a-r-j/proteinworkshop issues and pull requests

#99 - Reproducing the Fold Classification baselines

Issue - State: closed - Opened by anonymous-0545 about 2 months ago - 5 comments

#98 - question: fit for interface featurisation?

Issue - State: open - Opened by paoslaos 2 months ago - 2 comments

#97 - edge_index has edges across different data objects in a batch

Issue - State: closed - Opened by biochunan 3 months ago - 2 comments

#96 - 4v8m not found in raw directory. When processing go-bp dataset

Issue - State: closed - Opened by yangzhang33 6 months ago - 1 comment

#95 - Corrupted File in GeneOntology

Issue - State: open - Opened by AJB117 7 months ago - 1 comment

#94 - Unable to donwload dataset ec_reaction

Issue - State: closed - Opened by yangzhang33 7 months ago - 9 comments

#93 - Correct test file extension for GO dataset

Pull Request - State: closed - Opened by amorehead 10 months ago

#92 - [fix] notebook descriptions

Pull Request - State: closed - Opened by kierandidi 10 months ago - 1 comment

#91 - Unable to reproduce the results on fold classification task

Issue - State: closed - Opened by huangtinglin 10 months ago - 2 comments

#90 - Make plotting dependencies optional

Pull Request - State: closed - Opened by a-r-j 10 months ago - 3 comments

#89 - changed time_cutoff option

Pull Request - State: closed - Opened by kierandidi 11 months ago - 3 comments

#88 - added sequence clustering to pdb dataset

Pull Request - State: closed - Opened by kierandidi 11 months ago - 1 comment

#87 - remove breakpoint

Pull Request - State: closed - Opened by kierandidi 11 months ago

#86 - Pdb dataset fix

Pull Request - State: closed - Opened by kierandidi 11 months ago

#85 - Update GCPNet paper link

Pull Request - State: closed - Opened by amorehead 11 months ago

#84 - Deprecate torsional denoising task temporarily

Pull Request - State: closed - Opened by amorehead 11 months ago

#83 - Add wrapper for catching OOMs during backward pass

Pull Request - State: closed - Opened by amorehead 11 months ago

#82 - Minor fix: update ICLR paper citation and add link

Pull Request - State: closed - Opened by chaitjo 11 months ago - 1 comment

#81 - Add support for handling training/validation OOMs gracefully

Pull Request - State: closed - Opened by amorehead 11 months ago - 1 comment

#80 - Fix `sequence_edges` when b is a Data object

Pull Request - State: closed - Opened by linusyh 11 months ago - 1 comment

#79 - Update pipeline figure

Pull Request - State: closed - Opened by chaitjo 11 months ago

#78 - Add forced cuda version to `workshop install`

Pull Request - State: closed - Opened by linusyh 12 months ago - 1 comment

#77 - Fix PDB download

Pull Request - State: closed - Opened by linusyh 12 months ago - 3 comments

#76 - Lazy init refactor

Pull Request - State: closed - Opened by a-r-j 12 months ago

#75 - Update torch versions, CI

Pull Request - State: open - Opened by a-r-j 12 months ago - 2 comments

#74 - add pos to gearnet `required_batch_attributes` #73

Pull Request - State: closed - Opened by a-r-j 12 months ago

#73 - Required batch attributes for GearNet encoder

Issue - State: closed - Opened by Katja-Jagd 12 months ago - 3 comments

#72 - refactor multi test set datasets; add seq id test splits to GO

Pull Request - State: closed - Opened by a-r-j 12 months ago - 1 comment

#71 - Add `InverseSquareRootLR` scheduler

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#70 - Add `torchdrug` to project dependencies

Issue - State: open - Opened by amorehead about 1 year ago - 1 comment
Labels: dependency

#69 - Error encountered during training on GO datasets.

Issue - State: closed - Opened by gokceuludogan about 1 year ago - 4 comments

#68 - Fix data_dir creation error in download_processed_data.py

Pull Request - State: closed - Opened by gokceuludogan about 1 year ago - 1 comment

#67 - Ensure log_dir points to RUN_PATH from .env file

Pull Request - State: closed - Opened by chaitjo about 1 year ago - 2 comments

#66 - Update EC Reaction Sweep config

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#65 - Fix dataset names in README

Pull Request - State: closed - Opened by chaitjo about 1 year ago

#64 - Version bump for 0.2.5 release

Pull Request - State: closed - Opened by a-r-j about 1 year ago

#63 - Fix minor virtual angle feature documentation

Pull Request - State: closed - Opened by chaitjo about 1 year ago

#62 - Getting predictions for PTM model

Issue - State: closed - Opened by ann-las about 1 year ago - 2 comments

#61 - Mismatch of dimensions for PTM data

Issue - State: closed - Opened by asaksager about 1 year ago - 4 comments

#60 - Add a pre-trained model API

Issue - State: open - Opened by a-r-j about 1 year ago
Labels: enhancement

#59 - Add simple memory saving techniques to GCPNet encoder

Pull Request - State: closed - Opened by amorehead about 1 year ago - 1 comment

#58 - Fix `orientation` batching

Pull Request - State: closed - Opened by amorehead about 1 year ago - 2 comments

#57 - Fix `orientations` batching

Pull Request - State: closed - Opened by amorehead about 1 year ago

#56 - Issues with feature-computations

Issue - State: closed - Opened by martinaegidius about 1 year ago - 3 comments

#55 - Add UMAP embedding visualisation script

Pull Request - State: closed - Opened by amorehead over 1 year ago - 5 comments

#54 - `fold_fold` dataset cannot be downloaded

Issue - State: closed - Opened by amorehead over 1 year ago - 14 comments

#53 - Linting and updates

Pull Request - State: closed - Opened by a-r-j over 1 year ago - 6 comments

#52 - Fix tuple iteration in the `ProteinDataset`'s `process` method

Pull Request - State: closed - Opened by amorehead over 1 year ago

#51 - `process` function of the `ProteinDataset` class iterates over tuples instead of PDB codes

Issue - State: closed - Opened by amorehead over 1 year ago - 3 comments

#50 - Wire up argument for `create_example_batch`

Pull Request - State: closed - Opened by amorehead over 1 year ago

#49 - Bump urllib3 from 2.0.4 to 2.0.6

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependency

#48 - Bump pillow from 10.0.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependency

#47 - Update sequence encoder title

Pull Request - State: closed - Opened by chaitjo over 1 year ago

#46 - Update available encoders

Pull Request - State: closed - Opened by chaitjo over 1 year ago - 1 comment

#45 - Add `flash`

Pull Request - State: open - Opened by amorehead over 1 year ago - 1 comment

#44 - Default to using DDP

Pull Request - State: closed - Opened by amorehead over 1 year ago

#43 - Add fix for scheduler initialization with FoldComp datasets

Pull Request - State: closed - Opened by amorehead over 1 year ago

#42 - Bump gevent from 23.9.0.post1 to 23.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependency

#41 - Add configs and optional post embedding MLP for ESM encoder

Pull Request - State: closed - Opened by chaitjo over 1 year ago - 1 comment

#40 - Reduce number of layers for TFN model

Pull Request - State: closed - Opened by chaitjo over 1 year ago

#39 - unable to process mmtf file to pyg

Issue - State: closed - Opened by pengzhangzhi over 1 year ago - 4 comments

#38 - Improved TFN and MACE implementation

Pull Request - State: closed - Opened by chaitjo over 1 year ago - 1 comment

#37 - Release v0.2.4

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#36 - Bump gitpython from 3.1.32 to 3.1.35

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependency

#35 - Standardize `poetry` in README.md, and fix up docs

Pull Request - State: closed - Opened by amorehead over 1 year ago - 1 comment

#34 - fail to activate poetry

Issue - State: closed - Opened by pengzhangzhi over 1 year ago - 10 comments

#33 - Add preliminary ESM baseline

Pull Request - State: closed - Opened by amorehead over 1 year ago - 3 comments

#32 - Fix paths for new directory structure

Pull Request - State: closed - Opened by chaitjo over 1 year ago - 1 comment

#31 - [fix] typo

Pull Request - State: closed - Opened by Croydon-Brixton over 1 year ago

#30 - Fix W&B run name setting

Pull Request - State: closed - Opened by chaitjo over 1 year ago - 1 comment

#29 - Highlight local pip install option in docs

Issue - State: closed - Opened by a-r-j over 1 year ago - 2 comments
Labels: documentation

#28 - Update checksums and fnames in download script #27

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#27 - Metal3D Download URL incorrect

Issue - State: closed - Opened by a-r-j over 1 year ago - 1 comment
Labels: bug, data

#26 - Fix small notebook typos

Pull Request - State: closed - Opened by amorehead over 1 year ago

#25 - Patch cath

Pull Request - State: closed - Opened by a-r-j over 1 year ago - 1 comment

#24 - Raw files hotfix #23

Pull Request - State: closed - Opened by a-r-j over 1 year ago - 2 comments

#23 - Using processed datasets without a local copy of the PDB triggers download of raw data

Issue - State: closed - Opened by a-r-j over 1 year ago - 1 comment
Labels: bug

#22 - Bump version strings for 0.2.1 release

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#21 - Add a simple hyperlink in the README to point to the GitHub repository

Pull Request - State: closed - Opened by amorehead over 1 year ago

#20 - Add sanity check for CLI install

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#19 - Correct ENV var detection #18

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#18 - `constants.py` not correctly detecting env vars.

Issue - State: closed - Opened by a-r-j over 1 year ago - 1 comment
Labels: bug

#17 - Minor docs corrections

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#16 - Bump for version 0.2.0 release

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#15 - Update docs

Pull Request - State: closed - Opened by amorehead over 1 year ago

#14 - Add export example

Pull Request - State: closed - Opened by amorehead over 1 year ago

#13 - Torch 2.0.1 unsupported by Poetry

Issue - State: closed - Opened by a-r-j over 1 year ago - 2 comments
Labels: dependency

#12 - Poetry dist

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#11 - Add `foldcomp` to dependencies

Pull Request - State: closed - Opened by amorehead over 1 year ago

#10 - Fix/publish hotfixes

Pull Request - State: closed - Opened by amorehead over 1 year ago

#9 - Docs

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#8 - Fix/publish hotfixes

Pull Request - State: closed - Opened by Croydon-Brixton over 1 year ago

#7 - Update README

Pull Request - State: closed - Opened by amorehead over 1 year ago

#6 - Small updates to the notebook tutorials

Pull Request - State: closed - Opened by amorehead over 1 year ago

#5 - Notebooks

Pull Request - State: closed - Opened by kierandidi over 1 year ago

#4 - Model docstrings and miscellaneous fixes

Pull Request - State: closed - Opened by chaitjo over 1 year ago

#3 - W&B logging fixes

Pull Request - State: closed - Opened by chaitjo over 1 year ago

#2 - Publish package

Pull Request - State: closed - Opened by a-r-j over 1 year ago

#1 - Add tests & build configuration with Poetry

Pull Request - State: closed - Opened by a-r-j over 1 year ago

GitHub / a-r-j/proteinworkshop issues and pull requests