0.3.0

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

New Contributors

• @ellabarkan made their first contribution in #245

Full Changelog: 0.2.9...0.3.0

0.2.9

What's Changed

• Color aug fix by @avihu111 in #213
• feat: added support for logits in some classification metrics #215 by @afoncubierta in #216
• adding check for class attribute, fixes issue #217 by @agiova in #218

Full Changelog: 0.2.8...0.2.9

0.2.8

What's Changed

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

New Contributors

• @ishita1805 made their first contribution in #198
• @avihu111 made their first contribution in #200

Full Changelog: 0.2.7...0.2.8

0.2.7

What's Changed

• fix: explicitly exclude vulnerable protobuf version by @vagenas in #195

Full Changelog: 0.2.6...0.2.7

0.2.6

What's Changed

• fix(#192): relax protobuf constraint by @vagenas in #193
• added silent mode to evaluator by @smartdanny in #194

New Contributors

• @vagenas made their first contribution in #193
• @smartdanny made their first contribution in #194

Full Changelog: 0.2.5...0.2.6

0.2.5

What's Changed

• Lightweight mode in DatasetDefault which alllows good GPU utilization in large datasets (e.g. 100M samples) by @YoelShoshan in #177
• classification/regression Heads by @liamhazan in #164
• OpCond and knight sample ids by @mosheraboh in #191

Full Changelog: 0.2.4...0.2.5

0.2.4

What's Changed

• Add supported python versions badge by @SagiPolaczek in #183
• multimodal modifications by @mosheraboh in #184

Full Changelog: 0.2.3...0.2.4

0.2.3

What's Changed

• fix the case in dataset_default when sample_ids are integers by @simona-rc in #171
• fix (#172): support cpu in knight example by @agiova in #173
• Yoels by @YoelShoshan in #174
• Small documentation fixes by @SagiPolaczek in #175
• ML pipeline ("one click" cross validation) in fuse2 style by @alex-golts in #154
• Support Python 3.10 by @SagiPolaczek in #179
• Make ISIC multimodal again by @SagiPolaczek in #168
• PyPi update - bump version and classifiers by @SagiPolaczek in #182

New Contributors

• @simona-rc made their first contribution in #171
• @agiova made their first contribution in #173

Full Changelog: 0.2.2...0.2.3

0.2.2

What's Changed

• added remove_extension, changed default deepdiff to ignore nans, added proper implementation of keys() values() and items() to NDict, tried to also highlight more the faulting op in pipeline ops error by @YoelShoshan in #152
• Knight test by @liamhazan in #149
• override first backbone layers only when necessary by @mosheraboh in #156
• 🌐 Some small general (handle URLError, Ops Debugs, etc) by @SagiPolaczek in #157
• new wrapper by @itaijj in #160
• Improve knight by @liamhazan in #158
• move to BiomedSciAI org by @mosheraboh in #166
• remove opencv version limitation by @mosheraboh in #169

Full Changelog: 0.2.1...0.2.2

0.2.1

What's Changed

• remove managers - training is based on PyTorch lightning
• Added debug operations in data pipeline
• Added more imaging operations
• Model should return now batch_dict and not batch_dict["model"]
• Minor bugfixes

Full Changelog: 0.2.0...0.2.1