Implementing alignment based optimization for single-cell data - #72

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scjlee wants to merge 46 commits into

artyomovlab:mainfrom

scjlee:dsa_optimization

Commits on Aug 10, 2026

Implement additional regularization with alignment theorem
scjlee
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12c4a27
Implement GitHub Action workflow for Rcpp/roxygen sync
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c767588
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
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scjlee
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4339b2a
feat: adding `coef_hinge_H` argument back to `optimize_alignment` to provide freedom of tuning
scjlee
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fd9840f
bug-fix: recover `coef_hinge_H` in `optimize_solution` for alignment optimization
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6d844fc
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
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scjlee
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c58992a
bug-fix: remove coefficient re-weighting
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4ebcc08
feat: remove not used regularization and refactor `optimize_alignment`
scjlee
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6663875
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
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scjlee
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8e13a27
doc: save implementation plan for refactoring error logging
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dc96880
doc: add 5th milestone: compatibility layer
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7cd758a
feat: implement modular error calculation and logging system
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16b7ebd
feat: expose new long format optimization log to `DualSimplexSolver`
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7179fff
doc: refine implementation plan for the new logging mechanism
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866d77f
feat: single-pass hinge loss calculation
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54bdcf8
refactor: transition error tracking to logger-based architecture and add legacy matrix conversion support
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995b173
refactor: decouple optimization metrics and logging logic into dedicated header and source files
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61a98b4
feat: implement `AlignmentErrorCalculator` for optimize_alignment
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4f5df8f
fix: align iteration numbers in optimization history when appending new results
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bd0ab56
refactor: implement logging for initial optimization state and update iteration loop to start from 1
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735a224
refactor: simplify metric extraction by using ensemble metrics and helper functions in the optimization loop
scjlee
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cd36c0f
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
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scjlee
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a51e250
feat: add `legacy_random_invertible` for testing.
scjlee
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499c7db
refactor: rename variable names for clariy and in sync with mathematical formulas
scjlee
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8e0781d
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
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scjlee
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61ce8b8
feat: Prioritize error plotting to use new long-form history with backward compatibility
scjlee
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6ce3f1b
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
authored and
scjlee
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3bfa8c4
refactor: remove legacy logging in matrix from `optimize_alignment`
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f46d2e5
doc: manually update documentation and RcppExport [skip ci]
scjlee
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4e495d3
fix: proper `from_idx` calculation in `optimize_solution` [skip ci]
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9492e63
feat: implement new alignment optimization algorithm using progected gradient descent (PGD)
scjlee
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291bc01
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
authored and
scjlee
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6ae01c7
fix: add `alignment_pgd` to the list of optimization method
scjlee
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e2f442e
chore: auto-update RcppExports and documentation [skip ci]

github-actions[bot]
authored and
scjlee
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605e23d
feat: remove inverse-base alignment optimization in favor PGD-based algorithm.
scjlee
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1b1028f
chore: auto-update RcppExports and documentation [skip ci]
github-actions[bot]
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8cb9afd
fix: remove unused CSVLogger
scjlee
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14988ba
feat: implement getters for optimization history from the logger
scjlee
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1fa16e4
chore: auto-update RcppExports and documentation [skip ci]
github-actions[bot]
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9ba36d0

Commits on Aug 11, 2026

Commits on Aug 12, 2026

fix: calculating true gradients without any shortcut
scjlee
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1f55d05

Commits on Aug 13, 2026

Commits on Aug 27, 2026

fix: prevent matrix dimension drop in `optimize_solution` for edge case k=2
scjlee
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a3024d0