Bionemo demos #2968
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Bionemo demos #2968
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/build |
holgerroth
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Sep 27, 2024
holgerroth
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Sep 27, 2024
holgerroth
requested changes
Sep 27, 2024
examples/advanced/bionemo/task_fitting/jobs/embeddings/app/custom/bionemo_inference.py
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...ples/advanced/bionemo/task_fitting/jobs/embeddings/app/custom/bionemo_inference_processor.py
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holgerroth
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holgerroth
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...les/advanced/bionemo/downstream/sabdab/jobs/fedavg_sabdab_esm1nv/app/custom/base_config.yaml
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| @@ -36,9 +40,9 @@ exp_manager: | |||
| tags: | |||
| - ${name} | |||
| offline: True # set to True if there are issues uploading to WandB during training | |||
| resume_if_exists: False # automatically resume if checkpoint exists | |||
| resume_if_exists: True # automatically resume if checkpoint exists | |||
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if there are multiple global rounds, I vaguely remember in previous integration we need to set this to False? @holgerroth
...advanced/bionemo/downstream/tap/jobs/central_tap_esm1nv/app1/custom/downstream_flip_tap.yaml
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...ples/advanced/bionemo/downstream/tap/jobs/central_tap_esm1nv/app3/custom/pretrain_small.yaml
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examples/advanced/bionemo/task_fitting/jobs/embeddings/app/config/infer copy.yaml
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YuanTingHsieh
previously approved these changes
Oct 1, 2024
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/build |
...es/advanced/bionemo/downstream/sabdab/jobs/central_sabdab_esm1nv/app/custom/base_config.yaml
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.../bionemo/downstream/scl/jobs/fedavg_scl_finetune_esm2nv/app1/custom/downstream_flip_scl.yaml
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add few comments and questions
Overall, too many duplicated files with minor variation. For 2.5.1 this might be ok. But the final example for BioNemo 2.0, we should replace the duplication files with new Job APIs so we don't have so many files for just few minor changes
holgerroth
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...advanced/bionemo/downstream/tap/jobs/central_tap_esm1nv/app1/custom/downstream_flip_tap.yaml
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...advanced/bionemo/downstream/tap/jobs/central_tap_esm1nv/app2/custom/downstream_flip_tap.yaml
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holgerroth
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.../advanced/bionemo/downstream/tap/jobs/fedavg_tap_esm1nv/app1/custom/downstream_flip_tap.yaml
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…s, fixed column used for each site
…for sabdab fedavg changed to original ???
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@holgerroth we will need to add the PR for 2.5 branch if we want to include in 2.5.1 release |
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/build |
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updated bionemo demos examples from v1.0 to v1.8