arXiv subjects

Lixue Cheng

Publications and source records attributed to Lixue Cheng.

26 records · Page 2Linked to original sources

arXiv2022

Molecular-orbital-based Machine Learning for Open-shell and Multi-reference Systems with Kernel Addition Gaussian Process Regression

We introduce a novel machine learning strategy, kernel addition Gaussian process regression (KA-GPR), in molecular-orbital-based machine learning (MOB-ML) to learn the total correlation energies of general electronic structure theories for closed- and open-shell systems by introducing a machine learning strategy. The learning efficiency of MOB-ML (KA-GPR) is the same as the original MOB-ML method for the smallest criegee molecule, which is a closed-shell molecule with multi-reference characters. In addition, the prediction accuracies of different small free radicals could reach the chemical accuracy of 1 kcal/mol by training on one example structure. Accurate potential energy surfaces for the H10 chain (closed-shell) and water OH bond dissociation (open-shell) could also be generated by MOB-ML (KA-GPR). To explore the breadth of chemical systems that KA-GPR can describe, we further apply MOB-ML to accurately predict the large benchmark datasets for closed- (QM9, QM7b-T, GDB-13-T) and open-shell (QMSpin) molecules.

physics.chem-ph↗

arXiv2022

Molecular Dipole Moment Learning via Rotationally Equivariant Gaussian Process Regression with Derivatives in Molecular-orbital-based Machine Learning

This study extends the accurate and transferable molecular-orbital-based machine learning (MOB-ML) approach to modeling the contribution of electron correlation to dipole moments at the cost of Hartree-Fock computations. A molecular-orbital-based (MOB) pairwise decomposition of the correlation part of the dipole moment is applied, and these pair dipole moments could be further regressed as a universal function of molecular orbitals (MOs). The dipole MOB features consist of the energy MOB features and their responses to electric fields. An interpretable and rotationally equivariant Gaussian process regression (GPR) with derivatives algorithm is introduced to learn the dipole moment more efficiently. The proposed problem setup, feature design, and ML algorithm are shown to provide highly-accurate models for both dipole moment and energies on water and fourteen small molecules. To demonstrate the ability of MOB-ML to function as generalized density-matrix functionals for molecular dipole moments and energies of organic molecules, we further apply the proposed MOB-ML approach to train and test the molecules from the QM9 dataset. The application of local scalable GPR with Gaussian mixture model unsupervised clustering (GMM/GPR) scales up MOB-ML to a large-data regime while retaining the prediction accuracy. In addition, compared with literature results, MOB-ML provides the best test MAEs of 4.21 mDebye and 0.045 kcal/mol for dipole moment and energy models, respectively, when training on 110000 QM9 molecules. The excellent transferability of the resulting QM9 models is also illustrated by the accurate predictions for four different series of peptides.

physics.chem-ph↗

arXiv2022

Accurate Molecular-Orbital-Based Machine Learning Energies via Unsupervised Clustering of Chemical Space

We introduce an unsupervised clustering algorithm to improve training efficiency and accuracy in predicting energies using molecular-orbital-based machine learning (MOB-ML). This work determines clusters via the Gaussian mixture model (GMM) in an entirely automatic manner and simplifies an earlier supervised clustering approach [J. Chem. Theory Comput., 15, 6668 (2019)] by eliminating both the necessity for user-specified parameters and the training of an additional classifier. Unsupervised clustering results from GMM have the advantage of accurately reproducing chemically intuitive groupings of frontier molecular orbitals and having improved performance with an increasing number of training examples. The resulting clusters from supervised or unsupervised clustering is further combined with scalable Gaussian process regression (GPR) or linear regression (LR) to learn molecular energies accurately by generating a local regression model in each cluster. Among all four combinations of regressors and clustering methods, GMM combined with scalable exact Gaussian process regression (GMM/GPR) is the most efficient training protocol for MOB-ML. The numerical tests of molecular energy learning on thermalized datasets of drug-like molecules demonstrate the improved accuracy, transferability, and learning efficiency of GMM/GPR over not only other training protocols for MOB-ML, i.e., supervised regression-clustering combined with GPR(RC/GPR) and GPR without clustering. GMM/GPR also provide the best molecular energy predictions compared with the ones from literature on the same benchmark datasets. With a lower scaling, GMM/GPR has a 10.4-fold speedup in wall-clock training time compared with scalable exact GPR with a training size of 6500 QM7b-T molecules.

physics.chem-ph↗

arXiv2021

Molecular Energy Learning Using Alternative Blackbox Matrix-Matrix Multiplication Algorithm for Exact Gaussian Process

We present an application of the blackbox matrix-matrix multiplication (BBMM) algorithm to scale up the Gaussian Process (GP) training of molecular energies in the molecular-orbital based machine learning (MOB-ML) framework. An alternative implementation of BBMM (AltBBMM) is also proposed to train more efficiently (over four-fold speedup) with the same accuracy and transferability as the original BBMM implementation. The training of MOB-ML was limited to 220 molecules, and BBMM and AltBBMM scale the training of MOB-ML up by over 30 times to 6500 molecules (more than a million pair energies). The accuracy and transferability of both algorithms are examined on the benchmark datasets of organic molecules with 7 and 13 heavy atoms. These lower-scaling implementations of the GP preserve the state-of-the-art learning efficiency in the low-data regime while extending it to the large-data regime with better accuracy than other available machine learning works on molecular energies.

physics.chem-ph↗

arXiv2020

Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states

Molecular-orbital-based machine learning (MOB-ML) provides a general framework for the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. We demonstrate the importance of preserving physical constraints, including invariance conditions and size consistency, when generating the input for the machine learning model. Numerical improvements are demonstrated for different data sets covering total and relative energies for thermally accessible organic and transition-metal containing molecules, non-covalent interactions, and transition-state energies. MOB-ML requires training data from only 1% of the QM7b-T data set (i.e., only 70 organic molecules with seven and fewer heavy atoms) to predict the total energy of the remaining 99% of this data set with sub-kcal/mol accuracy. This MOB-ML model is significantly more accurate than other methods when transferred to a data set comprised of thirteen heavy atom molecules, exhibiting no loss of accuracy on a size intensive (i.e., per-electron) basis. It is shown that MOB-ML also works well for extrapolating to transition-state structures, predicting the barrier region for malonaldehyde intramolecular proton-transfer to within 0.35 kcal/mol when only trained on reactant/product-like structures. Finally, the use of the Gaussian process variance enables an active learning strategy for extending MOB-ML model to new regions of chemical space with minimal effort. We demonstrate this active learning strategy by extending a QM7b-T model to describe non-covalent interactions in the protein backbone-backbone interaction data set to an accuracy of 0.28 kcal/mol.

physics.chem-ph↗

arXiv2019

Regression-clustering for Improved Accuracy and Training Cost with Molecular-Orbital-Based Machine Learning

Machine learning (ML) in the representation of molecular-orbital-based (MOB) features has been shown to be an accurate and transferable approach to the prediction of post-Hartree-Fock correlation energies. Previous applications of MOB-ML employed Gaussian Process Regression (GPR), which provides good prediction accuracy with small training sets; however, the cost of GPR training scales cubically with the amount of data and becomes a computational bottleneck for large training sets. In the current work, we address this problem by introducing a clustering/regression/classification implementation of MOB-ML. In a first step, regression clustering (RC) is used to partition the training data to best fit an ensemble of linear regression (LR) models; in a second step, each cluster is regressed independently, using either LR or GPR; and in a third step, a random forest classifier (RFC) is trained for the prediction of cluster assignments based on MOB feature values. Upon inspection, RC is found to recapitulate chemically intuitive groupings of the frontier molecular orbitals, and the combined RC/LR/RFC and RC/GPR/RFC implementations of MOB-ML are found to provide good prediction accuracy with greatly reduced wall-clock training times. For a dataset of thermalized geometries of 7211 organic molecules of up to seven heavy atoms, both implementations reach chemical accuracy (1 kcal/mol error) with only 300 training molecules, while providing 35000-fold and 4500-fold reductions in the wall-clock training time, respectively, compared to MOB-ML without clustering. The resulting models are also demonstrated to retain transferability for the prediction of large-molecule energies with only small-molecule training data. Finally, it is shown that capping the number of training datapoints per cluster leads to further improvements in prediction accuracy with negligible increases in wall-clock training time.

physics.chem-ph↗

arXiv2019

A Universal Density Matrix Functional from Molecular Orbital-Based Machine Learning: Transferability across Organic Molecules

We address the degree to which machine learning can be used to accurately and transferably predict post-Hartree-Fock correlation energies. Refined strategies for feature design and selection are presented, and the molecular-orbital-based machine learning (MOB-ML) method is applied to several test systems. Strikingly, for the MP2, CCSD, and CCSD(T) levels of theory, it is shown that the thermally accessible (350 K) potential energy surface for a single water molecule can be described to within 1 millihartree using a model that is trained from only a single reference calculation at a randomized geometry. To explore the breadth of chemical diversity that can be described, MOB-ML is also applied to a new dataset of thermalized (350 K) geometries of 7211 organic models with up to seven heavy atoms. In comparison with the previously reported $Δ$-ML method, MOB-ML is shown to reach chemical accuracy with three-fold fewer training geometries. Finally, a transferability test in which models trained for seven-heavy-atom systems are used to predict energies for thirteen-heavy-atom systems reveals that MOB-ML reaches chemical accuracy with 36-fold fewer training calculations than $Δ$-ML (140 versus 5000 training calculations).

physics.chem-ph↗

arXiv2018

Transferability in Machine Learning for Electronic Structure via the Molecular Orbital Basis

We present a machine learning (ML) method for predicting electronic structure correlation energies using Hartree-Fock input.The total correlation energy is expressed in terms of individual and pair contributions from occupied molecular orbitals, and Gaussian process regression is used to predict these contributions from a feature set that is based on molecular orbital properties, such as Fock, Coulomb, and exchange matrix elements. With the aim of maximizing transferability across chemical systems and compactness of the feature set, we avoid the usual specification of ML features in terms of atom- or geometry-specific information, such atom/element-types, bond-types, or local molecular structure. ML predictions of MP2 and CCSD energies are presented for a range of systems, demonstrating that the method maintains accuracy while providing transferability both within and across chemical families; this includes predictions for molecules with atom-types and elements that are not included in the training set. The method holds promise both in its current form and as a proof-of-principle for the use of ML in the design of generalized density-matrix functionals.

physics.chem-ph↗