PyHealth 2.0.0

[jhnwu3]

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 Bump jinja2 from 3.0.3 to 3.1.3 in /docs #258
• Bump gradio from 3.44.2 to 4.19.2 in /chat-assistant by @dependabot[bot] in Bump gradio from 3.44.2 to 4.19.2 in /chat-assistant #272
• Bump langchain from 0.0.329 to 0.1.11 in /chat-assistant by @dependabot[bot] in Bump langchain from 0.0.329 to 0.1.11 in /chat-assistant #275
• fix minor bugs in omop.py by @ycq091044 in fix minor bugs in omop.py #287
• Bump jinja2 from 3.1.3 to 3.1.4 in /docs by @dependabot[bot] in Bump jinja2 from 3.1.3 to 3.1.4 in /docs #291
• Update doc by @zzachw in Update doc #312
• Dev by @jhnwu3 in Dev #320
• Updated Docs to Reflect New Incoming Communication Platforms by @jhnwu3 in Updated Docs to Reflect New Incoming Communication Platforms #322
• Fix/update doc by @zzachw in Fix/update doc #323
• Update pyhealth.datasets.TUABDataset.rst by @mosheber in Update pyhealth.datasets.TUABDataset.rst #296
• Validate YAML configs with Pydantic by @zzachw in Validate YAML configs with Pydantic #333
• Refactor MedicalTranscriptionsDataset by @zzachw in Refactor MedicalTranscriptionsDataset #336
• Refactor COVID19CXRDataset by @zzachw in Refactor COVID19CXRDataset #337
• MIMIC4 Refactor to Encompass Vision, Language, and EHR by @jhnwu3 in MIMIC4 Refactor to Encompass Vision, Language, and EHR #335
• Add EHRShot dataset and benchmarking tasks by @zzachw in Add EHRShot dataset and benchmarking tasks #350
• Fix issues with BaseDataset.load_table() by @zzachw in Fix issues with BaseDataset.load_table() #368
• Doc Updates to about.rst, index.rst, and tutorials.rst by @jhnwu3 in Doc Updates to about.rst, index.rst, and tutorials.rst #374
• fix bug with mortality label always being zero if hospital_expire_flag is a string by @PranavHerur in fix bug with mortality label always being zero if hospital_expire_flag is a string #391
• 2-3× Speedup for BaseDataset.set_task() by @zzachw in 2-3× Speedup for BaseDataset.set_task() #378
• Add NLP metrics package by @plandes in Add NLP metrics package #513
• fix readthedoc dependency error by @jhnwu3 in fix readthedoc dependency error #519
• readthedocs python update so huggingface can stop breaking by @jhnwu3 in readthedocs python update so huggingface can stop breaking #520
• fix docs python version incompatibility by @jhnwu3 in fix docs python version incompatibility #521
• fix doc requirements breaking from incompatibilities with numpy by @jhnwu3 in fix doc requirements breaking from incompatibilities with numpy #522
• test_dependencies by @jhnwu3 in test_dependencies #523
• fixed dependency errors in building autodocs by @jhnwu3 in fixed dependency errors in building autodocs #525
• Switch from Python setuptools to Pixi by @plandes in Switch from Python setuptools to Pixi #524
• MIMIC3 Initialize Test Case for Tests/Core by @jhnwu3 in MIMIC3 Initialize Test Case for Tests/Core #527
• more tutorial and doc updates by @jhnwu3 in more tutorial and doc updates #529
• project toml changes by @jhnwu3 in project toml changes #531
• readthedocs dependency fix by @jhnwu3 in readthedocs dependency fix #533
• SDOH Coding Model by @jhnwu3 in SDOH Coding Model #538
• crucial doc updates by @jhnwu3 in crucial doc updates #540
• Fix/auto docs pathing by @jhnwu3 in Fix/auto docs pathing #541
• Add/load tsv by @jhnwu3 in Add/load tsv #542
• make MLP compatible with the new pyhealth 2.0 loaders by @jhnwu3 in make MLP compatible with the new pyhealth 2.0 loaders #543
• Fix/mlp embedding by @jhnwu3 in Fix/mlp embedding #544
• legacy bug fix for the trainer assuming there exists a model.mode att… by @jhnwu3 in legacy bug fix for the trainer assuming there exists a model.mode att… #545
• added the ability to link visits by their ids instead of just their t… by @jhnwu3 in added the ability to link visits by their ids instead of just their t… #547
• Add/use processor class directly instead of just string by @jhnwu3 in Add/use processor class directly instead of just string #548
• Add/processor docs by @jhnwu3 in Add/processor docs #549
• Enhance mortality label check for string flags by @v1xerunt in Enhance mortality label check for string flags #551
• remove inactive link by @ycq091044 in remove inactive link #552
• Add/task caching by @jhnwu3 in Add/task caching #546
• huge docs update incoming by @jhnwu3 in huge docs update incoming #553
• Update/docs landing page by @jhnwu3 in Update/docs landing page #554
• Update/docs landing page by @jhnwu3 in Update/docs landing page #555
• tiny final update to badges by @jhnwu3 in tiny final update to badges #556
• fixing bold fonts and emojis by @jhnwu3 in fixing bold fonts and emojis #558
• Fix/model force dataset features by @jhnwu3 in Fix/model force dataset features #557
• more tasks, hopefully fix the lack of pages here by @jhnwu3 in more tasks, hopefully fix the lack of pages here #559
• change to autoclass instead of automod by @jhnwu3 in change to autoclass instead of automod #560
• Feat/accommodate legacy api by @jhnwu3 in Feat/accommodate legacy api #562
• fix to make model.mode compatible with trainers using new Processors … by @jhnwu3 in fix to make model.mode compatible with trainers using new Processors … #564
• small change to transformersmodel to not explicitly use a deprecated … by @jhnwu3 in small change to transformersmodel to not explicitly use a deprecated … #565
• update on pyhealth alpha release in the docs for installation by @jhnwu3 in update on pyhealth alpha release in the docs for installation #563
• init commit attempt for multihot embeddings, and other basic modeling… by @jhnwu3 in init commit attempt for multihot embeddings, and other basic modeling… #567
• docs update by @jhnwu3 in docs update #568
• init versioning control with Pixi and makefiles by @jhnwu3 in init versioning control with Pixi and makefiles #561
• Update/stagenet by @jhnwu3 in Update/stagenet #571
• init commit for stagenet documentation by @jhnwu3 in init commit for stagenet documentation #572
• update logo to newer, more streamlined colors logo by @jhnwu3 in update logo to newer, more streamlined colors logo #573
• clean up scratchiness of edges on pyhealth 2 logo by @jhnwu3 in clean up scratchiness of edges on pyhealth 2 logo #574
• Fix/pypi ver by @jhnwu3 in Fix/pypi ver #575
• Add/sample dataset processor transfer by @jhnwu3 in Add/sample dataset processor transfer #576
• [Bounty] Transformer PyHealth 2.0 ver. by @Logiquo in [Bounty] Transformer PyHealth 2.0 ver. #580
• Fix/drug recommendation by @jhnwu3 in Fix/drug recommendation #579
• Support mode parameter in the ImageProcessor by @Logiquo in Support mode parameter in the ImageProcessor #581
• init commit to fix documentation around interp and drug rec by @jhnwu3 in init commit to fix documentation around interp and drug rec #582
• [Bounty] CNN PyHealth 2.0 ver. by @Logiquo in [Bounty] CNN PyHealth 2.0 ver. #578
• add additional docs about pyhealth researchers and students by @jhnwu3 in add additional docs about pyhealth researchers and students #583
• Add/conformal cov pred by @jhnwu3 in Add/conformal cov pred #584
• make better instructions on dev environment by @jhnwu3 in make better instructions on dev environment #585
• init commit for omop extension by @jhnwu3 in init commit for omop extension #586
• commit to improve docs template for research initiative and our calib… by @jhnwu3 in commit to improve docs template for research initiative and our calib… #590
• Add/stagenet interp pipeline by @jhnwu3 in Add/stagenet interp pipeline #589
• init commit fix to enable portability of processors by @jhnwu3 in init commit fix to enable portability of processors #591
• [Bounty] SafeDrug by @lehendo in [Bounty] SafeDrug #588
• [Bounty] MICRON model adapted for PyHeatlh 2.0 version by @naveenkcb in [Bounty] MICRON model adapted for PyHeatlh 2.0 version #592
• update docs to include more details about the pyhealth research initi… by @jhnwu3 in update docs to include more details about the pyhealth research initi… #598
• Update/pyhealth community by @jhnwu3 in Update/pyhealth community #599
• [CS 598] Add DREAMT sleep dataset by @dalvg in [CS 598] Add DREAMT sleep dataset #595
• [Bounty] MoleRec by @lehendo in [Bounty] MoleRec #596
• Dataset: (BMD-HS) Heart Sound Recordings for Automated Cardiovascular Disease Diagnosis by @Razin93937 in Dataset: (BMD-HS) Heart Sound Recordings for Automated Cardiovascular Disease Diagnosis #600
• Add early stopping patience parameter to Trainer by @Razin93937 in Add early stopping patience parameter to Trainer #597
• Add/interp metrics by @jhnwu3 in Add/interp metrics #602
• Support processor tuple specs with kwargs in SampleDataset by @Razin93937 in Support processor tuple specs with kwargs in SampleDataset #603
• [Bounty] GNN PyHeatlh 2.0 ver. by @Logiquo in [Bounty] GNN PyHeatlh 2.0 ver. #587
• [BMS] Deeplift for MIMIC4 Mortality Prediction by @Logiquo in [BMS] Deeplift for MIMIC4 Mortality Prediction #593
• init commit to fix speed issues with mimic3 test cases by @jhnwu3 in init commit to fix speed issues with mimic3 test cases #607
• init commit to enable users to extend their processing beyond initial… by @jhnwu3 in init commit to enable users to extend their processing beyond initial… #606
• more navigation doc updates for users by @jhnwu3 in more navigation doc updates for users #608
• Update/docs by @jhnwu3 in Update/docs #609
• [Bounty] GAMENet by @lehendo in [Bounty] GAMENet #610
• [Bounty] ContraWR PyHealth 2.0 by @Razin93937 in [Bounty] ContraWR PyHealth 2.0 #604
• ChestX-ray14 Dataset and Classification Tasks by @EricSchrock in ChestX-ray14 Dataset and Classification Tasks #392
• init commit with more doc changes and the addition of a newsletter by @jhnwu3 in init commit with more doc changes and the addition of a newsletter #617
• small doc typo fix on task_fn vs. taskclass() by @jhnwu3 in small doc typo fix on task_fn vs. taskclass() #618
• Add Support for FeatureProcessor Instances in Schemas by @Razin93937 in Add Support for FeatureProcessor Instances in Schemas #615
• Example notebook with list of Datasets by @dalloliogm in Example notebook with list of Datasets #616
• Add dataset SUPPORT2 by @ningyuan-xie in Add dataset SUPPORT2 #614
• Basic gradient saliency visualization by @Nimanui in Basic gradient saliency visualization #594
• [BMS] Gradient Interaction Modification by @Logiquo in [BMS] Gradient Interaction Modification #605
• [Memory] Fix large memory usage during init call. by @Logiquo in [Memory] Fix large memory usage during __init__ call.  #620
• new update to phri links by @jhnwu3 in new update to phri links #628
• Add cancer genomics datasets and tasks (ClinVar, COSMIC, TCGA-PRAD) by @AbrahamArellano in Add cancer genomics datasets and tasks (ClinVar, COSMIC, TCGA-PRAD) #625
• update to status of phri to be year long and in constant rotation by @jhnwu3 in update to status of phri to be year long and in constant rotation #637
• add december newsletter surrounding call to the research initiative by @jhnwu3 in add december newsletter surrounding call to the research initiative #641
• [Bounty] Adacare PyHealth 2.0 by @Razin93937 in [Bounty] Adacare PyHealth 2.0 #613
• quick visual updates to the newsletter by @jhnwu3 in quick visual updates to the newsletter #643
• fix typos and make it easier to know how to join phri by @jhnwu3 in fix typos and make it easier to know how to join phri #650
• Fix/inference new tok new dim by @jhnwu3 in Fix/inference new tok new dim #623
• update to give a rough time estimate of the program by @jhnwu3 in update to give a rough time estimate of the program #653
• more typo fixes by @jhnwu3 in more typo fixes #655
• Update/phri call by @jhnwu3 in Update/phri call #656
• make change to add a table of contents so hopefully itll be easy to r… by @jhnwu3 in make change to add a table of contents so hopefully itll be easy to r… #657
• fix visual error for table of contents by @jhnwu3 in fix visual error for table of contents #658
• another year typo sigh* by @jhnwu3 in another year typo sigh* #659
• quick edits to have an actual official start date with communication … by @jhnwu3 in quick edits to have an actual official start date with communication … #661
• update pyprojectoml alpha version to 2.0a10 by @jhnwu3 in update pyprojectoml alpha version to 2.0a10 #660
• Fix SequenceProcessor by @Logiquo in Fix SequenceProcessor #691
• change overrides to none by @jhnwu3 in change overrides to none #731
• fix hopefully override by @jhnwu3 in fix hopefully override #734
• Fix/los pred by @jhnwu3 in Fix/los pred #735
• init commit to clarify install docs by @jhnwu3 in init commit to clarify install docs #736
• Mem 9 - Memory Efficiency Update by @jhnwu3 in Mem 9 - Memory Efficiency Update #739
• Update/pyproject by @jhnwu3 in Update/pyproject #741
• Fix/processors fit process by @jhnwu3 in Fix/processors fit process #744
• Add num_workers to BaseDataset by @Logiquo in Add num_workers to BaseDataset #743
• Fix incorrect null handling for patient_id and timestamp by @Logiquo in Fix incorrect null handling for patient_id and timestamp #746
• newsletter and doc updates for memory optimizations by @jhnwu3 in newsletter and doc updates for memory optimizations #745
• revision added to denote benchmarking setup by @jhnwu3 in revision added to denote benchmarking setup #747
• [Bounty] Update Dr. Agent model (PyHealth 2.0) by @joshuasteier in [Bounty] Update Dr. Agent model (PyHealth 2.0) #663
• [Bounty] ConCare PyHealth 2.0 ver by @joshuasteier in [Bounty] ConCare PyHealth 2.0 ver #649
• [Bounty] Deepr PyHealth 2.0 ver. by @joshuasteier in [Bounty] Deepr PyHealth 2.0 ver. #645
• Multiprocess task transformation by @Logiquo in Multiprocess task transformation #748
• Furthur optimization on task transformation. by @Logiquo in Furthur optimization on task transformation.  #750
• Clean up tmpdir correctly, cache task transformation result, and better notebook support. by @Logiquo in Clean up tmpdir correctly, cache task transformation result, and better notebook support.  #753
• Fix MIMIC3 unit tests by @EricSchrock in Fix MIMIC3 unit tests #757
• SHAP Interpretability method implementation by @naveenkcb in SHAP Interpretability method implementation #611
• Add/comp benchmark by @jhnwu3 in Add/comp benchmark #759
• init commit, will need to test the readme later, but should reflect m… by @jhnwu3 in init commit, will need to test the readme later, but should reflect m… #760
• [PyHealth2.0 Bounty] MIMIC3 Readmission Prediction by @EricSchrock in [PyHealth2.0 Bounty] MIMIC3 Readmission Prediction #751
• [Conformal EEG] TUEV Dataset and Task by @Razin93937 in [Conformal EEG] TUEV Dataset and Task #752
• update benchmark examples and pypi ver. by @jhnwu3 in update benchmark examples and pypi ver. #762
• Update the default task cache path to include task parameter names and values by @EricSchrock in Update the default task cache path to include task parameter names and values #766
• fix pixi deprecation warnings by @plandes in fix pixi deprecation warnings #769
• update benchmark examples and pypi ver. by @jhnwu3 in update benchmark examples and pypi ver. #771
• [Conformal EEG] TUEV Dataset ContraWR Example by @Razin93937 in [Conformal EEG] TUEV Dataset ContraWR Example #761
• TCN Bounty Implementation by @bilalarif3197 in TCN Bounty Implementation #729
• Remove trailing space in file name : timeseries_mimic4.py by @ekazum in Remove trailing space in file name : timeseries_mimic4.py #772
• Tidy up the ChestX-ray14 dataset for the PyHealth 2.0 release by @EricSchrock in Tidy up the ChestX-ray14 dataset for the PyHealth 2.0 release #777
• Typo in "How to Get Started" Documentation by @will-pang in Typo in "How to Get Started" Documentation #779
• LIME Interpretability by @naveenkcb in LIME Interpretability #758
• Add IgnoreProcessor to support remove a key in schema. by @Logiquo in Add IgnoreProcessor to support remove a key in schema.  #776
• [Conformal EEG] Add TUEV Conformal Prediction Examples - Conventional and Covariate Shift by @Razin93937 in [Conformal EEG] Add TUEV Conformal Prediction Examples - Conventional and Covariate Shift #780
• Add option to cache transformed data from processors and skip pipeline entirely by @Logiquo in Add option to cache transformed data from processors and skip pipeline entirely #783
• [BMS] StageNet with Attention by @Logiquo in [BMS] StageNet with Attention #707
• Fix the code will hang at set_task if any of the worker have 0 sample written by @Logiquo in Fix the code will hang at set_task if any of the worker have 0 sample written #784
• Allow change vocabs for processor that take vocabs by @Logiquo in Allow change vocabs for processor that take vocabs #778
• [PyHealth2.0 Bounty] OMOP Readmission Prediction by @EricSchrock in [PyHealth2.0 Bounty] OMOP Readmission Prediction #788
• [Conformal EEG] Fix TUEV dataset metadata permissions for shared cluster storage - main by @lehendo in [Conformal EEG] Fix TUEV dataset metadata permissions for shared cluster storage - main #787
• bump packages and remove pandarallel to see what happens, will need t… by @jhnwu3 in bump packages and remove pandarallel to see what happens, will need t… #791
• [Conformal EEG] Add TFM-Tokenizer model for EEG signal tokenization by @lehendo in [Conformal EEG] Add TFM-Tokenizer model for EEG signal tokenization #781
• Conformal prediction by @siddharthal in Conformal prediction #793
• MedLink Bounty by @Rian354 in MedLink Bounty #728
• init commit with additional visit ids for tables as attributes, altho… by @jhnwu3 in init commit with additional visit ids for tables as attributes, altho… #792
• Add/cxr comprehensive tutorial and benchmarks for PyHealth paper by @jhnwu3 in Add/cxr comprehensive tutorial and benchmarks for PyHealth paper #773
• Add/newsletter + update install docs for early release of PyHealth 2.0 by @jhnwu3 in Add/newsletter + update install docs for early release of PyHealth 2.0 #798
• Add multimodal RNN support by @jhnwu3 in Add multimodal RNN support #797
• make pyproject.toml reflect pypi changes by @jhnwu3 in make pyproject.toml reflect pypi changes #799
• Fix Deeplift Crash for Some Unlucky Embedding Values by @Logiquo in Fix Deeplift Crash for Some Unlucky Embedding Values #803
• Change hook-based non-linearity replacement to module-swap-based. by @Logiquo in Change hook-based non-linearity replacement to module-swap-based.  #805
• Fix pkg_resources warning by @Logiquo in Fix pkg_resources warning #804
• Add VisionEmbeddingModel for medical imaging by @joshuasteier in Add VisionEmbeddingModel for medical imaging #806
• Add/dka task by @jhnwu3 in Add/dka task #749
• TextEmbedding Module for Multimodality Reproducibility Study by @Rian354 in TextEmbedding Module for Multimodality Reproducibility Study #808
• Fix multi-class interpretability metric by @Logiquo in Fix multi-class interpretability metric #810
• out of memory error should be fixed since it should be iterative now … by @jhnwu3 in out of memory error should be fixed since it should be iterative now … #807
• [Conformal EEG] K-means clustering by @lehendo in [Conformal EEG] K-means clustering #795
• EHRMamba Implementation Into PyHealth by @lehendo in EHRMamba Implementation Into PyHealth #809
• Fix the MIMIC4 LoS and DKA task unit tests by @EricSchrock in Fix the MIMIC4 LoS and DKA task unit tests #813
• Fix lime CUDA OOM by @Logiquo in Fix lime CUDA OOM #811
• Add multi-class support for lime & shap by @Logiquo in Add multi-class support for lime & shap #814
• MIMIC4 Readmission Prediction by @EricSchrock in MIMIC4 Readmission Prediction #815
• BMS interpretability project runs scripts by @Logiquo in BMS interpretability project runs scripts #816
• Change UNK for token-ralated processor to 1 by @Logiquo in Change UNK for token-ralated processor to 1 #822
• Add auto-close PR workflow for old PRs. by @jhnwu3 in Add auto-close PR workflow for old PRs. #825
• Fix ChestX-ray14 Example Notebooks by @EricSchrock in Fix ChestX-ray14 Example Notebooks #828
• add example docs to all datasets and tasks possible by @jhnwu3 in add example docs to all datasets and tasks possible #823
• [Contribution] TimeImageProcessor for multimodal pipelines by @joshuasteier in [Contribution] TimeImageProcessor for multimodal pipelines #826
• Add TupleTimeTextProcessor for Temporal Text Data by @Rian354 in Add TupleTimeTextProcessor for Temporal Text Data #829
• Improve/docs by @jhnwu3 in Improve/docs #831
• [Conformal EEG] Neighborhood Conformal Prediction by @lehendo in [Conformal EEG] Neighborhood Conformal Prediction #824
• Update MIMIC3 example python scripts by @EricSchrock in Update MIMIC3 example python scripts #834
• Standard forward_from_embedding in BaseModel by @Logiquo in Standard forward_from_embedding in BaseModel #821
• TUAB Dataset PR by @Jathurshan0330 in TUAB Dataset PR #837
• Updated TUH dataset EEG tasks with preprocessing parameters by @Jathurshan0330 in Updated TUH dataset EEG tasks with preprocessing parameters #838
• Cleaned and Updated SpaRCNET examples for EEG event classification and abnormal prediction by @Jathurshan0330 in Cleaned and Updated SpaRCNET examples for EEG event classification and abnormal prediction #839
• Fix Chefer and add standardized API by @Logiquo in Fix Chefer and add standardized API #841
• Improve/docs by @jhnwu3 in Improve/docs #842
• Fix/eicu by @jhnwu3 in Fix/eicu #832
• Improve/docs - will merge without review since it's just quick doc changes that won't break anything. by @jhnwu3 in Improve/docs - will merge without review since it's just quick doc changes that won't break anything. #845
• Improve/docs by @jhnwu3 in Improve/docs #846
• more corrections to the documentation by @jhnwu3 in more corrections to the documentation #847
• [Contribution] JambaEHR: Hybrid Transformer-Mamba model for EHR prediction by @joshuasteier in [Contribution] JambaEHR: Hybrid Transformer-Mamba model for EHR prediction #848
• EEG Model PR: BIOT by @Jathurshan0330 in EEG Model PR: BIOT #849
• Fix flaky test_gradient_flow in JambaEHR (The core.test_jamba_ehr.TestJambaLayer.test_gradient_flow unit test is unstable #855) by @joshuasteier in Fix flaky test_gradient_flow in JambaEHR (#855) #857
• init commit, tldr the cache_dir or files should probably indicate tab… by @jhnwu3 in init commit, tldr the cache_dir or files should probably indicate tab… #835
• [Contribution] pyhealth.graph: Native knowledge graph support + GraphProcessor by @joshuasteier in [Contribution] pyhealth.graph: Native knowledge graph support + GraphProcessor #853
• init commit for guidelines by @jhnwu3 in init commit for guidelines #861
• Smart Processor + Unified Multimodal Embedding Support + HF Tokenization by @Rian354 in Smart Processor + Unified Multimodal Embedding Support + HF Tokenization #863
• [PyHealth 2.0 Bounty] Sparcnet fix for pyhealth 2.0 by @joshuxchn in [PyHealth 2.0 Bounty] Sparcnet fix for pyhealth 2.0 #864
• Make SHAP & LIME black box by @Logiquo in Make SHAP & LIME black box #856
• Add Ensemble Interpreter by @Logiquo in Add Ensemble Interpreter #850
• Fix/calendar link by @jhnwu3 in Fix/calendar link #870
• Fixed issues in reproducing inference results in TFM-Tokenizer by @Jathurshan0330 in Fixed issues in reproducing inference results in TFM-Tokenizer #860
• tldr; add improved check to task and dataset cache by @jhnwu3 in tldr; add improved check to task and dataset cache #876
• [Contribution] GraphCare: KG-enhanced EHR predictions (ICLR 2024) by @joshuasteier in [Contribution] GraphCare: KG-enhanced EHR predictions (ICLR 2024) #882
• small fix so that agents no longer get confused that its 1.14 installed by @jhnwu3 in small fix so that agents no longer get confused that its 1.14 installed #888
• Update/core docs by @jhnwu3 in Update/core docs #889
• [Conformal EEG] TUEV/TUAB Compatibility by @lehendo in [Conformal EEG] TUEV/TUAB Compatibility #894
• Updated Conformal Test Scripts by @lehendo in Updated Conformal Test Scripts #895
• fix: prevent batch_size=1 crashes, secure torch.load, fix device/contiguity issues by @haoyu-haoyu in fix: prevent batch_size=1 crashes, secure torch.load, fix device/contiguity issues #901
• fix: improve research reliability — metrics mutation, eval mode, reproducible splits by @haoyu-haoyu in fix: improve research reliability — metrics mutation, eval mode, reproducible splits #902
• fix: port GRASP model to PyHealth 2.0 API (fixes [Bug] GRASP model broken in 2.0.0: Incompatible with new BaseModel API (unexpected keyword argument 'feature_keys') #891) by @haoyu-haoyu in fix: port GRASP model to PyHealth 2.0 API (fixes #891) #903
• making the PyHealth Research Initiative page way less confusing and d… by @jhnwu3 in making the PyHealth Research Initiative page way less confusing and d… #907

New Contributors

• @mosheber made their first contribution in Update pyhealth.datasets.TUABDataset.rst #296
• @PranavHerur made their first contribution in fix bug with mortality label always being zero if hospital_expire_flag is a string #391
• @plandes made their first contribution in Add NLP metrics package #513
• @Logiquo made their first contribution in [Bounty] Transformer PyHealth 2.0 ver. #580
• @lehendo made their first contribution in [Bounty] SafeDrug #588
• @naveenkcb made their first contribution in [Bounty] MICRON model adapted for PyHeatlh 2.0 version #592
• @dalvg made their first contribution in [CS 598] Add DREAMT sleep dataset #595
• @Razin93937 made their first contribution in Dataset: (BMD-HS) Heart Sound Recordings for Automated Cardiovascular Disease Diagnosis #600
• @EricSchrock made their first contribution in ChestX-ray14 Dataset and Classification Tasks #392
• @dalloliogm made their first contribution in Example notebook with list of Datasets #616
• @ningyuan-xie made their first contribution in Add dataset SUPPORT2 #614
• @Nimanui made their first contribution in Basic gradient saliency visualization #594
• @AbrahamArellano made their first contribution in Add cancer genomics datasets and tasks (ClinVar, COSMIC, TCGA-PRAD) #625
• @joshuasteier made their first contribution in [Bounty] Update Dr. Agent model (PyHealth 2.0) #663
• @bilalarif3197 made their first contribution in TCN Bounty Implementation #729
• @ekazum made their first contribution in Remove trailing space in file name : timeseries_mimic4.py #772
• @will-pang made their first contribution in Typo in "How to Get Started" Documentation #779
• @siddharthal made their first contribution in Conformal prediction #793
• @Rian354 made their first contribution in MedLink Bounty #728
• @joshuxchn made their first contribution in [PyHealth 2.0 Bounty] Sparcnet fix for pyhealth 2.0 #864
• @haoyu-haoyu made their first contribution in fix: prevent batch_size=1 crashes, secure torch.load, fix device/contiguity issues #901

Full Changelog: v1.1.6...v2.0.0

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This discussion was created from the release PyHealth 2.0.0.