BiomedSciAI/fuse-med-ml issues and pull requests

#371 - adding r2 metric

Pull Request - State: closed - Opened by mosheraboh 10 days ago - 1 comment

#370 - multi test dataloaders

Pull Request - State: closed - Opened by mosheraboh 17 days ago

#369 - avoid from gpu sync attempt when using single gpu

Pull Request - State: closed - Opened by mosheraboh 18 days ago

#368 - Integrate `ModularTokenizerOp` with Hugging Face remote 🤗

Pull Request - State: closed - Opened by SagiPolaczek 21 days ago

#367 - support custom configure_optimizers method and avoid from saving random model by default

Pull Request - State: closed - Opened by mosheraboh 21 days ago

#366 - move modular tokenizer to fuse

Pull Request - State: closed - Opened by mosheraboh 24 days ago

#365 - to backward support packages importing metrics from a previous sub module

Pull Request - State: closed - Opened by YoelShoshan 25 days ago - 1 comment

#364 - added new metrics for regression tasks

Pull Request - State: closed - Opened by IdoAmosIBM 26 days ago - 2 comments

#363 - clearml offline mode

Pull Request - State: closed - Opened by mosheraboh about 1 month ago

#362 - Support tuples as sample IDs in Bootstrapping

Pull Request - State: open - Opened by ellabarkan about 2 months ago

#361 - Oai example

Pull Request - State: closed - Opened by liamhazan about 2 months ago

#360 - new OpRandCrop for augmentation

Pull Request - State: closed - Opened by bensha6757 2 months ago

#359 - fixed bug of specificity calculation

Pull Request - State: closed - Opened by ellabarkan 3 months ago

#358 - Matching keys lengths and new metrics

Pull Request - State: closed - Opened by IdoAmosIBM 3 months ago

#357 - Upper bound `numpy<2.0`

Pull Request - State: closed - Opened by SagiPolaczek 3 months ago - 1 comment

#356 - implement hdf5 dataset reader op

Pull Request - State: closed - Opened by mosheraboh 4 months ago

#355 - use scipy implementation for Pearson correlation

Pull Request - State: closed - Opened by alex-golts 5 months ago

#354 - min_size_per_dim + changes for scalars inputs+outputs support

Pull Request - State: closed - Opened by YoelShoshan 5 months ago

#353 - add workaround to support fsdp

Pull Request - State: closed - Opened by mosheraboh 5 months ago - 1 comment

#352 - MetricCountSeqAndTokens counst tokens in label (if exist) + improving epoch metrics print

Pull Request - State: closed - Opened by michalozeryflato 5 months ago

#351 - Remove usage of `xmlrunner` package

Issue - State: open - Opened by SagiPolaczek 5 months ago

#350 - Bump GitHub workflows' python version to `3.9`

Pull Request - State: closed - Opened by SagiPolaczek 6 months ago

#349 - collate now supports minimal dimension + added more support in samples cacher + added interface validation utility

Pull Request - State: closed - Opened by YoelShoshan 6 months ago

#348 - Crop pad fix

Pull Request - State: closed - Opened by IdoAmosIBM 6 months ago

#347 - shared memory utility helping to speedup reading from files significantly if enough RAM is available

Pull Request - State: closed - Opened by YoelShoshan 6 months ago

#346 - adds count num sequences and tokens metric

Pull Request - State: closed - Opened by mosheraboh 7 months ago - 2 comments

#345 - Perplexity gpu mem optimization

Pull Request - State: closed - Opened by mosheraboh 7 months ago

#344 - support pl module test step

Pull Request - State: closed - Opened by sivanravidos 7 months ago

#343 - Crop padding in collate

Pull Request - State: closed - Opened by liamhazan 8 months ago

#342 - Make `NDict` (hopefully) lighter to import

Pull Request - State: closed - Opened by SagiPolaczek 9 months ago

#341 - Support TSV files in `file_io`

Pull Request - State: closed - Opened by SagiPolaczek 9 months ago

#340 - Add OpReplaceAnyElements to ops_common

Pull Request - State: closed - Opened by sivanravidos 9 months ago

#339 - Added readthedocs config for documentation

Pull Request - State: closed - Opened by rakesh9177 10 months ago - 8 comments

#338 - pearson correlation metric

Pull Request - State: closed - Opened by alex-golts 10 months ago

#337 - Make `op_id` a really optional argument in `OpCast`

Pull Request - State: closed - Opened by SagiPolaczek 11 months ago

#336 - address tuple in collate

Pull Request - State: closed - Opened by michalozeryflato 11 months ago - 1 comment

#335 - OpSetRandomChoice

Pull Request - State: closed - Opened by mosheraboh about 1 year ago

#334 - Bfloat16 support

Pull Request - State: closed - Opened by mosheraboh about 1 year ago

#333 - Added `len` to `PipelineDefault`

Pull Request - State: closed - Opened by SagiPolaczek about 1 year ago

#332 - add a method to add sample ids to a dataset

Pull Request - State: closed - Opened by michalozeryflato about 1 year ago

#331 - adding torch_utils with select method similar to numpy

Pull Request - State: closed - Opened by michalozeryflato about 1 year ago

#330 - clearml logger + improved mnist starter

Pull Request - State: closed - Opened by shatz01 about 1 year ago

#329 - add ignore_index to auc_roc metric

Pull Request - State: closed - Opened by michalozeryflato about 1 year ago

#328 - Support a better string representation for `NDict`

Pull Request - State: closed - Opened by SagiPolaczek about 1 year ago - 2 comments
Labels: enhancement

#327 - Shaked fuse

Pull Request - State: closed - Opened by shakedpe over 1 year ago

#326 - OpFunc: input=None passes the entire sample_dict

Pull Request - State: closed - Opened by michalozeryflato over 1 year ago

#325 - add weight to extract loss class

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#324 - add an option in CollateDefault to add fixed items to batch_dict

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#323 - Remove `pyproject.toml`

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#322 - I got “NameError: name 'NDict' is not defined” from ndict.py, how can I fix it

Issue - State: closed - Opened by Betty-J over 1 year ago - 4 comments
Labels: question

#321 - multiple validation dataloaders in common lightning module

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#320 - Poriya Checkpointing Aid

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago - 3 comments

#319 - Refactoring: `.flake8` & `.mypy.ini` -> `setup.cfg`

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#318 - cleaning and reorganizing fuse core code on segmentation

Pull Request - State: closed - Opened by itaijj over 1 year ago

#317 - Shaked fuse

Pull Request - State: closed - Opened by shakedpe over 1 year ago

#316 - `TestCrossAttentionTransformerEncoder` randomly fails

Issue - State: open - Opened by SagiPolaczek over 1 year ago
Labels: bug

#315 - small fix. more intuitive condition for main process run

Pull Request - State: closed - Opened by alex-golts over 1 year ago

#314 - update resnet with pool option, added contrastive supervised loss

Pull Request - State: closed - Opened by shakedpe over 1 year ago

#313 - Prep for long train

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#312 - Fix ISIC's ResNet run (Poriya)

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#311 - add a flag to metric to avoid multigpu collection

Pull Request - State: closed - Opened by mosheraboh over 1 year ago - 1 comment

#310 - new picai seg

Pull Request - State: closed - Opened by itaijj over 1 year ago

#309 - Resnet3d bug fix

Pull Request - State: closed - Opened by itaijj over 1 year ago

#308 - resnet 3d with first channels dim != 64 bugfix

Pull Request - State: closed - Opened by itaijj over 1 year ago

#307 - bug in resnet3d following latest change

Issue - State: closed - Opened by itaijj over 1 year ago - 2 comments
Labels: bug

#306 - Picai detection

Pull Request - State: closed - Opened by itaijj over 1 year ago - 2 comments

#305 - make components more general

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#304 - `mypy` typing fix

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#303 - Integrate `isort`

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago - 1 comment

#302 - added an op to replace elements of value X with value Y - supporting numpy array, torch tensors, lists, and strings

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago - 2 comments

#301 - Support Lightning >=2.0.0 and Pandas >=2.0.0

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago - 2 comments

#300 - fixed num_available_cores to work correctly in distributed setting in LSF (using cores affinity)

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#299 - Shatz batch sampler

Pull Request - State: closed - Opened by smartdanny over 1 year ago - 1 comment

#298 - cindex: make pred np.array to allow negation

Pull Request - State: closed - Opened by michalozeryflato over 1 year ago - 1 comment

#297 - add postprocess to lostDefault

Pull Request - State: closed - Opened by itaijj over 1 year ago

#296 - multiprocessing improvements

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#295 - backbone resnet and resnet 3d - better pretrained support

Issue - State: open - Opened by mosheraboh over 1 year ago

#294 - Support for pl2 in simple mnist example

Pull Request - State: closed - Opened by smartdanny over 1 year ago

#293 - add backbone mvit

Pull Request - State: closed - Opened by liamhazan over 1 year ago - 1 comment

#292 - Support pytorch lightning 2.0.0

Issue - State: closed - Opened by mosheraboh over 1 year ago
Labels: enhancement

#291 - few fixes to enable pl2 - and limit pl version until all tests will …

Pull Request - State: closed - Opened by mosheraboh over 1 year ago - 1 comment

#290 - Failure in running mutliple GPUs with dp strategy for ehr_transformer

Issue - State: open - Opened by ellabarkan over 1 year ago - 1 comment
Labels: bug, wontfix

#289 - Make logging optional

Pull Request - State: closed - Opened by smartdanny over 1 year ago

#288 - perplexity impl + post collect func process fix

Pull Request - State: closed - Opened by mosheraboh over 1 year ago

#287 - 🧹 Integrate `nb-clean`

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#286 - added ability to ignore kwargs in function string descriptor building logic, and solved an issue in run_multiprocessed in verbose=0 case

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#285 - Adding participation in PyTorch Ecosystem to Readme

Pull Request - State: closed - Opened by simona-rc over 1 year ago

#284 - Caching should only be done on rank 0

Issue - State: open - Opened by smartdanny over 1 year ago - 1 comment
Labels: bug

#283 - Mention in readme that FuseMedML is part of PyTorch ecosystem

Issue - State: closed - Opened by mosheraboh over 1 year ago
Labels: enhancement

#282 - Yoels

Pull Request - State: closed - Opened by YoelShoshan over 1 year ago

#281 - Pl model save + export the entire dataset (all keys) to dataframe

Pull Request - State: closed - Opened by mosheraboh over 1 year ago - 1 comment

#280 - Update hello_world.ipynb

Pull Request - State: closed - Opened by alex-golts over 1 year ago

#278 - Update hello_world.ipynb example

Issue - State: closed - Opened by simona-rc over 1 year ago - 3 comments
Labels: bug

#277 - make examples subpackage (fuse_examples)

Pull Request - State: closed - Opened by mosheraboh over 1 year ago - 4 comments

#276 - remove examples. prefix

Pull Request - State: closed - Opened by alex-golts over 1 year ago

#275 - Fixes for the Hello World notebook

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago

#274 - made knight datamodule for DDP support

Pull Request - State: open - Opened by smartdanny over 1 year ago

#273 - NDict API change - missing pre-existing features

Issue - State: closed - Opened by avihu111 over 1 year ago - 2 comments
Labels: bug

#272 - Display CI output on Jenkins' console while building

Issue - State: open - Opened by SagiPolaczek over 1 year ago
Labels: enhancement, DEV

#271 - `NDict` optimization

Pull Request - State: closed - Opened by SagiPolaczek over 1 year ago - 1 comment
Labels: enhancement

GitHub / BiomedSciAI/fuse-med-ml issues and pull requests