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
Provinciehuis Vlaams-Brabant is located within walking distance of the Leuven railway and bus station. When exiting the station, go left across the Roger Van Overstraetenplein.
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
There is a dedicated cycling path next to the Leuven ring road where you can ride in both directions. You can park your bike right next to or underneath the building. Using your bike for longer distances? Check out Cycle Highways?
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
From the E40, take the E314 and immediately exit at junction 15 towards Leuven city center. Follow the road to the Leuven ring road, turn right towards Tienen and Diest, and continue past the Tiense Poort. As you approach the Provinciehuis, stay in the right lane and continue towards the station until the end. Then, carefully turn right and drive slowly, respecting pedestrians and cyclists, under the pedestrian bridge (Roger Van Overstraetenplein) until you reach the railway. Turn right and follow the tracks towards Provinciehuis.
Park on Bezoekersparking floor -2.
Using GPS? Older GPS software may not recognize 'Provincieplein' as an address. In that case, enter 'Tiensevest - intersection with Justus Lipsiusstraat' instead.
06 March 2024
Leuven - Provinciehuis Vlaams-Brabant
+32 16 26 70 15
provinciehuis@vlaamsbrabant.be