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Accurate and fast prediction of materials properties is central to the digital transformation of materials design. However, the vast design space and diverse operating conditions pose significant challenges for accurately modeling arbitrary material candidates and forecasting their properties. We present MatterSim, a deep learning model actively learned from large-scale first-principles computations, for efficient atomistic simulations at first-principles level and accurate prediction of broad material properties across the periodic table, spanning temperatures from 0 to 5000 K and pressures up to 1000 GPa. Out-of-the-box, the model serves as a machine learning force field, and shows remarkable capabilities not only in predicting ground-state material structures and energetics, but also in simulating their behavior under realistic temperatures and pressures, signifying an up to ten-fold enhancement in precision compared to the prior best-in-class. This enables MatterSim to compute materials' lattice dynamics, mechanical and thermodynamic properties, and beyond, to an accuracy comparable with first-principles methods. Specifically, MatterSim predicts Gibbs free energies for a wide range of inorganic solids with near-first-principles accuracy and achieves a 15 meV/atom resolution for temperatures up to 1000K compared with experiments. This opens an opportunity to predict experimental phase diagrams of materials at minimal computational cost. Moreover, MatterSim also serves as a platform for continuous learning and customization by integrating domain-specific data. The model can be fine-tuned for atomistic simulations at a desired level of theory or for direct structure-to-property predictions, achieving high data efficiency with a reduction in data requirements by up to 97%.

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design., Comment: 13 pages main text, 35 pages supplementary information

Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive computational costs when the simulation contains over a few hundred atoms in practice. We present an In-Distribution substructure Embedding Active Learner (IDEAL) to enable efficient simulation of large complex systems with quantum accuracy by maintaining a machine learning force field (MLFF) as an accurate surrogate to the first principles methods. By extracting high-uncertainty substructures into low-uncertainty atom environments, the active learner is allowed to concentrate on and learn from small substructures of interest rather than carrying out intractable quantum chemical computations on large structures. IDEAL is benchmarked on various systems and shows sub-linear complexity, accelerating the simulation thousands of times compared with conventional active learning and millions of times compared with pure first principles simulations. To demonstrate the capability of IDEAL in practical applications, we simulated a polycrystalline lithium system composed of one million atoms and the full ammonia formation process in a Haber-Bosch reaction on a 3-nm Iridium nanoparticle catalyst on a computing node comprising one single A100 GPU and 24 CPU cores.

Machine learning-based inverse materials discovery has attracted enormous attention recently due to its flexibility in dealing with black box models. Yet, many metaheuristic algorithms are not as widely applied to materials discovery applications as machine learning methods. There are ongoing challenges in applying different optimization algorithms to discover crystals with single- or multi-elemental compositions and how these algorithms differ in mining the ideal materials. We comprehensively compare 11 different optimization algorithms for the design of single- and multi-elemental crystals with targeted properties. By maximizing the bulk modulus and minimizing the Fermi energy through perturbing the parameterized elemental composition representations, we estimated the unique counts of elemental compositions, mean density scan of the objectives space, mean objectives and frequency distributed over the materials' representations and objectives. We found that nature-inspired algorithms contain more uncertainties in the defined elemental composition design tasks, which correspond to their dependency on multiple hyperparameters. Runge Kutta optimization (RUN) exhibits higher mean objectives whereas Bayesian optimization (BO) displayed low mean objectives compared with other methods. Combined with materials count and density scan, we propose that BO strives to approximate a more accurate surrogate of the design space by sampling more elemental compositions and hence have lower mean objectives, yet RUN will repeatedly sample the targeted elemental compositions with higher objective values. Our work shed light on the automated digital design of crystals with single- and multi-elemental compositions and is expected to elicit future studies on materials optimization such as composite and alloy design based on specific desired properties., Comment: 16 pages, 6 figures. 15 pages for Supplementary Information

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science., Comment: 80 pages, 11 figures

We report a new deep learning message passing network that takes inspiration from Newton's equations of motion to learn interatomic potentials and forces. With the advantage of directional information from trainable latent force vectors, and physics-infused operators that are inspired by the Newtonian physics, the entire model remains rotationally equivariant, and many-body interactions are inferred by more interpretable physical features. We test NewtonNet on the prediction of several reactive and non-reactive high quality ab initio data sets including single small molecule dynamics, a large set of chemically diverse molecules, and methane and hydrogen combustion reactions, achieving state-of-the-art test performance on energies and forces with far greater data and computational efficiency than other deep learning models.

We review recent advances in the capabilities of the open source ab initio Quantum Monte Carlo (QMC) package QMCPACK and the workflow tool Nexus used for greater efficiency and reproducibility. The auxiliary field QMC (AFQMC) implementation has been greatly expanded to include k-point symmetries, tensor-hypercontraction, and accelerated graphical processing unit (GPU) support. These scaling and memory reductions greatly increase the number of orbitals that can practically be included in AFQMC calculations, increasing accuracy. Advances in real space methods include techniques for accurate computation of band gaps and for systematically improving the nodal surface of ground state wavefunctions. Results of these calculations can be used to validate application of more approximate electronic structure methods including GW and density functional based techniques. To provide an improved foundation for these calculations we utilize a new set of correlation-consistent effective core potentials (pseudopotentials) that are more accurate than previous sets; these can also be applied in quantum-chemical and other many-body applications, not only QMC. These advances increase the efficiency, accuracy, and range of properties that can be studied in both molecules and materials with QMC and QMCPACK.

Nanoconfined aqueous environments and the recent advent of accelerated chemistry in microdroplets are increasingly being investigated for catalysis. The mechanisms underlying the enhanced reactivity in alternate solvent environments, and whether the enhanced reactivity due to nanoconfinement is a universal phenomenon, are not fully understood. Here, we use ab initio molecular dynamics simulations to characterize the free energy of a retro-Diels-Alder reaction in bulk water at very different densities and in water nanoconfined by parallel graphene sheets. We find that the broadly different global solvation environments accelerate the reactions to a similar degree with respect to the gas phase reaction, with activation free energies that do not differ by more than kbT from each other. The reason for the same acceleration factor in the extremely different solvation environments is that it is the microsolvation of the dienophile's carbonyl group that governs the transition state stabilization and mechanism, which is not significantly disrupted by either the lower density in bulk water or the strong nanoconfinement conditions used here. Our results also suggest that significant acceleration of Diels Alder reactions in microdroplets or on-water conditions can't arise from local microsolvation when water is present, but instead must come from highly altered reaction environments that drastically change the reaction mechanisms.

Layered perovskite ruthenium oxides exhibit a striking series of metal-insulator and magnetic-nonmagnetic phase transitions easily tuned by temperature, pressure, epitaxy, and nonlinear drive. In this work, we combine results from two complementary state of the art many-body methods, Auxiliary Field Quantum Monte Carlo and Dynamical Mean Field Theory, to determine the low-temperature phase diagram of Ca$_2$RuO$_4$. Both methods predict a low temperature, pressure-driven metal-insulator transition accompanied by a ferromagnetic-antiferromagnetic transition. The properties of the ferromagnetic state vary non-monotonically with pressure and are dominated by the ruthenium $d_{xy}$ orbital, while the properties of the antiferromagnetic state are dominated by the $d_{xz}$ and $d_{yz}$ orbitals. Differences of detail in the predictions of the two methods are analyzed. This work is theoretically important as it presents the first application of the Auxiliary Field Quantum Monte Carlo method to an orbitally-degenerate system with both Mott and Hunds physics, and provides an important comparison of the Dynamical Mean Field and Auxiliary Field Quantum Monte Carlo methods., Comment: 6 pages, 4 figures

In the study of strongly-correlated, many-electron systems, the Hubbard Kanamori (HK) model has emerged as one of the prototypes for transition metal oxide physics. The model is multi-band in nature and contains Hund's coupling terms, which have pronounced effects on metal-insulator transitions, high-temperature superconductivity, and other physical properties. In the following, we present a complete theoretical framework for treating the HK model using the ground state Auxiliary Field Quantum Monte Carlo (AFQMC) method and analyze its performance on few-band models whose parameters approximate those observed in ruthenate, rhodates, and other materials exhibiting Hund's physics. Unlike previous studies, the constrained path and phaseless approximations are used to respectively control the sign and phase problems, which enables high accuracy modeling of the HK model's ground state properties within parameter regimes of experimental interest. We demonstrate that, after careful consideration of the Hubbard-Stratonovich transformations and trial wave functions employed, relative errors in the energy of less than 1% can routinely be achieved for moderate to large values of the Hund's coupling constant. Crucially, our methodology also accurately predicts magnetic ordering and phase transitions. The results presented open the door to more predictive modeling of Hund's physics within a wide range of strongly-correlated materials using AFQMC., Comment: 14 pages, 7 figures, 2 tables

Neutral molecules with sufficiently large dipole moments can bind electrons in diffuse nonvalence orbitals with most of their charge density far from the nuclei, forming so-called dipole-bound anions. Because long-range correlation effects play an important role in the binding of an excess electron and overall binding energies are often only of the order of 10-100s of wave numbers, predictively modeling dipole-bound anions remains a challenge. Here, we demonstrate that quantum Monte Carlo methods can accurately characterize molecular dipole-bound anions with near threshold dipole moments. We also show that correlated sampling Auxiliary Field Quantum Monte Carlo is particularly well-suited for resolving the fine energy differences between the neutral and anionic species. These results shed light on the fundamental limitations of quantum Monte Carlo methods and pave the way toward using them for the study of weakly-bound species that are too large to model using traditional electron structure methods.

To predict lung nodule malignancy with a high sensitivity and specificity, we propose a fusion algorithm that combines handcrafted features (HF) into the features learned at the output layer of a 3D deep convolutional neural network (CNN). First, we extracted twenty-nine handcrafted features, including nine intensity features, eight geometric features, and twelve texture features based on grey-level co-occurrence matrix (GLCM) averaged from thirteen directions. We then trained 3D CNNs modified from three state-of-the-art 2D CNN architectures (AlexNet, VGG-16 Net and Multi-crop Net) to extract the CNN features learned at the output layer. For each 3D CNN, the CNN features combined with the 29 handcrafted features were used as the input for the support vector machine (SVM) coupled with the sequential forward feature selection (SFS) method to select the optimal feature subset and construct the classifiers. The fusion algorithm takes full advantage of the handcrafted features and the highest level CNN features learned at the output layer. It can overcome the disadvantage of the handcrafted features that may not fully reflect the unique characteristics of a particular lesion by combining the intrinsic CNN features. Meanwhile, it also alleviates the requirement of a large scale annotated dataset for the CNNs based on the complementary of handcrafted features. The patient cohort includes 431 malignant nodules and 795 benign nodules extracted from the LIDC/IDRI database. For each investigated CNN architecture, the proposed fusion algorithm achieved the highest AUC, accuracy, sensitivity, and specificity scores among all competitive classification models., Comment: 11 pages, 5 figures, 5 tables. This work has been submitted to the IEEE for possible publication

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org .

Radiomics aims to extract and analyze large numbers of quantitative features from medical images and is highly promising in staging, diagnosing, and predicting outcomes of cancer treatments. Nevertheless, several challenges need to be addressed to construct an optimal radiomics predictive model. First, the predictive performance of the model may be reduced when features extracted from an individual imaging modality are blindly combined into a single predictive model. Second, because many different types of classifiers are available to construct a predictive model, selecting an optimal classifier for a particular application is still challenging. In this work, we developed multi-modality and multi-classifier radiomics predictive models that address the aforementioned issues in currently available models. Specifically, a new reliable classifier fusion strategy was proposed to optimally combine output from different modalities and classifiers. In this strategy, modality-specific classifiers were first trained, and an analytic evidential reasoning (ER) rule was developed to fuse the output score from each modality to construct an optimal predictive model. One public data set and two clinical case studies were performed to validate model performance. The experimental results indicated that the proposed ER rule based radiomics models outperformed the traditional models that rely on a single classifier or simply use combined features from different modalities.

Purpose To develop and demonstrate a novel tumor shell feature for predicting distant failure in non-small cell lung cancer (NSCLC) and cervical cancer (CC) patients. Patients and Methods The shell predictive model was constructed using pretreatment positron emission tomography (PET) images from 48 NSCLC patients received stereotactic body radiation therapy (SBRT) and 52 CC patients underwent external beam radiation therapy and concurrent chemotherapy followed with high-dose-rate intracavitary brachytherapy. A shell feature, consisting of outer voxels around the tumor boundary, was extracted from a series of axial PET slices. The hypothesis behind this feature is that non-invasive and invasive tumors may have different morphologic patterns in the tumor periphery, in turn reflecting the differences in radiological presentations in the PET images. The utility of the shell was evaluated by the support vector machine (SVM) classifier in comparison with intensity, geometry, gray level co-occurrence matrix (GLCM) based texture, neighborhood gray tone difference matrix (NGTDM) based texture, and a combination of these four features. The results were assessed in terms of accuracy, sensitivity, specificity, and the area under the receiver operating curve (AUC). Results For NSCLC, the AUC achieved by the shell feature was 0.82 while the highest AUC achieved by the other features was 0.76. Similarly, for CC, the AUC achieved by the shell feature was 0.83 while the highest AUC achieved by the other features was 0.76. Also, the difference in performance between shell and the other features was significant (P < 0.005) in all cases. Conclusions We propose a boundary-based shell feature that correlates with tumor metastasis. The shell feature showed better predictive performance than all the other features for distant failure prediction in both NSCLC and CC., Comment: 12 pages,3 figures, 3 tables

For polarimetric SAR (PolSAR) image classification, it is a challenge to classify the aggregated terrain types, such as the urban area, into semantic homogenous regions due to sharp bright-dark variations in intensity. The aggregated terrain type is formulated by the similar ground objects aggregated together. In this paper, a polarimetric hierarchical semantic model (PHSM) is firstly proposed to overcome this disadvantage based on the constructions of a primal-level and a middle-level semantic. The primal-level semantic is a polarimetric sketch map which consists of sketch segments as the sparse representation of a PolSAR image. The middle-level semantic is a region map which can extract semantic homogenous regions from the sketch map by exploiting the topological structure of sketch segments. Mapping the region map to the PolSAR image, a complex PolSAR scene is partitioned into aggregated, structural and homogenous pixel-level subspaces with the characteristics of relatively coherent terrain types in each subspace. Then, according to the characteristics of three subspaces above, three specific methods are adopted, and furthermore polarimetric information is exploited to improve the segmentation result. Experimental results on PolSAR data sets with different bands and sensors demonstrate that the proposed method is superior to the state-of-the-art methods in region homogeneity and edge preservation for terrain classification.