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  • docs: expand README with full methods + refs; drop bacar_marker.hmm - README: correct InfoNCE description (SCG hard negatives, not positive pairs), remove SCG-SupCon, fix HMM default to checkm_markers_only.hmm, add 16 references (COMEBin, InfoNCE, Leiden, HNSW, CheckM, CheckM2, MapDamage, MIMAG, MetaBAT2, SemiBin2, CGR, EM, Briggs) - Remove auxiliary/bacar_marker.hmm (40 markers, replaced by checkm_markers_only.hmm with 206 CheckM universal markers) - Update --hmm defaults in cmd_bin.cpp, cmd_seeds.cpp, seed_generator.h - Clean up bacar_marker comments in seed_generator.cpp

    @genomewalker genomewalker committed Feb 26, 2026
    56ad573

  • docs: fix three feature dimension errors caught by code audit (mismatch spectrum, CGR layout, damage coverage)

    @genomewalker genomewalker committed Feb 26, 2026
    06f4f35

  • docs: humanize README prose, remove redundant damage-weight explanation

    @genomewalker genomewalker committed Feb 26, 2026
    f6ead53

  • docs: add COMEBin benchmark results, remove chimera subcommand

    @genomewalker genomewalker committed Feb 26, 2026
    2c004ee

  • docs: credit COMEBin baseline, frame AMBER as extension not replacement

    @genomewalker genomewalker committed Feb 26, 2026
    41fda1e

  • docs: add loss formula, fix encoder row, expand resolve math - README: show full SCG-SupCon loss with damage weights inline; fix encoder feature table row; add p_cobin formula for resolve section - Methods wiki: add LaTeX p_cobin formula + explain per-pair denominator rationale; add resolve reproducibility note (3 runs → 10 HQ core, ≥5 runs → borderline bins accumulate evidence)

    @genomewalker genomewalker committed Feb 26, 2026
    3176f8d

  • docs: add SCG-SupCon and internal C++ quality estimation - README: rename section to SCG-supervised damage-aware contrastive learning; explain P(i) = aug_views ∪ SCG co-members; 6 augmented views - Methods wiki: full SCG-SupCon loss derivation with positive set definition, exclusion mask, 6-view augmentation, damage weighting - Methods wiki: new internal quality estimation section — 107-marker C++ SCG engine, completeness/contamination formulae, dup_excess definition; clarify CheckM2 is post-hoc only, not called during binning

    @genomewalker genomewalker committed Feb 26, 2026
    6b653bb

  • production-ready repo: README, wiki, cmake refactor, CPU build path - CMakeLists.txt: rename target amber_gpu→amber, AMBER_USE_TORCH default OFF, split CORE vs TORCH sources, git version detection, install target, CTest - cmake/version.h.in: git-based version header - include/amber/config.hpp: VERSION from generated version.h - src/bin2/encoder/damage_aware_infonce.h: move DamageProfile/DamageAccumulator outside #ifdef USE_LIBTORCH (pure C++ structs, no LibTorch dependency) - src/cli/cmd_bin_stub.cpp: amber bin error with CPU/GPU build instructions - src/algorithms/damage_extraction_stub.cpp: amber damage stub when TORCH=OFF - README.md: comprehensive with math overview, install paths, benchmarks, citation - wiki/: Home, Methods-and-Model, aDNA-Features, Command-Reference, Output-Formats, Quick-Start-Tutorial, Benchmarks, _Sidebar - .github/workflows/ci.yml + release.yml: CI and tag-triggered releases - conda_recipe/meta.yaml: Bioconda recipe skeleton - environment.yml: dev environment - .gitignore: fix 'amber' → '/amber' (was excluding include/amber/ directory) - polish.cpp, strain_deconvolution.h: --write-modern-bam + deconv stats - Snakefile: assemble_s17_modern rule, deconvolve modern_bam output

    @genomewalker genomewalker committed Feb 26, 2026
    7198679