Computational modeling of chemical and biological systems at atomic resolution is a crucial tool in the chemist’s toolset. The use of computer simulations requires a balance between cost and accuracy: quantum-mechanical methods provide high accuracy but are computationally expensive and scale poorly to large systems, while classical force fields are cheap and scalable, but lack transferability to new systems. Machine learning can be used to achieve the best of both approaches. Here we train a general-purpose neural network potential (ANI-1ccx) that approaches CCSD(T)/CBS accuracy on benchmarks for reaction thermochemistry, isomerization, and drug-like molecular torsions. This is achieved by training a network to DFT data then using transfer learning techniques to retrain on a dataset of gold standard QM calculations (CCSD(T)/CBS) that optimally spans chemical space. The resulting potential is broadly applicable to materials science, biology, and chemistry, and billions of times faster than CCSD(T)/CBS calculations.
This content will become publicly available on December 1, 2023
- Award ID(s):
- NSF-PAR ID:
- Date Published:
- Journal Name:
- Astronomy & Astrophysics
- Page Range / eLocation ID:
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
Abstract—Materials Genomics initiative has the goal of rapidly synthesizing materials with a given set of desired properties using data science techniques. An important step in this direction is the ability to predict the outcomes of complex chemical reactions. Some graph-based feature learning algorithms have been proposed recently. However, the comprehensive relationship between atoms or structures is not learned properly and not explainable, and multiple graphs cannot be handled. In this paper, chemical reaction processes are formulated as translation processes. Both atoms and edges are mapped to vectors represent- ing the structural information. We employ the graph convolution layers to learn meaningful information of atom graphs, and further employ its variations, message passing networks (MPNN) and edge attention graph convolution network (EAGCN) to learn edge representations. Particularly, multi-view EAGCN groups and maps edges to a set of representations for the properties of the chemical bond between atoms from multiple views. Each bond is viewed from its atom type, bond type, distance and neighbor environment. The final node and edge representations are mapped to a sequence defined by the SMILES of the molecule and then fed to a decoder model with attention. To make full usage of multi-view information, we propose multi-view attention model to handle self correlation inside each atom or edge, and mutual correlation between edges and atoms, both of which are important in chemical reaction processes. We have evaluated our method on the standard benchmark datasets (that have been used by all the prior works), and the results show that edge embedding with multi-view attention achieves superior accuracy compared to existing techniques.more » « less
Estimating the quality of transmission (QoT) of a lightpath before its establishment is a critical procedure for efficient design and management of optical networks. Recently, supervised machine learning (ML) techniques for QoT estimation have been proposed as an effective alternative to well-established, yet approximated, analytic models that often require the introduction of conservative margins to compensate for model inaccuracies and uncertainties. Unfortunately, to ensure high estimation accuracy, the training set (i.e., the set of historical field data, or “samples,” required to train these supervised ML algorithms) must be very large, while in real network deployments, the number of monitored/monitorable lightpaths is limited by several practical considerations. This is especially true for lightpaths with an above-threshold bit error rate (BER) (i.e., malfunctioning or wrongly dimensioned lightpaths), which are infrequently observed during network operation. Samples with above-threshold BERs can be acquired by deploying probe lightpaths, but at the cost of increased operational expenditures and wastage of spectral resources. In this paper, we propose to use
active learningto reduce the number of probes needed for ML-based QoT estimation. We build an estimation model based on Gaussian processes, which allows iterative identification of those QoT instances that minimize estimation uncertainty. Numerical results using synthetically generated datasets show that, by using the proposed active learning approach, we can achieve the same performance of standard offline supervised ML methods, but with a remarkable reduction (at least 5% and up to 75%) in the number of training samples.
Deep neural networks (DNNs) are widely used to handle many difficult tasks, such as image classification and malware detection, and achieve outstanding performance. However, recent studies on adversarial examples, which have maliciously undetectable perturbations added to their original samples that are indistinguishable by human eyes but mislead the machine learning approaches, show that machine learning models are vulnerable to security attacks. Though various adversarial retraining techniques have been developed in the past few years, none of them is scalable. In this paper, we propose a new iterative adversarial retraining approach to robustify the model and to reduce the effectiveness of adversarial inputs on DNN models. The proposed method retrains the model with both Gaussian noise augmentation and adversarial generation techniques for better generalization. Furthermore, the ensemble model is utilized during the testing phase in order to increase the robust test accuracy. The results from our extensive experiments demonstrate that the proposed approach increases the robustness of the DNN model against various adversarial attacks, specifically, fast gradient sign attack, Carlini and Wagner (C&W) attack, Projected Gradient Descent (PGD) attack, and DeepFool attack. To be precise, the robust classifier obtained by our proposed approach can maintain a performance accuracy of 99% on average on the standard test set. Moreover, we empirically evaluate the runtime of two of the most effective adversarial attacks, i.e., C&W attack and BIM attack, to find that the C&W attack can utilize GPU for faster adversarial example generation than the BIM attack can. For this reason, we further develop a parallel implementation of the proposed approach. This parallel implementation makes the proposed approach scalable for large datasets and complex models.
Relevance to proposal: This project evaluates the generalizability of real and synthetic training datasets which can be used to train model-free techniques for multi-agent applications. We evaluate different methods of generating training corpora and machine learning techniques including Behavior Cloning and Generative Adversarial Imitation Learning. Our results indicate that the utility-guided selection of representative scenarios to generate synthetic data can have significant improvements on model performance. Paper abstract: Crowd simulation, the study of the movement of multiple agents in complex environments, presents a unique application domain for machine learning. One challenge in crowd simulation is to imitate the movement of expert agents in highly dense crowds. An imitation model could substitute an expert agent if the model behaves as good as the expert. This will bring many exciting applications. However, we believe no prior studies have considered the critical question of how training data and training methods affect imitators when these models are applied to novel scenarios. In this work, a general imitation model is represented by applying either the Behavior Cloning (BC) training method or a more sophisticated Generative Adversarial Imitation Learning (GAIL) method, on three typical types of data domains: standard benchmarks for evaluating crowd models, random sampling of state-action pairs, and egocentric scenarios that capture local interactions. Simulated results suggest that (i) simpler training methods are overall better than more complex training methods, (ii) training samples with diverse agent-agent and agent-obstacle interactions are beneficial for reducing collisions when the trained models are applied to new scenarios. We additionally evaluated our models in their ability to imitate real world crowd trajectories observed from surveillance videos. Our findings indicate that models trained on representative scenarios generalize to new, unseen situations observed in real human crowds.more » « less