pwc-archive/papers-with-abstracts huggingface dataset:
Advanced Nanostructured Topical Therapeutics for Psoriasis: Strategic Synthesis, Multimodal Characterization, and Preliminary Pharmacodynamic Profiling
Authors: Iqra Yousaf, Aqsa Yousaf
Date: 2025-06-02 00:00:00

Psoriasis is a long-term inflammatory skin disease that remains difficult to treat. In this study, we developed a new topical treatment by combining metal oxide nanoparticles: cerium oxide (CeO2), zinc oxide (ZnO), and silver (Ag), with natural plant extracts in a gel made from fish collagen and agar. The nanoparticles were characterized using UV-Vis spectroscopy, dynamic light scattering (DLS), Fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM), showing good stability and a uniform particle size distribution (ZnO averaged 66 nm). To enhance therapeutic potential, the gel was enriched with plant-derived antioxidants from bitter melon, ginger, and neem. This formulation was tested on an animal model of psoriasis. The treated group exhibited faster wound healing and reduced inflammation compared to both placebo and untreated groups, with statistically significant results (p < 0.01 to p < 0.001) observed from Day 3, becoming more pronounced by Day 14. These results indicate that the combination of nanoparticles with plant-based components in a topical gel may provide a promising new approach to psoriasis treatment. Further studies are recommended to evaluate long-term safety and therapeutic effectiveness.
The Dynamic Role of Aerosol and Exudate Transport in the Diffusion of Lung Infection in Respiratory Infectious Diseases (taking SARS-CoV-2 as an example): A Hypothesis Model
Authors: Shi Qiru
Date: 2025-05-29 00:00:00

This paper proposes a hypothetical model for the dual role of respiratory aerosols and inflammatory exudates in the dynamics and progression of SARS-CoV-2 lung infection. Starting from a new paradigm in infectious disease transmission, we reflect on the often-overlooked role of physical transmission media within the host individual. The hypothesis posits that tiny aerosols (including those inhaled externally and those self-generated and re-inhaled by the host) play a crucial role in the initial seeding and early expansion of the infection in the lungs, explaining the multifocal characteristics observed in early CT imaging. As the infection progresses, inflammatory exudates, formed due to lung inflammation, become a new efficient vehicle, driving the large-scale spread of the virus within the lungs and accounting for the development of diffuse lesions. This model reveals a "dynamic equilibrium point" where the dominant mechanism shifts from aerosol-mediated to exudate-mediated spread. Although direct validation of this hypothesis faces ethical and technical challenges, existing clinical imaging, viral kinetics, and epidemiological patterns provide indirect support. The paper also conceptualizes ideal experimental designs and retrospective analyses to validate the hypothesis. Finally, we discuss the implications of this hypothesis for public health practice, emphasizing the importance of improving ventilation in the microenvironment of infected individuals to achieve a "for all, by all" (literally "everyone for me, I for everyone") bidirectional protection. This research aims to provide a new framework for understanding the pathophysiology of respiratory infectious diseases and to offer theoretical basis for developing more cost-effective and broadly applicable intervention strategies.
Unlocking Chemical Insights: Superior Molecular Representations from Intermediate Encoder Layers
Authors: Luis Pinto
Date: 2025-06-06 00:00:00
Tasks: Computational chemistry, Computational Efficiency, Property Prediction

Pretrained molecular encoders have become indispensable in computational chemistry for tasks such as property prediction and molecular generation. However, the standard practice of relying solely on final-layer embeddings for downstream tasks may discard valuable information. In this work, we challenge this convention by conducting a comprehensive layer-wise analysis of five diverse molecular encoders across 22 ADMET property prediction tasks. Our results demonstrate that embeddings from intermediate layers consistently outperform final-layer representations. Specifically, using fixed embeddings from the optimal intermediate layers improved downstream performance by an average of 5.4%, reaching gains up to 28.6%. Furthermore, finetuning up to these intermediate layers yielded even greater average improvements of 8.5%, with performance increases as high as 40.8%, achieving new state-of-the-art results on several benchmarks. Additionally, a strong positive correlation between fixed embedding performance and finetuning outcomes supports an efficient evaluate-then-finetune approach, enabling identification of optimal layers with reduced computational cost. These findings highlight the importance of exploring the full representational depth of molecular encoders to achieve substantial performance improvements and computational efficiency. The code is made publicly available at https://github.com/luispintoc/Unlocking-Chemical-Insights.
chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations
Authors: Paul Fuchs, Weilong Chen, Stephan Thaler, Julija Zavadlav
Date: 2025-06-04 00:00:00
Tasks: Graph Neural Network

Machine learning potentials (MLPs) have advanced rapidly and show great promise to transform molecular dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard MD packages, or are not parallelizable across GPUs. To address these challenges, we present chemtrain-deploy, a framework that enables model-agnostic deployment of MLPs in LAMMPS. chemtrain-deploy supports any JAX-defined semi-local potential, allowing users to exploit the functionality of LAMMPS and perform large-scale MLP-based MD simulations on multiple GPUs. It achieves state-of-the-art efficiency and scales to systems containing millions of atoms. We validate its performance and scalability using graph neural network architectures, including MACE, Allegro, and PaiNN, applied to a variety of systems, such as liquid-vapor interfaces, crystalline materials, and solvated peptides. Our results highlight the practical utility of chemtrain-deploy for real-world, high-performance simulations and provide guidance for MLP architecture selection and future design.
Efficient Prediction of SO(3)-Equivariant Hamiltonian Matrices via SO(2) Local Frames
Authors: Haiyang Yu, Yuchao Lin, Xuan Zhang, Xiaofeng Qian, Shuiwang Ji
Date: 2025-06-11 00:00:00

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.
Diffusion-Based Hierarchical Graph Neural Networks for Simulating Nonlinear Solid Mechanics
Authors: Tobias Würth, Niklas Freymuth, Gerhard Neumann, Luise Kärger
Date: 2025-06-06 00:00:00
Tasks: Denoising, Graph Neural Network

Graph-based learned simulators have emerged as a promising approach for simulating physical systems on unstructured meshes, offering speed and generalization across diverse geometries. However, they often struggle with capturing global phenomena, such as bending or long-range correlations, and suffer from error accumulation over long rollouts due to their reliance on local message passing and direct next-step prediction. We address these limitations by introducing the Rolling Diffusion-Batched Inference Network (ROBIN), a novel learned simulator that integrates two key innovations: (i) Rolling Diffusion, a parallelized inference scheme that amortizes the cost of diffusion-based refinement across physical time steps by overlapping denoising steps across a temporal window. (ii) A Hierarchical Graph Neural Network built on algebraic multigrid coarsening, enabling multiscale message passing across different mesh resolutions. This architecture, implemented via Algebraic-hierarchical Message Passing Networks, captures both fine-scale local dynamics and global structural effects critical for phenomena like beam bending or multi-body contact. We validate ROBIN on challenging 2D and 3D solid mechanics benchmarks involving geometric, material, and contact nonlinearities. ROBIN achieves state-of-the-art accuracy on all tasks, substantially outperforming existing next-step learned simulators while reducing inference time by up to an order of magnitude compared to standard diffusion simulators.
PMNO: A novel physics guided multi-step neural operator predictor for partial differential equations
Authors: Jin Song, Kenji Kawaguchi, Zhenya Yan
Date: 2025-06-02 00:00:00
Tasks: Operator learning

Neural operators, which aim to approximate mappings between infinite-dimensional function spaces, have been widely applied in the simulation and prediction of physical systems. However, the limited representational capacity of network architectures, combined with their heavy reliance on large-scale data, often hinder effective training and result in poor extrapolation performance. In this paper, inspired by traditional numerical methods, we propose a novel physics guided multi-step neural operator (PMNO) architecture to address these challenges in long-horizon prediction of complex physical systems. Distinct from general operator learning methods, the PMNO framework replaces the single-step input with multi-step historical data in the forward pass and introduces an implicit time-stepping scheme based on the Backward Differentiation Formula (BDF) during backpropagation. This design not only strengthens the model's extrapolation capacity but also facilitates more efficient and stable training with fewer data samples, especially for long-term predictions. Meanwhile, a causal training strategy is employed to circumvent the need for multi-stage training and to ensure efficient end-to-end optimization. The neural operator architecture possesses resolution-invariant properties, enabling the trained model to perform fast extrapolation on arbitrary spatial resolutions. We demonstrate the superior predictive performance of PMNO predictor across a diverse range of physical systems, including 2D linear system, modeling over irregular domain, complex-valued wave dynamics, and reaction-diffusion processes. Depending on the specific problem setting, various neural operator architectures, including FNO, DeepONet, and their variants, can be seamlessly integrated into the PMNO framework.
An analysis of capital market through the lens of integral transforms: exploring efficient markets and information asymmetry
Authors: Kiran Sharma, Abhijit Dutta, Rupak Mukherjee
Date: 2025-06-02 00:00:00

Post Modigliani and Miller (1958), the concept of usage of arbitrage created a permanent mark on the discourses of financial framework. The arbitrage process is largely based on information dissemination amongst the stakeholders operating in the financial market. The advent of the efficient market Hypothesis draws close to the M&M hypothesis. Giving importance to the arbitrage process, which effects the price discovery in the stock market. This divided the market as random and efficient cohort system. The focus was on which information forms a key factor in deciding the price formation in the market. However, the conventional techniques of analysis do not permit the price cycles to be interpreted beyond its singular wave-like cyclical movement. The apparent cyclic measurement is not coherent as the technical analysis does not give sustained result. Hence adaption of theories and computation from mathematical methods of physics ensures that these cycles are decomposed and the effect of the broken-down cycles is interpreted to understand the overall effect of information on price formation and discovery. In order to break the cycle this paper uses spectrum analysis to decompose and understand the above-said phenomenon in determining the price behavior in National Stock Exchange of India (NSE).
DiffPINN: Generative diffusion-initialized physics-informed neural networks for accelerating seismic wavefield representation
Authors: Shijun Cheng, Tariq Alkhalifah
Date: 2025-05-31 00:00:00

Physics-informed neural networks (PINNs) offer a powerful framework for seismic wavefield modeling, yet they typically require time-consuming retraining when applied to different velocity models. Moreover, their training can suffer from slow convergence due to the complexity of of the wavefield solution. To address these challenges, we introduce a latent diffusion-based strategy for rapid and effective PINN initialization. First, we train multiple PINNs to represent frequency-domain scattered wavefields for various velocity models, then flatten each trained network's parameters into a one-dimensional vector, creating a comprehensive parameter dataset. Next, we employ an autoencoder to learn latent representations of these parameter vectors, capturing essential patterns across diverse PINN's parameters. We then train a conditional diffusion model to store the distribution of these latent vectors, with the corresponding velocity models serving as conditions. Once trained, this diffusion model can generate latent vectors corresponding to new velocity models, which are subsequently decoded by the autoencoder into complete PINN parameters. Experimental results indicate that our method significantly accelerates training and maintains high accuracy across in-distribution and out-of-distribution velocity scenarios.
Toward Knowledge-Guided AI for Inverse Design in Manufacturing: A Perspective on Domain, Physics, and Human-AI Synergy
Authors: Hugon Lee, Hyeonbin Moon, Junhyeong Lee, Seunghwa Ryu
Date: 2025-05-29 00:00:00
Tasks: Physics-informed machine learning

Artificial intelligence (AI) is reshaping inverse design across manufacturing domain, enabling high-performance discovery in materials, products, and processes. However, purely data-driven approaches often struggle in realistic settings characterized by sparse data, high-dimensional design spaces, and nontrivial physical constraints. This perspective argues for a new generation of design systems that transcend black-box modeling by integrating domain knowledge, physics-informed learning, and intuitive human-AI interfaces. We first demonstrate how expert-guided sampling strategies enhance data efficiency and model generalization. Next, we discuss how physics-informed machine learning enables physically consistent modeling in data-scarce regimes. Finally, we explore how large language models emerge as interactive design agents connecting user intent with simulation tools, optimization pipelines, and collaborative workflows. Through illustrative examples and conceptual frameworks, we advocate that inverse design in manufacturing should evolve into a unified ecosystem, where domain knowledge, physical priors, and adaptive reasoning collectively enable scalable, interpretable, and accessible AI-driven design systems.
Scientific machine learning in Hydrology: a unified perspective
Authors: Adoubi Vincent De Paul Adombi
Date: 2025-05-24 00:00:00
Tasks: Physics-informed machine learning

Scientific machine learning (SciML) provides a structured approach to integrating physical knowledge into data-driven modeling, offering significant potential for advancing hydrological research. In recent years, multiple methodological families have emerged, including physics-informed machine learning, physics-guided machine learning, hybrid physics-machine learning, and data-driven physics discovery. Within each of these families, a proliferation of heterogeneous approaches has developed independently, often without conceptual coordination. This fragmentation complicates the assessment of methodological novelty and makes it difficult to identify where meaningful advances can still be made in the absence of a unified conceptual framework. This review, the first focused overview of SciML in hydrology, addresses these limitations by proposing a unified methodological framework for each SciML family, bringing together representative contributions into a coherent structure that fosters conceptual clarity and supports cumulative progress in hydrological modeling. Finally, we highlight the limitations and future opportunities of each unified family to guide systematic research in hydrology, where these methods remain underutilized.
Simulation-trained conditional normalizing flows for likelihood approximation: a case study in stress regulation kinetics in yeast
Authors: Pedro Pessoa, Juan Andres Martinez, Vincent Vandenbroucke, Frank Delvigne, Steve Pressé
Date: 2025-06-11 00:00:00
Tasks: parameter estimation

Physics-inspired inference often hinges on the ability to construct a likelihood, or the probability of observing a sequence of data given a model. These likelihoods can be directly maximized for parameter estimation, incorporated into Bayesian frameworks, or even used as loss functions in neural networks. Yet, many models, despite being conceptually simple, lack tractable likelihoods. A notable example arises in estimating protein production from snapshot measurements of actively dividing cells. Here, the challenge stems from cell divisions occurring at non-Exponentially distributed intervals with each division stochastically partitioning protein content between daughter cells, making protein counts in any given cell a function of its full division history. Such history dependence precludes a straightforward likelihood based on a (standard Markovian) master equation. Instead, we employ conditional normalizing flows (a class of neural network models designed to learn probability distributions) to approximate otherwise intractable likelihoods from simulated data. As a case study, we examine activation of the \emph{glc3} gene in yeast involved in glycogen synthesis and expressed under nutrient-limiting conditions. We monitor this activity using snapshot fluorescence measurements via flow cytometry, where GFP expression reflects \emph{glc3} promoter activity. A na\"ive analysis of flow cytometry data ignoring cell division suggests many cells are active with low expression. However, fluorescent proteins persist and can be inherited, so cells may appear active from retaining ancestral fluorescence. Explicitly accounting for the (non-Markovian) effects of cell division reveals \emph{glc3} is mostly inactive under stress, showing that while cells occasionally activate it, expression is brief and transient.
Multi-Exit Kolmogorov-Arnold Networks: enhancing accuracy and parsimony
Authors: James Bagrow, Josh Bongard
Date: 2025-06-03 00:00:00
Tasks: Kolmogorov-Arnold Networks, scientific discovery

Kolmogorov-Arnold Networks (KANs) uniquely combine high accuracy with interpretability, making them valuable for scientific modeling. However, it is unclear a priori how deep a network needs to be for any given task, and deeper KANs can be difficult to optimize. Here we introduce multi-exit KANs, where each layer includes its own prediction branch, enabling the network to make accurate predictions at multiple depths simultaneously. This architecture provides deep supervision that improves training while discovering the right level of model complexity for each task. Multi-exit KANs consistently outperform standard, single-exit versions on synthetic functions, dynamical systems, and real-world datasets. Remarkably, the best predictions often come from earlier, simpler exits, revealing that these networks naturally identify smaller, more parsimonious and interpretable models without sacrificing accuracy. To automate this discovery, we develop a differentiable "learning to exit" algorithm that balances contributions from exits during training. Our approach offers scientists a practical way to achieve both high performance and interpretability, addressing a fundamental challenge in machine learning for scientific discovery.
Localizing synergies of hidden factors across complex systems: resting brain networks and HeLa gene expression profile as case studies
Authors: Marlis Ontivero-Ortega, Gorana Mijatovic, Luca Faes, Daniele Marinazzo, Sebastiano Stramaglia
Date: 2025-05-27 00:00:00

Factor analysis is a well-known statistical method to describe the variability of observed variables in terms of a smaller number of unobserved latent variables called factors. Even though latent factors are conceptually independent of each other, their influence on the observed variables is often joint and synergistic. We propose to quantify the synergy of the joint influence of factors on the observed variables using the O-information, a recently introduced metrics to assess high order dependencies in complex systems, in a new framework where latent factors and observed variables are jointly analyzed in terms of their joint informational character. Two case studies are reported: analyzing resting fMRI data, we find that DMN and FP networks show the highest synergy, consistently with their crucial role in higher cognitive functions; concerning HeLa cells, we find that the most synergistic gene is STK-12 (AURKB), suggesting that this gene is involved in controlling the HeLa cell cycle. We believe that this approach, representing a bridge between factor analysis and the field of high-order interactions, will find wide application across several domains.