Correct Shape of scdl output matirx #708
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Intron7
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jstjohn,
malcolmgreaves,
polinabinder1 and
skothenhill-nv
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trvachov
requested changes
Feb 27, 2025
| @@ -27,14 +29,19 @@ def collate_sparse_matrix_batch(batch: list[torch.Tensor]) -> torch.Tensor: | |||
| Returns: | |||
| The tensors collated into a CSR (Compressed Sparse Row) Format. | |||
| """ | |||
| n_features = batch[0][1][0] | |||
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Could you add a comment explaining the hardcoded indexes?
| @@ -240,6 +240,7 @@ def __init__( | |||
| paginated_load_cutoff: int = 10_000, | |||
| load_block_row_size: int = 1_000_000, | |||
| feature_index_name="feature_id", | |||
| return_padded: bool = False, | |||
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High level, how does the code know what the pad size is? Or max size to pad to?
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This uses the return get_row_padded for __getitem__
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Could you update the docstring?
Signed-off-by: Intron7 <[email protected]>
sub-packages/bionemo-scdl/src/bionemo/scdl/util/torch_dataloader_utils.py
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skothenhill-nv
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Mar 4, 2025
…er_utils.py Co-authored-by: Steven Kothen-Hill <[email protected]> Signed-off-by: Severin Dicks <[email protected]>
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I'll add a test tomorrow morning |
Signed-off-by: Intron7 <[email protected]>
Signed-off-by: Intron7 <[email protected]>
Signed-off-by: Intron7 <[email protected]>
Signed-off-by: Intron7 <[email protected]>
Signed-off-by: Intron7 <[email protected]>
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updated the tests to work with the returned tuple. Also I added 2 new tests for return padded and the shape |
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I also updated the |
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This fixes the size of the output matrix for scdl.
It also enables users to return a dense array