Fuse-med-ml

What's Changed
* Adding participation in PyTorch Ecosystem to Readme by simona-rc in https://github.com/BiomedSciAI/fuse-med-ml/pull/285
* 🧹 Integrate `nb-clean` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/287
* added ability to ignore kwargs in function string descriptor building logic, and solved an issue in run_multiprocessed in verbose=0 case by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/286
* perplexity impl + post collect func process fix by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/288
* Make logging optional by shatz01 in https://github.com/BiomedSciAI/fuse-med-ml/pull/289
* few fixes to enable pl2 - and limit pl version until all tests will … by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/291
* Support for pl2 in simple mnist example by shatz01 in https://github.com/BiomedSciAI/fuse-med-ml/pull/294
* multiprocessing improvements by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/296
* Shatz batch sampler by shatz01 in https://github.com/BiomedSciAI/fuse-med-ml/pull/299
* fixed num_available_cores to work correctly in distributed setting in LSF (using cores affinity) by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/300
* cindex: make pred np.array to allow negation by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/298
* add backbone mvit by liamhazan in https://github.com/BiomedSciAI/fuse-med-ml/pull/293
* added an op to replace elements of value X with value Y - supporting numpy array, torch tensors, lists, and strings by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/302
* Support Lightning >=2.0.0 and Pandas >=2.0.0 by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/301
* make components more general by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/305
* `mypy` typing fix by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/304
* resnet 3d with first channels dim != 64 bugfix by itaijj in https://github.com/BiomedSciAI/fuse-med-ml/pull/308
* Resnet3d bug fix by itaijj in https://github.com/BiomedSciAI/fuse-med-ml/pull/309
* add a flag to metric to avoid multigpu collection by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/311
* Fix ISIC's ResNet run (Poriya) by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/312
* Prep for long train by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/313
* small fix. more intuitive condition for main process run by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/315
* update resnet with pool option, added contrastive supervised loss by shakedpe in https://github.com/BiomedSciAI/fuse-med-ml/pull/314
* new picai seg by itaijj in https://github.com/BiomedSciAI/fuse-med-ml/pull/310
* Shaked fuse by shakedpe in https://github.com/BiomedSciAI/fuse-med-ml/pull/317
* cleaning and reorganizing fuse core code on segmentation by itaijj in https://github.com/BiomedSciAI/fuse-med-ml/pull/318
* Refactoring: `.flake8` & `.mypy.ini` -> `setup.cfg` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/319
* multiple validation dataloaders in common lightning module by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/321
* Remove `pyproject.toml` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/323
* add an option in CollateDefault to add fixed items to batch_dict by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/324
* add weight to extract loss class by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/325
* Shaked fuse by shakedpe in https://github.com/BiomedSciAI/fuse-med-ml/pull/327
* OpFunc: input=None passes the entire sample_dict by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/326
* Support a better string representation for `NDict` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/328
* add ignore_index to auc_roc metric by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/329
* adding torch_utils with select method similar to numpy by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/331
* clearml logger + improved mnist starter by shatz01 in https://github.com/BiomedSciAI/fuse-med-ml/pull/330
* Added `__len__` to `PipelineDefault` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/333
* Bfloat16 support by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/334
* add a method to add sample ids to a dataset by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/332
* OpSetRandomChoice by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/335
* Make `op_id` a really optional argument in `OpCast` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/337
* pearson correlation metric by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/338
* Added readthedocs config for documentation by rakesh9177 in https://github.com/BiomedSciAI/fuse-med-ml/pull/339
* Make `NDict` (hopefully) lighter to import by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/342
* Support TSV files in `file_io` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/341
* Add OpReplaceAnyElements to ops_common by sivanravidos in https://github.com/BiomedSciAI/fuse-med-ml/pull/340
* Crop padding in collate by liamhazan in https://github.com/BiomedSciAI/fuse-med-ml/pull/343
* support pl module test step by sivanravidos in https://github.com/BiomedSciAI/fuse-med-ml/pull/344
* Perplexity gpu mem optimization by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/345
* adds count num sequences and tokens metric by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/346
* shared memory utility helping to speedup reading from files significantly if enough RAM is available by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/347
* Crop pad fix by IdoAmosIBM in https://github.com/BiomedSciAI/fuse-med-ml/pull/348
* Bump GitHub workflows' python version to `3.9` by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/350
* add workaround to support fsdp by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/353
* collate now supports minimal dimension + added more support in samples cacher + added interface validation utility by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/349
* MetricCountSeqAndTokens counst tokens in label (if exist) + improving epoch metrics print by michalozeryflato in https://github.com/BiomedSciAI/fuse-med-ml/pull/352
* implement hdf5 dataset reader op by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/356
* use scipy implementation for Pearson correlation by alex-golts in https://github.com/BiomedSciAI/fuse-med-ml/pull/355
* Matching keys lengths and new metrics by IdoAmosIBM in https://github.com/BiomedSciAI/fuse-med-ml/pull/358
* min_size_per_dim + changes for scalars inputs+outputs support by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/354
* new OpRandCrop for augmentation by bensha6757 in https://github.com/BiomedSciAI/fuse-med-ml/pull/360
* Oai example by liamhazan in https://github.com/BiomedSciAI/fuse-med-ml/pull/361
* fixed bug of specificity calculation by ellabarkan in https://github.com/BiomedSciAI/fuse-med-ml/pull/359
* clearml offline mode by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/363
* added new metrics for regression tasks by IdoAmosIBM in https://github.com/BiomedSciAI/fuse-med-ml/pull/364
* to backward support packages importing metrics from a previous sub module by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/365
* move modular tokenizer to fuse by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/366
* support custom configure_optimizers method and avoid from saving random model by default by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/367
* avoid from gpu sync attempt when using single gpu by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/369
* Integrate `ModularTokenizerOp` with Hugging Face remote 🤗 by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/368
* multi test dataloaders by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/370
* adding r2 metric by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/371
* Add new tokens to tokenizer op by matanninio in https://github.com/BiomedSciAI/fuse-med-ml/pull/373
* rmse score fix by mosheraboh in https://github.com/BiomedSciAI/fuse-med-ml/pull/372
* advancing to scalars gen2 by YoelShoshan in https://github.com/BiomedSciAI/fuse-med-ml/pull/374
* Tokenizer's default behavior on unknown token by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/375
* Bug fix in `ModularTokenizer.decode()` when the input is `torch.Tensor` type by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/376
* Bump python version for MAMMAL release by SagiPolaczek in https://github.com/BiomedSciAI/fuse-med-ml/pull/377

New Contributors
* shakedpe made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/314
* rakesh9177 made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/339
* sivanravidos made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/340
* IdoAmosIBM made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/348
* bensha6757 made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/360
* matanninio made their first contribution in https://github.com/BiomedSciAI/fuse-med-ml/pull/373

**Full Changelog**: https://github.com/BiomedSciAI/fuse-med-ml/compare/0.3.0...0.4.0

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