# Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats

arXiv: https://arxiv.org/abs/2308.01921 · HTML: https://mlsanity.com/paper/2308.01921/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 70 references that are in the map.
- First posted on arXiv 17 Jul 2023.

## Builds on (most cited first, 12 of 12)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Residual Gated Graph ConvNets](https://mlsanity.com/paper/1711.07553/) (2017)
- [Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks](https://mlsanity.com/paper/1909.01315/) (2019)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [DeepDTA: Deep Drug-Target Binding Affinity Prediction](https://mlsanity.com/paper/1801.10193/) (2018)
- [Deep Molecular Dreaming: Inverse machine learning for de-novo molecular design and interpretability with surjective representations](https://mlsanity.com/paper/2012.09712/) (2020)
- [Combining docking pose rank and structure with deep learning improves protein-ligand binding mode prediction](https://mlsanity.com/paper/1910.02845/) (2019)

## Abstract (arXiv)

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and great fidelity. In this study, we built a COVID-19 drug docking dataset of about 300,000 drug candidates on 23 coronavirus protein targets. With this dataset, we trained graph neural fingerprint docking models for high-throughput virtual COVID-19 drug screening. The graph neural fingerprint models yield high prediction accuracy on docking scores with the mean squared error lower than 0.21 kcal/mol for most of the docking targets, showing significant improvement over conventional circular fingerprint methods. To make the neural fingerprints transferable for unknown targets, we also propose a transferable graph neural fingerprint method trained on multiple targets. With comparable accuracy to target-specific graph neural fingerprint models, the transferable model exhibits superb training and data efficiency. We highlight that the impact of this study extends beyond COVID-19 dataset, as our approach for fast virtual ligand screening can be easily adapted and integrated into a general machine learning-accelerated pipeline to battle future bio-threats.