Changes related to data processing and fine-tuning new models #16
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avantikalal
commented
Jul 9, 2025
avantikalal
commented
- Enabled finetuning via CLI
- Added new arguments to CLI training and finetuning scripts
- Modified the CLI inference script to enable running separately on train/val/test genes
- Enabled inference by changing predict_on_dataset to have separate logic depending on the dataset class (HDF5Dataset or VariantDataset)
- Added a new preprocessing function that searches for gene metadata on ensembl using mygene.
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@avantikalal Can you added finetuning data similar to https://github.com/Genentech/decima/blob/main/tests/test_cli.py with may be dumy test and just runs new steps? It is easier to add unittest for I am preparing unittests for |
Shall I do these in a separate PR? |
…nd fine-tuning (#19) * ensemble vep init * backward compability of grelu, ensembling, testcases, custom fasta * gene dataset * gene expression prediction and sequence shifting * fix testcase * conflig * Changes related to data processing and fine-tuning new models (#16) * enable finetune via cli * split input and output directories * add mygene * added ensembl * added N padding * add more params * added args to cli finetune * add csv logging * add csv logging * add run name to checkpoints * gene pearson metric * training 202506 * added new params * added topk * reset unnecessary changes * reset unnecessary changes * reset unnecessary changes * reset unnecessary changes * reset unnecessary changes * fixed savek typo * more useful print * finetuning updates --------- Co-authored-by: Muhammed Hasan Celik <celik.muhammed_hasan@gene.com> * fix testcases * branch review updates --------- Co-authored-by: Muhammed Hasan Celik <celik.muhammed_hasan@gene.com> Co-authored-by: Avantika Lal <avantikalal1990@gmail.com>
