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remove label requirement related to 24.10 (#315)
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remove label requirement related to 24.10

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Signed-off-by: Yang Zhang <yangzhang@nvidia.com>
Signed-off-by: Tyler Shimko <tshimko@nvidia.com>
Co-authored-by: Peter St. John <pstjohn@nvidia.com>
Co-authored-by: Tyler Shimko <tshimko@nvidia.com>
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1 change: 0 additions & 1 deletion .github/pull_request_template.md
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Expand Up @@ -43,4 +43,3 @@ pytest -v tests/your/new/or/existing/test_functions.py::test_function
- [ ] Can you add [the `SKIP_CI` label](https://github.com/NVIDIA/bionemo-framework/-/blob/dev/CONTRIBUTING.md?ref_type=heads#skip-ci) to your PR?
- [ ] Can you add [the `PYTEST_NOT_REQUIRED` label](https://github.com/NVIDIA/bionemo-framework/-/blob/dev/CONTRIBUTING.md?ref_type=heads#skip-pytest) to your PR?
- [ ] Can you add [the `JET_NOT_REQUIRED` label](https://github.com/NVIDIA/bionemo-framework/-/blob/dev/CONTRIBUTING.md?ref_type=heads#skip-jet) to your PR?
- [ ] You need to add one of the labels `bug_fix_for_v24.10` or `NOT_related_to_v24.10` or `feature_for_v24.10`
27 changes: 0 additions & 27 deletions .github/workflows/label-check-for-24-10.yml

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30 changes: 30 additions & 0 deletions docs/docs/user-guide/appendix/releasenotes-fw.md
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# Release Notes


## BioNeMo Framework v2.0

### New Features:
* ESM2 implementation
* State of the art training performance and equivalent accuracy to the reference implementation
* 650M, and 3B scale checkpoints available which mirror the reference model
* Flexible fine-tuning examples that can be copied and modified to accomplish a wide variety of downstream tasks
* First version of our NeMo v2 based reference implementation which re-imagines bionemo as a repository of megatron models, dataloaders, and training recipes which make use of NeMo v2 for training loops.
* Modular design and permissible Apache 2 OSS licenses enables the import and use of our framework in proprietary applications.
* NeMo2 training abstractions allows the user to focus on the model implementation while the training strategy handles distribution and model parallelism.
* Documentation and documentation build system for BioNeMo 2.

### Known Issues:
* PEFT support is not yet fully functional.
* Partial implementation of Geneformer is present, use at your own risk. It will be optimized and officially released in the future.
* Command line interface is currently based on one-off training recipes and scripts. We are working on a configuration based approach that will be released in the future.
* Fine-tuning workflow is implemented for BERT based architectures and could be adapted for others, but it requires you to inherit from the biobert base model config. You can follow similar patterns in the short term to load weights from an old checkpoint partially into a new model, however in the future we will have a more direct API which is easier to follow.

## BioNeMo Framework v1.9

### New Features
* [Documentation] Updated, executable ESM-2nv notebooks demonstrating: Data preprocessing and model training with custom datasets, Fine-tuning on FLIP data, Inference on OAS sequences, Pre-training from scratch and continuing training
* [Documentation] New notebook demonstrating Zero-Shot Protein Design Using ESM-2nv. Thank you to @awlange from A-Alpha Bio for contributing the original version of this recipe!

### Bug fixes and Improvements
* [Geneformer] Fixed bug in preprocessing due to a relocation of dependent artifacts.
* [Geneformer] Fixes bug in finetuning to use the newer preprocessing constructor.

## BioNeMo Framework v1.8
### New Features
* [Documentation] Updated, executable MolMIM notebooks demonstrating: Training on custom data, Inference and downstream prediction, ZINC15 dataset preprocesing, and CMA-ES optimization
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