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PyTorch DataLoader #499
PyTorch DataLoader #499
Commits on May 18, 2023
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add PyTorch DataLoader support
introduce this under a new "incubation" sub-package
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Commits on May 19, 2023
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rm explicit timeout param handling
user to specify as normal DataLoader param
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Commits on May 22, 2023
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swap order of obs and labels in DataLoader rows/batches
"X, y" is common ordering in ML training usage
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Commits on May 23, 2023
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support access to ExperimentAccessQuery from ExperimentDataPipe
allows model training code access query dim sizes required refactoring to initialize ExperimentDataPipe when needed
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take Experiment obj instead of URI
cleans up experiment open logic, providing s3 region param
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support split and shuffle via PyTorch DataPipes
separate the ExperimentDataPipe instantation from the experiment_data_loader() method, to allow user to specify additional pipe operations, per her use case.
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Commits on May 24, 2023
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invert sparse_X option to dense_X
Sparse Tensors are experimental and are currently known not to work with multiprocessing or LR models. So let's make use of dense Tensors the default. Use of sparse Tensors now requires the explicit option `sparse_X=True`. Also fix bug where dense, non-batched results were returned as 1-row batches, instead of being unwrapped.
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run experimental tests conditionally (#501)
* experimental tests only run with explicit pytest option * only run experimental tests with Python 3.10 on GHA, since not all experimental package dependencies are available for lower version (e.g. pytorch 2.0.1 not available for Python 3.7)
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Commits on May 25, 2023
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use API's default buffer_bytes value
rename buffer_bytes to soma_buffer_bytes for clarity
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- rename ms_name to measurement_name - remove ExperimentDataPipe num_workers param (unused except for an invalid usage check)
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rename layer_name to X_name, to align with Census API get_anndata
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Commits on May 30, 2023
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