EEG-GCNN: Dataset, Task, Models, and Neurological Disease Detection Pipeline#1059

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Commits on Dec 3, 2025

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Commits on Dec 24, 2025

[Bounty] Update Dr. Agent model (PyHealth 2.0) (#663)

joshuasteier
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Steier
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[Bounty] ConCare PyHealth 2.0 ver (#649)

joshuasteier
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Steier
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[Bounty] Deepr PyHealth 2.0 ver. (#645)

joshuasteier
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Steier
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Multiprocess task transformation (#748)
Logiquo
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Commits on Dec 26, 2025

Furthur optimization on task transformation. (#750)
Logiquo
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Commits on Dec 27, 2025

Clean up tmpdir correctly, cache task transformation result, and better notebook support. (#753)
Logiquo
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Commits on Dec 28, 2025

Fix MIMIC3 unit tests (#757)
EricSchrock
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Commits on Dec 29, 2025

Commits on Dec 30, 2025

[PyHealth2.0 Bounty] MIMIC3 Readmission Prediction (#751)
EricSchrock
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Commits on Dec 31, 2025

[Conformal EEG] TUEV Dataset and Task (#752)
Razin93937
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Commits on Jan 1, 2026

update benchmark examples and pypi ver. (#762)
jhnwu3
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Commits on Jan 2, 2026

Update the default task cache path to include task parameter names and values (#766)
EricSchrock
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Commits on Jan 5, 2026

Fix pixi deprecation warnings in CI (#769)
plandes
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Commits on Jan 6, 2026

Commits on Jan 9, 2026

Rename timeseries_mimic4.py to timeseries_mimic4.py (#772)
ekazum
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Commits on Jan 15, 2026

Allow change vocabs for processor that take vocabs (#778)
Logiquo
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Commits on Jan 19, 2026

Commits on Jan 22, 2026

Add/cxr comprehensive tutorial and benchmarks for PyHealth paper (#773)
jhnwu3
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Commits on Jan 27, 2026

Commits on Jan 31, 2026

Commits on Feb 2, 2026

Add VisionEmbeddingModel for medical imaging (#806)

joshuasteier
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Steier
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Add/dka task (#749)

jhnwu3
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Logiquo
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Commits on Feb 3, 2026

Commits on Feb 5, 2026

BMS interpretability project runs scripts (#816)

Logiquo
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jhnwu3
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Commits on Feb 6, 2026

Commits on Feb 8, 2026

Commits on Feb 11, 2026

Fix Chefer and add standardized API (#841)
Logiquo
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Commits on Feb 13, 2026

Commits on Feb 15, 2026

EEG Model PR: BIOT (#849)
Jathurshan0330
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Commits on Feb 16, 2026

Commits on Feb 17, 2026

Commits on Feb 19, 2026

Smart Processor + Unified Multimodal Embedding Support + HF Tokenization (#863)
Rian354
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Commits on Feb 20, 2026

sparcnet fix for pyhealth 2.0 (#864)
joshuxchn
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Commits on Feb 23, 2026

Commits on Feb 24, 2026

Commits on Feb 28, 2026

tldr; add improved check to task and dataset cache (#876)
jhnwu3
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Commits on Mar 7, 2026

Add GraphCare model using pyhealth.graph infrastructure (#882)

joshuasteier
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Steier
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Commits on Mar 12, 2026

small fix so that agents no longer get confused that its 1.14 installed (#888)
jhnwu3
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Commits on Mar 13, 2026

Update/core docs (#889)
jhnwu3
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Commits on Mar 15, 2026

[Conformal EEG] TUEV/TUAB Compatibility (#894)
lehendo
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Commits on Mar 16, 2026

Updated Conformal Test Scripts (#895)
lehendo
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Commits on Mar 22, 2026

Commits on Mar 23, 2026

making the PyHealth Research Initiative page way less confusing and dense (#907)
jhnwu3
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Commits on Mar 25, 2026

add new reference to the top of the pyhealth page for our new project page so users who join can hopefully find a more easy to navigate page that isn't so documentation heavy to find what they're l…
jhnwu3
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Commits on Mar 30, 2026

Commits on Mar 31, 2026

Commits on Apr 1, 2026

Commits on Apr 6, 2026

feat: align schema keys with teammate's model and add combined pipeline

Jimmy Burhan
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Jimmy Burhan
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feat: align schema keys with teammate's model and add combined pipeline

Jimmy Burhan
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Jimmy Burhan
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Commits on Apr 8, 2026

Commits on Apr 9, 2026

Initial dataset, config and task, prepared for edge weight and frequency band ablations.

Robert Coffey
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Robert Coffey
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Initial dataset, config and task, prepared for edge weight and frequency band ablations.

Robert Coffey
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Robert Coffey
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Initial dataset, config and task, prepared for edge weight and frequency band ablations.

Robert Coffey
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Robert Coffey
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Approach adjusted so frequency bands are sampled on inference only and not also on training to reduce the time needed

Robert Coffey
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Robert Coffey
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Approach adjusted so frequency bands are sampled on inference only and not also on training to reduce the time needed

Robert Coffey
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Robert Coffey
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Approach adjusted so frequency bands are sampled on inference only and not also on training to reduce the time needed

Robert Coffey
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Robert Coffey
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Commits on Apr 10, 2026

Commits on Apr 12, 2026

Fix Interpretability Methods `target_class_idx` (#926)
Logiquo
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Commits on Apr 13, 2026

Models added and documentation updates made to dataset and classifier.

Robert Coffey
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Robert Coffey
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Models added and documentation updates made to dataset and classifier.

Robert Coffey
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Robert Coffey
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Models added and documentation updates made to dataset and classifier.

Robert Coffey
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Robert Coffey
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heldout_test_run_gatcnn and training_pipeline_short_gatcnn added to examples/eeg_gatcnn

Robert Coffey
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Robert Coffey
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heldout_test_run_gatcnn and training_pipeline_short_gatcnn added to examples/eeg_gatcnn

Robert Coffey
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Robert Coffey
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heldout_test_run_gatcnn and training_pipeline_short_gatcnn added to examples/eeg_gatcnn

Robert Coffey
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Robert Coffey
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Training_pipeline_shallow_gcnn, heldout_test_run_gcnn and run_band_ablation added.

Robert Coffey
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Robert Coffey
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Training_pipeline_shallow_gcnn, heldout_test_run_gcnn and run_band_ablation added.

Robert Coffey
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Robert Coffey
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Training_pipeline_shallow_gcnn, heldout_test_run_gcnn and run_band_ablation added.

Robert Coffey
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Robert Coffey
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refactor: rename EEGGCNNDataset -> EEGGCNNRawDataset to avoid collision with teammate's implementation

Jimmy Burhan
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Jimmy Burhan
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refactor: rename EEGGCNNDataset -> EEGGCNNRawDataset to avoid collision with teammate's implementation

Jimmy Burhan
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Jimmy Burhan
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Merge remote-tracking branch 'origin/roberts' into eeg-gcnn-contribution

Jimmy Burhan
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Jimmy Burhan
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Merge remote-tracking branch 'origin/roberts' into eeg-gcnn-contribution

Jimmy Burhan
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Jimmy Burhan
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Documentation rst files added and updated for dataset, models and related task.

Robert Coffey
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Robert Coffey
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Documentation rst files added and updated for dataset, models and related task.

Robert Coffey
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Robert Coffey
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feat: add LEMON channel aliases, processed sample outputs, and fix broken imports

Jimmy Burhan
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Jimmy Burhan
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feat: add LEMON channel aliases, processed sample outputs, and fix broken imports

Jimmy Burhan
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Jimmy Burhan
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Unit tests added for gcnn_dataset, gcnn_model and gat_model

Robert Coffey
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Robert Coffey
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Unit tests added for gcnn_dataset, gcnn_model and gat_model

Robert Coffey
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Robert Coffey
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small fix + bump to pyproject.toml ver. for bug fixed release on pypi (#927)
jhnwu3
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test: add unit tests for RNN and MultimodalRNN models (#936)
haoyu-haoyu
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Conformal Methods and Scripts (#942)
lehendo
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Commits on Apr 14, 2026

Merge Robert's latest: model docs, model tests, dataset tests

Jimmy Burhan
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Jimmy Burhan
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Merge Robert's latest: model docs, model tests, dataset tests

Jimmy Burhan
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Jimmy Burhan
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Dev/grasp full pipeline (#905)

authored

Commits on Apr 18, 2026

Model, training, and holdout scripts updated. Docs and tests added.

Robert Coffey
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Robert Coffey
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Model, training, and holdout scripts updated. Docs and tests added.

Robert Coffey
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Robert Coffey
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Merge Robert's latest (a074d3f): updated models, training scripts, pipeline docs, and tests

Jimmy Burhan
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Jimmy Burhan
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Merge Robert's latest (a074d3f): updated models, training scripts, pipeline docs, and tests

Jimmy Burhan
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Jimmy Burhan
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fix: correct prepare_metadata test to use EEGGCNNRawDataset for TUAB/LEMON CSV generation

Jimmy Burhan
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Jimmy Burhan
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fix: correct prepare_metadata test to use EEGGCNNRawDataset for TUAB/LEMON CSV generation

Jimmy Burhan
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Jimmy Burhan
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Merge master into branch: keep our newer versions of all EEG-GCNN files

Jimmy Burhan
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Jimmy Burhan
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Merge master into branch: keep our newer versions of all EEG-GCNN files

Jimmy Burhan
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Jimmy Burhan
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feat: add pre-compute pipeline scripts for GCN and GAT with raw TUAB/LEMON data, expand pipeline docs with dataset processing section

Jimmy Burhan
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Jimmy Burhan
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feat: add pre-compute pipeline scripts for GCN and GAT with raw TUAB/LEMON data, expand pipeline docs with dataset processing section

Jimmy Burhan
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Jimmy Burhan
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fix: align EEGGCNNDiseaseDetection task_name to match class name convention

Jimmy Burhan
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Jimmy Burhan
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fix: align EEGGCNNDiseaseDetection task_name to match class name convention

Jimmy Burhan
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Jimmy Burhan
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refactor: rename eeg_gcnn_nd_detection -> eeg_gcnn_disease_detection to match EEGGCNNDiseaseDetection class name

Jimmy Burhan
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Jimmy Burhan
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refactor: rename eeg_gcnn_nd_detection -> eeg_gcnn_disease_detection to match EEGGCNNDiseaseDetection class name

Jimmy Burhan
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Jimmy Burhan
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docs: rewrite eeg_gcnn_pipeline.rst to cover full end-to-end pipeline

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Jimmy Burhan
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docs: rewrite eeg_gcnn_pipeline.rst to cover full end-to-end pipeline

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Jimmy Burhan
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docs: correct ablation section to reflect actual studies performed

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Jimmy Burhan
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docs: correct ablation section to reflect actual studies performed

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Jimmy Burhan
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docs: update adjacency ablation with full GCN + GAT results and paper comparison

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Jimmy Burhan
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docs: update adjacency ablation with full GCN + GAT results and paper comparison

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Jimmy Burhan
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docs: add Robert's spectral frequency analysis results table

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Jimmy Burhan
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docs: add Robert's spectral frequency analysis results table

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Jimmy Burhan
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docs: fix spectral frequency analysis table — correct all values from slides

authored and
Jimmy Burhan
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docs: fix spectral frequency analysis table — correct all values from slides

authored and
Jimmy Burhan
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docs: add F1 column to adjacency ablation tables for GCN and GAT

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Jimmy Burhan
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docs: add F1 column to adjacency ablation tables for GCN and GAT

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Jimmy Burhan
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Commits on Apr 19, 2026

Adjustments made to save output files. Also end to end pipeline checking has been removed.

Robert Coffey
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Robert Coffey
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Adjustments made to save output files. Also end to end pipeline checking has been removed.

Robert Coffey
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Robert Coffey
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Corrected labelling of TUAB normal from health to diseased. Updated documentation.

Robert Coffey
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Robert Coffey
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Corrected labelling of TUAB normal from health to diseased. Updated documentation.

Robert Coffey
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Robert Coffey
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Adding the possibility to configure the number of TUAB and LEMON patients to include in the precompute step.

Robert Coffey
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Robert Coffey
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Adding the possibility to configure the number of TUAB and LEMON patients to include in the precompute step.

Robert Coffey
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Robert Coffey
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Correction made to the name convention for the LEMON files. Those downloaded recently have a different external directory numbering

Robert Coffey
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Robert Coffey
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Correction made to the name convention for the LEMON files. Those downloaded recently have a different external directory numbering

Robert Coffey
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Robert Coffey
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Name of pre_compute_gcnn.py changed to pre-compute.py

Robert Coffey
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Robert Coffey
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Name of pre_compute_gcnn.py changed to pre-compute.py

Robert Coffey
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Robert Coffey
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docs: address Robert's review feedback

authored and
Jimmy Burhan
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docs: address Robert's review feedback

authored and
Jimmy Burhan
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Introduced a new LR approach to the GAT model and deleted two old files.

Robert Coffey
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Robert Coffey
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Introduced a new LR approach to the GAT model and deleted two old files.

Robert Coffey
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Robert Coffey
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Merge branch 'eeg-gcnn-contribution' of https://github.com/jburhan/PyHealth into eeg-gcnn-contribution

Robert Coffey
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Robert Coffey
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Merge branch 'eeg-gcnn-contribution' of https://github.com/jburhan/PyHealth into eeg-gcnn-contribution

Robert Coffey
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Robert Coffey
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Add PhysioNet De-Identification dataset, NER task, and TransformerDeID model (#981)
mtmckenna
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dl4h final project kobeguo2 - CaliForest (#999)
KobeGuo99
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Commits on Apr 20, 2026

Commits on Apr 21, 2026

Adding updated GAT training pipeline and also sample data.

Robert Coffey
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Robert Coffey
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Merge remote-tracking branch 'origin/eeg-gcnn-contribution' into eeg-gcnn-contribution

Robert Coffey
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Robert Coffey
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docs: clarify EEGGCNNDiseaseDetection vs EEGGCNNRawDataset in signal processing section

authored and
Jimmy Burhan
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Naming of /example files updated to required convention.

Robert Coffey
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Robert Coffey
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Merge remote-tracking branch 'origin/eeg-gcnn-contribution' into eeg-gcnn-contribution

Robert Coffey
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Robert Coffey
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Sample raw and precomputed data added to the eeg_gcnn folder

Robert Coffey
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Robert Coffey
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feat: add examples/eeg_gcnn_classification_eeg_graph_conv_net.py

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Jimmy Burhan
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chore: remove redundant top-level example script

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Jimmy Burhan
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Links to raw data added to documentation and duplicate test_eeg_gcnn.py removed

Robert Coffey
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Robert Coffey
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tests: merge raw-path tests into test_eeg_gcnn_dataset.py

Jimmy Burhan
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claude
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Merge eeg-gcnn-contribution into master

Jimmy Burhan
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claude
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tests: add precompute_features integration tests using sample raw data

Jimmy Burhan
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claude
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Commits on Apr 22, 2026

tests: split into test_eeg_gcnn_dataset.py and test_eeg_gcnn_raw_dataset.py

Jimmy Burhan
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claude
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tests: fully revert test_eeg_gcnn_dataset.py to Robert's original

Jimmy Burhan
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claude
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tests: remove pyhealth/tests/test_eeg_gcnn.py

Jimmy Burhan
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claude
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docs: fix band Hz ranges and remove non-existent download_lemon.py

Jimmy Burhan
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claude
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chore: remove pyhealth/eeg-gcnn-data/processed_samples from repo

Jimmy Burhan
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claude
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tests: remove tests/test_eeg_gcnn.py

Jimmy Burhan
and
claude
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Deleted redundanct documents and minor updates made to .rst and raw test documents.

Robert Coffey
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Robert Coffey
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