set min seq len by default #621
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Signed-off-by: Peter St. John <pstjohn@nvidia.com>
farhadrgh
approved these changes
Jan 17, 2025
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Can you add this change to finetune Datamodule here:
https://github.com/NVIDIA/bionemo-framework/blob/main/sub-packages/bionemo-esm2/src/bionemo/esm2/model/finetune/datamodule.py
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #621 +/- ##
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Coverage 86.62% 86.62%
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Files 116 116
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Hits 6030 6030
Misses 931 931 ☔ View full report in Codecov by Sentry. |
jstjohn
approved these changes
Jan 18, 2025
polinabinder1
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Jan 22, 2025
### Description In https://nvbugspro.nvidia.com/bug/5060664 they notice a warning message about performance when pretraining with variable sequence lengths. This is largely an oversight since our test scripts didn't set both minimum and maximum seq_lens. We should have the default if min_seq_length is omitted be to just pad to the maximum sequence length for performance reasons. ### Type of changes <!-- Mark the relevant option with an [x] --> - [x] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [ ] Documentation update - [ ] Other (please describe): ### CI Pipeline Configuration Configure CI behavior by applying the relevant labels: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. ### Usage <!--- How does a user interact with the changed code --> ```python TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [x] I have tested these changes locally - [x] I have updated the documentation accordingly - [x] I have added/updated tests as needed - [x] All existing tests pass successfully Signed-off-by: Peter St. John <pstjohn@nvidia.com> Signed-off-by: Polina Binder <pbinder@nvidia.com>
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Description
In https://nvbugspro.nvidia.com/bug/5060664 they notice a warning message about performance when pretraining with variable sequence lengths. This is largely an oversight since our test scripts didn't set both minimum and maximum seq_lens. We should have the default if min_seq_length is omitted be to just pad to the maximum sequence length for performance reasons.
Type of changes
CI Pipeline Configuration
Configure CI behavior by applying the relevant labels:
Note
By default, the notebooks validation tests are skipped unless explicitly enabled.
Usage
Pre-submit Checklist