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History / Technical algorithm

Revisions

  • Update default model scaling method

    @glarue glarue committed Dec 13, 2025
    130a60d

  • Update algorithm details

    @glarue glarue committed Dec 8, 2025
    7e2daf8

  • Fix schematic labels

    @glarue glarue committed Dec 7, 2025
    13bad34

  • Update toy transcript diagram

    @glarue glarue committed Dec 7, 2025
    59a52c9

  • docs: add references from U12 training data sources Add 4 publications cited in the reference intron training files: - Pineda & Bradley 2018 (branch point tissue-specificity) - Niemelä et al. 2014 (U12 intron nuclear processing) - Madan et al. 2015 (ZRSR2 mutations in MDS) - Cologne et al. 2019 (TALS patient transcriptomics) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>

    @glarue glarue committed Dec 6, 2025
    7d4b290

  • docs: use LaTeX math formatting for equations Convert plaintext math expressions to proper LaTeX notation: - Log-odds ratios with fraction notation - Probability expressions P(U12-type) - IQR quartile notation (Q75 - Q25) - Feature formulas with min() and absolute values - Platt scaling equation with bold vector notation 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>

    @glarue glarue committed Dec 6, 2025
    dd34658

  • docs: document intron extraction design decisions - Add Mixed CDS/Exon handling explanation - Add Touching Exons annotation artifacts behavior - Update Quick-start runtime estimates

    @glarue glarue committed Dec 6, 2025
    6482375

  • docs: standardize U12/U2 terminology (U12-type intron, U12-dependent spliceosome)

    @glarue glarue committed Dec 6, 2025
    a6fd6f0

  • docs: update Technical-algorithm.md for v2 defaults - Note that streaming mode is now the default - Remove outdated normalizer save/reload advice (pretrained model includes scaler) - Simplify PWM table to compact bullet list format

    @glarue glarue committed Dec 6, 2025
    30f8e76

  • Fix normalization documentation: describe actual RobustScaler(with_centering=True) implementation - Technical-algorithm.md: Replace ASCII pipeline diagram with nested list format - Technical-algorithm.md: Correct Stage 3 description - uses standard robust z-score WITH centering, not zero-anchored scaling - Overview.md: Update normalization description to match - Note: ZeroAnchoredRobustScaler exists in codebase but is deprecated/unused

    @glarue glarue committed Dec 3, 2025
    d7acb76

  • Comprehensive wiki update: technical details, citations, v2 features - Home.md: Added key features, quick links, proper citation - Overview.md: Added scientific background, classification method summary - Quick-start.md: Updated installation methods, dependencies - Data-filtering-notes.md: Expanded with filtering tables, boundary correction - Output-files.md: Added score interpretation, common operations - Training-data-and-PWMs.md: Updated for JSON format, added citations - Example-usage.md: Reorganized, added cross-species section - Usage-info.md: Added intro linking to examples - About.md: Expanded with citations, related resources - _Sidebar.md: Added Technical details link - NEW Technical-algorithm.md: Complete technical documentation - Pipeline overview diagram - PWM scoring details with equations - Zero-anchored robust scaling explanation - SVM architecture and feature augmentation - Training process description - Memory/performance considerations - Scientific references

    @glarue glarue committed Dec 3, 2025
    4d762d6