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model + task + dataset implementation, tested #1112

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model + task + dataset implementation, tested
sanyamahesh2 Apr 22, 2026
330ca04
improved docstrings
sanyamahesh2 Apr 22, 2026
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1 change: 1 addition & 0 deletions docs/api/datasets.rst
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Expand Up @@ -244,5 +244,6 @@ Available Datasets
datasets/pyhealth.datasets.ClinVarDataset
datasets/pyhealth.datasets.COSMICDataset
datasets/pyhealth.datasets.TCGAPRADDataset
datasets/pyhealth.datasets.TCGARNASeqDataset
datasets/pyhealth.datasets.splitter
datasets/pyhealth.datasets.utils
13 changes: 13 additions & 0 deletions docs/api/datasets/pyhealth.datasets.TCGARNASeqDataset.rst
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pyhealth.datasets.TCGARNASeqDataset
===================================

Dataset is available at https://portal.gdc.cancer.gov/

The TCGA RNA-Seq dataset contains pan-cancer bulk RNA sequencing data along with associated clinical information.

This dataset supports preprocessing and tokenization for downstream modeling tasks, following the methodology used in BulkRNABert.

.. autoclass:: pyhealth.datasets.TCGARNASeqDataset
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions docs/api/models.rst
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Expand Up @@ -204,5 +204,6 @@ API Reference
models/pyhealth.models.VisionEmbeddingModel
models/pyhealth.models.TextEmbedding
models/pyhealth.models.BIOT
models/pyhealth.models.BulkRNABert
models/pyhealth.models.unified_multimodal_embedding_docs
models/pyhealth.models.califorest
11 changes: 11 additions & 0 deletions docs/api/models/pyhealth.models.BulkRNABert.rst
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pyhealth.models.BulkRNABert
===================================

The separate callable BulkRNABert model.

.. autoclass:: pyhealth.models.bulk_rna_bert.BulkRNABert
:members:
:undoc-members:
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.. autofunction:: pyhealth.models.bulk_rna_bert.cox_partial_likelihood_loss
1 change: 1 addition & 0 deletions docs/api/tasks.rst
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Expand Up @@ -230,3 +230,4 @@ Available Tasks
Mutation Pathogenicity (COSMIC) <tasks/pyhealth.tasks.MutationPathogenicityPrediction>
Cancer Survival Prediction (TCGA) <tasks/pyhealth.tasks.CancerSurvivalPrediction>
Cancer Mutation Burden (TCGA) <tasks/pyhealth.tasks.CancerMutationBurden>
TCGA RNA-seq (BulkRNABert) <tasks/pyhealth.tasks.tcga_rnaseq_tasks>
12 changes: 12 additions & 0 deletions docs/api/tasks/pyhealth.tasks.tcga_rnaseq_tasks.rst
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pyhealth.tasks.tcga_rnaseq_tasks
=================================

.. autoclass:: pyhealth.tasks.tcga_rnaseq_tasks.TCGACancerTypeTask
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:undoc-members:
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.. autoclass:: pyhealth.tasks.tcga_rnaseq_tasks.TCGASurvivalTask
:members:
:undoc-members:
:show-inheritance:
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