Feature/prosit improvements dataset caching #34
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omsh
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May 3, 2024
* Feature/migrate to huggingface datasets (#32) * new file structure * skeleton rt dataset * [Testing] abstraction + intensity + alphabet updates * pprint args dict * modified seq utils not to add empty n-c terms * parallel and batch processing - faster pipeline * removed datasets_sql and pyteomics parser from base class * Added a working version of time delta and updated prosit model * minor fixes * minor fix + added tf prob dep * refactoring, improvements, feature extraction * Added different PTM features * Added dict in pkl file * refactoring * updated .gitignore * refactored ptm handling workflow with naive and unmod schemes * updated feature tables from wassim * refactored tests to new hf datasets style * package restructure for clean install + minor fixes * updates to package dir in gitignore, makefile, docs conf * clean-up of unnecessary files and code * unified parsed column names + cleaner user messages * minor user message edits * docs system improvements * refactored vocab to alphabet and minor fixed * updates to runscripts and notebooks + minor fixes * example intensity data in parquet to lists as strings in csv * [WIP]: adding tests * model tests and run files for features and ptms * added docstrings --------- Co-authored-by: WassimG <wassim.gabriel@gmail.com> * Update setup.py * gh actions improvements - docs - README.md * fixed docs * more and more fixes * version update * fixes * updates to docstrings + docs conf.py * Feature/reduced smiles (#33) * Added reduced smiles feature extractor and pkl file * splitting logic refactored + comments for lookup features --------- Co-authored-by: victorgiurcoiu <victor.giurcoiu@tum.de> * Feature/prosit improvements dataset caching (#34) * improvements to prosit intensity + dataset caching + others * removed extra notebook * cleaned up print statements * dev install command fix * added flag for tf dataset cache + notebook minor updates * remove wandb from report init + notebook updates * uncommented notebook pip install * pumbed up version to 0.1.0 --------- Co-authored-by: WassimG <wassim.gabriel@gmail.com> Co-authored-by: victorgiurcoiu <victor.giurcoiu@tum.de>
omsh
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May 5, 2024
* Feature/migrate to huggingface datasets (#32) * new file structure * skeleton rt dataset * [Testing] abstraction + intensity + alphabet updates * pprint args dict * modified seq utils not to add empty n-c terms * parallel and batch processing - faster pipeline * removed datasets_sql and pyteomics parser from base class * Added a working version of time delta and updated prosit model * minor fixes * minor fix + added tf prob dep * refactoring, improvements, feature extraction * Added different PTM features * Added dict in pkl file * refactoring * updated .gitignore * refactored ptm handling workflow with naive and unmod schemes * updated feature tables from wassim * refactored tests to new hf datasets style * package restructure for clean install + minor fixes * updates to package dir in gitignore, makefile, docs conf * clean-up of unnecessary files and code * unified parsed column names + cleaner user messages * minor user message edits * docs system improvements * refactored vocab to alphabet and minor fixed * updates to runscripts and notebooks + minor fixes * example intensity data in parquet to lists as strings in csv * [WIP]: adding tests * model tests and run files for features and ptms * added docstrings --------- Co-authored-by: WassimG <wassim.gabriel@gmail.com> * Update setup.py * gh actions improvements - docs - README.md * fixed docs * more and more fixes * version update * fixes * updates to docstrings + docs conf.py * Feature/reduced smiles (#33) * Added reduced smiles feature extractor and pkl file * splitting logic refactored + comments for lookup features --------- Co-authored-by: victorgiurcoiu <victor.giurcoiu@tum.de> * Feature/prosit improvements dataset caching (#34) * improvements to prosit intensity + dataset caching + others * removed extra notebook * cleaned up print statements * dev install command fix * added flag for tf dataset cache + notebook minor updates * remove wandb from report init + notebook updates * uncommented notebook pip install * pumbed up version to 0.1.0 --------- Co-authored-by: WassimG <wassim.gabriel@gmail.com> Co-authored-by: victorgiurcoiu <victor.giurcoiu@tum.de>
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