Updates docs for geneformer training, inference, and cellxclassification #823
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We also will need to upload artifacts and update the resource yaml file.
Signed-off-by: Jonathan Mitchell <[email protected]>
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…ion (#823) ### Description Updates the documentation for Geneformer 10m and 106M models, and their respective training curves and MLM loss benchmark scores. All data is also tracked inside this google sheet https://docs.google.com/spreadsheets/d/1OB28ArwR_-huNyfi4M2I_Q8jKEpvcINNqLhd-LGqKBY/edit?gid=521924651#gid=521924651 ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [X] 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 - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### 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 --> - [ ] I have tested these changes locally - [X] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully Signed-off-by: Jonathan Mitchell <[email protected]> Signed-off-by: Cory Ye <[email protected]>
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…ion (#823) ### Description Updates the documentation for Geneformer 10m and 106M models, and their respective training curves and MLM loss benchmark scores. All data is also tracked inside this google sheet https://docs.google.com/spreadsheets/d/1OB28ArwR_-huNyfi4M2I_Q8jKEpvcINNqLhd-LGqKBY/edit?gid=521924651#gid=521924651 ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [X] 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 - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### 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 --> - [ ] I have tested these changes locally - [X] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully Signed-off-by: Jonathan Mitchell <[email protected]> Signed-off-by: Farhad Ramezanghorbani <[email protected]>
camirr-nv
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…ion (#823) ### Description Updates the documentation for Geneformer 10m and 106M models, and their respective training curves and MLM loss benchmark scores. All data is also tracked inside this google sheet https://docs.google.com/spreadsheets/d/1OB28ArwR_-huNyfi4M2I_Q8jKEpvcINNqLhd-LGqKBY/edit?gid=521924651#gid=521924651 ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Refactor - [X] 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 - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) to manage authorization of CI runs on NVIDIA's compute resources. * If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123) * If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an `/ok to test` comment on the pull request to trigger CI. This will need to be done for each new commit. ### 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 --> - [ ] I have tested these changes locally - [X] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully Signed-off-by: Jonathan Mitchell <[email protected]> Signed-off-by: Ubuntu <[email protected]>
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Description
Updates the documentation for Geneformer 10m and 106M models, and their respective training curves and MLM loss benchmark scores.
All data is also tracked inside this google sheet https://docs.google.com/spreadsheets/d/1OB28ArwR_-huNyfi4M2I_Q8jKEpvcINNqLhd-LGqKBY/edit?gid=521924651#gid=521924651
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.
Authorizing CI Runs
We use copy-pr-bot to manage authorization of CI
runs on NVIDIA's compute resources.
automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123)
/ok to testcomment on the pull request to trigger CI. This will need to be done for each new commit.Usage
Pre-submit Checklist