arXiv subjects

Youzhi Luo

Publications and source records attributed to Youzhi Luo.

21 records · Page 2Linked to original sources

arXiv2021

Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery

Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum. However, there lacks customized and advanced methods and comprehensive tools for this task currently. Here we develop a suite of comprehensive machine learning methods and tools spanning different computational models, molecular representations, and loss functions for molecular property prediction and drug discovery. Specifically, we represent molecules as both graphs and sequences. Built on these representations, we develop novel deep models for learning from molecular graphs and sequences. In order to learn effectively from highly imbalanced datasets, we develop advanced loss functions that optimize areas under precision-recall curves. Altogether, our work not only serves as a comprehensive tool, but also contributes towards developing novel and advanced graph and sequence learning methodologies. Results on both online and offline antibiotics discovery and molecular property prediction tasks show that our methods achieve consistent improvements over prior methods. In particular, our methods achieve #1 ranking in terms of both ROC-AUC and PRC-AUC on the AI Cures Open Challenge for drug discovery related to COVID-19. Our software is released as part of the MoleculeX library under AdvProp.

q-bio.QM↗

arXiv2021

Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks

Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically favorable since obtaining 3D equilibrium structures requires extremely expensive calculations. In this work, we design a deep graph neural network to predict quantum properties by directly learning from 2D molecular graphs. In addition, we propose a 3D graph neural network to learn from low-cost conformer sets, which can be obtained with open-source tools using an affordable budget. We employ our methods to participate in the 2021 KDD Cup on OGB Large-Scale Challenge (OGB-LSC), which aims to predict the HOMO-LUMO energy gap of molecules. Final evaluation results reveal that we are one of the winners with a mean absolute error of 0.1235 on the holdout test set. Our implementation is available as part of the MoleculeX package (https://github.com/divelab/MoleculeX).

cs.LG↗

arXiv2021

GraphDF: A Discrete Flow Model for Molecular Graph Generation

We consider the problem of molecular graph generation using deep models. While graphs are discrete, most existing methods use continuous latent variables, resulting in inaccurate modeling of discrete graph structures. In this work, we propose GraphDF, a novel discrete latent variable model for molecular graph generation based on normalizing flow methods. GraphDF uses invertible modulo shift transforms to map discrete latent variables to graph nodes and edges. We show that the use of discrete latent variables reduces computational costs and eliminates the negative effect of dequantization. Comprehensive experimental results show that GraphDF outperforms prior methods on random generation, property optimization, and constrained optimization tasks.

cs.LG↗