Chemical-Reaction-Aware Molecule Representation Learning

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take SMILES strings as input that have difficulty in encoding molecule structure information, or over-emphasize the importance of GNN architectures but neglect their generalization ability. Here we propose using chemical reactions to assist learning molecule representation. The key idea of our approach is to preserve the equivalence of molecules with respect to chemical reactions in the embedding space, i.e., forcing the sum of reactant embeddings and the sum of product embeddings to be equal for each chemical equation. This constraint is proven effective to 1) keep the embedding space well-organized and 2) improve the generalization ability of molecule embeddings. Moreover, our model can use any GNN as the molecule encoder and is thus agnostic to GNN architectures. Experimental results demonstrate that our method achieves state-of-the-art performance in a variety of downstream tasks, e.g., 17.4% absolute Hit@1 gain in chemical reaction prediction, 2.3% absolute AUC gain in molecule property prediction, and 18.5% relative RMSE gain in graph-edit-distance prediction, respectively, over the best baseline method. The code is available at https://github.com/hwwang55/MolR.

On the Sensitivity of Adversarial Robustness to Input Data Distributions

Neural networks are vulnerable to small adversarial perturbations. Existing literature largely focused on understanding and mitigating the vulnerability of learned models. In this paper, we demonstrate an intriguing phenomenon about the most popular robust training method in the literature, adversarial training: Adversarial robustness, unlike clean accuracy, is sensitive to the input data distribution. Even a semantics-preserving transformations on the input data distribution can cause a significantly different robustness for the adversarial trained model that is both trained and evaluated on the new distribution. Our discovery of such sensitivity on data distribution is based on a study which disentangles the behaviors of clean accuracy and robust accuracy of the Bayes classifier. Empirical investigations further confirm our finding. We construct semantically-identical variants for MNIST and CIFAR10 respectively, and show that standardly trained models achieve comparable clean accuracies on them, but adversarially trained models achieve significantly different robustness accuracies. This counter-intuitive phenomenon indicates that input data distribution alone can affect the adversarial robustness of trained neural networks, not necessarily the tasks themselves. Lastly, we discuss the practical implications on evaluating adversarial robustness, and make initial attempts to understand this complex phenomenon.

advertorch v0.1: An Adversarial Robustness Toolbox based on PyTorch

advertorch is a toolbox for adversarial robustness research. It contains various implementations for attacks, defenses and robust training methods. advertorch is built on PyTorch (Paszke et al., 2017), and leverages the advantages of the dynamic computational graph to provide concise and efficient reference implementations. The code is licensed under the LGPL license and is open sourced at https://github.com/BorealisAI/advertorch .