks covering all
classification levels, risk scoring, vector encoding, population
generation, streaming, anomaly/trend detection
- index.d.ts: Full TypeScript definitions for all biomarker APIs
- package.json: Bump to v0.3.0, add biomarker keywords
Benchmark results (Node.js):
computeRiskScores: 7.33 us/op
encodeProfileVector: 9.51 us/op
RingBuffer push+iter: 3.32 us/op
https://claude.ai/code/session_014FpaYVohmyLH5dcBZTgmSY
2026-02-22 15:27:37 +00:00
Claude
81ab90f6b0
feat(rvdna): add health biomarker analysis engine with streaming simulation
...
Implement ADR-014 Health Biomarker Analysis Architecture:
- biomarker.rs: Composite risk scoring engine with 17-SNP weight matrix,
gene-gene interaction modifiers (COMT×OPRM1, MTHFR compound, BRCA1×TP53),
64-dim HNSW-aligned profile vectors, clinical reference ranges for 12
biomarkers, and deterministic synthetic population generation
- biomarker_stream.rs: Streaming biomarker simulator with generic RingBuffer,
configurable noise/drift/anomaly injection, z-score anomaly detection,
linear regression trend analysis, and exponential moving averages
- 35 unit tests + 15 integration tests (168 total, 0 failures)
- Criterion benchmark suite targeting ADR-014 performance budgets
https://claude.ai/code/session_014FpaYVohmyLH5dcBZTgmSY
2026-02-22 05:19:23 +00:00
Claude
53214e7ade
feat(dna): add RVDNA AI-native format, real gene data, 8-stage pipeline
...
New RVDNA binary format (.rvdna) purpose-built for AI genomic analysis:
- 2-bit nucleotide encoding (4x compression vs ASCII FASTA)
- Pre-computed k-mer vectors with int8 quantization for instant HNSW search
- Sparse attention matrices in COO format for direct tensor consumption
- Variant probability tensors with f16 genotype likelihoods
- Zero-copy memory-mappable with 64-byte aligned sections
- CRC32 checksums, section-level integrity verification
Real human gene sequences from NCBI RefSeq:
- HBB (hemoglobin beta, NM_000518.5) - sickle cell gene
- TP53 (tumor suppressor, NM_000546.6) - exons 5-8 hotspot
- BRCA1 (DNA repair, NM_007294.4) - exon 11 fragment
- CYP2D6 (drug metabolism, NM_000106.6) - pharmacogenomic
- INS (insulin, NM_000207.3) - preproinsulin
Pipeline upgraded to 8 stages using real data:
1. Load 5 real human genes (2,340 bp total)
2. K-mer similarity matrix across gene panel
3. Smith-Waterman alignment on HBB
4. Sickle cell variant detection at HBB codon 6
5. HBB → hemoglobin beta translation (MVHLTPEEKSAVTALWGKVN verified)
6. Horvath epigenetic clock
7. CYP2D6 *4/*10 pharmacogenomics
8. RVDNA format conversion with pre-computed vectors
87 tests, 0 failures. ADR-013 documents the format specification.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 04:48:28 +00:00
Claude
fc6818f54b
feat(dna): optimize all 12 ADRs + add DDD docs, README
...
All ADRs updated with:
- Implementation Status sections (Working/Buildable/Research)
- SOTA algorithm references with citations
- Crate API mappings to actual RuVector functions
- Concrete performance math and targets
New documents:
- ADR-011: Performance targets and benchmark suite (755 lines)
- ADR-012: Genomic security and privacy (596 lines)
- DDD Bounded Context Map (602 lines)
- DDD Domain Model with Rust types (1,047 lines)
- README with features, comparisons, QuickStart (541 lines)
9,326 lines of architecture documentation total.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 04:02:06 +00:00
Claude
06f8c58cfb
feat(dna): add ADR-006 temporal epigenomics, ADR-008 WASM edge, ADR-010 pharmacogenomics
...
ADR-006: Temporal Epigenomic & Lifespan Analysis Engine (1,177 lines)
ADR-008: WebAssembly Edge Genomics & Universal Deployment (1,117 lines)
ADR-010: Quantum-Enhanced Pharmacogenomics & Precision Medicine (1,136 lines)
10 of 15 documents now complete (10,935 total lines).
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 03:43:38 +00:00
Claude
bd08a5c6e8
feat(dna): add 7 ADR documents for DNA analyzer architecture
...
ADR-001: Vision & Context - world's fastest DNA analyzer strategy
ADR-002: Quantum Genomics Engine - Grover's, QAOA, VQE for genomics
ADR-003: HNSW Genomic Vector Index - hyperbolic space phylogenetics
ADR-004: Flash Attention Genomic Architecture - hierarchical 6-level
ADR-005: GNN Protein Structure Engine - SE(3)-equivariant folding
ADR-007: Distributed Genomics Consensus - global biosurveillance
ADR-009: Zero-False-Negative Variant Calling Pipeline
7,505 lines of scientifically-grounded architecture decisions.
Remaining ADRs (006, 008, 010-012) and DDD docs in progress.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 01:32:49 +00:00
Claude
b1af4f0ab2
feat(dna): scaffold DNA analyzer example with claude-flow init
...
- Initialize claude-flow v3 with hierarchical-mesh swarm (15 agents)
- Create examples/dna/ directory structure for ADR/DDD documents
- Update .claude/ agents, helpers, settings, and skills from init --force
- 15-agent swarm actively producing ADR-001 through ADR-012 and DDD docs
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 00:25:19 +00:00
