pwc-archive/papers-with-abstracts huggingface dataset:
Global Universal Scaling and Ultra-Small Parameterization in Machine Learning Interatomic Potentials with Super-Linearity
Authors: Yanxiao Hu, Ye Sheng, Jing Huang, Xiaoxin Xu, Yuyan Yang, Mingqiang Zhang, Yabei Wu, Caichao Ye, Jiong Yang, Wenqing Zhang
Date: 2025-02-11 00:00:00
Tasks: Computational Efficiency, Property Prediction

Using machine learning (ML) to construct interatomic interactions and thus potential energy surface (PES) has become a common strategy for materials design and simulations. However, those current models of machine learning interatomic potential (MLIP) provide no relevant physical constrains, and thus may owe intrinsic out-of-domain difficulty which underlies the challenges of model generalizability and physical scalability. Here, by incorporating physics-informed Universal-Scaling law and nonlinearity-embedded interaction function, we develop a Super-linear MLIP with both Ultra-Small parameterization and greatly expanded expressive capability, named SUS2-MLIP. Due to the global scaling rooting in universal equation of state (UEOS), SUS2-MLIP not only has significantly-reduced parameters by decoupling the element space from coordinate space, but also naturally outcomes the out-of-domain difficulty and endows the potentials with inherent generalizability and scalability even with relatively small training dataset. The nonlinearity-enbeding transformation for interaction function expands the expressive capability and make the potentials super-linear. The SUS2-MLIP outperforms the state-of-the-art MLIP models with its exceptional computational efficiency especially for multiple-element materials and physical scalability in property prediction. This work not only presents a highly-efficient universal MLIP model but also sheds light on incorporating physical constraints into artificial-intelligence-aided materials simulation.
WyckoffDiff -- A Generative Diffusion Model for Crystal Symmetry
Authors: Filip Ekström Kelvinius, Oskar B. Andersson, Abhijith S. Parackal, Dong Qian, Rickard Armiento, Fredrik Lindsten
Date: 2025-02-10 00:00:00
Tasks: model, Position

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fr\'echet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. As a proof-of-concept study, we use WyckoffDiff to find new materials below the convex hull of thermodynamical stability.
A physics-based data-driven model for CO$_2$ gas diffusion electrodes to drive automated laboratories
Authors: Ivan Grega, Félix Therrien, Abhishek Soni, Karry Ocean, Kevan Dettelbach, Ribwar Ahmadi, Mehrdad Mokhtari, Curtis P. Berlinguette, Yoshua Bengio
Date: 2025-02-10 00:00:00
Tasks: Active Learning

The electrochemical reduction of atmospheric CO$_2$ into high-energy molecules with renewable energy is a promising avenue for energy storage that can take advantage of existing infrastructure especially in areas where sustainable alternatives to fossil fuels do not exist. Automated laboratories are currently being developed and used to optimize the composition and operating conditions of gas diffusion electrodes (GDEs), the device in which this reaction takes place. Improving the efficiency of GDEs is crucial for this technology to become viable. Here we present a modeling framework to efficiently explore the high-dimensional parameter space of GDE designs in an active learning context. At the core of the framework is an uncertainty-aware physics model calibrated with experimental data. The model has the flexibility to capture various input parameter spaces and any carbon products which can be modeled with Tafel kinetics. It is interpretable, and a Gaussian process layer can capture deviations of real data from the function space of the physical model itself. We deploy the model in a simulated active learning setup with real electrochemical data gathered by the AdaCarbon automated laboratory and show that it can be used to efficiently traverse the multi-dimensional parameter space.
Machine learning-guided construction of an analytic kinetic energy functional for orbital free density functional theory
Authors: Sergei Manzhos, Johann Luder, Pavlo Golub, Manabu Ihara
Date: 2025-02-08 00:00:00
Tasks: GPR

Machine learning (ML) of kinetic energy functionals (KEF) for orbital-free density functional theory (OF-DFT) holds the promise of addressing an important bottleneck in large-scale ab initio materials modeling where sufficiently accurate analytic KEFs are lacking. However, ML models are not as easily handled as analytic expressions; they need to be provided in the form of algorithms and associated data. Here, we bridge the two approaches and construct an analytic expression for a KEF guided by interpretative machine learning of crystal cell-averaged kinetic energy densities ({\tau}) of several hundred materials. A previously published dataset including multiple phases of 433 unary, binary, and ternary compounds containing Li, Al, Mg, Si, As, Ga, Sb, Na, Sn, P, and In was used for training, including data at the equilibrium geometry as well as strained structures. A hybrid Gaussian process regression - neural network (GPR-NN) method was used to understand the type of functional dependence of {\tau} on the features which contained cell-averaged terms of the 4th order gradient expansion and the product of the electron density and Kohn-Sham effective potential. Based on this analysis, an analytic model is constructed that can reproduce Kohn-Sham DFT energy-volume curves with sufficient accuracy (pronounced minima that are sufficiently close to the minima of the Kohn-Sham DFT-based curves and with sufficiently close curvatures) to enable structure optimizations and elastic response calculations.
Diagonal Symmetrization of Neural Network Solvers for the Many-Electron Schrödinger Equation
Authors: Kevin Han Huang, Ni Zhan, Elif Ertekin, Peter Orbanz, Ryan P. Adams
Date: 2025-02-07 00:00:00
Tasks: Data Augmentation, Variational Monte Carlo

Incorporating group symmetries into neural networks has been a cornerstone of success in many AI-for-science applications. Diagonal groups of isometries, which describe the invariance under a simultaneous movement of multiple objects, arise naturally in many-body quantum problems. Despite their importance, diagonal groups have received relatively little attention, as they lack a natural choice of invariant maps except in special cases. We study different ways of incorporating diagonal invariance in neural network ans\"atze trained via variational Monte Carlo methods, and consider specifically data augmentation, group averaging and canonicalization. We show that, contrary to standard ML setups, in-training symmetrization destabilizes training and can lead to worse performance. Our theoretical and numerical results indicate that this unexpected behavior may arise from a unique computational-statistical tradeoff not found in standard ML analyses of symmetrization. Meanwhile, we demonstrate that post hoc averaging is less sensitive to such tradeoffs and emerges as a simple, flexible and effective method for improving neural network solvers.
Honegumi: An Interface for Accelerating the Adoption of Bayesian Optimization in the Experimental Sciences
Authors: Sterling G. Baird, Andrew R. Falkowski, Taylor D. Sparks
Date: 2025-02-04 00:00:00
Tasks: Bayesian Optimization, Experimental Design

Bayesian optimization (BO) has emerged as a powerful tool for guiding experimental design and decision- making in various scientific fields, including materials science, chemistry, and biology. However, despite its growing popularity, the complexity of existing BO libraries and the steep learning curve associated with them can deter researchers who are not well-versed in machine learning or programming. To address this barrier, we introduce Honegumi, a user-friendly, interactive tool designed to simplify the process of creating advanced Bayesian optimization scripts. Honegumi offers a dynamic selection grid that allows users to configure key parameters of their optimization tasks, generating ready-to-use, unit-tested Python scripts tailored to their specific needs. Accompanying the interface is a comprehensive suite of tutorials that provide both conceptual and practical guidance, bridging the gap between theoretical understanding and practical implementation. Built on top of the Ax platform, Honegumi leverages the power of existing state-of-the-art libraries while restructuring the user experience to make advanced BO techniques more accessible to experimental researchers. By lowering the barrier to entry and providing educational resources, Honegumi aims to accelerate the adoption of advanced Bayesian optimization methods across various domains.
On the use of neural networks for the structural characterization of polymeric porous materials
Authors: Jorge Torre, Suset Barroso-Solares, M. A. Rodríguez-Pérez, Javier Pinto
Date: 2025-01-25 00:00:00

The structural characterization is an essential task in the study of porous materials. To achieve reliable results, it requires to evaluate images with hundreds of pores. Current methods require large time amounts and are subjected to human errors and subjectivity. A completely automatic tool would not only speed up the process but also enhance its reliability and reproducibility. Therefore, the main objective of this article is the study of a deep-learning-based technique for the structural characterization of porous materials, through the use of a convolutional neural network. Several fine-tuned Mask R CNN models are evaluated using different training configurations in four separate datasets each composed of numerous SEM images of diverse polymeric porous materials: closed-pore extruded polystyrene (XPS), polyurethane (PU), and poly(methyl methacrylate) (PMMA), and open-pore PU. Results prove the tool capable of providing very accurate results, equivalent to those achieved by time consuming manual methods, in a matter of seconds.
Neurophysiological correlates to the human brain complexity through $q$-statistical analysis of electroencephalogram
Authors: Dimitri Marques Abramov, Daniel de Freitas Quintanilha, Henrique Santos Lima, Roozemeria Pereira Costa, Carla Kamil-Leite, Vladimir V. Lazarev, Constantino Tsallis
Date: 2025-02-09 00:00:00
Tasks: EEG

The prospects of assessing neural complexity (NC) by $q$-statistics of the systemic organization of different types and levels of brain activity were studied. In 70 adult subjects, NC was assessed via the parameter $q$ of $q$-statistics, applied to the ongoing and EEG and its spectral power of 20 scalp points (channels). The NC were estimated both globally for all channels (AllCh) and locally (for each single channel) in different Functional States (FSs). The values of $q$ was compared among FSs and single channels, as well they were correlated with the power of $\theta$ (4-8Hz), $\beta_1$ (15-25Hz) and others EEG bands, in each FS. The value of $q$ across all FSs was higher for AllCh than for the single channels FSs. Consistently with previous studies, we found a negative correlation between NC and age. The FSs did not influence the $q$ of the EEG in AllCh, although locally the FS modulated $q$ in a consistent manner (e.g., reducing $q$ in posterior sites with eyes closed). The $q$ was correlated positively with the power of the $\theta$ and negatively with that of the $\beta_1$ band in general. These findings support the idea that, as a first approach, $q$-statistics can describe the human NC. The relationship between $q$ and $\theta$ power aligns with greater NC during FSs such as listening music and resting with eyes open, which is consistent with high-order representations rather than low-informative attentional tasks (OddBall).
Physics-Conditioned Diffusion Models for Lattice Gauge Theory
Authors: Qianteng Zhu, Gert Aarts, Wei Wang, Kai Zhou, Lingxiao Wang
Date: 2025-02-08 00:00:00
Tasks: Quantization

We develop diffusion models for simulating lattice gauge theories, where stochastic quantization is explicitly incorporated as a physical condition for sampling. We demonstrate the applicability of this novel sampler to U(1) gauge theory in two spacetime dimensions and find that a model trained at a small inverse coupling constant can be extrapolated to larger inverse coupling regions without encountering the topological freezing problem. Additionally, the trained model can be employed to sample configurations on different lattice sizes without requiring further training. The exactness of the generated samples is ensured by incorporating Metropolis-adjusted Langevin dynamics into the generation process. Furthermore, we demonstrate that this approach enables more efficient sampling of topological quantities compared to traditional algorithms such as Hybrid Monte Carlo and Langevin simulations.
DGenNO: A Novel Physics-aware Neural Operator for Solving Forward and Inverse PDE Problems based on Deep, Generative Probabilistic Modeling
Authors: Yaohua Zang, Phaedon-Stelios Koutsourelakis
Date: 2025-02-10 00:00:00

Solving parametric partial differential equations (PDEs) and associated PDE-based, inverse problems is a central task in engineering and physics, yet existing neural operator methods struggle with high-dimensional, discontinuous inputs and require large amounts of {\em labeled} training data. We propose the Deep Generative Neural Operator (DGenNO), a physics-aware framework that addresses these challenges by leveraging a deep, generative, probabilistic model in combination with a set of lower-dimensional, latent variables that simultaneously encode PDE-inputs and PDE-outputs. This formulation can make use of unlabeled data and significantly improves inverse problem-solving, particularly for discontinuous or discrete-valued input functions. DGenNO enforces physics constraints without labeled data by incorporating as virtual observables, weak-form residuals based on compactly supported radial basis functions (CSRBFs). These relax regularity constraints and eliminate higher-order derivatives from the objective function. We also introduce MultiONet, a novel neural operator architecture, which is a more expressive generalization of the popular DeepONet that significantly enhances the approximating power of the proposed model. These innovations make DGenNO particularly effective for challenging forward and inverse, PDE-based problems, such as those involving multi-phase media. Numerical experiments demonstrate that DGenNO achieves higher accuracy across multiple benchmarks while exhibiting robustness to noise and strong generalization to out-of-distribution cases. Its adaptability, and the ability to handle sparse, noisy data while providing probabilistic estimates, make DGenNO a powerful tool for scientific and engineering applications.
Invariant Measures for Data-Driven Dynamical System Identification: Analysis and Application
Authors: Jonah Botvinick-Greenhouse
Date: 2025-01-31 00:00:00

We propose a novel approach for performing dynamical system identification, based upon the comparison of simulated and observed physical invariant measures. While standard methods adopt a Lagrangian perspective by directly treating time-trajectories as inference data, we take on an Eulerian perspective and instead seek models fitting the observed global time-invariant statistics. With this change in perspective, we gain robustness against pervasive challenges in system identification including noise, chaos, and slow sampling. In the first half of this paper, we pose the system identification task as a partial differential equation (PDE) constrained optimization problem, in which synthetic stationary solutions of the Fokker-Planck equation, obtained as fixed points of a finite-volume discretization, are compared to physical invariant measures extracted from observed trajectory data. In the latter half of the paper, we improve upon this approach in two crucial directions. First, we develop a Galerkin-inspired modification to the finite-volume surrogate model, based on data-adaptive unstructured meshes and Monte-Carlo integration, enabling the approach to efficiently scale to high-dimensional problems. Second, we leverage Takens' seminal time-delay embedding theory to introduce a critical data-dependent coordinate transformation which can guarantee unique system identifiability from the invariant measure alone. This contribution resolves a major challenge of system identification through invariant measures, as systems exhibiting distinct transient behaviors may still share the same time-invariant statistics in their state-coordinates. Throughout, we present comprehensive numerical tests which highlight the effectiveness of our approach on a variety of challenging system identification tasks.
Spatial Pattern Formation in Eco-Evolutionary Games with Environment-Driven Motion
Authors: Tianyong Yao, Daniel B. Cooney
Date: 2025-02-10 00:00:00

The sustainable management of common resources often leads to a social dilemma known as the tragedy of the commons: individuals benefit from rapid extraction of resources, while communities as a whole benefit from more sustainable extraction strategies. Such a social dilemma can be further complicated by the role played by space for both resources and harvesters, where spatial diffusion of resources and directed motion of harvesters can potentially feature the emergence of clusters of environmental resource and sustainable harvesting strategies. In this paper, we explore a PDE model of evolutionary game theory with environmental feedback, describing how the spatial distribution of resource extraction strategies and environmental resources can change due to both local eco-evolutionary dynamics and environmental-driven directed motion of harvesters. Through linear stability analysis, we show that this biased motion towards higher-quality environments can lead to spatial patterns in the distribution of extraction strategies, creating local regions with improved environmental quality and increase payoff for resource extractors. However, by measuring the average payoff and environmental quality across the spatial domain, we see that this pattern-forming mechanism can actually decrease the overall success of the population relative to the equilibrium outcome in the absence of spatial motion. This suggests that environmental-driven motion can produce a spatial social dilemma, in which biased motion towards more beneficial regions can produce emergent patterns featuring a worse overall environment for the population.
Diffusion-LAM: Probabilistic Limited Area Weather Forecasting with Diffusion
Authors: Erik Larsson, Joel Oskarsson, Tomas Landelius, Fredrik Lindsten
Date: 2025-02-11 00:00:00
Tasks: Weather Forecasting

Machine learning methods have been shown to be effective for weather forecasting, based on the speed and accuracy compared to traditional numerical models. While early efforts primarily concentrated on deterministic predictions, the field has increasingly shifted toward probabilistic forecasting to better capture the forecast uncertainty. Most machine learning-based models have been designed for global-scale predictions, with only limited work targeting regional or limited area forecasting, which allows more specialized and flexible modeling for specific locations. This work introduces Diffusion-LAM, a probabilistic limited area weather model leveraging conditional diffusion. By conditioning on boundary data from surrounding regions, our approach generates forecasts within a defined area. Experimental results on the MEPS limited area dataset demonstrate the potential of Diffusion-LAM to deliver accurate probabilistic forecasts, highlighting its promise for limited-area weather prediction.
QuantumDNA: A Python Package for Analyzing Quantum Charge Dynamics in DNA and Exploring Its Biological Relevance
Authors: Dennis Herb, Marco Trenti, Marilena Mantela, Constantinos Simserides, Joachim Ankerhold, Mirko Rossini
Date: 2025-02-08 00:00:00

The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant advances in each of these areas, knowledge often remains inaccessible to other scientific communities, limiting the broader impact of advances across disciplines. To bridge this gap, we present QuantumDNA, an open-source Python package for simulating DNA charge transfer (CT) and excited states using quantum-physical methods. QuantumDNA combines an efficient Linear Combination of Atomic Orbitals (LCAO) approach with tight-binding (TB) models, incorporating open quantum systems techniques to account for environmental effects. This approach allows rapid yet accurate analysis of large DNA ensembles, enabling statistical studies of genetic and epigenetic phenomena. To ensure accessibility, the package features a graphical user interface (GUI), making it suitable for researchers across disciplines.
Teacher-student training improves accuracy and efficiency of machine learning interatomic potentials
Authors: Sakib Matin, Alice E. A. Allen, Emily Shinkle, Aleksandra Pachalieva, Galen T. Craven, Benjamin Nebgen, Justin S. Smith, Richard Messerly, Ying Wai Li, Sergei Tretiak, Kipton Barros, Nicholas Lubbers
Date: 2025-02-07 00:00:00

Machine learning interatomic potentials (MLIPs) are revolutionizing the field of molecular dynamics (MD) simulations. Recent MLIPs have tended towards more complex architectures trained on larger datasets. The resulting increase in computational and memory costs may prohibit the application of these MLIPs to perform large-scale MD simulations. Here, we present a teacher-student training framework in which the latent knowledge from the teacher (atomic energies) is used to augment the students' training. We show that the light-weight student MLIPs have faster MD speeds at a fraction of the memory footprint compared to the teacher models. Remarkably, the student models can even surpass the accuracy of the teachers, even though both are trained on the same quantum chemistry dataset. Our work highlights a practical method for MLIPs to reduce the resources required for large-scale MD simulations.