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gnn-thesis's Introduction

Binding Affinity Prediction with Graph Neural Networks

  • The repository contains the notebooks for the final chapter of my Master's Thesis.

  • The notebooks contain the implementation of a novel fusion-based architecture, which combines a graph neural network (AttentiveFP) and biologically-motivated learned protein embeddings (ProtTransBert) for drug-target interaction prediction. The model architecture is outlined below: proteinafp

The model is benchmarked on Davis and KIBA standard datasets, as well as on an in-house dataset of ~400K de novo generated molecules against 6 targets.

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gnn-thesis's Issues

Problem with library installtation

encountering a problem with installation of bio-embeddings library.
error is as follows:
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
tried everything but nothing works for this

because of this cannot use ProtTransBertBFDEmbedder()

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