Prediction of Atomization Energy Using Graph Kernel and Active Learning

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules with high accuracy. The framework employs Gaussian process regression to perform predictions based on the similarity between molecules, which is computed using the marginalized graph kernel. To apply the marginalized graph kernel, a spatial adjacency rule is first employed to convert molecules into graphs whose vertices and edges are labeled by elements and interatomic distances, respectively. We then derive formulas for the efficient evaluation of the kernel. Specific functional components for the marginalized graph kernel are proposed, while the effect of the associated hyperparameters on accuracy and predictive confidence are examined. We show that the graph kernel is particularly suitable for predicting extensive properties because its convolutional structure coincides with that of the covariance formula between sums of random variables. Using an active learning procedure, we demonstrate that the proposed method can achieve a mean absolute error of 0.62 +- 0.01 kcal/mol using as few as 2000 training samples on the QM7 data set

Unfolding Quantum Computer Readout Noise

In the current era of noisy intermediate-scale quantum (NISQ) computers, noisy qubits can result in biased results for early quantum algorithm applications. This is a significant challenge for interpreting results from quantum computer simulations for quantum chemistry, nuclear physics, high energy physics, and other emerging scientific applications. An important class of qubit errors are readout errors. The most basic method to correct readout errors is matrix inversion, using a response matrix built from simple operations to probe the rate of transitions from known initial quantum states to readout outcomes. One challenge with inverting matrices with large off-diagonal components is that the results are sensitive to statistical fluctuations. This challenge is familiar to high energy physics, where prior-independent regularized matrix inversion techniques (`unfolding') have been developed for years to correct for acceptance and detector effects when performing differential cross section measurements. We study various unfolding methods in the context of universal gate-based quantum computers with the goal of connecting the fields of quantum information science and high energy physics and providing a reference for future work. The method known as iterative Bayesian unfolding is shown to avoid pathologies from commonly used matrix inversion and least squares methods.Comment: 13 pages, 16 figures; v2 has a typo fixed in Eq. 3 and a series of minor modification

Resource-Efficient Chemistry on Quantum Computers with the Variational Quantum Eigensolver and the Double Unitary Coupled-Cluster Approach.

Applications of quantum simulation algorithms to obtain electronic energies of molecules on noisy intermediate-scale quantum (NISQ) devices require careful consideration of resources describing the complex electron correlation effects. In modeling second-quantized problems, the biggest challenge confronted is that the number of qubits scales linearly with the size of the molecular basis. This poses a significant limitation on the size of the basis sets and the number of correlated electrons included in quantum simulations of chemical processes. To address this issue and enable more realistic simulations on NISQ computers, we employ the double unitary coupled-cluster (DUCC) method to effectively downfold correlation effects into the reduced-size orbital space, commonly referred to as the active space. Using downfolding techniques, we demonstrate that properly constructed effective Hamiltonians can capture the effect of the whole orbital space in small-size active spaces. Combining the downfolding preprocessing technique with the variational quantum eigensolver, we solve for the ground-state energy of H2, Li2, and BeH2 in the cc-pVTZ basis using the DUCC-reduced active spaces. We compare these results to full configuration-interaction and high-level coupled-cluster reference calculations

ML4Chem: A Machine Learning Package for Chemistry and Materials Science

ML4Chem is an open-source machine learning library for chemistry and materials science. It provides an extendable platform to develop and deploy machine learning models and pipelines and is targeted to the non-expert and expert users. ML4Chem follows user-experience design and offers the needed tools to go from data preparation to inference. Here we introduce its atomistic module for the implementation, deployment, and reproducibility of atom-centered models. This module is composed of six core building blocks: data, featurization, models, model optimization, inference, and visualization. We present their functionality and easiness of use with demonstrations utilizing neural networks and kernel ridge regression algorithms.Comment: 32 pages, 11 Figure

ArQTiC: A full-stack software package for simulating materials on quantum computers

ArQTiC is an open-source, full-stack software package built for the simulations of materials on quantum computers. It currently can simulate materials that can be modeled by any Hamiltonian derived from a generic, one-dimensional, time-dependent Heisenberg Hamiltonain. ArQTiC includes modules for generating quantum programs for real- and imaginary-time evolution, quantum circuit optimization, connection to various quantum backends via the cloud, and post-processing of quantum results. By enabling users to seamlessly perform and analyze materials simulations on quantum computers by simply providing a minimal input text file, ArQTiC opens this field to a broader community of scientists from a wider range of scientific domains.Comment: 8 pages, 7 figure

Density Functional Studies on the Complexation and Spectroscopy of Uranyl Ligated with Acetonitrile and Acetone Derivatives

The coordination of nitrile (acetonitrile, propionitrile, and benzonitrile) and carbonyl (formaldehyde, acetaldehyde, and acetone) ligands to the uranyl dication (UO22+) has been examined using density functional theory (DFT) utilizing relativistic effective core potentials (RECPs). Complexes containing up to six ligands have been modeled in the gas phase for all ligands except formaldehyde, for which no minimum could be found. A comparison of relative binding energies indicates that 5-coordinate complexes are predominant, while 6-coordinate complexes involving propionitrile and acetone ligands might be possible. Additionally, the relative binding energy and the weakening of the uranyl bond is related to the size of the ligand, and in general, nitriles bind more strongly to uranyl than carbonyls

Detecting Label Noise via Leave-One-Out Cross-Validation

We present a simple algorithm for identifying and correcting real-valued noisy labels from a mixture of clean and corrupted sample points using Gaussian process regression. A heteroscedastic noise model is employed, in which additive Gaussian noise terms with independent variances are associated with each and all of the observed labels. Optimizing the noise model using maximum likelihood estimation leads to the containment of the GPR model's predictive error by the posterior standard deviation in leave-one-out cross-validation. A multiplicative update scheme is proposed for solving the maximum likelihood estimation problem under non-negative constraints. While we provide proof of convergence for certain special cases, the multiplicative scheme has empirically demonstrated monotonic convergence behavior in virtually all our numerical experiments. We show that the presented method can pinpoint corrupted sample points and lead to better regression models when trained on synthetic and real-world scientific data sets