Geometric Deep Learning for Protein Structure Data with PyTorch Lightning
6 March 9:30h-17h
General context
In this course we will develop a geometric deep learning model that takes a protein structure as input and predicts binding site residues. Through the process, we will cover the basics of data processing, tracking performance, hyperparameter configuration, training and validation of a production-level deep learning model using PyTorch Lightning.
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Construct featurised graphs from protein structures
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Create a geometric deep learning (GDL) architecture by combining off-the-shelf graph layers
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Efficiently load and batch graph representations
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Implement evaluation metrics and tracking specific to the task at hand
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Train and checkpoint the model, log and visualise validation performance
We ask the participants to use their own laptop.
Python programmers with some experience in machine learning and/or protein structure data.
Python
Trainers
Janani Durairaj
I’m a postdoctoral researcher in Torsten Schwede’s Protein Bioinformatics in 3D research group at the Biozentrum, University of Basel. I work at the interface of protein structural bioinformatics and machine learning, developing efficient algorithms and software to represent, explore and understand protein structures for applications ranging from enzyme engineering to drug discovery.
Program
Graph construction from protein structures with PyTorch-geometric
GDL architecture with PyTorch-geometric and LightningModule
Loading and batching graph data with LightningDataModule
Implementing metrics for tracking performance
Hyperparameter configuration, training, and checkpointing
Wrap-up
Practical info
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
Provincieplein 1
3010 Leuven
Belgium
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
Leuven is easy to reach by train from all Belgian and European cities. Leuven is a 20-minute train ride from Brussels, 45 minutes from Antwerp, 50 minutes from Liège, 1.5 hours from Paris and 2.5 hours from London, Amsterdam or Cologne.
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
Leuven is located at the junction of two important highways: the E40 and the E314. The 'P' signposts will guide you to the different car parks. If you are using a GPS, please enter “Tiensevest” and not “Provincieplein 1”.
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
+32 16 26 70 15
provinciehuis@vlaamsbrabant.be