pwc-archive/papers-with-abstracts huggingface dataset:
Rewards-based image analysis in microscopy
Authors: Kamyar Barakati, Yu Liu, Utkarsh Pratiush, Boris N. Slautin, Sergei V. Kalinin
Date: 2025-02-23 00:00:00
Tasks: Decision Making, Denoising, Dimensionality Reduction, Image Segmentation, Keypoint Detection, Semantic Segmentation, Transfer Learning

Analyzing imaging and hyperspectral data is crucial across scientific fields, including biology, medicine, chemistry, and physics. The primary goal is to transform high-resolution or high-dimensional data into an interpretable format to generate actionable insights, aiding decision-making and advancing knowledge. Currently, this task relies on complex, human-designed workflows comprising iterative steps such as denoising, spatial sampling, keypoint detection, feature generation, clustering, dimensionality reduction, and physics-based deconvolutions. The introduction of machine learning over the past decade has accelerated tasks like image segmentation and object detection via supervised learning, and dimensionality reduction via unsupervised methods. However, both classical and NN-based approaches still require human input, whether for hyperparameter tuning, data labeling, or both. The growing use of automated imaging tools, from atomically resolved imaging to biological applications, demands unsupervised methods that optimize data representation for human decision-making or autonomous experimentation. Here, we discuss advances in reward-based workflows, which adopt expert decision-making principles and demonstrate strong transfer learning across diverse tasks. We represent image analysis as a decision-making process over possible operations and identify desiderata and their mappings to classical decision-making frameworks. Reward-driven workflows enable a shift from supervised, black-box models sensitive to distribution shifts to explainable, unsupervised, and robust optimization in image analysis. They can function as wrappers over classical and DCNN-based methods, making them applicable to both unsupervised and supervised workflows (e.g., classification, regression for structure-property mapping) across imaging and hyperspectral data.
Generative adversarial neural networks for simulating neutrino interactions
Authors: Jose L. Bonilla, Krzysztof M. Graczyk, Artur M. Ankowski, Rwik Dharmapal Banerjee, Beata E. Kowal, Hemant Prasad, Jan T. Sobczyk
Date: 2025-02-27 00:00:00

We propose a new approach to simulate neutrino scattering events as an alternative to the standard Monte Carlo generator approach. Generative adversarial neural network (GAN) models are developed to simulate neutrino-carbon collisions in the few-GeV energy range. The models produce scattering events for a given neutrino energy. GAN models are trained on simulation data from NuWro Monte Carlo event generator. Two GAN models have been obtained: one simulating only quasielastic neutrino-nucleus scatterings and another simulating all interactions at given neutrino energy. The performance of both models has been assessed using two statistical metrics. It is shown that both GAN models successfully reproduce the event distributions.
Colored Jones Polynomials and the Volume Conjecture
Authors: Mark Hughes, Vishnu Jejjala, P. Ramadevi, Pratik Roy, Vivek Kumar Singh
Date: 2025-02-25 00:00:00

Using the vertex model approach for braid representations, we compute polynomials for spin-1 placed on hyperbolic knots up to 15 crossings. These polynomials are referred to as 3-colored Jones polynomials or adjoint Jones polynomials. Training a subset of the data using a fully connected feedforward neural network, we predict the volume of the knot complement of hyperbolic knots from the adjoint Jones polynomial or its evaluations with 99.34% accuracy. A function of the adjoint Jones polynomial evaluated at the phase $q=e^{ 8 \pi i / 15 }$ predicts the volume with nearly the same accuracy as the neural network. From an analysis of 2-colored and 3-colored Jones polynomials, we conjecture the best phase for $n$-colored Jones polynomials, and use this hypothesis to motivate an improved statement of the volume conjecture. This is tested for knots for which closed form expressions for the $n$-colored Jones polynomial are known, and we show improved convergence to the volume.
Optimal COVID-19 vaccine prioritization by age depends critically on inter-group contacts and vaccination rates
Authors: Iker Atienza-Diez, Gabriel Rodriguez-Maroto, Saúl Ares, Susanna Manrubia
Date: 2025-02-26 00:00:00

The limited availability of COVID-19 vaccines has prompted extensive research on optimal vaccination strategies. Previous studies have considered various non-pharmaceutical interventions, vaccine efficacy, and distribution strategies. In this work, we address the combined effects of inter-group contacts and vaccination rates under contact reduction, analyzing the Spanish population's demographic and age group contact patterns and incorporating reinfection dynamics. We conduct an exhaustive analysis, evaluating 362,880 permutations of 9 age groups across 6 vaccination rates and two distinct, empirically quantified scenarios for social contacts. Our results show that at intermediate-to-high vaccination rates with unrestricted social contacts, optimal age-based vaccination strategies only slightly deviate from older-to-younger prioritization, yielding marginal reductions in deaths and infections. However, when significant reductions in social contacts are enforced -similar to the lockdowns in 2020-, there are substantial improvements, particularly at moderate vaccination rates. These restrictions lead to a transition where infection propagation is halted, a scenario that became achievable during the pandemic with the observed vaccination rates. Our findings emphasize the importance of combining appropriate social contact reductions with vaccination to optimize age-based vaccination strategies, underscoring the complex, nonlinear dynamics involved in pandemic dynamics and the necessity for tailored, context-specific interventions.
Global Framework for Emulation of Nuclear Calculations
Authors: Antoine Belley, Jose M. Munoz, Ronald F. Garcia Ruiz
Date: 2025-02-27 00:00:00
Tasks: Sensitivity, Uncertainty Quantification

We introduce a hierarchical framework that combines ab initio many-body calculations with a Bayesian neural network, developing emulators capable of accurately predicting nuclear properties across isotopic chains simultaneously and being applicable to different regions of the nuclear chart. We benchmark our developments using the oxygen isotopic chain, achieving accurate results for ground-state energies and nuclear charge radii, while providing robust uncertainty quantification. Our framework enables global sensitivity analysis of nuclear binding energies and charge radii with respect to the low-energy constants that describe the nuclear force.
Adaptive conditional latent diffusion maps beam loss to 2D phase space projections
Authors: Alexander Scheinker, Alan Williams
Date: 2025-02-25 00:00:00

Beam loss (BLM) and beam current monitors (BCM) are ubiquitous at particle accelerator around the world. These simple devices provide non-invasive high level beam measurements, but give no insight into the detailed 6D (x,y,z,px,py,pz) beam phase space distributions or dynamics. We show that generative conditional latent diffusion models can learn intricate patterns to map waveforms of tens of BLMs or BCMs along an accelerator to detailed 2D projections of a charged particle beam's 6D phase space density. This transformational method can be used at any particle accelerator to transform simple non-invasive devices into detailed beam phase space diagnostics. We demonstrate this concept via multi-particle simulations of the high intensity beam in the kilometer-long LANSCE linear proton accelerator.
A Novel P-bit-based Probabilistic Computing Approach for Solving the 3-D Protein Folding Problem
Authors: Chao Fang, Yihan He, Xiao Gong, Gengchiau Liang
Date: 2025-02-27 00:00:00
Tasks: Protein Folding

In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic bits (p-bits) has attracted attention due to the widespread availability of p-bits and support for large-scale simulations. This study marks the first work to apply probabilistic computing to tackle protein folding, a significant NP-complete problem challenge in biology. We represent proteins as sequences of hydrophobic (H) and polar (P) beads within a three-dimensional (3-D) grid and introduce a novel many-body interaction-based encoding method to map the problem onto an Ising model. Our simulations show that this approach significantly simplifies the energy landscape for short peptide sequences of six amino acids, halving the number of energy levels. Furthermore, the proposed mapping method achieves approximately 100 times acceleration for sequences consisting of ten amino acids in identifying the correct folding configuration. We predicted the optimal folding configuration for a peptide sequence of 36 amino acids by identifying the ground state. These findings highlight the unique potential of the proposed encoding method for solving protein folding and, importantly, provide new tools for solving similar NP-complete problems in biology by probabilistic computing approach.
Noise-induced Extreme Events in Hodgkin-Huxley Neural Networks
Authors: Bruno R. R. Boaretto, Elbert E. N. Macau, Cristina Masoller
Date: 2025-02-26 00:00:00

Extreme events are rare, large-scale deviations from typical system behavior that can occur in nonlinear dynamical systems. In this study, we explore the emergence of extreme events within a network of identical stochastic Hodgkin-Huxley neurons with mean-field coupling. The neurons are exposed to uncorrelated noise, which introduces stochastic electrical fluctuations that influence their spiking activity. Analyzing the variations in the amplitude of the mean field, we observe a smooth transition from small-amplitude, out-of-sync activity to synchronized spiking activity as the coupling parameter increases, while an abrupt transition occurs with increasing noise intensity. However, beyond a certain threshold, the coupling abruptly suppresses the spiking activity of the network. Our analysis reveals that the influence of noise combined with neuronal coupling near the abrupt transitions can trigger cascades of synchronized spiking activity, identified as extreme events. The analysis of the entropy of the mean field allows us to detect the parameter region where these events occur. We characterize the statistics of these events and find that, as the network size increases, the parameter range where they occur decreases significantly. Our findings shed light on the mechanisms driving extreme events in neural networks and how noise and neural coupling shape collective behavior.
Design of Cavity Backed Slotted Antenna using Machine Learning Regression Model
Authors: Vijay Kumar Sutrakar, Anjana PK, Rohit Bisariya, Soumya KK, Gopal Chawan M
Date: 2025-02-26 00:00:00
Tasks: regression

In this paper, a regression-based machine learning model is used for the design of cavity backed slotted antenna. This type of antenna is commonly used in military and aviation communication systems. Initial reflection coefficient data of cavity backed slotted antenna is generated using electromagnetic solver. These reflection coefficient data is then used as input for training regression-based machine learning model. The model is trained to predict the dimensions of cavity backed slotted antenna based on the input reflection coefficient for a wide frequency band varying from 1 GHz to 8 GHz. This approach allows for rapid prediction of optimal antenna configurations, reducing the need for repeated physical testing and manual adjustments, may lead to significant amount of design and development cost saving. The proposed model also demonstrates its versatility in predicting multi frequency resonance across 1 GHz to 8 GHz. Also, the proposed approach demonstrates the potential for leveraging machine learning in advanced antenna design, enhancing efficiency and accuracy in practical applications such as radar, military identification systems and secure communication networks.
Graph Neural Networks embedded into Margules model for vapor-liquid equilibria prediction
Authors: Edgar Ivan Sanchez Medina, Kai Sundmacher
Date: 2025-02-26 00:00:00

Predictive thermodynamic models are crucial for the early stages of product and process design. In this paper the performance of Graph Neural Networks (GNNs) embedded into a relatively simple excess Gibbs energy model, the extended Margules model, for predicting vapor-liquid equilibrium is analyzed. By comparing its performance against the established UNIFAC-Dortmund model it has been shown that GNNs embedded in Margules achieves an overall lower accuracy. However, higher accuracy is observed in the case of various types of binary mixtures. Moreover, since group contribution methods, like UNIFAC, are limited due to feasibility of molecular fragmentation or availability of parameters, the GNN in Margules model offers an alternative for VLE estimation. The findings establish a baseline for the predictive accuracy that simple excess Gibbs energy models combined with GNNs trained solely on infinite dilution data can achieve.
Transported Memory Networks accelerating Computational Fluid Dynamics
Authors: Matthias Schulz, Gwendal Jouan, Daniel Berger, Stefan Gavranovic, Dirk Hartmann
Date: 2025-02-25 00:00:00
Tasks: Computational Efficiency

In recent years, augmentation of differentiable PDE solvers with neural networks has shown promising results, particularly in fluid simulations. However, most approaches rely on convolutional neural networks and custom solvers operating on Cartesian grids with efficient access to cell data. This particular choice poses challenges for industrial-grade solvers that operate on unstructured meshes, where access is restricted to neighboring cells only. In this work, we address this limitation using a novel architecture, named Transported Memory Networks. The architecture draws inspiration from both traditional turbulence models and recurrent neural networks, and it is fully compatible with generic discretizations. Our results show that it is point-wise and statistically comparable to, or improves upon, previous methods in terms of both accuracy and computational efficiency.
Data-Driven and Theory-Guided Pseudo-Spectral Seismic Imaging Using Deep Neural Network Architectures
Authors: Christopher Zerafa
Date: 2025-02-26 00:00:00
Tasks: Seismic Imaging

Full Waveform Inversion (FWI) reconstructs high-resolution subsurface models via multi-variate optimization but faces challenges with solver selection and data availability. Deep Learning (DL) offers a promising alternative, bridging data-driven and physics-based methods. While FWI in DL has been explored in the time domain, the pseudo-spectral approach remains underutilized, despite its success in classical FWI. This thesis integrates pseudo-spectral FWI into DL, formulating both data-driven and theory-guided approaches using Deep Neural Networks (DNNs) and Recurrent Neural Networks (RNNs). These methods were theoretically derived, tested on synthetic and Marmousi datasets, and compared with deterministic and time-domain approaches. Results show that data-driven pseudo-spectral DNNs outperform classical FWI in deeper and over-thrust regions due to their global approximation capability. Theory-guided RNNs yield greater accuracy, with lower error and better fault identification. While DNNs excel in velocity contrast recovery, RNNs provide superior edge definition and stability in shallow and deep sections. Beyond enhancing FWI performance, this research identifies broader applications of DL-based inversion and outlines future directions for these frameworks.
FPGA-Accelerated SpeckleNN with SNL for Real-time X-ray Single-Particle Imaging
Authors: Abhilasha Dave, Cong Wang, James Russell, Ryan Herbst, Jana Thayer
Date: 2025-02-27 00:00:00
Tasks: GPU

We implement a specialized version of our SpeckleNN model for real-time speckle pattern classification in X-ray Single-Particle Imaging (SPI) using the SLAC Neural Network Library (SNL) on an FPGA. This hardware is optimized for inference near detectors in high-throughput X-ray free-electron laser (XFEL) facilities like the Linac Coherent Light Source (LCLS). To fit FPGA constraints, we optimized SpeckleNN, reducing parameters from 5.6M to 64.6K (98.8% reduction) with 90% accuracy. We also compressed the latent space from 128 to 50 dimensions. Deployed on a KCU1500 FPGA, the model used 71% of DSPs, 75% of LUTs, and 48% of FFs, with an average power consumption of 9.4W. The FPGA achieved 45.015us inference latency at 200 MHz. On an NVIDIA A100 GPU, the same inference consumed ~73W and had a 400us latency. Our FPGA version achieved an 8.9x speedup and 7.8x power reduction over the GPU. Key advancements include model specialization and dynamic weight loading through SNL, eliminating time-consuming FPGA re-synthesis for fast, continuous deployment of (re)trained models. These innovations enable real-time adaptive classification and efficient speckle pattern vetoing, making SpeckleNN ideal for XFEL facilities. This implementation accelerates SPI experiments and enhances adaptability to evolving conditions.
Sustainable intensification of small-scale aquaculture systems depends on the local context and characteristics of producers
Authors: Sonja Radosavljevic, Ezio Venturino, Francesca Acotto, Quanli Wang, Jie Su, Alexandros Gasparatos
Date: 2025-02-15 00:00:00

Aquaculture has been the fastest growing food production sector globally due to its potential to improve food security, stimulate economic growth, and reduce poverty. Its rapid development has been linked to sustainability challenges, many of which are still unresolved and poorly understood. Small-scale producers account for an increasing fraction of aquacultural output. At the same time, many of these producers experience poverty, food insecurity, and rely on unimproved production practices. We develop a stylized mathematical model to explore the effects of ecological, social, and economic factors on the dynamics of a small-scale pond aquaculture system. Using analytical and numerical methods, we explore the stability, asymptotic dynamics, and bifurcations of the model. Depending on the characteristics of the system, the model exhibits one of three distinct configurations: monostability with a global poverty trap in a nutrient-dominated or fish-dominated system; bistability with poverty trap and well-being attractors; multistability with poverty trap and two well-being attractors with different characteristics. The model results show that intensification can be sustainable only if it takes into account the local social-ecological context. In addition, the heterogeneity of small-scale aquaculture producers matters, as the effects of intensification can be unevenly distributed among them. Finally, more is not always better because too high nutrient input or productivity can lead to a suboptimal attractor or system collapse.
Viral mutation spread controlled by inter-host network dynamics
Authors: Javier López-Pedrares, M. Elena Vázquez-Cendón, Alberto P. Muñuzuri
Date: 2025-02-04 00:00:00

The increase in the connectivity between hosts in recent times has facilitated the emergence of more aggressive mutant viral strains, making their containment and eradication significantly more challenging compared to the original variants. We focus on the evolution of a new more aggressive mutant strain that appears in the system and competes with a previous version. The role of host interaction network topology in the emergence and spatial diffusion of these highly contagious strains is analyzed, as well as how network-based interventions can help mitigate their spread. To address these issues, we present simplified mathematical models that qualitatively describe the occurrence, propagation, and impact of such mutations within host-interaction networks. By incorporating the topology of the host network into the analysis, a more advanced framework is proposed to curb the growth of mutant strains. Extensive numerical simulations of these models offer insights into the mechanisms driving viral evolution, the dynamics of contagion, and the topological influence of host networks on viral spread and containment strategies.
Efficient and Universal Neural-Network Decoder for Stabilizer-Based Quantum Error Correction
Authors: Gengyuan Hu, Wanli Ouyang, Chao-Yang Lu, Chen Lin, Han-sen Zhong
Date: 2025-02-27 00:00:00
Tasks: Decoder, Graph Neural Network

Quantum error correction is crucial for large-scale quantum computing, but the absence of efficient decoders for new codes like quantum low-density parity-check (QLDPC) codes has hindered progress. Here we introduce a universal decoder based on linear attention sequence modeling and graph neural network that operates directly on any stabilizer code's graph structure. Our numerical experiments demonstrate that this decoder outperforms specialized algorithms in both accuracy and speed across diverse stabilizer codes, including surface codes, color codes, and QLDPC codes. The decoder maintains linear time scaling with syndrome measurements and requires no structural modifications between different codes. For the Bivariate Bicycle code with distance 12, our approach achieves a 39.4% lower logical error rate than previous best decoders while requiring only ~1% of the decoding time. These results provide a practical, universal solution for quantum error correction, eliminating the need for code-specific decoders.
Quantum Annealing Feature Selection on Light-weight Medical Image Datasets
Authors: Merlin A. Nau, Luca A. Nutricati, Bruno Camino, Paul A. Warburton, Andreas K. Maier
Date: 2025-02-26 00:00:00
Tasks: feature selection

We investigate the use of quantum computing algorithms on real quantum hardware to tackle the computationally intensive task of feature selection for light-weight medical image datasets. Feature selection is often formulated as a k of n selection problem, where the complexity grows binomially with increasing k and n. As problem sizes grow, classical approaches struggle to scale efficiently. Quantum computers, particularly quantum annealers, are well-suited for such problems, offering potential advantages in specific formulations. We present a method to solve larger feature selection instances than previously presented on commercial quantum annealers. Our approach combines a linear Ising penalty mechanism with subsampling and thresholding techniques to enhance scalability. The method is tested in a toy problem where feature selection identifies pixel masks used to reconstruct small-scale medical images. The results indicate that quantum annealing-based feature selection is effective for this simplified use case, demonstrating its potential in high-dimensional optimization tasks. However, its applicability to broader, real-world problems remains uncertain, given the current limitations of quantum computing hardware.
Economic Causal Inference Based on DML Framework: Python Implementation of Binary and Continuous Treatment Variables
Authors: Shunxin Yao
Date: 2025-02-27 00:00:00
Tasks: Causal Inference

This study utilizes a simulated dataset to establish Python code for Double Machine Learning (DML) using Anaconda's Jupyter Notebook and the DML software package from GitHub. The research focuses on causal inference experiments for both binary and continuous treatment variables. The findings reveal that the DML model demonstrates relatively stable performance in calculating the Average Treatment Effect (ATE) and its robustness metrics. However, the study also highlights that the computation of Conditional Average Treatment Effect (CATE) remains a significant challenge for future DML modeling, particularly in the context of continuous treatment variables. This underscores the need for further research and development in this area to enhance the model's applicability and accuracy.