From 3e735c83c861405e37cd76b3835f48a3d0ed0c17 Mon Sep 17 00:00:00 2001 From: Jamasb Date: Tue, 26 Dec 2023 14:51:19 -0800 Subject: [PATCH] add changelog --- CHANGELOG.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a19ad8e..14328430 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,33 @@ +### 0.2.6 (Unreleased) + + + +#### Datasets + +* Adds to antibody-specific datasets using the IGFold corpuses for paired OAS and Jaffe 2022 [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Set `in_memory=True` as default for most (small) datasets for improved performance [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Fix `num_classes` for GO datamodules * Set `in_memory=True` as default for most (downstream) datasets for improved performance [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Fixes GO labelling [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) + + +### Features +* Improves positional encoding performance by adding a `seq_pos` attribute on `Data/Protein` objects in the base dataset getter. [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) + +### Models +* Adds CDConv implementation [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Adds tuned hparams for models [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) + +### Framework +* Refactors beartype/jaxtyping to use latest recommended syntax [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Adds explainability module for performing attribution on a trained model [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Change default finetuning features in config: `ca_base` -> `ca_seq` [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Add optional hparam entry point to finetuning config [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Fixes GPU memory accumulation for some metrics [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Updates zenodo URL for processed datasets to reflect upstream API change [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Adds multi-hot label encoding transform [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Fixes auto PyG install for `torch>2.1.0` [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) +* Adds `proteinworkshop.model_io` containing utils for loading trained models [#53](https://github.com/a-r-j/ProteinWorkshop/pull/53/) + ### 0.2.5 (25/09/2024) * Implement ESM embedding encoder ([#33](https://github.com/a-r-j/ProteinWorkshop/pull/33), [#41](https://github.com/a-r-j/ProteinWorkshop/pull/33))