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Implementation of new MIL algorithms and editing existing files to accommodate such algorithms #5

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awxlong wants to merge 8 commits intosecrierlab:mainfrom
awxlong:mil-architectures
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Implementation of new MIL algorithms and editing existing files to accommodate such algorithms #5
awxlong wants to merge 8 commits intosecrierlab:mainfrom
awxlong:mil-architectures

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@awxlong awxlong commented Jan 18, 2025

  1. I first deleted MIL.py from PL_protocol/ and replaced it with my own BaseMIL.py. This implements the abstract class BaseMIL from which all MIL algorithms inherit.
  2. I modified Image/MIL/init.py's list of available MIL models. I also modified Image/MIL/utils.py's file to include more helper functions relevant to the MIL algorithms, such as transformer layers and multimodal fusion.
  3. I modified the Image/init.py create_img_model() function to be more flexible to call the newly implemented MIL algorithms
  4. I added the definition of the following MIL algorithms, their paras, and pytorch lightning wrapper: AttentionMIL, CAMIL, CLAM, DTFD_MIL, DTFDMultimodal (please ignore this one I shouldn't push this), GraphTransformer, Transformer, TransMIL, and TransMILMultimodal and TransMILRegression.

Xuelong An Wang added 8 commits August 27, 2024 17:54
…onfig.py for better naming of directories created (avoid creating repetitive Data/ directory); 3. update pre_processing.py to extract features with foundation models UNI, prov-gigapath, resnet-50 and also compute weighted adjacency matrices as in CAMIL
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