Alex Morehead

Add graph batching support to `dgl.knn_graph()`

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## 🚀 Feature Adding graph batching support to `dgl.knn_graph()` ## Motivation Being able to provide a batch of coordinates/features to `knn_graph()` would allow users to develop much more efficient graph...

Cross-Attention?

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Hi, @lucidrains. Thank you for sharing this excellent implementation with us all! Do you have any thoughts as to what changes would need to be made to make cross-attention possible...

* Add EQGAT paper and fix up equivariance paper indices

Add Kendall's Rank Correlation

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## 🚀 Feature A `Metric` that computes Kendall's Rank Correlation (https://en.wikipedia.org/wiki/Kendall_rank_correlation_coefficient). ### Motivation This metric would be useful for many regressive tasks. ### Pitch Add a new `Metric` that computes...

Add support to `saving.py` for loading GPU-trained models on CPU-only machines

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## What does this PR do? - Adds support to `saving.py` for loading GPU-trained models on CPU-only machines. - Without this fix, a `.to()` call in the context of CPU-only...

Hello. Thank you for your work on OmegaFold! I am trying to find out whether OmegaFold supports unknown (i.e., masked) residue types as part of an input FASTA sequence. For...

Add support for using custom `Environments` and `Strategies` :zap:

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## What does this PR do? Adds the ability for one to employ custom (e.g., Lightning Fabric) `Environments` (e.g., `SlurmEnvironment`) and `Strategies` (e.g., `DeepSpeedStrategy`) during model training or evaluation. ##...

Update model_checkpoint.yaml for Lightning 2.1.0

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## What does this PR do? Updates `model_checkpoint.yaml` for Lightning 2.1.0. ## Before submitting - [x] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?...

Add `DensePaddingDataLoader` for flexible (padded) dense batching of `BaseData` objects

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### 🚀 The new functionality, motivation and pitch * This PR adds a new `DensePaddingDataLoader` class that enables flexible dense batching of `BaseData` objects. * Such functionality supports fast and...

Add the ability for the `PDBManager` to perform interface-based chain filtering

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#### What does this implement/fix? Explain your changes This allows one to select PDB complex chains satisfying certain interface contact or hydrogen bonding constraints.