Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / datamol-io/graphium issues and pull requests

#532 - Added C++ file description comments

Pull Request - State: closed - Opened by ndickson-nvidia 3 months ago

#531 - Packaging of Graphium 3.0

Pull Request - State: open - Opened by Andrewq11 3 months ago - 1 comment
Labels: ASAP priority

#530 - Remove IPU (again)

Pull Request - State: closed - Opened by WenkelF 3 months ago
Labels: fix

#529 - Integrate finetuning & fingerprinting

Pull Request - State: closed - Opened by WenkelF 3 months ago
Labels: enhancement, feature

#527 - Adding the gcc, gxx, pybind to the env file. Preparing for packaging

Pull Request - State: closed - Opened by DomInvivo 5 months ago - 3 comments

#526 - Graphium 3.0

Pull Request - State: closed - Opened by AnujaSomthankar 5 months ago

#525 - Remove ipu

Pull Request - State: closed - Opened by DomInvivo 5 months ago - 1 comment

#524 - Torchmetrics error: AttributeError: 'Tensor' object has no attribute 'clear'

Issue - State: closed - Opened by AnujaSomthankar 6 months ago - 1 comment
Labels: bug

#523 - Weak baseline

Issue - State: closed - Opened by SteshinSS 7 months ago - 6 comments

#522 - Updating dep versions for bh2 install

Pull Request - State: closed - Opened by Andrewq11 7 months ago
Labels: fix

#521 - Reorder atoms in label data (Fixes 502) + documenting C++

Pull Request - State: closed - Opened by ndickson-nvidia 7 months ago

#520 - Access to intermediate embeddings

Pull Request - State: closed - Opened by blazejba 7 months ago - 2 comments

#519 - Graphium 3.0

Pull Request - State: open - Opened by DomInvivo 7 months ago - 2 comments

#518 - Global molecular features support

Issue - State: closed - Opened by VladVin 8 months ago - 5 comments
Labels: enhancement, feature

#517 - Torchmetrics usage improvements with classes instead of functionals

Pull Request - State: closed - Opened by DomInvivo 8 months ago
Labels: enhancement, fix

#516 - Revert "Revert "fix: Remove compromised link to polyfill.io""

Pull Request - State: closed - Opened by DomInvivo 8 months ago

#515 - fix: Remove compromised link to polyfill.io

Pull Request - State: closed - Opened by DomInvivo 8 months ago

#514 - Revert "fix: Remove compromised link to polyfill.io"

Pull Request - State: closed - Opened by DomInvivo 8 months ago

#513 - fix: Remove compromised link to polyfill.io

Pull Request - State: closed - Opened by jstlaurent 8 months ago
Labels: fix

#512 - Remove forced constraint to cuda 11.2 with Graphium 3.0

Issue - State: open - Opened by DomInvivo 10 months ago - 1 comment

#511 - Torchmetrics

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

#505 - remove Gradient links in README

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

#504 - Properly testing the node ordering in `test_featurizer.py`

Issue - State: open - Opened by DomInvivo about 1 year ago - 1 comment
Labels: bug, ASAP priority

#502 - Re-order atoms and edges when matching molecules from different datasets

Pull Request - State: closed - Opened by DomInvivo about 1 year ago
Labels: ASAP priority, fix

#490 - Use custom `isnan` for IPU

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

#488 - WIP: 0 GNN layers on last IPU + Fingerprinting

Pull Request - State: closed - Opened by callumm-graphcore about 1 year ago - 5 comments

#466 - Update `MetricWrapper` to work with the update/compute from torchmetrics

Issue - State: open - Opened by DomInvivo over 1 year ago - 1 comment
Labels: enhancement

#234 - Replace the `pre-nn` and `pre-nn-edges` by the `MLPEncoder`

Issue - State: open - Opened by DomInvivo almost 2 years ago - 1 comment
Labels: enhancement

#197 - Consider muP suggestions made in Appendix D of Tensor Programs V

Issue - State: closed - Opened by callumm-graphcore about 2 years ago - 1 comment
Labels: enhancement, mup

#100 - Speedy

Pull Request - State: closed - Opened by DomInvivo almost 3 years ago - 2 comments

#99 - Make PR for high-level review

Pull Request - State: closed - Opened by graphriela almost 3 years ago - 1 comment

#98 - Fixed the added mode in the lr scheduler

Pull Request - State: closed - Opened by DomInvivo almost 3 years ago - 4 comments

#97 - Fixes

Pull Request - State: closed - Opened by DomInvivo almost 3 years ago - 1 comment

#96 - Compatibility with PyTorch 1.9 and above

Issue - State: closed - Opened by hadim almost 3 years ago - 3 comments
Labels: medium priority

#95 - Increase training speed

Issue - State: closed - Opened by DomInvivo almost 3 years ago - 3 comments
Labels: enhancement, medium priority

#94 - Add RWPE

Issue - State: closed - Opened by DomInvivo almost 3 years ago - 1 comment

#93 - compatibility with PCQM4M and PCQM4Mv2

Pull Request - State: closed - Opened by DomInvivo almost 3 years ago

#92 - Need some integration tests, and more unit-tests for predictor and datamodule

Issue - State: closed - Opened by DomInvivo almost 3 years ago - 1 comment
Labels: Low priority

#91 - Improvements to make Goli more modular

Pull Request - State: closed - Opened by DomInvivo almost 3 years ago

#90 - Added concatenation of last layers

Pull Request - State: closed - Opened by DomInvivo about 3 years ago

#89 - Make eigenvectors deterministic

Pull Request - State: closed - Opened by DomInvivo about 3 years ago - 6 comments
Labels: bug

#88 - Flag

Pull Request - State: closed - Opened by DomInvivo about 3 years ago - 4 comments

#87 - PCBA performance and GPU usage with FLAG

Issue - State: closed - Opened by DomInvivo about 3 years ago - 1 comment

#86 - feat: Implement FLAG (adversarial data augmentation) for training GNNs

Pull Request - State: closed - Opened by graphriela about 3 years ago - 1 comment

#85 - Added ResidualConnectionRandom

Pull Request - State: closed - Opened by DomInvivo about 3 years ago

#84 - Improve logging

Issue - State: closed - Opened by DomInvivo about 3 years ago
Labels: enhancement, Low priority

#83 - Improved dgn

Pull Request - State: closed - Opened by DomInvivo about 3 years ago

#82 - Log training metrics at step end

Issue - State: closed - Opened by DomInvivo about 3 years ago - 2 comments
Labels: bug, High priority

#81 - Remove batch_size warning

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment
Labels: enhancement, Low priority

#80 - PL1.5, better NaN handling, and better RAM

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 6 comments
Labels: bug, enhancement

#79 - Implement multi-task manager

Issue - State: closed - Opened by DomInvivo over 3 years ago - 2 comments
Labels: enhancement, High priority

#78 - Significant Memory Consumption Reduction

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 4 comments
Labels: enhancement

#77 - Implement FLAG

Issue - State: closed - Opened by DomInvivo over 3 years ago
Labels: enhancement, medium priority

#76 - Multiple small changes

Pull Request - State: closed - Opened by DomInvivo over 3 years ago

#75 - Saving the featurizer?

Issue - State: closed - Opened by DomInvivo over 3 years ago
Labels: enhancement, medium priority

#74 - n_params no longer appears in the Tensorboard HParams

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment

#73 - Fixed test set of size 0

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 2 comments

#72 - Changed usage of the batch-normalization

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 1 comment

#71 - Change batch_norm naming?

Issue - State: closed - Opened by DomInvivo over 3 years ago - 2 comments

#70 - Fix issues

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 2 comments

#69 - New try for LSC pull request

Pull Request - State: closed - Opened by DomInvivo over 3 years ago

#68 - Ogb lsc

Pull Request - State: closed - Opened by alip67 over 3 years ago - 1 comment

#67 - Minor fixes

Pull Request - State: closed - Opened by DomInvivo over 3 years ago

#66 - Incompatible with pytorch 1.9 and Python 3.9

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment

#65 - Implement random residual connection

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment
Labels: medium priority

#64 - Deal with NaN featurization

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment

#63 - Support for multi-GPUs

Issue - State: closed - Opened by DomInvivo over 3 years ago - 4 comments
Labels: medium priority, On hold

#62 - Save a compressed dataset file

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment

#61 - Implemented larger dataset, and fixing GPU memory leaks

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 2 comments

#60 - Dev

Pull Request - State: closed - Opened by hadim over 3 years ago - 3 comments

#59 - Implemented basic transfer learning and prediction capabilities

Pull Request - State: closed - Opened by DomInvivo over 3 years ago
Labels: bug, enhancement

#58 - Ignore molecules that fail featurization

Issue - State: closed - Opened by DomInvivo over 3 years ago - 3 comments
Labels: bug

#57 - [Meta] Next

Issue - State: closed - Opened by hadim over 3 years ago - 4 comments

#56 - Improved metrics handling of NaNs

Pull Request - State: closed - Opened by DomInvivo over 3 years ago - 3 comments
Labels: bug, enhancement

#55 - Improve naming of models

Issue - State: closed - Opened by DomInvivo over 3 years ago - 4 comments
Labels: enhancement

#54 - Implement graph norm

Issue - State: closed - Opened by DomInvivo over 3 years ago - 1 comment
Labels: enhancement, Low priority, On hold

#53 - Improved performance on PCBA dataset, and few fixes

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 3 comments

#52 - Pretrained models

Issue - State: closed - Opened by hadim almost 4 years ago - 1 comment
Labels: enhancement

#51 - Cache

Pull Request - State: closed - Opened by hadim almost 4 years ago - 2 comments

#50 - Too much GPU memory?

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#49 - Works on OGB datasets

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#48 - Add virtual batch sizes

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment
Labels: enhancement

#47 - Implement bond-length without conformer

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#46 - Deal with class imbalance

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 3 comments
Labels: enhancement

#45 - Implemented DGN and positional encoding

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 3 comments
Labels: enhancement

#44 - Load model checkpoint and run test set

Issue - State: closed - Opened by DomInvivo almost 4 years ago

#43 - Ogb

Pull Request - State: closed - Opened by hadim almost 4 years ago - 1 comment

#42 - Fixed some bugs with Windows and PL

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#41 - Update pna_layer.py

Pull Request - State: closed - Opened by HannesStark almost 4 years ago

#40 - Fixed training not being tracked by the logger

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#39 - Fix the docs search

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 2 comments
Labels: bug

#38 - Use custom callback to log the YAML files

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment
Labels: Low priority

#37 - Add logic to only load cache if the same graph features are used

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 3 comments
Labels: bug

#36 - Add support for the OGB datasets

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 2 comments
Labels: enhancement

#35 - Add support for Bench-GNN datasets

Issue - State: closed - Opened by DomInvivo almost 4 years ago - 2 comments
Labels: enhancement

#34 - Finished alpha version

Pull Request - State: closed - Opened by DomInvivo almost 4 years ago - 1 comment

#33 - Track learning rate in tensorboard

Issue - State: closed - Opened by DomInvivo almost 4 years ago
Labels: enhancement