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Release 0.2.0

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@haipinglu haipinglu released this 11 May 18:08
· 142 commits to main since this release
a53a64b

New Features

  • #281: Add quantile binning for uncertainty estimation including error bound estimation and evaluation metrics
  • #360: Add multimodal neural network for multimodal data integration with AVMNIST example
  • #361: Add MOGONET for multiomics integration
  • #395: Create main.py, cross_validation for multisite_neuroimg_adapt example
  • #407: Add prototypical network
  • #437: Add mida_trainer pipeline
  • #458: Add example DrugBAN PyG
  • #460: Update cross-validation for transductive domain adaptation
  • #463: Add symmetric weights and connectome vizualization
  • #464: Implement AutoMIDAClassificationTrainer and MIDA enhancement
  • #471: Add multimodal tri-stream pre-training and fine-tuning for image and signal modalities
  • #475: Add feature importance interpretation to MOGONET example
  • #476: Allow custom param_grid for AutoMIDAClassificationTrainer
  • #477: Add Integrated Gradients interpretation method and minor refinements

Bug Fixes

  • #423: Update the default checkpoint (ckpt) resume and test file name to None
  • #444: Pin Torch to 2.0.0 to fix test OSError and update related packages
  • #445: Pin torch to 2.3.0
  • #453: Fix device allocation error and resolve type mismatches
  • #455: Fix device allocation error, resolve type mismatches, and update repo configurations
  • #456: Support Python 3.11 and stop support Python 3.8
  • #459: Upgrade minimum sklearn version from 0.23.2 to 1.6.1
  • #472: Fix auto-unwrapping in the multiomics example
  • #481: Support torch 2.6
  • #482: Set neurokit2<=0.2.11 in setup.py
  • #487: Fix circular import and refactor correlation analysis
  • #494: Update weight norm imports for DrugBAN
  • #511: Fix torch-numpy type mismatch

Code Improvements

  • #383: Update keyword param for pretrained ResNet
  • #401: Upgrade to support PyTorch 2.0+ and Lightning 2.0+
  • #403: Refine examples via unifying device settings and output folder names
  • #409: Refactor ResNet
  • #417: Add resume and test checkpoint loading to main.py in example/cifas_cn…
  • #426: Refactor documentation and resolve module visibility issues
  • #429: Cache preload data
  • #438: Upgrade to support Numpy 2.0.0+
  • #441: Refactor merge modules losses distance and metrics to one
  • #449: Fix DANN torch2.0
  • #467: Unify API for mida_trainer and multi_domain_trainer, and improve mida_trainer test
  • #469: Refactor DomainNetSmallImage
  • #480: Make the output of interpretation in cancer more clean
  • #483: Refactor DrugBAN
  • #484: Reorganize kale.embed APIs
  • #492: Refactor uncertainty_quantile with BoxPlotter class
  • #497: Support Python 3.12
  • #498: Refactor Jaccard evaluation in uncertainty metrics
  • #502: Refactor uncertainty quantiles by implementing QuantileBinningAnalyzer
  • #505: Unify domain adapter loader
  • #508: Refactor Squeeze-and-Excitation Layers
  • #509: Stop support Python 3.9
  • #514: Refactor/embed.BaseCnn address issue #513
  • #520: Fix #518: [Refactor] Variable naming in CNN modules

Tests

  • #461: Add codecov token for testing
  • #470: Improve code test coverage
  • #491: Improve test coverage for predict APIs

Documentation Updates

  • #432: Refine test ReadMe
  • #436: Fix bugs of greek letters in docstring
  • #493: Update embed ReadMe
  • #499: Add workshop and tutorial repository links
  • #501: Update EMBC workshop link