a-r-j ProteinWorkshop issues

a-r-j / ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

https://proteins.sh/

MIT License

194 stars 16 forks source link

issues

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4v8m not found in raw directory. When processing go-bp dataset

#96 yangzhang33 opened 2 months ago
1
Corrupted File in GeneOntology

#95 AJB117 opened 2 months ago
1
Unable to donwload dataset ec_reaction

#94 yangzhang33 closed 2 months ago
9
Correct test file extension for GO dataset

#93 amorehead closed 5 months ago
0
[fix] notebook descriptions

#92 kierandidi closed 5 months ago
1
Unable to reproduce the results on fold classification task

#91 huangtinglin closed 6 months ago
2
Make plotting dependencies optional

#90 a-r-j closed 6 months ago
3
changed time_cutoff option

#89 kierandidi closed 6 months ago
3
added sequence clustering to pdb dataset

#88 kierandidi closed 6 months ago
1
remove breakpoint

#87 kierandidi closed 6 months ago
0
Pdb dataset fix

#86 kierandidi closed 6 months ago
0
Update GCPNet paper link

#85 amorehead closed 7 months ago
0
Deprecate torsional denoising task temporarily

#84 amorehead closed 7 months ago
0
Add wrapper for catching OOMs during backward pass

#83 amorehead closed 7 months ago
0
Minor fix: update ICLR paper citation and add link

#82 chaitjo closed 7 months ago
1
Add support for handling training/validation OOMs gracefully

#81 amorehead closed 7 months ago
1
Fix `sequence_edges` when b is a Data object

#80 linusyh closed 7 months ago
1
Update pipeline figure

#79 chaitjo closed 7 months ago
0
Add forced cuda version to `workshop install`

#78 linusyh closed 7 months ago
1
Fix PDB download

#77 linusyh closed 7 months ago
3
Lazy init refactor

#76 a-r-j closed 8 months ago
0
Update torch versions, CI

#75 a-r-j opened 8 months ago
2
add pos to gearnet `required_batch_attributes` #73

#74 a-r-j closed 8 months ago
0
Required batch attributes for GearNet encoder

#73 Katja-Jagd closed 8 months ago
3
refactor multi test set datasets; add seq id test splits to GO

#72 a-r-j closed 8 months ago
1
Add `InverseSquareRootLR` scheduler

#71 a-r-j closed 8 months ago
0
Add `torchdrug` to project dependencies

#70 amorehead opened 8 months ago
1
Error encountered during training on GO datasets.

#69 gokceuludogan closed 8 months ago
4
Fix data_dir creation error in download_processed_data.py

#68 gokceuludogan closed 8 months ago
1
Ensure log_dir points to RUN_PATH from .env file

#67 chaitjo closed 8 months ago
2
Update EC Reaction Sweep config

#66 a-r-j closed 8 months ago
0
Fix dataset names in README

#65 chaitjo closed 9 months ago
0
Version bump for 0.2.5 release

#64 a-r-j closed 9 months ago
0
Fix minor virtual angle feature documentation

#63 chaitjo closed 9 months ago
0
Getting predictions for PTM model

#62 ann-las closed 10 months ago
2
Mismatch of dimensions for PTM data

#61 asaksager closed 9 months ago
4
Add a pre-trained model API

#60 a-r-j opened 10 months ago
0
Add simple memory saving techniques to GCPNet encoder

#59 amorehead closed 9 months ago
1
Fix `orientation` batching

#58 amorehead closed 9 months ago
2
Fix `orientations` batching

#57 amorehead closed 10 months ago
0
Issues with feature-computations

#56 martinaegidius closed 10 months ago
3
Add UMAP embedding visualisation script

#55 amorehead closed 11 months ago
5
`fold_fold` dataset cannot be downloaded

#54 amorehead closed 11 months ago
14
Linting and updates

#53 a-r-j closed 9 months ago
6
Fix tuple iteration in the `ProteinDataset`'s `process` method

#52 amorehead closed 11 months ago
0
`process` function of the `ProteinDataset` class iterates over tuples instead of PDB codes

#51 amorehead closed 11 months ago
3
Wire up argument for `create_example_batch`

#50 amorehead closed 12 months ago
0
Bump urllib3 from 2.0.4 to 2.0.6

#49 dependabot[bot] closed 11 months ago
1
Bump pillow from 10.0.0 to 10.0.1

#48 dependabot[bot] closed 11 months ago
1
Update sequence encoder title

#47 chaitjo closed 1 year ago
0