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Revision updates - #118

Merged

tonyliang19 merged 68 commits into

mainfrom

Oct 9, 2026

Commits on Sep 4, 2026
- fix: make sure sklearn cv search works even with make_pipeline
  tonyliang19
  committed
  0ce67f6
Commits on Sep 11, 2026
Commits on Sep 15, 2026
Commits on Sep 26, 2026
Commits on Sep 28, 2026
- fix: remove old skipper of methods
  tonyliang19
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  8f4a27e
- feat: add sksurv modules (not tested, need to add container def too
  tonyliang19
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  b598a38
- feat: mofa try survival, need to run later
  tonyliang19
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  6fbc86f
- feat: this THU specific launcher local script wrapper, del later
  tonyliang19
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  bb719ea
Commits on Sep 29, 2026
Commits on Oct 1, 2026
Commits on Oct 2, 2026
- feat: add common json writers to store method hyperparams
  tonyliang19
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  fac2baa
- feat: add module to merge selected hyperparams from model_selection
  tonyliang19
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  01d72ae
- feat: add caretMultimodal report hyperparms
  tonyliang19
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  0e581e5
- feat: add cooperativeLearning report hyperparms
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  7fd5f75
- feat: add DIABLO report hyperparms
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  9413887
- feat add IntegrAO report hyperparams
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  26d8efc
- feat add MOGONET report hyperparams
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  e376042
- feat add RGCCA report hyperparams
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  2cd5de7
- feat add sklearn report hyperparams
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  1cf25b8
- feat add MOFA report hyperparams
  tonyliang19
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  a3acce8
- feat: finalize feature hyperparams report
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  d2f3d2f
- fix: clean target should also remove subfolders inside work/ after each nxf run
  tonyliang19
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  db1c6d4
- fix: make sure to also report selected hyperparameters when want publish relevant files only
  tonyliang19
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  61d6854
- feat: include sksurv as part of pipeline run
  tonyliang19
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  71e75b9
- feat: add sksurv label into config
  tonyliang19
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  5f11aa3
Commits on Oct 3, 2026
- fix: fallback strategy for sim data on caretMultimodal
  tonyliang19
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  f5d784f
- feat: include outcome type to mergers
  tonyliang19
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  c77126f
- feat: include calc metrics for survival data
  tonyliang19
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  c580fd2
- fix： add fallback of caretMultimodal to not fail with sim data with all noise
  tonyliang19
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  09e8af4
- fix: complete the data configs
  tonyliang19
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  6cfd126
- fix: survival model to work with rsf only
  tonyliang19
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  267e028
- fix: include outcome type for calculating metrics
  tonyliang19
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  15481b8
- fix: let merge result to parse a file of input of paths instead of list of paths, otherwise exceed arg length when long filenames
  tonyliang19
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  18e313c
- fix: splitting by outcome type
  tonyliang19
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  19780fa
- Merge branch 'dev' of github.com:CompBio-Lab/MESSI-pipeline into dev
  tonyliang19
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  31dd400
- dummy?
  tonyliang19
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  82179e9
- merge conf
  tonyliang19
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  912f387
- fix: update the container label for sksurv related modules
  tonyliang19
  committed
  351506d
Commits on Oct 4, 2026
- Merge branch 'dev' of github.com:CompBio-Lab/MESSI-pipeline into dev
  tonyliang19
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  144bece
- feat: handle checking survival
  tonyliang19
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  f7bc5bb
- fix: make sure preprare data not drop columns
  tonyliang19
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  0aa138e
- feat: finalize mofa on survival prediction
  tonyliang19
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  ef8579d
- feat: skip method dynamically from config opt or if not support other task
  tonyliang19
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  4982932
- feat: implement cplr to do survival
  tonyliang19
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  217c95e
- fix: update the skipper and include right arg
  tonyliang19
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  77766d6
- BUG: cplr not returning right lp?
  tonyliang19
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  d034011
- feat: add survival profile
  tonyliang19
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  e4b032f
- feat: include right skippers
  tonyliang19
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  3107b0c
Commits on Oct 9, 2026
- fix: finalize the launcher scripts
  tonyliang19
  committed
  7139b1e