Articles
Get started
Install, the five-minute path, and the full tour from variants to a reference comparison.
Core workflows
The task guides: bring data in, build catalogs, extract de novo, fit and test.
Statistics and comparison
The calibrated-similarity comparison and the MSU-Fit calibration statistics.
Applications and QC
The scenario atlas, the QC/reporting faces and the figure-type gallery.
Performance and peer evidence
Frozen floors, witness censuses and the sealed peer-evidence face.
Repository governance corpus
The converted docs/ tree: architecture, capability matrix, roadmap, performance, the FFI surface, ADRs, the paper lane and the corpus navigation index.
- msuiter architecture design (ARCHITECTURE)
- msuiter capability coverage matrix (CAPABILITY-MATRIX)
- The FFI export surface (ffi-surface) review artifact
- msuiter implementation plan (IMPLEMENTATION-PLAN) -- the executable decomposition of ROADMAP v3
- The MSU concept map (MSU-MAP)
- msuiter — manuscript spine (PP-1 draft)
- msuiter performance anchoring
- v0.1 release-engineering preparation checklist (the non-blocking preparation batch)
- Reproduction proof — msuiter paper lane (PP-1)
- msuiter roadmap (ROADMAP) -- v3 (dual-track versioning + organizational action gates)
- ADR 0001: the 2bit reader selection — adopting the `twobit` crate (over `Cursor<Mmap>`)
- ADR 0002: the vendor size budget and the MSRV build proof (the U-M0-02 spike)
- Docs bridge: the governance & technical corpus
Research dossiers
The pre-implementation survey corpus (methods, fitting, applications, source audits, standards).
- msuiter research executive summary (Executive Summary)
- Research report 01: the de novo signature-extraction method panorama and the NMF compute engines
- Research report 02: fitting/attribution, exposure statistical inference and post-processing analysis
- Research report 03: the application literature and the application-scenario panorama (2012–2026)
- Research report 04: the per-repository deep source audit
- Research report 05: the data standards, the licenses, the genome readers, the visualization, the benchmarks and the engineering practice
- Research report 06: the state of play of the S7 class system, the design patterns and the method-framework blueprint
- Research report 07: the complete algorithm-zoo inventory and the self-development opportunity list
- Research report 08: the fact-check audit report of the existing research documents
- 09 · sigminer v3 parity plan — closing the SigProfiler result-performance gap via msuiter asset integration
Independent reviews
The five-expert adversarial review round and its synthesis.
- The five-expert review synthesis adjudication (Synthesis, 2026-09-28)
- The review 01: the computational biologist (an independent review, 2026-09-28)
- The review 02: the Rust/R systems-development expert (an independent review, 2026-09-28)
- The review 03: the machine-learning/statistics expert (an independent review, 2026-09-28)
- The review 04: the software-development expert (an independent review, 2026-09-28)
- The review 05: the Nature journal-editor perspective (an independent assessment, 2026-09-28)
Extending msuiter
The third-party engine extension guide and the registry contract.
Campaign devlog
The dated decision and delivery records of the whole campaign, oldest first.
- Devlog · G0 先导覆盖实验——PI 裁决与待冻结项（2026-09-28）
- G0 先导覆盖实验协议设计备忘（冻结前草案 v0.1，2026-09-28）
- G0 先导覆盖实验——生物学与数据现实性备忘
- Devlog · G3 事件驱动竞争复核：Cornet 预印本正式发表（2026-09-28）
- Devlog · U-M0-01 rextendr 脚手架 + Cargo workspace（2026-09-28）
- Devlog · U-M0-02 M0 spike（2026-09-28）
- Devlog · U-M0-03 S7 类骨架（2026-09-28，W2 轮）
- Devlog · U-M0-04 引擎注册表 + 契约测试套件（2026-09-28，W3 轮）
- Devlog · U-M0-05 通道注册表单一事实来源 + docs-sync（2026-09-28，W2 轮）
- Devlog · U-M0-06 自研 RNG 模块（2026-09-28，W2 轮）
- Devlog · U-M0-09 FFI 硬契约落地 + ms_sitrep()（2026-09-28，W3 轮）
- Devlog · 假设审计备忘：Cornet 之后的领域共同假设地图（2026-09-28）
- Devlog · G0 harness 开建与修复（2026-09-29）
- Devlog · U-M0-07 CI + U-M0-08 治理文件（2026-09-29，W4 轮，联合）
- Devlog · U-M1s-01 linalg + Lawson–Hanson NNLS（2026-09-29，W4 轮，M1s 轨道开闸）
- Devlog · U-M1s-02 修复 + U-M1s-03 green pass + U-M1s-04（2026-09-29）
- GMM 超突变分层语义设计备忘（U-M1c-02·先设计后实现）
- ID83 语义设计备忘（M1c 头号单元·先设计后实现）
- Devlog · U-M1c-02/03/04 GMM 分层器 + CN48/SV32（2026-09-30）
- Devlog · U-M1c-02 GMM 超突变分层器（2026-09-30）
- Devlog · M1c 输入层收尾（2026-09-30）——M1c 里程碑 4/4 关闭
- Devlog · U-M1s-05 线程不变性接线 + 审核轮（2026-09-30）
- Devlog · U-M1s-09/10/11 组装层 + 审计修复（2026-09-30）
- Devlog · U-M1s-12/14 收尾批次 + 审核轮（2026-09-30）
- Devlog · U-M1s-12 审核 + U-M1s-13 正式化 + M1s 验收门 bench（2026-09-30）
- Devlog · 并行 tally 优化 + sigminer/MP 交叉验证（2026-09-30）
- 设计备忘 · M2 统一提取流水线（共识 Hungarian 语义 + SUITOR CV 语义 + K 仲裁规则）
- Devlog · M1c/M2/M3a 联合批次（2026-10-01 夜间）
- Devlog · U-M3a-04/05/06 收官批（2026-10-02 凌晨）
- Devlog · U-M3a-03 presence P0 + bootstrap CI P1 修复记录（2026-10-03）
- Devlog · M3b 收官三件：U-M3b-04 / 05 / 06（2026-10-04）
- Devlog · M3b 设计备忘 + M3a 关闭确认轮（2026-10-04）
- 设计备忘 · M3b MSU-Fit 校准统计（2026-10-04）
- U-M4-01 设计备忘：ms_compare() 校准相似度库
- U-M4-02 设计备忘：ms_downsample() + 格式互操作首批
- U-M4-02b 设计备忘：ms_qc_report() 初版（样本 QC 报告）
- U-M4-02c 设计备忘：ms_convert() 机会转换（exome↔genome）
- U-M4-03 设计备忘：viz 首批 8 图型
- bench/jiang 设计备忘：Jiang 2025 拟合协议对标（v0.2 验收门证据）
- M7 前置设计备忘：ms_benchmark() 网格驱动器
- U-M7 前置设计备忘：ms_simulate() 第一版（场景目录模拟器）
- CI contract closure (round-7, 2026-10-07)
- G0 authoritative run — measured cost basis for the PI go/no-go (2026-10-07)
- M6s · ms_hrd_report() — ground-truth anchoring & design (U-M6s-01, A12)
- U-M6s-01 RED batch adjudications (T1 → T2 GREEN handoff)
- G0 degraded authoritative run — PI-gate closure (2026-10-08)
- U-M7-02 competitor benchmark harness — design memo (2026-10-08)
- U-M7-03 benchmark matrix — Phase-A pilot, projection, and the sigminer interpreter catch (2026-10-09)
- M7 benchmark ergonomics — the three-function trio stays three
- GO-05 bootstrap-vs-sigminer campaign — pre-registered protocol (2026-10-10)
- GO-05 hardware-pin completeness — the authoritative table must attest its machine (2026-10-10)
- RB-11 restoration — instrument liveness attestation and evidence-snapshot laws (2026-10-10)
- GO-05 anchor-gate amendment — the median clause moves to the CI-noise envelope
- GO-05 tier-oracle amendment — consumed vs report-only fits, the floor-gate
- 2026-10-21 -- CI wall-clock restructure: shard-parallel attested arms
- Valgrind leg, child instrumentation: the execve escape, the last-writer
- M4-03b — viz batch 2 design memo
- P8-CS-3 — treatment-forensics reporting face design memo
- Build-pin drift attestation -- blob-form re-anchor of the arm-recipe digest pins (2026-11-04)
- 2026-11-05 -- CI PR-gate tiering ruling: three arms, one tier, nightly depth
- 2026-11-05 -- P7cap batch-face no-stamp ruling: archival record (audit #74 P2)
- 2026-11-07 -- Generator-emitted artifacts: dead `docs/` citation sweep
- 2026-11-07 -- Runner-image pin ruling: the valgrind leg adjudicates a pinned environment