pwc-archive/papers-with-abstracts huggingface dataset:
Prediction of Halo Coronal Mass Ejections Using SDO/HMI Vector Magnetic Data Products and a Transformer Model
Authors: Hongyang Zhang, Ju Jing, Jason T. L. Wang, Haimin Wang, Yasser Abduallah, Yan Xu, Khalid A. Alobaid, Hameedullah Farooki, Vasyl Yurchyshyn
Date: 2025-03-05 00:00:00

We present a transformer model, named DeepHalo, to predict the occurrence of halo coronal mass ejections (CMEs). Our model takes as input an active region (AR) and a profile, where the profile contains a time series of data samples in the AR that are collected 24 hours before the beginning of a day, and predicts whether the AR would produce a halo CME during that day. Each data sample contains physical parameters, or features, derived from photospheric vector magnetic field data taken by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). We survey and match CME events in the Space Weather Database Of Notification, Knowledge, Information (DONKI) and Large Angle and Spectrometric Coronagraph (LASCO) CME Catalog, and compile a list of CMEs including halo CMEs and non-halo CMEs associated with ARs in the period between November 2010 and August 2023. We use the information gathered above to build the labels (positive versus negative) of the data samples and profiles at hand, where the labels are needed for machine learning. Experimental results show that DeepHalo with a true skill statistics (TSS) score of 0.907 outperforms a closely related long short-term memory network with a TSS score of 0.821. To our knowledge, this is the first time that the transformer model has been used for halo CME prediction.
Les Houches lectures on Theoretical Ecology: High-dimensional models and extreme events
Authors: Ada Altieri
Date: 2025-03-04 00:00:00

The study of ecological systems is gaining momentum in modern scientific research, driven by an abundance of empirical data and advancements in bioengineering techniques. However, a full understanding of their dynamical and thermodynamical properties, also in light of the ongoing biodiversity crisis, remains a formidable endeavor. From a theoretical standpoint, modeling the interactions within these complex systems -- such as bacteria in microbial communities, plant-pollinator networks in forests, or starling murmurations -- presents a significant challenge. Given the characteristic high dimensionality of the datasets, alternative elegant approaches employ random matrix formalism and techniques from disordered systems. In these lectures, we will explore two cornerstone models in theoretical ecology: the MacArthur/Resource-Consumer model, and the Generalized Lotka-Volterra model, with a special focus on systems composed of a large number of interacting species. In the second part, we will highlight timely directions, particularly to bridge the gap with empirical observations and detect macroecological patterns.
Time-Irreversible Quantum-Classical Dynamics of Molecular Models in the Brain
Authors: Alessandro Sergi, Antonino Messina, Rosalba Saija, Gabriella Martino, Maria Teresa Caccamo, Min-Fang Kuo, Michael A. Nitsche
Date: 2025-02-18 00:00:00

This manuscript aims to illustrate a quantum-classical dissipative theory (suited to be converted to effective algorithms for numerical simulations) within the long-term project of studying molecular processes in the brain. Other approaches, briefly sketched in the text, have advocated the need to deal with both quantum and classical dynamic variables when studying the brain. At variance with these other frameworks, the manuscript's formalism allows us to explicitly treat the classical dynamical variables. The theory must be dissipative not because of formal requirements but because brain processes appear to be dissipative at the molecular, physiological, and high functional levels. We discuss theoretically that using Brownian dynamics or the Nos\`e-Hoover-Chain thermostat to perform computer simulations provides an effective way to introduce an arrow of time for open quantum systems in a classical environment. In the future, We plan to study classical models of neurons and astrocytes, as well as their networks, coupled to quantum dynamical variables describing, e.g., nuclear and electron spins, HOMO and LUMO orbitals of phenyl and indole rings, ion channels, and tunneling protons.
Integrating Predictive and Generative Capabilities by Latent Space Design via the DKL-VAE Model
Authors: Boris N. Slautin, Utkarsh Pratiush, Doru C. Lupascu, Maxim A. Ziatdinov, Sergei V. Kalinin
Date: 2025-03-04 00:00:00
Tasks: Property Prediction

We introduce a Deep Kernel Learning Variational Autoencoder (VAE-DKL) framework that integrates the generative power of a Variational Autoencoder (VAE) with the predictive nature of Deep Kernel Learning (DKL). The VAE learns a latent representation of high-dimensional data, enabling the generation of novel structures, while DKL refines this latent space by structuring it in alignment with target properties through Gaussian Process (GP) regression. This approach preserves the generative capabilities of the VAE while enhancing its latent space for GP-based property prediction. We evaluate the framework on two datasets: a structured card dataset with predefined variational factors and the QM9 molecular dataset, where enthalpy serves as the target function for optimization. The model demonstrates high-precision property prediction and enables the generation of novel out-of-training subset structures with desired characteristics. The VAE-DKL framework offers a promising approach for high-throughput material discovery and molecular design, balancing structured latent space organization with generative flexibility.
SAGE-Amine: Generative Amine Design with Multi-Property Optimization for Efficient CO2 Capture
Authors: Hocheol Lim, Hyein Cho, Jeonghoon Kim
Date: 2025-03-04 00:00:00

Efficient CO2 capture is vital for mitigating climate change, with amine-based solvents being widely used due to their strong reactivity with CO2. However, optimizing key properties such as basicity, viscosity, and absorption capacity remains challenging, as traditional methods rely on labor-intensive experimentation and predefined chemical databases, limiting the exploration of novel solutions. Here, SAGE-Amine was introduced, a generative modeling approach that integrates Scoring-Assisted Generative Exploration (SAGE) with quantitative structure-property relationship models to design new amines tailored for CO2 capture. Unlike conventional virtual screening restricted to existing compounds, SAGE-Amine generates novel amines by leveraging autoregressive natural language processing models trained on amine datasets. SAGE-Amine identified known amines for CO2 capture from scratch and successfully performed single-property optimization, increasing basicity or reducing viscosity or vapor pressure. Furthermore, it facilitated multi-property optimization, simultaneously achieving high basicity with low viscosity and vapor pressure. The 10 top-ranked amines were suggested using SAGE-Amine and their thermodynamic properties were further assessed using COSMO-RS simulations, confirming their potential for CO2 capture. These results highlight the potential of generative modeling in accelerating the discovery of amine solvents and expanding the possibilities for industrial CO2 capture applications.
Wyckoff Transformer: Generation of Symmetric Crystals
Authors: Nikita Kazeev, Wei Nong, Ignat Romanov, Ruiming Zhu, Andrey Ustyuzhanin, Shuya Yamazaki, Kedar Hippalgaonkar
Date: 2025-03-04 00:00:00
Tasks: Inductive Bias, Property Prediction, valid

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.
CrystalFramer: Rethinking the Role of Frames for SE(3)-Invariant Crystal Structure Modeling
Authors: Yusei Ito, Tatsunori Taniai, Ryo Igarashi, Yoshitaka Ushiku, Kanta Ono
Date: 2025-03-04 00:00:00
Tasks: Property Prediction

Crystal structure modeling with graph neural networks is essential for various applications in materials informatics, and capturing SE(3)-invariant geometric features is a fundamental requirement for these networks. A straightforward approach is to model with orientation-standardized structures through structure-aligned coordinate systems, or"frames." However, unlike molecules, determining frames for crystal structures is challenging due to their infinite and highly symmetric nature. In particular, existing methods rely on a statically fixed frame for each structure, determined solely by its structural information, regardless of the task under consideration. Here, we rethink the role of frames, questioning whether such simplistic alignment with the structure is sufficient, and propose the concept of dynamic frames. While accommodating the infinite and symmetric nature of crystals, these frames provide each atom with a dynamic view of its local environment, focusing on actively interacting atoms. We demonstrate this concept by utilizing the attention mechanism in a recent transformer-based crystal encoder, resulting in a new architecture called CrystalFramer. Extensive experiments show that CrystalFramer outperforms conventional frames and existing crystal encoders in various crystal property prediction tasks.
Proliferating active disks with game dynamical interaction
Authors: Alejandro Almodóvar, Tobias Galla, Cristóbal López
Date: 2025-03-04 00:00:00

We study a system of self-propelled, proliferating finite-size disks with game-theoretical interactions, where growth rates depend on local population composition. We analyze how these interactions influence spatial distribution, coexistence, and extinction. Three scenarios emerge: (i) stable coexistence with well-mixed distributions, (ii) bistability, where the outcome depends on initial conditions, and (iii) dominance, where one species always outcompetes the other. We further show that activity enhances spatial mixing in coexistence and reduces extinction times in both dominance and bistability. Additionally, stronger interactions promote coexistence while accelerating extinction in the latter two regimes. By varying diffusivity, activity, and interaction strength, we show how movement and spatial constraints affect population dynamics.
Spatial competition and repulsion: pattern formation and the role of movement
Authors: Cristóbal López, Eduardo H. Colombo, Emilio Hernández-García, Ricardo Martinez-Garcia
Date: 2025-03-04 00:00:00

This chapter investigates some mechanisms behind pattern formation driven by competitive-only or repelling interactions, and explores how these patterns are influenced by different types of particle movement. Despite competition and repulsion are both anti-crowding interactions, collective effects may lead to clusters of individuals, which can arrange periodically. Through the analysis of two models, it provides insights into the similarities and differences in the patterns formed and underlines the role of movement in shaping the spatial distribution of biological populations.
Learning finite symmetry groups of dynamical systems via equivariance detection
Authors: Pablo Calvo-Barlés, Sergio G. Rodrigo, Luis Martín-Moreno
Date: 2025-03-04 00:00:00

In this work, we introduce the Equivariance Seeker Model (ESM), a data-driven method for discovering the underlying finite equivariant symmetry group of an arbitrary function. ESM achieves this by optimizing a loss function that balances equivariance preservation with the penalization of redundant solutions, ensuring the complete and accurate identification of all symmetry transformations. We apply this framework specifically to dynamical systems, identifying their symmetry groups directly from observed trajectory data. To demonstrate its versatility, we test ESM on multiple systems in two distinct scenarios: (i) when the governing equations are known theoretically and (ii) when they are unknown, and the equivariance finding relies solely on observed data. The latter case highlights ESM's fully data-driven capability, as it requires no prior knowledge of the system's equations to operate.
An Efficient Learning Method to Connect Observables
Authors: Hang Yu, Takayuki Miyagi
Date: 2025-03-03 00:00:00

Constructing fast and accurate surrogate models is a key ingredient for making robust predictions in many topics. We introduce a new model, the Multiparameter Eigenvalue Problem (MEP) emulator. The new method connects emulators and can make predictions directly from observables to observables. We present that the MEP emulator can be trained with data from Eigenvector Continuation (EC) and Parametric Matrix Model (PMM) emulators. A simple simulation on a one-dimensional lattice confirms the performance of the MEP emulator. Using $^{28}$O as an example, we also demonstrate that the predictive probability distribution of the target observables can be easily obtained through the new emulator.
Generative assimilation and prediction for weather and climate
Authors: Shangshang Yang, Congyi Nai, Xinyan Liu, Weidong Li, Jie Chao, Jingnan Wang, Leyi Wang, Xichen Li, Xi Chen, Bo Lu, Ziniu Xiao, Niklas Boers, Huiling Yuan, Baoxiang Pan
Date: 2025-03-04 00:00:00
Tasks: Prediction

Machine learning models have shown great success in predicting weather up to two weeks ahead, outperforming process-based benchmarks. However, existing approaches mostly focus on the prediction task, and do not incorporate the necessary data assimilation. Moreover, these models suffer from error accumulation in long roll-outs, limiting their applicability to seasonal predictions or climate projections. Here, we introduce Generative Assimilation and Prediction (GAP), a unified deep generative framework for assimilation and prediction of both weather and climate. By learning to quantify the probabilistic distribution of atmospheric states under observational, predictive, and external forcing constraints, GAP excels in a broad range of weather-climate related tasks, including data assimilation, seamless prediction, and climate simulation. In particular, GAP is competitive with state-of-the-art ensemble assimilation, probabilistic weather forecast and seasonal prediction, yields stable millennial simulations, and reproduces climate variability from daily to decadal time scales.
Improving Oil Slick Trajectory Simulations with Bayesian Optimization
Authors: Gabriele Accarino, Marco M. De Carlo, Igor Atake, Donatello Elia, Anusha L. Dissanayake, Antonio Augusto Sepp Neves, Juan Peña Ibañez, Italo Epicoco, Paola Nassisi, Sandro Fiore, Giovanni Coppini
Date: 2025-03-04 00:00:00
Tasks: Bayesian Optimization

Accurate simulations of oil spill trajectories are essential for supporting practitioners' response and mitigating environmental and socioeconomic impacts. Numerical models, such as MEDSLIK-II, simulate advection, dispersion, and transformation processes of oil particles. However, simulations heavily rely on accurate parameter tuning, still based on expert knowledge and manual calibration. To overcome these limitations, we integrate the MEDSLIK-II numerical oil spill model with a Bayesian optimization framework to iteratively estimate the best physical parameter configuration that yields simulation closer to satellite observations of the slick. We focus on key parameters, such as horizontal diffusivity and drift factor, maximizing the Fraction Skill Score (FSS) as a measure of spatio-temporal overlap between simulated and observed oil distributions. We validate the framework for the Baniyas oil incident that occurred in Syria between August 23 and September 4, 2021, which released over 12,000 $m^3$ of oil. We show that, on average, the proposed approach systematically improves the FSS from 5.82% to 11.07% compared to control simulations initialized with default parameters. The optimization results in consistent improvement across multiple time steps, particularly during periods of increased drift variability, demonstrating the robustness of our method in dynamic environmental conditions.
Weakly-Constrained 4D Var for Downscaling with Uncertainty using Data-Driven Surrogate Models
Authors: Philip Dinenis, Vishwas Rao, Mihai Anitescu
Date: 2025-03-04 00:00:00

Dynamic downscaling typically involves using numerical weather prediction (NWP) solvers to refine coarse data to higher spatial resolutions. Data-driven models such as FourCastNet have emerged as a promising alternative to the traditional NWP models for forecasting. Once these models are trained, they are capable of delivering forecasts in a few seconds, thousands of times faster compared to classical NWP models. However, as the lead times, and, therefore, their forecast window, increase, these models show instability in that they tend to diverge from reality. In this paper, we propose to use data assimilation approaches to stabilize them when used for downscaling tasks. Data assimilation uses information from three different sources, namely an imperfect computational model based on partial differential equations (PDE), from noisy observations, and from an uncertainty-reflecting prior. In this work, when carrying out dynamic downscaling, we replace the computationally expensive PDE-based NWP models with FourCastNet in a ``weak-constrained 4DVar framework" that accounts for the implied model errors. We demonstrate the efficacy of this approach for a hurricane-tracking problem; moreover, the 4DVar framework naturally allows the expression and quantification of uncertainty. We demonstrate, using ERA5 data, that our approach performs better than the ensemble Kalman filter (EnKF) and the unstabilized FourCastNet model, both in terms of forecast accuracy and forecast uncertainty.
Towards Environment-Sensitive Molecular Inference via Mixed Integer Linear Programming
Authors: Jianshen Zhu, Mao Takekida, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
Date: 2025-02-17 00:00:00

Traditional QSAR/QSPR and inverse QSAR/QSPR methods often assume that chemical properties are dictated by single molecules, overlooking the influence of molecular interactions and environmental factors. In this paper, we introduce a novel QSAR/QSPR framework that can capture the combined effects of multiple molecules (e.g., small molecules or polymers) and experimental conditions on property values. We design a feature function to integrate the information of multiple molecules and the environment. Specifically, for the property Flory-Huggins $\chi$-parameter, which characterizes the thermodynamic properties between the solute and the solvent, and varies in temperatures, we demonstrate through computational experimental results that our approach can achieve a competitively high learning performance compared to existing works on predicting $\chi$-parameter values, while inferring the solute polymers with up to 50 non-hydrogen atoms in their monomer forms in a relatively short time. A comparison study with the simulation software J-OCTA demonstrates that the polymers inferred by our methods are of high quality.
A new practical and effective source-independent full-waveform inversion with a velocity-distribution supported deep image prior: Applications to two real datasets
Authors: Chao Song, Tariq Alkhalifah, Umair bin Waheed, Silin Wang, Cai Liu
Date: 2025-03-01 00:00:00

Full-waveform inversion (FWI) is an advanced technique for reconstructing high-resolution subsurface physical parameters by progressively minimizing the discrepancy between observed and predicted seismic data. However, conventional FWI encounters challenges in real data applications, primarily due to its conventional objective of direct measurements of the data misfit. Accurate estimation of the source wavelet is essential for effective data fitting, alongside the need for low-frequency data and a reasonable initial model to prevent cycle skipping. Additionally, wave equation solvers often struggle to accurately simulate the amplitude of observed data in real applications. To address these challenges, we introduce a correlation-based source-independent objective function for FWI that aims to mitigate source uncertainty and amplitude dependency, which effectively enhances its practicality for real data applications. We develop a deep-learning framework constrained by this new objective function with a velocity-distribution supported deep image prior, which reparameterizes velocity inversion into trainable parameters within an autoencoder, thereby reducing the nonlinearity in the conventional FWI's objective function. We demonstrate the superiority of our proposed method using synthetic data from benchmark velocity models and, more importantly, two real datasets. These examples highlight its effectiveness and practicality even under challenging conditions, such as missing low frequencies, a crude initial velocity model, and an incorrect source wavelet.
Constructing balanced datasets for predicting failure modes in structural systems under seismic hazards
Authors: Jungho Kim, Taeyong Kim
Date: 2025-02-26 00:00:00

Accurate prediction of structural failure modes under seismic excitations is essential for seismic risk and resilience assessment. Traditional simulation-based approaches often result in imbalanced datasets dominated by non-failure or frequently observed failure scenarios, limiting the effectiveness in machine learning-based prediction. To address this challenge, this study proposes a framework for constructing balanced datasets that include distinct failure modes. The framework consists of three key steps. First, critical ground motion features (GMFs) are identified to effectively represent ground motion time histories. Second, an adaptive algorithm is employed to estimate the probability densities of various failure domains in the space of critical GMFs and structural parameters. Third, samples generated from these probability densities are transformed into ground motion time histories by using a scaling factor optimization process. A balanced dataset is constructed by performing nonlinear response history analyses on structural systems with parameters matching the generated samples, subjected to corresponding transformed ground motion time histories. Deep neural network models are trained on balanced and imbalanced datasets to highlight the importance of dataset balancing. To further evaluate the framework's applicability, numerical investigations are conducted using two different structural models subjected to recorded and synthetic ground motions. The results demonstrate the framework's robustness and effectiveness in addressing dataset imbalance and improving machine learning performance in seismic failure mode prediction.