Fuse-med-ml

Alert: major revision
FuseMedML new version introduces a few minor backward compatibility breaks.
Including new installation instructions.

What's Changed
* Add vit isic by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/221
* remove protobuf from dependencies by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/225
* Added more descriptive error messages and hints for common usage mistakes by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/226
* support arbitrary (not sequential and even not ints) balanced class values by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/227
* update DL readme according to JOSS reviewer comments by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/232
* Some changes from DTI task (Add doc' and some small features) by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/233
* knight data download script by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/235
* raise an exception in case of str input/outputs by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/234
* Auc metric fix by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/237
* CICD fix by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/239
* fix learning rate and added config options by liamhazan in https://github.com/BiomedSciAI/fuse-med-ml/pull/238
* Ensemble of multi-modal survival models by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/231
* add downsample option to BatchSamplerDefault by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/246
* Ehr transformer ICU example by ellabarkan in https://github.com/BiomedSciAI/fuse-med-ml/pull/245
* Simple MNIST Example by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/240
* Ehr transformer example by ellabarkan in https://github.com/BiomedSciAI/fuse-med-ml/pull/256
* a more configureable resnet3d implementation by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/257
* not strict mode in ProjectPatchesTokenizer by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/260
* allow non-int sample ids in DatasetDefault by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/259
* support not specifying number of channels in ModelMultiHead by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/244
* update JOSS paper citation and badge by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/263
* support shallow copy of pipelines by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/262
* fix bug with specific binary input format by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/264
* Ndict support hydra by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/265
* add props to dataset and pipelines + small fix to cacher by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/266
* optimized train time for a use case of small samples and large batch by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/268
* add multi-label metric cladd and func by egozi in https://github.com/BiomedSciAI/fuse-med-ml/pull/269
* `torchvision` version upper bound fix by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/254
* Additional model - `CrossAttentionTransformerEncoder` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/251
* ddp_fix by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/270
* `NDict` optimization by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/271
* remove examples. prefix by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/276
* make examples subpackage (fuse_examples) by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/277
* Fixes for the Hello World notebook by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/275
* Pl model save + export the entire dataset (all keys) to dataframe by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/281

New Contributors
* ellabarkan made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/245

**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.9...0.3.0

What's Changed
* Color aug fix by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/213
* feat: added support for logits in some classification metrics 215 by afoncubierta in https://github.com/BiomedSciAI/fuse-med-ml/pull/216
* adding check for class attribute, fixes issue 217 by agiova in https://github.com/BiomedSciAI/fuse-med-ml/pull/218


**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.8...0.2.9

What's Changed
* feat: add pre-commit hooks by ishita1805 in https://github.com/BiomedSciAI/fuse-med-ml/pull/198
* Transformer + 1D/2D/3D Vision Transformer by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/200
* net changes from plotly visualization by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/202
* Add csv logger to some examples (mnist & stoic) by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/204
* ISIC using DDP strategy by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/176
* Apply pre-commit changes (ex. `mypy`) on all files by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/209
* loss wrapper to batch dict by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/206
* Update backbone_vit.py by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/207
* Ukbb changes by avihu111 in https://github.com/BiomedSciAI/fuse-med-ml/pull/205
* fix: uncollate inference of batch size by afoncubierta in https://github.com/BiomedSciAI/fuse-med-ml/pull/211

New Contributors
* ishita1805 made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/198
* avihu111 made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/200

**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.7...0.2.8

What's Changed
* fix: explicitly exclude vulnerable protobuf version by vagenas in https://github.com/BiomedSciAI/fuse-med-ml/pull/195


**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.6...0.2.7

What's Changed
* fix(192): relax protobuf constraint by vagenas in https://github.com/BiomedSciAI/fuse-med-ml/pull/193
* added silent mode to evaluator by smartdanny in https://github.com/BiomedSciAI/fuse-med-ml/pull/194

New Contributors
* vagenas made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/193
* smartdanny made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/194

**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.5...0.2.6

What's Changed
* Lightweight mode in DatasetDefault which alllows good GPU utilization in large datasets (e.g. 100M samples) by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/177
* classification/regression Heads by liamhazan in https://github.com/BiomedSciAI/fuse-med-ml/pull/164
* OpCond and knight sample ids by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/191


**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.2.4...0.2.5