pwc-archive/papers-with-abstracts huggingface dataset:
ReGNet: Reciprocal Space-Aware Long-Range Modeling for Crystalline Property Prediction
Authors: Jianan Nie, Peiyao Xiao, Kaiyi Ji, Peng Gao
Date: 2025-02-04 00:00:00
Tasks: Computational Efficiency, Long-range modeling, Mixture-of-Experts, Prediction, Property Prediction

Predicting properties of crystals from their structures is a fundamental yet challenging task in materials science. Unlike molecules, crystal structures exhibit infinite periodic arrangements of atoms, requiring methods capable of capturing both local and global information effectively. However, most current works fall short of capturing long-range interactions within periodic structures. To address this limitation, we leverage \emph{reciprocal space} to efficiently encode long-range interactions with learnable filters within Fourier transforms. We introduce Reciprocal Geometry Network (ReGNet), a novel architecture that integrates geometric GNNs and reciprocal blocks to model short-range and long-range interactions, respectively. Experimental results on JARVIS, Materials Project, and MatBench demonstrate that ReGNet achieves state-of-the-art predictive accuracy across a range of crystal property prediction tasks. Additionally, we explore a model extension that employs the mixture-of-experts for multi-property prediction with promising results and high computational efficiency. These findings highlight the potential of our model as a scalable and accurate solution for crystal property prediction. The code will be released upon paper acceptance.
Frustration In Physiology And Molecular Medicine
Authors: R. Gonzalo Parra, Elizabeth A. Komives, Peter G. Wolynes, Diego U. Ferreiro
Date: 2025-02-06 00:00:00

Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains "locally frustrated". Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.
HEP-JEPA: A foundation model for collider physics using joint embedding predictive architecture
Authors: Jai Bardhan, Radhikesh Agrawal, Abhiram Tilak, Cyrin Neeraj, Subhadip Mitra
Date: 2025-02-06 00:00:00

We present a transformer architecture-based foundation model for tasks at high-energy particle colliders such as the Large Hadron Collider. We train the model to classify jets using a self-supervised strategy inspired by the Joint Embedding Predictive Architecture. We use the JetClass dataset containing 100M jets of various known particles to pre-train the model with a data-centric approach -- the model uses a fraction of the jet constituents as the context to predict the embeddings of the unseen target constituents. Our pre-trained model fares well with other datasets for standard classification benchmark tasks. We test our model on two additional downstream tasks: top tagging and differentiating light-quark jets from gluon jets. We also evaluate our model with task-specific metrics and baselines and compare it with state-of-the-art models in high-energy physics. Project site: https://hep-jepa.github.io/
Refining Integration-by-Parts Reduction of Feynman Integrals with Machine Learning
Authors: Matt von Hippel, Matthias Wilhelm
Date: 2025-02-07 00:00:00
Tasks: Code Generation, Language Modeling, Language Modelling, Large Language Model

Integration-by-parts reductions of Feynman integrals pose a frequent bottle-neck in state-of-the-art calculations in theoretical particle and gravitational-wave physics, and rely on heuristic approaches for selecting integration-by-parts identities, whose quality heavily influences the performance. In this paper, we investigate the use of machine-learning techniques to find improved heuristics. We use funsearch, a genetic programming variant based on code generation by a Large Language Model, in order to explore possible approaches, then use strongly typed genetic programming to zero in on useful solutions. Both approaches manage to re-discover the state-of-the-art heuristics recently incorporated into integration-by-parts solvers, and in one example find a small advance on this state of the art.
Harnessing omnipresent oscillator networks as computational resource
Authors: Thomas Geert de Jong, Hirofumi Notsu, Kohei Nakajima
Date: 2025-02-07 00:00:00

Nature is pervaded with oscillatory dynamics. In networks of coupled oscillators patterns can arise when the system synchronizes to an external input. Hence, these networks provide processing and memory of input. We present a universal framework for harnessing oscillator networks as computational resource. This computing framework is introduced by the ubiquitous model for phase-locking, the Kuramoto model. We force the Kuramoto model by a nonlinear target-system, then after substituting the target-system with a trained feedback-loop it emulates the target-system. Our results are two-fold. Firstly, the trained network inherits performance properties of the Kuramoto model, where all-to-all coupling is performed in linear time with respect to the number of nodes and parameters for synchronization are abundant. The latter implies that the network is generically successful since the system learns via sychronization. Secondly, the learning capabilities of the oscillator network, which describe a type of collective intelligence, can be explained using Kuramoto model's order parameter. In summary, this work provides the foundation for utilizing nature's oscillator networks as a new class of information processing systems.
Learning low-dimensional representations of ensemble forecast fields using autoencoder-based methods
Authors: Jieyu Chen, Kevin Höhlein, Sebastian Lerch
Date: 2025-02-06 00:00:00
Tasks: Dimensionality Reduction

Large-scale numerical simulations often produce high-dimensional gridded data that is challenging to process for downstream applications. A prime example is numerical weather prediction, where atmospheric processes are modeled using discrete gridded representations of the physical variables and dynamics. Uncertainties are assessed by running the simulations multiple times, yielding ensembles of simulated fields as a high-dimensional stochastic representation of the forecast distribution. The high-dimensionality and large volume of ensemble datasets poses major computing challenges for subsequent forecasting stages. Data-driven dimensionality reduction techniques could help to reduce the data volume before further processing by learning meaningful and compact representations. However, existing dimensionality reduction methods are typically designed for deterministic and single-valued inputs, and thus cannot handle ensemble data from multiple randomized simulations. In this study, we propose novel dimensionality reduction approaches specifically tailored to the format of ensemble forecast fields. We present two alternative frameworks, which yield low-dimensional representations of ensemble forecasts while respecting their probabilistic character. The first approach derives a distribution-based representation of an input ensemble by applying standard dimensionality reduction techniques in a member-by-member fashion and merging the member representations into a joint parametric distribution model. The second approach achieves a similar representation by encoding all members jointly using a tailored variational autoencoder. We evaluate and compare both approaches in a case study using 10 years of temperature and wind speed forecasts over Europe. The approaches preserve key spatial and statistical characteristics of the ensemble and enable probabilistic reconstructions of the forecast fields.
A Corrugated All-Metal Vivaldi Antenna for 5G Phased Array Applications
Authors: Mahyar Mehri Pashaki, Mohammad Hossein Koohi Ghamsari, Alireza Mallahzadeh, Gabriele Gradoni, Mohsen Khalily
Date: 2025-02-05 00:00:00
Tasks: All

In this paper, a corrugated Vivaldi phased array antenna in the 28 GHz frequency band is proposed for 5G communication applications. The presented configuration features an all-metal antipodal antenna structure with a broad bandwidth ranging from 26 to 30 GHz and beam steering capabilities from -30 to +30 degrees. The proposed antenna consists of a 4x4 array configuration, where each element has dimensions of 6.46x6.46x14.25 mm, resulting in an overall antenna structure with dimensions of 25.84x25.84x14.25 mm. The corrugation method is applied to minimize surface currents, resulting in a reduction in interelement mutual couplings. Therefore, the return loss in the array structure for central elements is decreased, and the antenna gain and radiation efficiency are improved. Moreover, the improved radiation efficiency allows for higher power transmission and reception from an antenna, resulting in potentially higher data rates and better performance.
Machine-Learning Interatomic Potentials for Long-Range Systems
Authors: Yajie Ji, Jiuyang Liang, Zhenli Xu
Date: 2025-02-07 00:00:00

Machine-learning interatomic potentials have emerged as a revolutionary class of force-field models in molecular simulations, delivering quantum-mechanical accuracy at a fraction of the computational cost and enabling the simulation of large-scale systems over extended timescales. However, they often focus on modeling local environments, neglecting crucial long-range interactions. We propose a Sum-of-Gaussians Neural Network (SOG-Net), a lightweight and versatile framework for integrating long-range interactions into machine learning force field. The SOG-Net employs a latent-variable learning network that seamlessly bridges short-range and long-range components, coupled with an efficient Fourier convolution layer that incorporates long-range effects. By learning sum-of-Gaussian multipliers across different convolution layers, the SOG-Net adaptively captures diverse long-range decay behaviors while maintaining close-to-linear computational complexity during training and simulation via non-uniform fast Fourier transforms. The method is demonstrated effective for a broad range of long-range systems.
Retro-Rank-In: A Ranking-Based Approach for Inorganic Materials Synthesis Planning
Authors: Thorben Prein, Elton Pan, Sami Haddouti, Marco Lorenz, Janik Jehkul, Tymoteusz Wilk, Cansu Moran, Menelaos Panagiotis Fotiadis, Artur P. Toshev, Elsa Olivetti, Jennifer L. M. Rupp
Date: 2025-02-06 00:00:00
Tasks: Multi-Label Classification, MUlTI-LABEL-ClASSIFICATION, Out-of-Distribution Generalization, Retrosynthesis

Retrosynthesis strategically plans the synthesis of a chemical target compound from simpler, readily available precursor compounds. This process is critical for synthesizing novel inorganic materials, yet traditional methods in inorganic chemistry continue to rely on trial-and-error experimentation. Emerging machine-learning approaches struggle to generalize to entirely new reactions due to their reliance on known precursors, as they frame retrosynthesis as a multi-label classification task. To address these limitations, we propose Retro-Rank-In, a novel framework that reformulates the retrosynthesis problem by embedding target and precursor materials into a shared latent space and learning a pairwise ranker on a bipartite graph of inorganic compounds. We evaluate Retro-Rank-In's generalizability on challenging retrosynthesis dataset splits designed to mitigate data duplicates and overlaps. For instance, for Cr2AlB2, it correctly predicts the verified precursor pair CrB + Al despite never seeing them in training, a capability absent in prior work. Extensive experiments show that Retro-Rank-In sets a new state-of-the-art, particularly in out-of-distribution generalization and candidate set ranking, offering a powerful tool for accelerating inorganic material synthesis.
First-Passage Approach to Optimizing Perturbations for Improved Training of Machine Learning Models
Authors: Sagi Meir, Tommer D. Keidar, Shlomi Reuveni, Barak Hirshberg
Date: 2025-02-06 00:00:00

Machine learning models have become indispensable tools in applications across the physical sciences. Their training is often time-consuming, vastly exceeding the inference timescales. Several protocols have been developed to perturb the learning process and improve the training, such as shrink and perturb, warm restarts, and stochastic resetting. For classifiers, these perturbations have been shown to result in enhanced speedups or improved generalization. However, the design of such perturbations is usually done ad hoc by intuition and trial and error. To rationally optimize training protocols, we frame them as first-passage processes and consider their response to perturbations. We show that if the unperturbed learning process reaches a quasi-steady state, the response at a single perturbation frequency can predict the behavior at a wide range of frequencies. We employ this approach to a CIFAR-10 classifier using the ResNet-18 model and identify a useful perturbation and frequency among several possibilities. We demonstrate the transferability of the approach to other datasets, architectures, optimizers and even tasks (regression instead of classification). Our work allows optimization of perturbations for improving the training of machine learning models using a first-passage approach.
Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization
Authors: Chanhui Lee, Hanbum Ko, Yuheon Song, Yongjun Jeong, Rodrigo Hormazabal, Sehui Han, Kyunghoon Bae, Sungbin Lim, Sungwoong Kim
Date: 2025-02-05 00:00:00
Tasks: Chemical Reaction Prediction, Molecular Property Prediction, Molecule Captioning, Prediction, Property Prediction

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.
Calibrated Physics-Informed Uncertainty Quantification
Authors: Vignesh Gopakumar, Ander Gray, Lorenzo Zanisi, Timothy Nunn, Daniel Giles, Matt J. Kusner, Stanislas Pamela, Marc Peter Deisenroth
Date: 2025-02-06 00:00:00
Tasks: Conformal Prediction, Uncertainty Quantification

Simulating complex physical systems is crucial for understanding and predicting phenomena across diverse fields, such as fluid dynamics and heat transfer, as well as plasma physics and structural mechanics. Traditional approaches rely on solving partial differential equations (PDEs) using numerical methods, which are computationally expensive and often prohibitively slow for real-time applications or large-scale simulations. Neural PDEs have emerged as efficient alternatives to these costly numerical solvers, offering significant computational speed-ups. However, their lack of robust uncertainty quantification (UQ) limits deployment in critical applications. We introduce a model-agnostic, physics-informed conformal prediction (CP) framework that provides guaranteed uncertainty estimates without requiring labelled data. By utilising a physics-based approach, we can quantify and calibrate the model's inconsistencies with the physics rather than the uncertainty arising from the data. Our approach utilises convolutional layers as finite-difference stencils and leverages physics residual errors as nonconformity scores, enabling data-free UQ with marginal and joint coverage guarantees across prediction domains for a range of complex PDEs. We further validate the efficacy of our method on neural PDE models for plasma modelling and shot design in fusion reactors.
Pseudo-Physics-Informed Neural Operators: Enhancing Operator Learning from Limited Data
Authors: Keyan Chen, Yile Li, Da Long, Zhitong Xu, Wei Xing, Jacob Hochhalter, Shandian Zhe
Date: 2025-02-04 00:00:00
Tasks: Operator learning

Neural operators have shown great potential in surrogate modeling. However, training a well-performing neural operator typically requires a substantial amount of data, which can pose a major challenge in complex applications. In such scenarios, detailed physical knowledge can be unavailable or difficult to obtain, and collecting extensive data is often prohibitively expensive. To mitigate this challenge, we propose the Pseudo Physics-Informed Neural Operator (PPI-NO) framework. PPI-NO constructs a surrogate physics system for the target system using partial differential equations (PDEs) derived from simple, rudimentary physics principles, such as basic differential operators. This surrogate system is coupled with a neural operator model, using an alternating update and learning process to iteratively enhance the model's predictive power. While the physics derived via PPI-NO may not mirror the ground-truth underlying physical laws -- hence the term ``pseudo physics'' -- this approach significantly improves the accuracy of standard operator learning models in data-scarce scenarios, which is evidenced by extensive evaluations across five benchmark tasks and a fatigue modeling application.
SpecTUS: Spectral Translator for Unknown Structures annotation from EI-MS spectra
Authors: Adam Hájek, Helge Hecht, Elliott J. Price, Aleš Křenek
Date: 2025-02-07 00:00:00

Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery and chemical engineering. We propose SpecTUS: Spectral Translator for Unknown Structures, a deep neural model that addresses the task of structural annotation of small molecules from low-resolution gas chromatography electron ionization mass spectra (GC-EI-MS). Our model analyzes the spectra in \textit{de novo} manner -- a direct translation from the spectra into 2D-structural representation. Our approach is particularly useful for analyzing compounds unavailable in spectral libraries. In a rigorous evaluation of our model on the novel structure annotation task across different libraries, we outperformed standard database search techniques by a wide margin. On a held-out testing set, including \numprint{28267} spectra from the NIST database, we show that our model's single suggestion perfectly reconstructs 43\% of the subset's compounds. This single suggestion is strictly better than the candidate of the database hybrid search (common method among practitioners) in 76\% of cases. In a~still affordable scenario of~10 suggestions, perfect reconstruction is achieved in 65\%, and 84\% are better than the hybrid search.
Practically Effective Adjustment Variable Selection in Causal Inference
Authors: Atsushi Noda, Takashi Isozaki
Date: 2025-02-04 00:00:00
Tasks: Causal Inference, Variable Selection

In the estimation of causal effects, one common method for removing the influence of confounders is to adjust the variables that satisfy the back-door criterion. However, it is not always possible to uniquely determine sets of such variables. Moreover, real-world data is almost always limited, which means it may be insufficient for statistical estimation. Therefore, we propose criteria for selecting variables from a list of candidate adjustment variables along with an algorithm to prevent accuracy degradation in causal effect estimation. We initially focus on directed acyclic graphs (DAGs) and then outlines specific steps for applying this method to completed partially directed acyclic graphs (CPDAGs). We also present and prove a theorem on causal effect computation possibility in CPDAGs. Finally, we demonstrate the practical utility of our method using both existing and artificial data.
Capturing Extreme Events in Turbulence using an Extreme Variational Autoencoder (xVAE)
Authors: Likun Zhang, Kiran Bhaganagar, Christopher K. Wikle
Date: 2025-02-07 00:00:00
Tasks: Uncertainty Quantification

Turbulent flow fields are characterized by extreme events that are statistically intermittent and carry a significant amount of energy and physical importance. To emulate these flows, we introduce the extreme variational Autoencoder (xVAE), which embeds a max-infinitely divisible process with heavy-tailed distributions into a standard VAE framework, enabling accurate modeling of extreme events. xVAEs are neural network models that reduce system dimensionality by learning non-linear latent representations of data. We demonstrate the effectiveness of xVAE in large-eddy simulation data of wildland fire plumes, where intense heat release and complex plume-atmosphere interactions generate extreme turbulence. Comparisons with the commonly used Proper Orthogonal Decomposition (POD) modes show that xVAE is more robust in capturing extreme values and provides a powerful uncertainty quantification framework using variational Bayes. Additionally, xVAE enables analysis of the so-called copulas of fields to assess risks associated with rare events while rigorously accounting for uncertainty, such as simultaneous exceedances of high thresholds across multiple locations. The proposed approach provides a new direction for studying realistic turbulent flows, such as high-speed aerodynamics, space propulsion, and atmospheric and oceanic systems that are characterized by extreme events.