Releases · sunlabuiuc/PyHealth

There's a huge chain of chnages from 1.1.6 to 2.0.0. But, functionally, we've revamped the entire framework to be faster, easier to use, more scalable, and just overall more useful for any task a researcher might want to do.

What's Changed

Bump jinja2 from 3.0.3 to 3.1.3 in /docs by @dependabot[bot] in #258
Bump gradio from 3.44.2 to 4.19.2 in /chat-assistant by @dependabot[bot] in #272
Bump langchain from 0.0.329 to 0.1.11 in /chat-assistant by @dependabot[bot] in #275
fix minor bugs in omop.py by @ycq091044 in #287
Bump jinja2 from 3.1.3 to 3.1.4 in /docs by @dependabot[bot] in #291
Update doc by @zzachw in #312
Dev by @jhnwu3 in #320
Updated Docs to Reflect New Incoming Communication Platforms by @jhnwu3 in #322
Fix/update doc by @zzachw in #323
Update pyhealth.datasets.TUABDataset.rst by @mosheber in #296
Validate YAML configs with Pydantic by @zzachw in #333
Refactor MedicalTranscriptionsDataset by @zzachw in #336
Refactor COVID19CXRDataset by @zzachw in #337
MIMIC4 Refactor to Encompass Vision, Language, and EHR by @jhnwu3 in #335
Add EHRShot dataset and benchmarking tasks by @zzachw in #350
Fix issues with BaseDataset.load_table() by @zzachw in #368
Doc Updates to about.rst, index.rst, and tutorials.rst by @jhnwu3 in #374
fix bug with mortality label always being zero if hospital_expire_flag is a string by @PranavHerur in #391
2-3× Speedup for BaseDataset.set_task() by @zzachw in #378
Add NLP metrics package by @plandes in #513
fix readthedoc dependency error by @jhnwu3 in #519
readthedocs python update so huggingface can stop breaking by @jhnwu3 in #520
fix docs python version incompatibility by @jhnwu3 in #521
fix doc requirements breaking from incompatibilities with numpy by @jhnwu3 in #522
test_dependencies by @jhnwu3 in #523
fixed dependency errors in building autodocs by @jhnwu3 in #525
Switch from Python setuptools to Pixi by @plandes in #524
MIMIC3 Initialize Test Case for Tests/Core by @jhnwu3 in #527
more tutorial and doc updates by @jhnwu3 in #529
project toml changes by @jhnwu3 in #531
readthedocs dependency fix by @jhnwu3 in #533
SDOH Coding Model by @jhnwu3 in #538
crucial doc updates by @jhnwu3 in #540
Fix/auto docs pathing by @jhnwu3 in #541
Add/load tsv by @jhnwu3 in #542
make MLP compatible with the new pyhealth 2.0 loaders by @jhnwu3 in #543
Fix/mlp embedding by @jhnwu3 in #544
legacy bug fix for the trainer assuming there exists a model.mode att… by @jhnwu3 in #545
added the ability to link visits by their ids instead of just their t… by @jhnwu3 in #547
Add/use processor class directly instead of just string by @jhnwu3 in #548
Add/processor docs by @jhnwu3 in #549
Enhance mortality label check for string flags by @v1xerunt in #551
remove inactive link by @ycq091044 in #552
Add/task caching by @jhnwu3 in #546
huge docs update incoming by @jhnwu3 in #553
Update/docs landing page by @jhnwu3 in #554
Update/docs landing page by @jhnwu3 in #555
tiny final update to badges by @jhnwu3 in #556
fixing bold fonts and emojis by @jhnwu3 in #558
Fix/model force dataset features by @jhnwu3 in #557
more tasks, hopefully fix the lack of pages here by @jhnwu3 in #559
change to autoclass instead of automod by @jhnwu3 in #560
Feat/accommodate legacy api by @jhnwu3 in #562
fix to make model.mode compatible with trainers using new Processors … by @jhnwu3 in #564
small change to transformersmodel to not explicitly use a deprecated … by @jhnwu3 in #565
update on pyhealth alpha release in the docs for installation by @jhnwu3 in #563
init commit attempt for multihot embeddings, and other basic modeling… by @jhnwu3 in #567
docs update by @jhnwu3 in #568
init versioning control with Pixi and makefiles by @jhnwu3 in #561
Update/stagenet by @jhnwu3 in #571
init commit for stagenet documentation by @jhnwu3 in #572
update logo to newer, more streamlined colors logo by @jhnwu3 in #573
clean up scratchiness of edges on pyhealth 2 logo by @jhnwu3 in #574
Fix/pypi ver by @jhnwu3 in #575
Add/sample dataset processor transfer by @jhnwu3 in #576
[Bounty] Transformer PyHealth 2.0 ver. by @Logiquo in #580
Fix/drug recommendation by @jhnwu3 in #579
Support mode parameter in the ImageProcessor by @Logiquo in #581
init commit to fix documentation around interp and drug rec by @jhnwu3 in #582
[Bounty] CNN PyHealth 2.0 ver. by @Logiquo in #578
add additional docs about pyhealth researchers and students by @jhnwu3 in #583
Add/conformal cov pred by @jhnwu3 in #584
make better instructions on dev environment by @jhnwu3 in #585
init commit for omop extension by @jhnwu3 in #586
commit to improve docs template for research initiative and our calib… by @jhnwu3 in #590
Add/stagenet interp pipeline by @jhnwu3 in #589
init commit fix to enable portability of processors by @jhnwu3 in #591
[Bounty] SafeDrug by @lehendo in #588
[Bounty] MICRON model adapted for PyHeatlh 2.0 version by @naveenkcb in #592
update docs to include more details about the pyhealth research initi… by @jhnwu3 in #598
Update/pyhealth community by @jhnwu3 in #599
[CS 598] Add DREAMT sleep dataset by @dalvg in #595
[Bounty] MoleRec by @lehendo in #596
Dataset: (BMD-HS) Heart Sound Recordings for Automated Cardiovascular Disease Diagnosis by @Razin93937 in #600
Add early stopping patience parameter to Trainer by @Razin93937 in #597
Add/interp metrics by @jhnwu3 in #602
Support processor tuple specs with kwargs in SampleDataset by @Razin93937 in #603
[Bounty] GNN PyHeatlh 2.0 ver. by @Logiquo in #587
[BMS] Deeplift for MIMIC4 Mortality Prediction by @Logiquo in #593
init commit to fix speed issues with mimic3 test cases by @jhnwu3 in #607
init commit to enable users to extend their processing beyond initial… by @jhnwu3 in #606
more navigation doc updates for users by @jhnwu3 in #608
Update/docs by @j...