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Recent Releases of helical

helical - v0.0.1a16

What's Changed

  • Include notebook workflow by @bputzeys in https://github.com/helicalAI/helical/pull/68
  • Include GitHub Action testing successfull runs for all Jupyter Notebooks in examples folder by @bputzeys in https://github.com/helicalAI/helical/pull/70
  • Remove condition to only run workflow on release branch by @bputzeys in https://github.com/helicalAI/helical/pull/72
  • Remove condition to only run workflow on release branch by @bputzeys in https://github.com/helicalAI/helical/pull/73
  • Remove requirement to run other workflow before this. by @bputzeys in https://github.com/helicalAI/helical/pull/74
  • Remove requirement to run other workflow before this by @bputzeys in https://github.com/helicalAI/helical/pull/75
  • fixed typing issue for python<3.11 by @maxiallard in https://github.com/helicalAI/helical/pull/77
  • Adjust alcs by @bputzeys in https://github.com/helicalAI/helical/pull/76
  • changed version python by @maxiallard in https://github.com/helicalAI/helical/pull/79
  • Fix typing issue for python<3.11 by @bputzeys in https://github.com/helicalAI/helical/pull/78
  • Include hydra configs for each model by @bputzeys in https://github.com/helicalAI/helical/pull/80
  • Adjust uce config by @bputzeys in https://github.com/helicalAI/helical/pull/82
  • Improve uce memory foodprint by @bputzeys in https://github.com/helicalAI/helical/pull/81
  • Fix data notebooks by @maxiallard in https://github.com/helicalAI/helical/pull/84
  • fixed naming of anndata by @maxiallard in https://github.com/helicalAI/helical/pull/85
  • Improvements UCE and Hydra introduction for configs by @maxiallard in https://github.com/helicalAI/helical/pull/83
  • Avoid mapping ensembl ids to ensembl ids by @bputzeys in https://github.com/helicalAI/helical/pull/86
  • Geneformer v2 by @JadSbai in https://github.com/helicalAI/helical/pull/88
  • Basic Fine-Tuning Capabilities For All RNA Models by @mattwoodx in https://github.com/helicalAI/helical/pull/90
  • Fix file not found issue in notebook by @mattwoodx in https://github.com/helicalAI/helical/pull/92
  • Fix notebook errors by @JadSbai in https://github.com/helicalAI/helical/pull/94
  • Fix Geneformer process_data by @mattwoodx in https://github.com/helicalAI/helical/pull/95
  • Reduce train sample to stop timeout by @mattwoodx in https://github.com/helicalAI/helical/pull/96
  • Changing to Helical Hugging Face Dataset In Repo by @mattwoodx in https://github.com/helicalAI/helical/pull/97
  • Added Geneformer v2, Fine-Tuning for RNA models, Bug Fixes for Mapping by @maxiallard in https://github.com/helicalAI/helical/pull/91
  • Typing fixes, refactoring and renaming by @bputzeys in https://github.com/helicalAI/helical/pull/99
  • Include converter tests by @bputzeys in https://github.com/helicalAI/helical/pull/102
  • Fix Weight Scrambling in scGPT by @mattwoodx in https://github.com/helicalAI/helical/pull/98
  • Typing updates, reordering and renaming by @bputzeys in https://github.com/helicalAI/helical/pull/100
  • Change workflow by @bputzeys in https://github.com/helicalAI/helical/pull/107
  • Bugfix: stop execution if no genes are present by @bputzeys in https://github.com/helicalAI/helical/pull/109
  • Change workflow to exectute tests and notebooks sequentially by @bputzeys in https://github.com/helicalAI/helical/pull/108
  • Adding downloads where initial files might not be available anymore. by @maxiallard in https://github.com/helicalAI/helical/pull/110
  • Change dependency strictness by @mattwoodx in https://github.com/helicalAI/helical/pull/111
  • HyenaDNA Fine-Tuning Capabilities and Regression Head by @mattwoodx in https://github.com/helicalAI/helical/pull/101
  • Refactor fine-tuning by @mattwoodx in https://github.com/helicalAI/helical/pull/112
  • Raise error if download fails and include log message by @bputzeys in https://github.com/helicalAI/helical/pull/113
  • Raise error if download fails by @bputzeys in https://github.com/helicalAI/helical/pull/114
  • Maxiallard patch 1 by @maxiallard in https://github.com/helicalAI/helical/pull/116
  • Merge updates in main into release by @mattwoodx in https://github.com/helicalAI/helical/pull/115
  • Include raw counts flag by @bputzeys in https://github.com/helicalAI/helical/pull/117
  • Include release build by @bputzeys in https://github.com/helicalAI/helical/pull/118
  • Add missing steps by @bputzeys in https://github.com/helicalAI/helical/pull/120
  • Include release process by @bputzeys in https://github.com/helicalAI/helical/pull/119
  • Docker by @maxiallard in https://github.com/helicalAI/helical/pull/121
  • Change docs to Mkdocs by @mattwoodx in https://github.com/helicalAI/helical/pull/122
  • Use logger to show warning message by @bputzeys in https://github.com/helicalAI/helical/pull/123
  • Fix GeneformerConfig Docstring by @mattwoodx in https://github.com/helicalAI/helical/pull/124
  • Filter logs and warnings by @mattwoodx in https://github.com/helicalAI/helical/pull/125
  • Filter loggging, improve README by @bputzeys in https://github.com/helicalAI/helical/pull/126
  • Feature/helix mrna by @bputzeys in https://github.com/helicalAI/helical/pull/127
  • Update forward of fine-tuning model by @mattwoodx in https://github.com/helicalAI/helical/pull/128
  • Add import to the package by @mattwoodx in https://github.com/helicalAI/helical/pull/130
  • Mamba2-mRNA and Helix-mRNA by @bputzeys in https://github.com/helicalAI/helical/pull/129
  • Include instructions for Colab run by @bputzeys in https://github.com/helicalAI/helical/pull/131
  • Address import issues in Colab by @bputzeys in https://github.com/helicalAI/helical/pull/132
  • Remove causal conv 1d by @mattwoodx in https://github.com/helicalAI/helical/pull/133
  • Add causal conv1d by @mattwoodx in https://github.com/helicalAI/helical/pull/136
  • Fix version by @maxiallard in https://github.com/helicalAI/helical/pull/135
  • Update HyenaDNA with new Dependencies by @mattwoodx in https://github.com/helicalAI/helical/pull/137
  • CPU bound unit tests and GPU integration tests by @mattwoodx in https://github.com/helicalAI/helical/pull/140
  • Modify pyproject.toml and make mamba_ssm optional. by @giogix2 in https://github.com/helicalAI/helical/pull/138
  • Add emb_mode option to scGPT and update docs by @mattwoodx in https://github.com/helicalAI/helical/pull/141
  • Fix mamba-ssm integration in release Pypi by @giogix2 in https://github.com/helicalAI/helical/pull/144
  • Test models using local files by @mattwoodx in https://github.com/helicalAI/helical/pull/145
  • Cleanup by @bputzeys in https://github.com/helicalAI/helical/pull/149
  • Add binning seed to scGPT by @bputzeys in https://github.com/helicalAI/helical/pull/148
  • Fix seeds v2 by @bputzeys in https://github.com/helicalAI/helical/pull/151
  • Update versions by @bputzeys in https://github.com/helicalAI/helical/pull/153
  • Bring back skipped tests, fix seed for reproducible results in scGPT, include updates in README by @bputzeys in https://github.com/helicalAI/helical/pull/150
  • Cleanup scgpt and remove torchtext dependency by @bputzeys in https://github.com/helicalAI/helical/pull/154
  • Bump torch and torchvision versions by @giogix2 in https://github.com/helicalAI/helical/pull/155
  • Fix broken model card link by @giogix2 in https://github.com/helicalAI/helical/pull/160
  • Remove tensorflow dependency by @bputzeys in https://github.com/helicalAI/helical/pull/156
  • Return ensembl ID for each embedding for emb_mode="gene" by @mattwoodx in https://github.com/helicalAI/helical/pull/157
  • Integrate Caduceus Model by @mattwoodx in https://github.com/helicalAI/helical/pull/159
  • Bug fix: HyenaDNA variable length input sequences by @mattwoodx in https://github.com/helicalAI/helical/pull/161
  • Transfer the benchmarking scripts to external repo by @giogix2 in https://github.com/helicalAI/helical/pull/162

New Contributors

  • @JadSbai made their first contribution in https://github.com/helicalAI/helical/pull/88
  • @mattwoodx made their first contribution in https://github.com/helicalAI/helical/pull/90
  • @giogix2 made their first contribution in https://github.com/helicalAI/helical/pull/138

Full Changelog: https://github.com/helicalAI/helical/compare/0.0.1a1...v0.0.1a16

- Python
Published by maxiallard about 1 year ago

helical - v0.0.1-alpha

First Pre-Release of Helical Package 🎉. It includes:

  • Geneformer, UCE and scGPT for RNA Expression Data
  • HyenaDNA for DNA Sequences
  • Benchmarking Framework
  • Example Notebooks and Scripts
  • BaseModel Definition
  • Classifier and Regressor Heads

- Python
Published by maxiallard over 1 year ago