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8 commits

Author SHA1 Message Date
rUv
e7a5096205 fix: format all files, add EXO crate READMEs, convert path deps to version deps 
- Run cargo fmt across entire workspace
- Create README.md files for all 9 EXO-AI crates
- Convert path dependencies to crates.io version dependencies for publishing
- Add [patch.crates-io] to exo workspace for local development

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-27 16:21:14 +00:00
Claude
0378bda78e feat(rvdna): add LPA cardiovascular SNPs from SOTA meta-analysis evidence 
Add rs10455872 (OR 1.6-1.75/allele CHD) and rs3798220 (OR 1.49-1.54/allele)
from 2024 LPA meta-analyses. Include Lp(a) biomarker reference (0-75 nmol/L)
and gene-biomarker correlation in population model. Separate NUM_ONEHOT_SNPS
(17) from NUM_SNPS (19) to preserve 64-dim vector layout with LPA encoded
in summary dimension 63.

https://claude.ai/code/session_014FpaYVohmyLH5dcBZTgmSY
 2026-02-22 06:41:06 +00:00
Claude
e35e7919c7 feat(rvdna): add gene-biomarker correlations, CUSUM changepoint detection, and interaction tests 
- Add gene→biomarker correlations in synthetic population: APOE e4→lower HDL/higher
  triglycerides, MTHFR→lower B12, NQO1 null→higher CRP
- Add CUSUM changepoint detection algorithm to StreamProcessor for detecting
  sustained biomarker shifts beyond simple anomaly detection
- Add 4 new integration tests: MTHFR×COMT interaction, DRD2×COMT interaction,
  APOE→HDL population correlation, CUSUM changepoint detection
- Remove unused variant_categories import
- All 172 tests pass, all ADR-014 performance targets exceeded

https://claude.ai/code/session_014FpaYVohmyLH5dcBZTgmSY
 2026-02-22 06:08:41 +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
rUv
161f890ddb fix: apply cargo fmt across workspace and fix CI issues 
- Run cargo fmt --all to fix formatting in 362 files across the entire workspace
- Add PGDG repository for PostgreSQL 17 in CI test-all-features and benchmark jobs
- Add missing rvf dependency crates to standalone Dockerfile for domain-expansion
- Add sona-learning and domain-expansion features to standalone Dockerfile build
- Create npu.rs stub for ruvector-sparse-inference (fixes rustfmt resolution error)

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-21 20:56:38 +00:00
rUv
829ca9f014 feat(rvdna): rename package to rvdna, publish to crates.io and npm 
Rename dna-analyzer-example to rvdna across all source files, tests,
and benchmarks. Add crates.io metadata (repository, docs, keywords).
Publish rvdna v0.1.0 to crates.io and @ruvector/rvdna v0.1.0 to npm
with NAPI-RS platform loader, JS fallbacks, and TypeScript definitions.

Also publishes workspace deps at v2.0.2: ruvector-math, ruvector-core,
ruvector-filter, ruvector-collections, ruvector-graph, ruvector-gnn.

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-12 15:47:00 +00:00
rUv
244bbffe54 feat: add package.json for rvdna example with WASM bindings and build scripts 2026-02-12 15:32:55 +00:00
Claude
541fc85e4b feat(dna): complete SOTA genomic analysis pipeline with full test suite 
Implements a comprehensive DNA analyzer demonstrating RuVector's vector
computing capabilities for bioinformatics:

Modules (9):
- types: Core domain types (DnaSequence, Nucleotide, ProteinSequence, etc.)
- kmer: HNSW k-mer indexing with FNV-1a hashing and MinHash sketching
- alignment: Smith-Waterman local alignment with CIGAR generation
- variant: SNP calling from pileup data with genotype classification
- protein: DNA-to-protein translation with contact graph prediction
- epigenomics: Horvath clock biological age prediction from CpG methylation
- pharma: CYP2D6 star allele calling and metabolizer phenotype prediction
- pipeline: DAG-based genomic analysis orchestration
- error: Typed error handling across all modules

Testing (41 tests, 0 mocks):
- 12 k-mer integration tests (encoding, HNSW search, MinHash Jaccard)
- 17 pipeline e2e tests (alignment, variant calling, pharmacogenomics)
- 12 security tests (buffer overflow, path traversal, concurrency, bounds)

Benchmarks: Criterion suite for kmer, alignment, variant, protein, pipeline

Binary: 7-stage demo (sequence gen, k-mer search, alignment, variant
calling, protein analysis, epigenomics, pharmacogenomics)

https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
 2026-02-11 04:29:28 +00:00