Releases: Genentech/gReLU
Releases · Genentech/gReLU
v1.0.11
What's Changed
- Compare motifs by @avantikalal in #162
- added attributions to compare_motifs by @avantikalal in #168
- Transform ensembles by @avantikalal in #111
- Fix wandb login, set anonymous to must by @jkanche in #169
Full Changelog: v1.0.10...v1.0.11
v1.0.10
What's Changed
- updated modiscolite version by @avantikalal in #161
- fixed filter_overlapping with anndata input by @avantikalal in #160
- fixed issue with gc matching by @avantikalal in #159
- Update to the JASPAR 2024 consensus motifs by @oriolfornes in #163
New Contributors
- @oriolfornes made their first contribution in #163
Full Changelog: 1.0.9...v1.0.10
1.0.9
What's Changed
- better-defaults-borzoi-activation-norm by @MuhammedHasan in #153
Full Changelog: v1.0.8...1.0.9
v1.0.8
What's Changed
- Update urls to public gReLU by @jkanche in #146
- Limit ledidi version by @avantikalal in #148
- fix error when return_seqs="best" by @cdedonno in #131
- added hocomoco v13 by @avantikalal in #151
- Tangermeme update by @avantikalal in #152
- fixed ledidi code to work with latest version and reran design tutorial by @avantikalal in #150
- custom fasta by @MuhammedHasan in #143
New Contributors
Full Changelog: v1.0.7...v1.0.8
v1.0.7
What's Changed
- allow poisson multinomial loss by @avantikalal in #142
- load catlas dataset from zoo by @avantikalal in #141
- Fixed small Borzoi discrepancies, fixes #144 by @johahi in #147
New Contributors
Full Changelog: v1.0.6...v1.0.7
v1.0.6
What's Changed
- Install tox in pypi-publish.yml by @avantikalal in #120
- set abs=False in saliency by @avantikalal in #124
- Typo in
correct_gradcausing it to not be applied by @suragnair in #126 - Zoo tutorial by @avantikalal in #122
- changed augmentation and VEP logic by @avantikalal in #121
- split modisco functions by @avantikalal in #128
- created simulation module and tutorial by @avantikalal in #118
- Simulations by @avantikalal in #129
- 🐞 Replace
positional argumentswithkeyword argumentsto avoid misassignment ofblacklistparameter by @fahimfarhan in #134 - Run fimo on multiple sequences by @jkanche in #136
- fix bug in scan_sequences in motifs.py by @ketringjoni in #137
- updated authors list by @avantikalal in #139
- updated test scan sequences by @avantikalal in #138
New Contributors
- @fahimfarhan made their first contribution in #134
- @ketringjoni made their first contribution in #137
Full Changelog: v1.0.5...v1.0.6
v1.0.5
What's Changed
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #97
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #100
- print a warning when random mutation augmentation is used by @avantikalal in #101
- add gradient accumulation and checkpoint versioning by @avantikalal in #96
- Prevent padded intervals from exceeding chromosome ends by @avantikalal in #95
- module docstrings by @avantikalal in #104
- corrected use of attr if no motif matches are found by @dagarfield in #99
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #108
- made model checkpoints more informative by @avantikalal in #107
- Revert "made model checkpoints more informative" by @avantikalal in #109
- Make model checkpoints more informative (this time without logging the extra info) by @avantikalal in #114
- added gradient correction by @avantikalal in #106
- Updated contribution guide by @avantikalal in #103
- added a tutorial on custom models by @avantikalal in #102
New Contributors
- @dagarfield made their first contribution in #99
Full Changelog: v1.0.4...v1.0.5
v1.0.4
What's Changed
- Use tangermeme backend for tomtom by @avantikalal in #75
- Bugfix by @avantikalal in #81
- updated available motif sets by @avantikalal in #83
- Score FIMO hits with attributions by @avantikalal in #73
- Fix CI failure by @avantikalal in #90
- fix bug in ism_predict on multiple sequences by @avantikalal in #89
Full Changelog: v1.0.3...v1.0.4
v1.0.3
What's Changed
- fixed bug in pypi-publish workflow by @avantikalal in #35
- Poisson losses bug fixes #31 by @MuhammedHasan in #32
- add python gitignore by @MuhammedHasan in #25
- Add support for half precision (bf16 and fp16) and on device model creation by @MuhammedHasan in #26
- replaced .A with .toarray() by @avantikalal in #37
- allow custom blacklist file by @avantikalal in #36
- replace bpnetlite with tangermeme by @avantikalal in #15
- updated pre-commit hooks by @ekageyama in #44
- Support alternative normalization methods by @MuhammedHasan in #42
- added preprint link by @avantikalal in #49
- Pin torchmetrics version by @gokceneraslan in #51
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #53
- Add precision to the pl.Trainer constructors by @gokceneraslan in #50
- fixed and updated plot_tracks by @avantikalal in #67
- Saliency by @avantikalal in #71
- Flash Attention support by @suragnair in #78
- updated merge_intervals function to account for strand by @avantikalal in #66
- Updated motif processing to Tangermeme 0.4 by @avantikalal in #69
- add multiomial axis option to poisson multinomial loss by @avantikalal in #79
New Contributors
- @MuhammedHasan made their first contribution in #32
- @ekageyama made their first contribution in #44
- @pre-commit-ci made their first contribution in #53
Full Changelog: v1.0.2...v1.0.3
v1.0.2
What's Changed
- Reset val/test metrics and losses after every epoch by @suragnair in #8
- updated readme with pip command by @avantikalal in #14
- convert indices to int8 before stacking by @avantikalal in #21
- fixed device parsing in embed_on_dataset by @avantikalal in #20
- added host and docstrings to resources module by @avantikalal in #13
- added map_location arg in load_model to load model onto any device by @avantikalal in #18
- added reset method to PearsonCorrCoef by @avantikalal in #30
New Contributors
- @suragnair made their first contribution in #8
Full Changelog: v1.0.1...v1.0.2