Releases: samsledje/D-SCRIPT
Releases · samsledje/D-SCRIPT
v0.2.8: 2024-09-16 -- Fix bug with model cuda assignment during prediction
v0.2.7: 2024-09-13 -- HuggingFace Models
What's Changed
- R notebooks added for baseline sequence-based analysis by @kap-devkota in #59
- Add HuggingFace support by @samsledje in #69
Full Changelog: v0.2.6...v0.2.7
v0.2.6b: 2023-08-24 -- Zenodo Release
Release to generate a DOI for the current state of the repository containing TT3D experiments.
What's Changed
- R notebooks added for baseline sequence-based analysis by @kap-devkota in #59
- Python notebooks for baseline structure-based analysis
Full Changelog: v0.2.6...v0.2.6b
v0.2.6: 2023-09-28 -- Add TT3D as a pretrained option
Full Changelog: v0.2.5...v0.2.6
v0.2.5: 2023-07-24 -- Integrating 3Di sequences into prediction
Update predict.py
so models trained with --allow_foldseek
(Topsy-Turvy 3D) can be used to make predictions, provided that a foldseek_fasta
is provided.
v0.2.4
v0.2.2: 2023-01-20 -- Bug Fixes and Topsy-Turvy
- Resolve #35 to use
require_dataset
-- can now add multiple .fasta files to the same h5 file - Update pretrained API and docs to include Topsy-Turvy
- Add retry decorator to get_pretrained if download fails
- Add ability to set a random seed for training
- Update
evaluate
code to also store metrics in a file
v0.2.1: 2022-06-28 -- Bug Fixes
- Update
setup.py
to includebiopython
so that it runs properly on a cleanpip
install.
v0.2.0: 2022-06-24 -- Integration of Topsy-Turvy
Topsy-Turvy Integration
- Integrate Topsy-Turvy to allow for top-down supervision
- See the GitHub repository
- See the landing page
- To appear at ISMB 2022 and in Bioinformatics as
Devkota*, Singh*, Sledzieski, Berger, Cowen, “Topsy-Turvy: integrating a global view into sequence-based PPI prediction”
Bug Fixes and Quality of Life
- Use
utils.log
function across all commands - Speed up loading embeddings into memory using parallel processing
- Update
fasta.parse
andfasta.write
to useBioPython SeqIO
(better error checking) - More comprehensive test suite for main commands
v0.1.9 Dealing with pypi and semvar fussiness
This is the same as v0.1.8b0 but it will actually take priority