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equivariant_electron_density

SAND2022-3548 O This code contains scripts that allow users to generate molecular electron densities, train a machine learning model to predict electron densities, and analyze the accuracy of machine learned electron densities. It accompanies a publication titled "Cracking the Quantum Scaling Limit with Machine Learned Electron Densities.” Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Rackers, Joshua↗

Off-shell Partition Functions in 3d Gravity

We explore three-dimensional gravity with negative cosmological constant via canonical quantization. We focus on chiral gravity which is related to a single copy of PSL(2,R) Chern-Simons theory and is simpler to treat in canonical quantization. Its phase space for an initial value surface Σ is given by the appropriate moduli space of Riemann surfaces. We use geometric quantization to compute partition functions of chiral gravity on three-manifolds of the form Σ×S 1 , where Σ can have asymptotic boundaries. Most of these topologies do not admit a classical solution and are thus not amenable to a direct semiclassical path integral computation. We use an index theorem that expresses the partition function as an integral of characteristic classes over phase space. In the presence of n asymptotic boundaries, we use techniques from equivariant cohomology to localize the integral to a finite-dimensional integral over $\overline{M}$ g,n , which we evaluate in low genus cases. Higher genus partition functions quickly become complicated since they depend in an oscillatory way on Newton's constant. There is a precise sense in which one can isolate the non-oscillatory part which we call the fake partition function. We establish that there is a topological recursion that computes the fake partition functions for arbitrary Riemann surfaces Σ. As a result, there is a scaling limit in which the model reduces to JT gravity and our methods give a novel way to compute JT partition functions via equivariant localization.

Classical and Quantum Gravity↗

MS25: Materials Science-Focused Benchmark Data Set for Machine Learning Interatomic Potentials

Here, we present MS25, a benchmark data set for evaluating machine learning interatomic potentials (MLIPs) across diverse materials-relevant systems including MgO surfaces, liquid water, zeolites, a catalytic Pt surface reaction, high-entropy alloys (HEAs), and disordered Zr-oxides. Five MLIP architectures (MACE, NequIP, Allegro, MTP, and Torch-ANI) are trained and tested, focusing not only on traditional metrics (energies, forces, and stresses) but also explicitly validating derived physical observables such as lattice constants, volumes, and reaction barriers. We find that most models reach comparable accuracy on standard error metrics across the simple systems, although equivariant MLIPs offer 1.5–2× improvements over nonequivariant MLIPs in energy and force error for structurally complex or compositionally disordered environments such as HEAs and Zr–O systems. Our analysis highlights that low errors in energy and force predictions do not guarantee reliable observables, emphasizing the necessity of explicit validation. We demonstrate limitations in cross-framework transferability, as models trained on one zeolite framework (CHA) fail to reliably generalize to predictions of structurally distinct frameworks (e.g., MFI). Size-extensive tests show some dependence on system size for MgO, resulting from forced periodicity. The HEA and Zr–O data sets are identified as challenging tests for future benchmarks and MLIP model architecture developments as they show significant differentiation in error between MLIP architectures and are still relatively difficult at 1000 training images. Moving forward, we recommend that benchmarking efforts shift their focus from marginal accuracy improvements in energy and force errors toward identifying and understanding model failure modes, rigorously assessing transferability, and evaluating how their errors affect observable predictions. For researchers looking to choose an MLIP architecture, we suggest selecting equivariant MLIP architectures if the complexity of the system is a challenge. For simple materials problems, auxiliary features such as integration with molecular dynamics engines, trade-offs between computational data set generation cost vs MLIP inference speed, and framework integration may play a more important decision factor than small differences in error metrics that are unlikely to matter for production-level research.

chemical structure↗

Local Noether theorem for quantum lattice systems and topological invariants of gapped states

Here, we study generalizations of the Berry phase for quantum lattice systems in arbitrary dimensions. For a smooth family of gapped ground states in d dimensions, we define a closed d + 2-form on the parameter space, which generalizes the curvature of the Berry connection. Its cohomology class is a topological invariant of the family. When the family is equivariant under the action of a compact Lie group G, topological invariants take values in the equivariant cohomology of the parameter space. These invariants unify and generalize the Hall conductance and the Thouless pump. A key role in these constructions is played by a certain differential graded Fréchet–Lie algebra attached to any quantum lattice system. As a by-product, we describe ambiguities in charge densities and conserved currents for arbitrary lattice systems with rapidly decaying interactions.

97 MATHEMATICS AND COMPUTING↗

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗

SIDDA: SInkhorn Dynamic Domain Adaptation

Modern neural networks (NNs) often do not generalize well in the presence of a "covariate shift"; that is, in situations where the training and test data distributions differ, but the conditional distribution of classification labels remains unchanged. In such cases, NN generalization can be reduced to a problem of learning more domain-invariant features. Domain adaptation (DA) methods include a range of techniques aimed at achieving this; however, these methods have struggled with the need for extensive hyperparameter tuning, which then incurs significant computational costs. In this work, we introduce SIDDA, an out-of-the-box DA training algorithm built upon the Sinkhorn divergence, that can achieve effective domain alignment with minimal hyperparameter tuning and computational overhead. We demonstrate the efficacy of our method on multiple simulated and real datasets of varying complexity, including simple shapes, handwritten digits, and real astronomical observations. SIDDA is compatible with a variety of NN architectures, and it works particularly well in improving classification accuracy and model calibration when paired with equivariant neural networks (ENNs). We find that SIDDA enhances the generalization capabilities of NNs, achieving up to a ≈40% improvement in classification accuracy on unlabeled target data. We also study the efficacy of DA on ENNs with respect to the varying group orders of the dihedral group DN, and find that the model performance improves as the degree of equivariance increases. Finally, we find that SIDDA enhances model calibration on both source and target data--achieving over an order of magnitude improvement in the ECE and Brier score. SIDDA's versatility, combined with its automated approach to domain alignment, has the potential to advance multi-dataset studies by enabling the development of highly generalizable models.

Pandya, Sneh [Northeastern U.]↗

Densely Connected G-invariant Deep Neural Networks with Signed Permutation Representations

We introduce and investigate, for finite groups G, G-invariant deep neural network (GDNN) architectures with ReLU activation that are densely connected- i.e., include all possible skip connections. In contrast to other G-invariant architectures in the literature, the preactivations of theG-DNNs presented here are able to transform by signed permutation representations (signed perm-reps) of G. Moreover, the individual layers of the G-DNNs are not required to be G-equivariant; instead, the preactivations are constrained to be G-equivariant functions of the network input in a way that couples weights across all layers. The result is a richer family of G-invariant architectures never seen previously. We derive an efficient implementation of G-DNNs after a reparameterization of weights, as well as necessary and sufficient conditions for an architecture to be "admissible"- i.e., nondegenerate and inequivalent to smaller architectures. We include code that allows a user to build a G-DNN interactively layer-by-layer, with the final architecture guaranteed to be admissible. We show that there are far more admissible G-DNN architectures than those accessible with the "concatenated ReLU" activation function from the literature. Finally, we apply G-DNNs to two example problems--(1) multiplication in --1, 1} (with theoretical guarantees) and (2) 3D object classification--finding that the inclusion of signed perm-reps significantly boosts predictive performance compared to baselines with only ordinary (i.e., unsigned) perm-reps.

97 MATHEMATICS AND COMPUTING↗

Analyzing the Free States of one Quantum Resource Theory as Resource States of Another

In the context of quantum resource theories (QRTs), free states are defined as those that can be obtained at no cost under a certain restricted set of conditions. However, when taking a free state from one QRT and evaluating it through the optics of another QRT, it might well turn out that the state is now extremely resourceful. Such realization has recently prompted numerous works characterizing states across several QRTs. Here, in this work, we contribute to this body of knowledge by analyzing the resourcefulness in free states for—and across witnesses of—the QRTs of multipartite entanglement, fermionic non-Gaussianity, imaginarity, realness, spin coherence, Clifford non-stabilizerness, $S_n$-equivariance, and non-uniform entanglement. We provide rigorous theoretical results as well as present numerical studies that showcase the rich and complex behavior that arises in this type of cross-examination.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the intermediate Jacobian of M5-branes

Abstract We study Euclidean M5-branes wrapping vertical divisors in elliptic Calabi-Yau fourfold compactifications of M/F-theory that admit a Sen limit. We construct these Calabi-Yau fourfolds as elliptic fibrations over coordinate flip O3/O7 orientifolds of toric hypersurface Calabi-Yau threefolds. We devise a method to analyze the Hodge structure (and hence the dimension of the intermediate Jacobian) of vertical divisors in these fourfolds, using only the data available from a type IIB compactification on the O3/O7 Calabi-Yau orientifold. Our method utilizes simple combinatorial formulae (that we prove) for the equivariant Hodge numbers of the Calabi-Yau orientifolds and their prime toric divisors, along with a formula for the Euler characteristic of vertical divisors in the corresponding elliptic Calabi-Yau fourfold. Our formula for the Euler characteristic includes a conjectured correction term that accounts for the contributions of pointlike terminal ℤ 2 singularities corresponding to perturbative O3-planes. We check our conjecture in a number of explicit examples and find perfect agreement with the results of direct computations.

Physics↗