pwc-archive/papers-with-abstracts huggingface dataset:
Sparks: Multi-Agent Artificial Intelligence Model Discovers Protein Design Principles
Authors: Alireza Ghafarollahi, Markus J. Buehler
Date: 2025-04-26 00:00:00
Tasks: Protein Design

Advances in artificial intelligence (AI) promise autonomous discovery, yet most systems still resurface knowledge latent in their training data. We present Sparks, a multi-modal multi-agent AI model that executes the entire discovery cycle that includes hypothesis generation, experiment design and iterative refinement to develop generalizable principles and a report without human intervention. Applied to protein science, Sparks uncovered two previously unknown phenomena: (i) a length-dependent mechanical crossover whereby beta-sheet-biased peptides surpass alpha-helical ones in unfolding force beyond ~80 residues, establishing a new design principle for peptide mechanics; and (ii) a chain-length/secondary-structure stability map revealing unexpectedly robust beta-sheet-rich architectures and a "frustration zone" of high variance in mixed alpha/beta folds. These findings emerged from fully self-directed reasoning cycles that combined generative sequence design, high-accuracy structure prediction and physics-aware property models, with paired generation-and-reflection agents enforcing self-correction and reproducibility. The key result is that Sparks can independently conduct rigorous scientific inquiry and identify previously unknown scientific principles.
Reshaping MOFs Text Mining with a Dynamic Multi-Agent Framework of Large Language Agents
Authors: Zuhong Lin, Daoyuan Ren, Kai Ran, Sun Jing, Xiaotiang Huang, Haiyang He, Pengxu Pan, Xiaohang Zhang, Ying Fang, Tianying Wang, Minli Wu, Zhanglin Li, Xiaochuan Zhang, Haipu Li, Jingjing Yao
Date: 2025-04-26 00:00:00
Tasks: Attribute

The mining of synthesis conditions for metal-organic frameworks (MOFs) is a significant focus in materials science. However, identifying the precise synthesis conditions for specific MOFs within the vast array of possibilities presents a considerable challenge. Large Language Models (LLMs) offer a promising solution to this problem. We leveraged the capabilities of LLMs, specifically gpt-4o-mini, as core agents to integrate various MOF-related agents, including synthesis, attribute, and chemical information agents. This integration culminated in the development of MOFh6, an LLM tool designed to streamline the MOF synthesis process. MOFh6 allows users to query in multiple formats, such as submitting scientific literature, or inquiring about specific MOF codes or structural properties. The tool analyzes these queries to provide optimal synthesis conditions and generates model files for density functional theory pre modeling. We believe MOFh6 will enhance efficiency in the MOF synthesis of all researchers.
Predicting Stress in Two-phase Random Materials and Super-Resolution Method for Stress Images by Embedding Physical Information
Authors: Tengfei Xing, Xiaodan Ren, Jie Li
Date: 2025-04-26 00:00:00
Tasks: Image Super-Resolution, Prediction, Super-Resolution, Transfer Learning

Stress analysis is an important part of material design. For materials with complex microstructures, such as two-phase random materials (TRMs), material failure is often accompanied by stress concentration. Phase interfaces in two-phase materials are critical for stress concentration. Therefore, the prediction error of stress at phase boundaries is crucial. In practical engineering, the pixels of the obtained material microstructure images are limited, which limits the resolution of stress images generated by deep learning methods, making it difficult to observe stress concentration regions. Existing Image Super-Resolution (ISR) technologies are all based on data-driven supervised learning. However, stress images have natural physical constraints, which provide new ideas for new ISR technologies. In this study, we constructed a stress prediction framework for TRMs. First, the framework uses a proposed Multiple Compositions U-net (MC U-net) to predict stress in low-resolution material microstructures. By considering the phase interface information of the microstructure, the MC U-net effectively reduces the problem of excessive prediction errors at phase boundaries. Secondly, a Mixed Physics-Informed Neural Network (MPINN) based method for stress ISR (SRPINN) was proposed. By introducing the constraints of physical information, the new method does not require paired stress images for training and can increase the resolution of stress images to any multiple. This enables a multiscale analysis of the stress concentration regions at phase boundaries. Finally, we performed stress analysis on TRMs with different phase volume fractions and loading states through transfer learning. The results show the proposed stress prediction framework has satisfactory accuracy and generalization ability.
Global Stress Generation and Spatiotemporal Super-Resolution Physics-Informed Operator under Dynamic Loading for Two-Phase Random Materials
Authors: Tengfei Xing, Xiaodan Ren, Jie Li
Date: 2025-04-26 00:00:00
Tasks: STS, Super-Resolution

Material stress analysis is a critical aspect of material design and performance optimization. Under dynamic loading, the global stress evolution in materials exhibits complex spatiotemporal characteristics, especially in two-phase random materials (TRMs). Such kind of material failure is often associated with stress concentration, and the phase boundaries are key locations where stress concentration occurs. In practical engineering applications, the spatiotemporal resolution of acquired microstructural data and its dynamic stress evolution is often limited. This poses challenges for deep learning methods in generating high-resolution spatiotemporal stress fields, particularly for accurately capturing stress concentration regions. In this study, we propose a framework for global stress generation and spatiotemporal super-resolution in TRMs under dynamic loading. First, we introduce a diffusion model-based approach, named as Spatiotemporal Stress Diffusion (STS-diffusion), for generating global spatiotemporal stress data. This framework incorporates Space-Time U-Net (STU-net), and we systematically investigate the impact of different attention positions on model accuracy. Next, we develop a physics-informed network for spatiotemporal super-resolution, termed as Spatiotemporal Super-Resolution Physics-Informed Operator (ST-SRPINN). The proposed ST-SRPINN is an unsupervised learning method. The influence of data-driven and physics-informed loss function weights on model accuracy is explored in detail. Benefiting from physics-based constraints, ST-SRPINN requires only low-resolution stress field data during training and can upscale the spatiotemporal resolution of stress fields to arbitrary magnifications.
Energy Transduction in Complex Networks with Multiple Resources: The Chemistry Paradigm
Authors: Massimo Bilancioni, Massimiliano Esposito
Date: 2025-05-02 00:00:00

We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when stoichiometrically balanced processes are driven against their spontaneous directions by coupling them with thermodynamically favorable ones. However, when multiple processes (resources) interact through a shared CRN, identifying the relevant set of processes for analyzing transduction becomes a critical and complex challenge. To address this, we introduce a systematic procedure based on elementary processes, which cannot be further decomposed into subprocesses. Our theory generalizes the methodology used to define transduction efficiency in thermal engines operating between multiple heat baths. By selecting a reference equilibrium environment, it explicitly reveals the inherently relative nature of transduction efficiency and ties its definition to exergy. This framework also allows one to exclude unusable outputs from efficiency calculations. We further extend the concept of chemical gears to multi-process transduction, demonstrating their versatility as an analytical tool in complex settings. Finally, we apply our framework to central metabolic pathways, uncovering deep insights into their operation and highlighting the crucial difference between thermodynamic efficiencies and stoichiometric yields.
Topology, Kinetics and Inheritance in Clonal Colonies of Bone Marrow Stromal Cells
Authors: Alessandro Allegrezza, Riccardo Beschi, Domenico Caudo, Andrea Cavagna, Alessandro Corsi, Antonio Culla, Samantha Donsante, Giuseppe Giannicola, Irene Giardina, Giorgio Gosti, Tomas S. Grigera, Stefania Melillo, Biagio Palmisano, Leonardo Parisi, Lorena Postiglione, Mara Riminucci, Francesco Saverio Rotondi
Date: 2025-04-30 00:00:00

Bone marrow stromal cells (BMSCs), whose populations contain multipotent skeletal stem cells with relevant therapeutic applications, are known to produce very heterogeneous colonies upon in vitro culture, a trait that may severely hinder the clinical usefulness of BMSC-based therapies. Therefore, reaching a better insight on the nature of such heterogeneity, as well as on the factors determining it, is important. Here, by using time-lapse microscopy, we study the structure of N=28 human BMSC colonies from six donors, each colony derived from a single cell, and trace their lineage trees up to the seventh generation. We confirm the presence of very significant inter-colony and intra-colony heterogeneities, both in the topology of the lineages and in the replicative kinetics of the colonies. We also find that topology and kinetics are strongly correlated, consistent with the existence of regulating factors linking the sub-population of inactive cells, which uniquely determine a lineage's topology, and that of active cells, which are the sole responsible for the proliferation rate of the colony. Finally, we submit each colony to an entropy-based inheritance test, which measures the degree of non-random clustering of inactive cells within the same branches of the lineage, and find a clear signature of hereditary transmission of the probability of emergence of inactive cells in the largest majority of the experimental lineages.
Explorative Curriculum Learning for Strongly Correlated Electron Systems
Authors: Kimihiro Yamazaki, Takuya Konishi, Yoshinobu Kawahara
Date: 2025-05-01 00:00:00
Tasks: Transfer Learning

Recent advances in neural network quantum states (NQS) have enabled high-accuracy predictions for complex quantum many-body systems such as strongly correlated electron systems. However, the computational cost remains prohibitive, making exploration of the diverse parameters of interaction strengths and other physical parameters inefficient. While transfer learning has been proposed to mitigate this challenge, achieving generalization to large-scale systems and diverse parameter regimes remains difficult. To address this limitation, we propose a novel curriculum learning framework based on transfer learning for NQS. This facilitates efficient and stable exploration across a vast parameter space of quantum many-body systems. In addition, by interpreting NQS transfer learning through a perturbative lens, we demonstrate how prior physical knowledge can be flexibly incorporated into the curriculum learning process. We also propose Pairing-Net, an architecture to practically implement this strategy for strongly correlated electron systems, and empirically verify its effectiveness. Our results show an approximately 200-fold speedup in computation and a marked improvement in optimization stability compared to conventional methods.
A Cyclical Baryonic Big Bang Explains the Universe
Authors: David E. Rosenberg
Date: 1998-10-21 00:00:00

Our universe has multiple examples of unexplained gravitational losses in black holes and neutron stars. The smallest black holes of about 4 solar masses means the maximum baryon density \rho \approx 10^{17} grams/cm^3. Any collapse of the universe will stop with a scale factor \approx 10^{13} cm. and radiation energy \approx 10 GeV. Due to higher squeezed core baryons, the outer part of the mass transferred energy to the core and became dark matter. After contraction reduced particle motion and gravitation, the core radiation energy propelled pieces of the shell into the universe. Each of these masses captured hot core gases according to its gravitational size, forming proto-galaxies. A cold shell and a hot core explain the Planck spectrum and large galaxy formation in the early universe. Thus the universe was never radiation dominant.The universe will remain cyclical as any increase in entropy of matter will be crushed back to neutrons during the contraction phase.
Scalable Multi-Task Learning for Particle Collision Event Reconstruction with Heterogeneous Graph Neural Networks
Authors: William Sutcliffe, Marta Calvi, Simone Capelli, Jonas Eschle, Julián García Pardiñas, Abhijit Mathad, Azusa Uzuki, Nicola Serra
Date: 2025-04-30 00:00:00
Tasks: Graph Neural Network, Multi-Task Learning

The growing luminosity frontier at the Large Hadron Collider is challenging the reconstruction and analysis of particle collision events. Increased particle multiplicities are straining latency and storage requirements at the data acquisition stage, while new complications are emerging, including higher background levels and more frequent particle vertex misassociations. This in turn necessitates the development of more holistic and scalable reconstruction methods that take advantage of recent advances in machine learning. We propose a novel Heterogeneous Graph Neural Network (HGNN) architecture featuring unique representations for diverse particle collision relationships and integrated graph pruning layers for scalability. Trained with a multi-task paradigm in an environment mimicking the LHCb experiment, this HGNN significantly improves beauty hadron reconstruction performance. Notably, it concurrently performs particle vertex association and graph pruning within a single framework. We quantify reconstruction and pruning performance, demonstrate enhanced inference time scaling with event complexity, and mitigate potential performance loss using a weighted message passing scheme.
Generative Models for Fast Simulation of Cherenkov Detectors at the Electron-Ion Collider
Authors: James Giroux, Michael Martinez, Cristiano Fanelli
Date: 2025-04-26 00:00:00
Tasks: Benchmarking, GPU

The integration of Deep Learning (DL) into experimental nuclear and particle physics has driven significant progress in simulation and reconstruction workflows. However, traditional simulation frameworks such as Geant4 remain computationally intensive, especially for Cherenkov detectors, where simulating optical photon transport through complex geometries and reflective surfaces introduces a major bottleneck. To address this, we present an open, standalone fast simulation tool for Detection of Internally Reflected Cherenkov Light (DIRC) detectors, with a focus on the High-Performance DIRC (hpDIRC) at the future Electron-Ion Collider (EIC). Our framework incorporates a suite of generative models tailored to accelerate particle identification (PID) tasks by offering a scalable, GPU-accelerated alternative to full Geant4-based simulations. Designed with accessibility in mind, our simulation package enables both DL researchers and physicists to efficiently generate high-fidelity large-scale datasets on demand, without relying on complex traditional simulation stacks. This flexibility supports the development and benchmarking of novel DL-driven PID methods. Moreover, this fast simulation pipeline represents a critical step toward enabling EIC-wide PID strategies that depend on virtually unlimited simulated samples, spanning the full acceptance of the hpDIRC.
Lecture Notes on Normalizing Flows for Lattice Quantum Field Theories
Authors: Miranda C. N. Cheng, Niki Stratikopoulou
Date: 2025-04-25 00:00:00

Numerical simulations of quantum field theories on lattices serve as a fundamental tool for studying the non-perturbative regime of the theories, where analytic tools often fall short. Challenges arise when one takes the continuum limit or as the system approaches a critical point, especially in the presence of non-trivial topological structures in the theory. Rapid recent advances in machine learning provide a promising avenue for progress in this area. These lecture notes aim to give a brief account of lattice field theories, normalizing flows, and how the latter can be applied to study the former. The notes are based on the lectures given by the first author in various recent research schools.
On the robustness of the emergent spatiotemporal dynamics in biophysically realistic and phenomenological whole-brain models at multiple network resolutions
Authors: Cristiana Dimulescu, Ronja Strömsdörfer, Agnes Flöel, Klaus Obermayer
Date: 2025-04-24 00:00:00
Tasks: Rhythm

The human brain is a complex dynamical system which displays a wide range of macroscopic and mesoscopic patterns of neural activity, whose mechanistic origin remains poorly understood. Whole-brain modelling allows us to explore candidate mechanisms causing the observed patterns. However, it is not fully established how the choice of model type and the networks' resolution influence the simulation results, hence, it remains unclear, to which extent conclusions drawn from these results are limited by modelling artefacts. Here, we compare the dynamics of a biophysically realistic, linear-nonlinear cascade model of whole-brain activity with a phenomenological Wilson-Cowan model using three structural connectomes based on the Schaefer parcellation scheme with 100, 200, and 500 nodes. Both neural mass models implement the same mechanistic hypotheses, which specifically address the interaction between excitation, inhibition, and a slow adaptation current, which affects the excitatory populations. We quantify the emerging dynamical states in detail and investigate how consistent results are across the different model variants. Then we apply both model types to the specific phenomenon of slow oscillations, which are a prevalent brain rhythm during deep sleep. We investigate the consistency of model predictions when exploring specific mechanistic hypotheses about the effects of both short- and long-range connections and of the antero-posterior structural connectivity gradient on key properties of these oscillations. Overall, our results demonstrate that the coarse-grained dynamics are robust to changes in both model type and network resolution. In some cases, however, model predictions do not generalize. Thus, some care must be taken when interpreting model results.
Tailored minimal reservoir computing: on the bidirectional connection between nonlinearities in the reservoir and in data
Authors: Davide Prosperino, Haochun Ma, Christoph Räth
Date: 2025-04-24 00:00:00
Tasks: Time Series

We study how the degree of nonlinearity in the input data affects the optimal design of reservoir computers, focusing on how closely the model's nonlinearity should align with that of the data. By reducing minimal RCs to a single tunable nonlinearity parameter, we explore how the predictive performance varies with the degree of nonlinearity in the reservoir. To provide controlled testbeds, we generalize to the fractional Halvorsen system, a novel chaotic system with fractional exponents. Our experiments reveal that the prediction performance is maximized when the reservoir's nonlinearity matches the nonlinearity present in the data. In cases where multiple nonlinearities are present in the data, we find that the correlation dimension of the predicted signal is reconstructed correctly when the smallest nonlinearity is matched. We use this observation to propose a method for estimating the minimal nonlinearity in unknown time series by sweeping the reservoir exponent and identifying the transition to a successful reconstruction. Applying this method to both synthetic and real-world datasets, including financial time series, we demonstrate its practical viability. Finally, we transfer these insights to classical RC by augmenting traditional architectures with fractional, generalized reservoir states. This yields performance gains, particularly in resource-constrained scenarios such as physical reservoirs, where increasing reservoir size is impractical or economically unviable. Our work provides a principled route toward tailoring RCs to the intrinsic complexity of the systems they aim to model.
Fourier analysis of the physics of transfer learning for data-driven subgrid-scale models of ocean turbulence
Authors: Moein Darman, Pedram Hassanzadeh, Laure Zanna, Ashesh Chattopadhyay
Date: 2025-04-21 00:00:00
Tasks: Transfer Learning

Transfer learning (TL) is a powerful tool for enhancing the performance of neural networks (NNs) in applications such as weather and climate prediction and turbulence modeling. TL enables models to generalize to out-of-distribution data with minimal training data from the new system. In this study, we employ a 9-layer convolutional NN to predict the subgrid forcing in a two-layer ocean quasi-geostrophic system and examine which metrics best describe its performance and generalizability to unseen dynamical regimes. Fourier analysis of the NN kernels reveals that they learn low-pass, Gabor, and high-pass filters, regardless of whether the training data are isotropic or anisotropic. By analyzing the activation spectra, we identify why NNs fail to generalize without TL and how TL can overcome these limitations: the learned weights and biases from one dataset underestimate the out-of-distribution sample spectra as they pass through the network, leading to an underestimation of output spectra. By re-training only one layer with data from the target system, this underestimation is corrected, enabling the NN to produce predictions that match the target spectra. These findings are broadly applicable to data-driven parameterization of dynamical systems.
Compton Form Factor Extraction using Quantum Deep Neural Networks
Authors: Brandon Le, Dustin Keller
Date: 2025-04-21 00:00:00
Tasks: Form

Extraction tests of Compton Form Factors are performed using pseudodata based on experimental data from Deeply Virtual Compton Scattering experiments conducted at Jefferson Lab. The standard Belitsky, Kirchner, and Muller formalism at twist-two is employed, along with a fitting procedure designed to reduce model dependency similar to traditional local fits. The extraction of the Compton Form Factors is performed using both Classical Deep Neural Networks (CDNNs) and Quantum Deep Neural Networks (QDNNs). Comparative studies reveal that QDNNs outperform CDNNs for this application, demonstrating improved predictive accuracy and precision even for limited model complexity. The results demonstrate the potential of QDNNs for future studies in which quantum algorithms can be fully optimized.