A prediction rigidity formalism for low-cost uncertainties in trained neural networks

Regression methods are fundamental for scientific and technological applications. However, fitted models can be highly unreliable outside of their training domain, and hence the quantification of their uncertainty is crucial in many of their applications. Based on the solution of a constrained optimization problem, we propose "prediction rigidities" as a method to obtain uncertainties of arbitrary pre-trained regressors. We establish a strong connection between our framework and Bayesian inference, and we develop a last-layer approximation that allows the new method to be applied to neural networks. This extension affords cheap uncertainties without any modification to the neural network itself or its training procedure. We show the effectiveness of our method on a wide range of regression tasks, ranging from simple toy models to applications in chemistry and meteorology.

Electronic excited states from physically-constrained machine learning

Data-driven techniques are increasingly used to replace electronic-structure calculations of matter. In this context, a relevant question is whether machine learning (ML) should be applied directly to predict the desired properties or be combined explicitly with physically-grounded operations. We present an example of an integrated modeling approach, in which a symmetry-adapted ML model of an effective Hamiltonian is trained to reproduce electronic excitations from a quantum-mechanical calculation. The resulting model can make predictions for molecules that are much larger and more complex than those that it is trained on, and allows for dramatic computational savings by indirectly targeting the outputs of well-converged calculations while using a parameterization corresponding to a minimal atom-centered basis. These results emphasize the merits of intertwining data-driven techniques with physical approximations, improving the transferability and interpretability of ML models without affecting their accuracy and computational efficiency, and providing a blueprint for developing ML-augmented electronic-structure methods.

Physics-inspired Equivariant Descriptors of Non-bonded Interactions

Most of the existing machine-learning schemes applied to atomic-scale simulations rely on a local description of the geometry of a structure, and struggle to model effects that are driven by long-range physical interactions. Efforts to overcome these limitations have focused on the direct incorporation of electrostatics, which is the most prominent effect, often relying on architectures that mirror the functional form of explicit physical models. Including other forms of non-bonded interactions, or predicting properties other than the interatomic potential, requires ad hoc modifications. We propose an alternative approach that extends the long-distance equivariant (LODE) framework to generate local descriptors of an atomic environment that resemble non-bonded potentials with arbitrary asymptotic behaviors, ranging from point-charge electrostatics to dispersion forces. We show that the LODE formalism is amenable to a direct physical interpretation in terms of a generalized multipole expansion, that simplifies its implementation and reduces the number of descriptors needed to capture a given asymptotic behavior. These generalized LODE features provide improved extrapolation capabilities when trained on structures dominated by a given asymptotic behavior, but do not help in capturing the wildly different energy scales that are relevant for a more heterogeneous data set. This approach provides a practical scheme to incorporate different types of non-bonded interactions, and a framework to investigate the interplay of physical and data-related considerations that underlie this challenging modeling problem.

Smooth, exact rotational symmetrization for deep learning on point clouds

Point clouds are versatile representations of 3D objects and have found widespread application in science and engineering. Many successful deep-learning models have been proposed that use them as input. Some application domains require incorporating exactly physical constraints, including chemical and materials modeling which we focus on in this paper. These constraints include smoothness, and symmetry with respect to translations, rotations, and permutations of identical particles. Most existing architectures in other domains do not fulfill simultaneously all of these requirements and thus are not applicable to atomic-scale simulations. Many of them, however, can be straightforwardly made to incorporate all the physical constraints except for rotational symmetry. We propose a general symmetrization protocol that adds rotational equivariance to any given model while preserving all the other constraints. As a demonstration of the potential of this idea, we introduce the Point Edge Transformer (PET) architecture, which is not intrinsically equivariant but achieves state-of-the-art performance on several benchmark datasets of molecules and solids. A-posteriori application of our general protocol makes PET exactly equivariant, with minimal changes to its accuracy. By alleviating the need to explicitly incorporate rotational symmetry within the model, our method bridges the gap between the approaches used in different communities, and simplifies the design of deep-learning schemes for chemical and materials modeling.

Wigner kernels: body-ordered equivariant machine learning without a basis

Machine-learning models based on a point-cloud representation of a physical object are ubiquitous in scientific applications and particularly well-suited to the atomic-scale description of molecules and materials. Among the many different approaches that have been pursued, the description of local atomic environments in terms of their neighbor densities has been used widely and very succesfully. We propose a novel density-based method which involves computing ``Wigner kernels''. These are fully equivariant and body-ordered kernels that can be computed iteratively with a cost that is independent of the radial-chemical basis and grows only linearly with the maximum body-order considered. This is in marked contrast to feature-space models, which comprise an exponentially-growing number of terms with increasing order of correlations. We present several examples of the accuracy of models based on Wigner kernels in chemical applications, for both scalar and tensorial targets, reaching state-of-the-art accuracy on the popular QM9 benchmark dataset, and we discuss the broader relevance of these ideas to equivariant geometric machine-learning.

Completeness of Atomic Structure Representations

Achieving a complete and symmetric description of a group of point particles, such as atoms in a molecule, is a common problem in physics and theoretical chemistry. The introduction of machine learning to science has made this issue even more critical, as it underpins the ability of a model to reproduce arbitrary physical relationships, and to do so while being consistent with basic symmetries and conservation laws. However, the descriptors that are commonly used to represent point clouds -- most notably those adopted to describe matter at the atomic scale -- are unable to distinguish between special arrangements of particles. This makes it impossible to machine learn their properties. Frameworks that are provably complete exist, but are only so in the limit in which they simultaneously describe the mutual relationship between all atoms, which is impractical. We introduce, and demonstrate on a particularly insidious class of atomic arrangements, a strategy to build descriptors that rely solely on information on the relative arrangement of triplets of particles, but can be used to construct symmetry-adapted models that have universal approximation power.

Fast evaluation of real spherical harmonics and their derivatives in Cartesian coordinates

Spherical harmonics provide a smooth, orthogonal, and symmetry-adapted basis to expand functions on a sphere, and they are used routinely in computer graphics, signal processing and different fields of science, from geology to quantum chemistry. More recently, spherical harmonics have become a key component of rotationally equivariant models for geometric deep learning, where they are used in combination with distance-dependent functions to describe the distribution of neighbors within local spherical environments within a point cloud. We present a fast and elegant algorithm for the evaluation of the real-valued spherical harmonics. Our construction integrates many of the desirable features of existing schemes and allows to compute Cartesian derivatives in a numerically stable and computationally efficient manner. We provide an efficient C implementation of the proposed algorithm, along with easy-to-use Python bindings.

A data-driven interpretation of the stability of molecular crystals

Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A particularly active and fruitful approach involves classifying the different combinations of interacting chemical moieties, as understanding the relative energetics of different interactions enables the design of molecular crystals and fine-tuning their stabilities. While this is usually performed based on the empirical observation of the most commonly encountered motifs in known crystal structures, we propose to apply a combination of supervised and unsupervised machine-learning techniques to automate the construction of an extensive library of molecular building blocks. We introduce a structural descriptor tailored to the prediction of the binding energy for a curated dataset of organic crystals and exploit its atom-centered nature to obtain a data-driven assessment of the contribution of different chemical groups to the lattice energy of the crystal. We then interpret this library using a low-dimensional representation of the structure-energy landscape and discuss selected examples of the insights that can be extracted from this analysis, providing a complete database to guide the design of molecular materials.

A smooth basis for atomistic machine learning

Machine learning frameworks based on correlations of interatomic positions begin with a discretized description of the density of other atoms in the neighbourhood of each atom in the system. Symmetry considerations support the use of spherical harmonics to expand the angular dependence of this density, but there is as yet no clear rationale to choose one radial basis over another. Here we investigate the basis that results from the solution of the Laplacian eigenvalue problem within a sphere around the atom of interest. We show that this generates the smoothest possible basis of a given size within the sphere, and that a tensor product of Laplacian eigenstates also provides the smoothest possible basis for expanding any higher-order correlation of the atomic density within the appropriate hypersphere. We consider several unsupervised metrics of the quality of a basis for a given dataset, and show that the Laplacian eigenstate basis has a performance that is much better than some widely used basis sets and is competitive with data-driven bases that numerically optimize each metric. In supervised machine learning tests, we find that the optimal function smoothness of the Laplacian eigenstates leads to comparable or better performance than can be obtained from a data-driven basis of a similar size that has been optimized to describe the atom-density correlation for the specific dataset. We conclude that the smoothness of the basis functions is a key and hitherto largely overlooked aspect of successful atomic density representations.