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666266b
Add CheXpert Plus dataset, RadiologyKGExtraction task, and ReXKG model
Sterilistic Apr 18, 2026
f5faa4d
Add API documentation pages and toctree entries for ReXKG contribution
Sterilistic Apr 18, 2026
874335d
Add end-to-end ReXKG notebook example and tutorials.rst entry
Sterilistic Apr 19, 2026
ea5d702
Add GPT-4o entity/relation extraction pipeline to ReXKG notebook
Sterilistic Apr 19, 2026
75f53de
Fix local vs Colab path setup; resolve ModuleNotFoundError for local …
Sterilistic Apr 19, 2026
7700200
fix: migrate openai v0->v1 API, fix Event access in task, tune BERT demo
Sterilistic Apr 19, 2026
7fa07d5
Apply suggestions from code review
Sterilistic Apr 19, 2026
dc4c89c
Merge branch 'master' into feature/rexkg-chexpert-plus
Sterilistic Apr 19, 2026
f3bda20
Added run result in ipynb
Sterilistic Apr 19, 2026
691641a
feat: add ReXKG span-level evaluation metrics
Sterilistic Apr 20, 2026
5634676
fix: align SpanNERHead architecture with pretrained checkpoint
Sterilistic Apr 20, 2026
9b7e4e2
fix: align label sets and evaluation metrics with checkpoint training…
Sterilistic Apr 20, 2026
7b2da46
feat: add NER fine-tuning pipeline to notebook (Step 6c)
Sterilistic Apr 20, 2026
5290eff
feat: add joint NER+RE training pipeline
Sterilistic Apr 20, 2026
6942216
fix: align ReXKG with PURE paper architecture
Sterilistic Apr 20, 2026
8d2ae8d
fix: collate rel_labels mismatch with entity_spans
Sterilistic Apr 20, 2026
e96e268
style: clean up inline comments and fix stale RE head docstring
Sterilistic Apr 20, 2026
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1 change: 1 addition & 0 deletions docs/api/datasets.rst
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Expand Up @@ -238,6 +238,7 @@ Available Datasets
datasets/pyhealth.datasets.BMDHSDataset
datasets/pyhealth.datasets.COVID19CXRDataset
datasets/pyhealth.datasets.ChestXray14Dataset
datasets/pyhealth.datasets.CheXpertPlusDataset
datasets/pyhealth.datasets.PhysioNetDeIDDataset
datasets/pyhealth.datasets.TUABDataset
datasets/pyhealth.datasets.TUEVDataset
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12 changes: 12 additions & 0 deletions docs/api/datasets/pyhealth.datasets.CheXpertPlusDataset.rst
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@@ -0,0 +1,12 @@
pyhealth.datasets.CheXpertPlusDataset
====================================

CheXpert Plus dataset wrapper for report-driven chest X-ray knowledge graph
extraction. For more information see the dataset page
`here <https://stanfordaimi.azurewebsites.net/datasets/5158c524-d3ab-4e02-96e9-6ee9efc110a1>`_
and paper `here <https://arxiv.org/abs/2405.19111>`_.

.. autoclass:: pyhealth.datasets.CheXpertPlusDataset
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions docs/api/models.rst
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Expand Up @@ -177,6 +177,7 @@ API Reference
models/pyhealth.models.GNN
models/pyhealth.models.Transformer
models/pyhealth.models.TransformersModel
models/pyhealth.models.ReXKGModel
models/pyhealth.models.TransformerDeID
models/pyhealth.models.RETAIN
models/pyhealth.models.GAMENet
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10 changes: 10 additions & 0 deletions docs/api/models/pyhealth.models.ReXKGModel.rst
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pyhealth.models.ReXKGModel
===========================

ReXKG model for span-based radiology NER, pairwise relation extraction,
and downstream knowledge graph construction.

.. autoclass:: pyhealth.models.ReXKGModel
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions docs/api/tasks.rst
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Expand Up @@ -226,6 +226,7 @@ Available Tasks
ChestX-ray14 Binary Classification <tasks/pyhealth.tasks.ChestXray14BinaryClassification>
De-Identification NER <tasks/pyhealth.tasks.DeIDNERTask>
ChestX-ray14 Multilabel Classification <tasks/pyhealth.tasks.ChestXray14MultilabelClassification>
Radiology KG Extraction <tasks/pyhealth.tasks.RadiologyKGExtractionTask>
Variant Classification (ClinVar) <tasks/pyhealth.tasks.VariantClassificationClinVar>
Mutation Pathogenicity (COSMIC) <tasks/pyhealth.tasks.MutationPathogenicityPrediction>
Cancer Survival Prediction (TCGA) <tasks/pyhealth.tasks.CancerSurvivalPrediction>
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9 changes: 9 additions & 0 deletions docs/api/tasks/pyhealth.tasks.RadiologyKGExtractionTask.rst
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pyhealth.tasks.RadiologyKGExtractionTask
========================================

Task for ReXKG-style entity and relation extraction from radiology reports.

.. autoclass:: pyhealth.tasks.RadiologyKGExtractionTask
:members:
:undoc-members:
:show-inheritance:
2 changes: 2 additions & 0 deletions docs/tutorials.rst
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Expand Up @@ -218,6 +218,8 @@ These examples are located in ``examples/cxr/``.
- VAE for chest X-ray image generation
* - ``cxr/ChestXray-image-generation-GAN.ipynb``
- GAN for chest X-ray image generation (notebook)
* - ``cxr/chexpert_plus_rexkg.ipynb``
- Radiology KG extraction with CheXpert Plus (ReXKG pipeline, notebook)

Interpretability
----------------
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