pwc-archive/papers-with-abstracts huggingface dataset:
BondMatcher: H-Bond Stability Analysis in Molecular Systems
Authors: Thomas Daniel, Malgorzata Olejniczak, Julien Tierny
Date: 2025-04-04 00:00:00

This application paper investigates the stability of hydrogen bonds (H-bonds), as characterized by the Quantum Theory of Atoms in Molecules (QTAIM). First, we contribute a database of 4544 electron densities associated to four isomers of water hexamers (the so-called Ring, Book, Cage and Prism), generated by distorting their equilibrium geometry under various structural perturbations, modeling the natural dynamic behavior of molecular systems. Second, we present a new stability measure, called bond occurrence rate, associating each bond path present at equilibrium with its rate of occurrence within the input ensemble. We also provide an algorithm, called BondMatcher, for its automatic computation, based on a tailored, geometry-aware partial isomorphism estimation between the extremum graphs of the considered electron densities. Our new stability measure allows for the automatic identification of densities lacking H-bond paths, enabling further visual inspections. Specifically, the topological analysis enabled by our framework corroborates experimental observations and provides refined geometrical criteria for characterizing the disappearance of H-bond paths. Our electron density database and our C++ implementation are available at this address: https://github.com/thom-dani/BondMatcher.
Transfer learning from first-principles calculations to experiments with chemistry-informed domain transformation
Authors: Yuta Yahagi, Kiichi Obuchi, Fumihiko Kosaka, Kota Matsui
Date: 2025-03-20 00:00:00
Tasks: Transfer Learning

Simulation-to-Real (Sim2Real) transfer learning, the machine learning technique that efficiently solves a real-world task by leveraging knowledge from computational data, has received increasing attention in materials science as a promising solution to the scarcity of experimental data. We proposed an efficient transfer learning scheme from first-principles calculations to experiments based on the chemistry-informed domain transformation, that integrates the heterogeneous source and target domains by harnessing the underlying physics and chemistry. The proposed method maps the computational data from the simulation space (source domain) into the space of experimental data (target domain). During this process, these qualitatively different domains are efficiently integrated by a couple of prior knowledge of chemistry, (1) the statistical ensemble, and (2) the relationship between source and target quantities. As a proof-of-concept, we predict the catalyst activity for the reverse water-gas shift reaction by using the abundant first-principles data in addition to the experimental data. Through the demonstration, we confirmed that the transfer learning model exhibits positive transfer in accuracy and data efficiency. In particular, a significantly high accuracy was achieved despite using a few (less than ten) target data in domain transformation, whose accuracy is one order of magnitude smaller than that of a full scratch model trained with over 100 target data. This result indicates that the proposed method leverages the high prediction performance with few target data, which helps to save the number of trials in real laboratories.
JanusDDG: A Thermodynamics-Compliant Model for Sequence-Based Protein Stability via Two-Fronts Multi-Head Attention
Authors: Guido Barducci, Ivan Rossi, Francesco Codicè, Cesare Rollo, Valeria Repetto, Corrado Pancotti, Virginia Iannibelli, Tiziana Sanavia, Piero Fariselli
Date: 2025-04-04 00:00:00

Understanding how residue variations affect protein stability is crucial for designing functional proteins and deciphering the molecular mechanisms underlying disease-related mutations. Recent advances in protein language models (PLMs) have revolutionized computational protein analysis, enabling, among other things, more accurate predictions of mutational effects. In this work, we introduce JanusDDG, a deep learning framework that leverages PLM-derived embeddings and a bidirectional cross-attention transformer architecture to predict $\Delta \Delta G$ of single and multiple-residue mutations while simultaneously being constrained to respect fundamental thermodynamic properties, such as antisymmetry and transitivity. Unlike conventional self-attention, JanusDDG computes queries (Q) and values (V) as the difference between wild-type and mutant embeddings, while keys (K) alternate between the two. This cross-interleaved attention mechanism enables the model to capture mutation-induced perturbations while preserving essential contextual information. Experimental results show that JanusDDG achieves state-of-the-art performance in predicting $\Delta \Delta G$ from sequence alone, matching or exceeding the accuracy of structure-based methods for both single and multiple mutations. Code Availability:https://github.com/compbiomed-unito/JanusDDG
Physics-informed 4D X-ray image reconstruction from ultra-sparse spatiotemporal data
Authors: Zisheng Yao, Yuhe Zhang, Zhe Hu, Robert Klöfkorn, Tobias Ritschel, Pablo Villanueva-Perez
Date: 2025-04-04 00:00:00
Tasks: 4D reconstruction, Image Reconstruction

The unprecedented X-ray flux density provided by modern X-ray sources offers new spatiotemporal possibilities for X-ray imaging of fast dynamic processes. Approaches to exploit such possibilities often result in either i) a limited number of projections or spatial information due to limited scanning speed, as in time-resolved tomography, or ii) a limited number of time points, as in stroboscopic imaging, making the reconstruction problem ill-posed and unlikely to be solved by classical reconstruction approaches. 4D reconstruction from such data requires sample priors, which can be included via deep learning (DL). State-of-the-art 4D reconstruction methods for X-ray imaging combine the power of AI and the physics of X-ray propagation to tackle the challenge of sparse views. However, most approaches do not constrain the physics of the studied process, i.e., a full physical model. Here we present 4D physics-informed optimized neural implicit X-ray imaging (4D-PIONIX), a novel physics-informed 4D X-ray image reconstruction method combining the full physical model and a state-of-the-art DL-based reconstruction method for 4D X-ray imaging from sparse views. We demonstrate and evaluate the potential of our approach by retrieving 4D information from ultra-sparse spatiotemporal acquisitions of simulated binary droplet collisions, a relevant fluid dynamic process. We envision that this work will open new spatiotemporal possibilities for various 4D X-ray imaging modalities, such as time-resolved X-ray tomography and more novel sparse acquisition approaches like X-ray multi-projection imaging, which will pave the way for investigations of various rapid 4D dynamics, such as fluid dynamics and composite testing.
Epicast 2.0: A large-scale, demographically detailed, agent-based model for simulating respiratory pathogen spread in the United States
Authors: Prescott C. Alexander, Thomas J. Harris, Joy Kitson, Joseph V. Tuccillo, Sara Y. Del Valle, Timothy C. Germann
Date: 2025-04-04 00:00:00
Tasks: Decision Making

The recent history of respiratory pathogen epidemics, including those caused by influenza and SARS-CoV-2, has highlighted the urgent need for advanced modeling approaches that can accurately capture heterogeneous disease dynamics and outcomes at the national scale, thereby enhancing the effectiveness of resource allocation and decision-making. In this paper, we describe Epicast 2.0, an agent-based model that utilizes a highly detailed, synthetic population and high-performance computing techniques to simulate respiratory pathogen transmission across the entire United States. This model replicates the contact patterns of over 320 million agents as they engage in daily activities at school, work, and within their communities. Epicast 2.0 supports vaccination and an array of non-pharmaceutical interventions that can be promoted or relaxed via highly granular, user specified policies. We illustrate the model's capabilities using a wide range of outbreak scenarios, highlighting the model's varied dynamics as well as its extensive support for policy exploration. This model provides a robust platform for conducting what if scenario analysis and providing insights into potential strategies for mitigating the impacts of infectious diseases.
Quantum Speedups for Markov Chain Monte Carlo Methods with Application to Optimization
Authors: Guneykan Ozgul, Xiantao Li, Mehrdad Mahdavi, Chunhao Wang
Date: 2025-04-04 00:00:00

We propose quantum algorithms that provide provable speedups for Markov Chain Monte Carlo (MCMC) methods commonly used for sampling from probability distributions of the form $\pi \propto e^{-f}$, where $f$ is a potential function. Our first approach considers Gibbs sampling for finite-sum potentials in the stochastic setting, employing an oracle that provides gradients of individual functions. In the second setting, we consider access only to a stochastic evaluation oracle, allowing simultaneous queries at two points of the potential function under the same stochastic parameter. By introducing novel techniques for stochastic gradient estimation, our algorithms improve the gradient and evaluation complexities of classical samplers, such as Hamiltonian Monte Carlo (HMC) and Langevin Monte Carlo (LMC) in terms of dimension, precision, and other problem-dependent parameters. Furthermore, we achieve quantum speedups in optimization, particularly for minimizing non-smooth and approximately convex functions that commonly appear in empirical risk minimization problems.
Optimizing Quantum Circuits via ZX Diagrams using Reinforcement Learning and Graph Neural Networks
Authors: Alexander Mattick, Maniraman Periyasamy, Christian Ufrecht, Abhishek Y. Dubey, Christopher Mutschler, Axel Plinge, Daniel D. Scherer
Date: 2025-04-04 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning

Quantum computing is currently strongly limited by the impact of noise, in particular introduced by the application of two-qubit gates. For this reason, reducing the number of two-qubit gates is of paramount importance on noisy intermediate-scale quantum hardware. To advance towards more reliable quantum computing, we introduce a framework based on ZX calculus, graph-neural networks and reinforcement learning for quantum circuit optimization. By combining reinforcement learning and tree search, our method addresses the challenge of selecting optimal sequences of ZX calculus rewrite rules. Instead of relying on existing heuristic rules for minimizing circuits, our method trains a novel reinforcement learning policy that directly operates on ZX-graphs, therefore allowing us to search through the space of all possible circuit transformations to find a circuit significantly minimizing the number of CNOT gates. This way we can scale beyond hard-coded rules towards discovering arbitrary optimization rules. We demonstrate our method's competetiveness with state-of-the-art circuit optimizers and generalization capabilities on large sets of diverse random circuits.
Detecting underdetermination in parameterized quantum circuits
Authors: Marie Kempkes, Jakob Spiegelberg, Evert van Nieuwenburg, Vedran Dunjko
Date: 2025-04-04 00:00:00
Tasks: Quantum Machine Learning

A central question in machine learning is how reliable the predictions of a trained model are. Reliability includes the identification of instances for which a model is likely not to be trusted based on an analysis of the learning system itself. Such unreliability for an input may arise from the model family providing a variety of hypotheses consistent with the training data, which can vastly disagree in their predictions on that particular input point. This is called the underdetermination problem, and it is important to develop methods to detect it. With the emergence of quantum machine learning (QML) as a prospective alternative to classical methods for certain learning problems, the question arises to what extent they are subject to underdetermination and whether similar techniques as those developed for classical models can be employed for its detection. In this work, we first provide an overview of concepts from Safe AI and reliability, which in particular received little attention in QML. We then explore the use of a method based on local second-order information for the detection of underdetermination in parameterized quantum circuits through numerical experiments. We further demonstrate that the approach is robust to certain levels of shot noise. Our work contributes to the body of literature on Safe Quantum AI, which is an emerging field of growing importance.
Weak instrumental variables due to nonlinearities in panel data: A Super Learner Control Function estimator
Authors: Monika Avila Marquez
Date: 2025-04-04 00:00:00

A triangular structural panel data model with additive separable individual-specific effects is used to model the causal effect of a covariate on an outcome variable when there are unobservable confounders with some of them time-invariant. In this setup, a linear reduced-form equation might be problematic when the conditional mean of the endogenous covariate and the instrumental variables is nonlinear. The reason is that ignoring the nonlinearity could lead to weak instruments As a solution, we propose a triangular simultaneous equation model for panel data with additive separable individual-specific fixed effects composed of a linear structural equation with a nonlinear reduced form equation. The parameter of interest is the structural parameter of the endogenous variable. The identification of this parameter is obtained under the assumption of available exclusion restrictions and using a control function approach. Estimating the parameter of interest is done using an estimator that we call Super Learner Control Function estimator (SLCFE). The estimation procedure is composed of two main steps and sample splitting. We estimate the control function using a super learner using sample splitting. In the following step, we use the estimated control function to control for endogeneity in the structural equation. Sample splitting is done across the individual dimension. We perform a Monte Carlo simulation to test the performance of the estimators proposed. We conclude that the Super Learner Control Function Estimators significantly outperform Within 2SLS estimators.
A Systematic Review on Women's Participation in Agricultural Work and Nutritional Outcomes
Authors: Pallavi Gupta
Date: 2025-04-04 00:00:00
Tasks: Nutrition

While agriculture is recognised as vital for improving nutrition, the evidence linking women's participation to sustained nutritional gains remains inconclusive. This review synthesizes studies published between 2000 and 2024 to reflect current agricultural practices and nutritional challenges. We examine how agricultural practices and time use affect nutritional outcomes among rural women through pathways such as income generation food preparation and intra-household labour allocation. A structured methodology with clear inclusion and exclusion criteria was used to assess gender-sensitive and nutrition-sensitive interventions. Using narrative synthesis the review categorizes findings around key themes and contextual factors including socio-economic status seasonality and labour intensity. The results show that while increased involvement in agriculture can boost household dietary diversity and income it also raises time burdens that affect food preparation childcare and self-care. Positive outcomes occur when interventions enhance women's decision-making power income access and use of time-saving technologies whereas negative outcomes emerge when excessive workloads compromise energy balance and limit rest. A conceptual framework is presented to map the dual pathways linking agriculture time use and nutrition capturing the roles of labour distribution social norms and resource access. The framework underscores the need to integrate gender equity time efficiency and nutritional objectives into agricultural policies. In conclusion agricultural interventions have potential for nutritional improvement if they are carefully designed to avoid unintended negative impacts on women.
Brewing Discontent: How U.S. Reciprocal Tariffs on Coffee Could Echo the Boston Tea Party
Authors: Muhammad Sukri Bin Ramli
Date: 2025-04-03 00:00:00
Tasks: Clustering, regression

This research employs quantitative techniques interpreted through relevant economic theories to analyze a proposed U.S. "Discounted Reciprocal Tariff" structure. Statistical modeling (linear regression) quantifies the policy's consistent 'discounted reciprocity' pattern, which is interpreted using a Game Theory perspective on strategic interaction. Machine learning (K-Means clustering) identifies distinct country typologies based on tariff exposure and Economic Complexity Index (ECI), linking the policy to Economic Complexity theory. The study's primary application focuses on the major coffee exporting sector, utilizing simulation modeling grounded in principles of demand elasticity and substitution to project potential trade flow impacts. Specifically, for coffee, this simulation demonstrates how the proposed tariff differentials can induce significant substitution effects, projecting a potential shift in U.S. import demand away from high-tariff origins toward lower-tariff competitors. This disruption, stemming from the tariffs impacting exporting countries, is projected to ultimately increase coffee prices for consumers in the United States. Findings throughout are contextualized within Political Economy considerations. Overall, the study demonstrates how integrating regression, clustering, and simulation with economic theory exemplified through the coffee sector analysis provides a robust framework for assessing the potential systemic impacts, including consumer price effects, of strategic trade policies.
Separable choices
Authors: Davide Carpentiere, Alfio Giarlotta, Angelo Petralia, Ester Sudano
Date: 2025-04-03 00:00:00

We introduce the novel setting of joint choices, in which options are vectors with components associated to different dimensions. In this framework, menus are multidimensional, being vectors whose components are one-dimensional menus, that is, nonempty subsets of elements associated to each dimension. We provide a natural notion of separability, requiring that selections from some dimensions are never affected by those performed on the remaining dimensions. Stability of separability across dimensions is throughly investigated. Moreover, we analyze rationalizable joint choices, which are those explained by the maximization of a revealed preference. The interplay between rationalizability e separability of joint choices allows to show that latter extends the classical definition of separability of discrete preference relations, and to assess the consistency of the former across dimensions.
MedSAM2: Segment Anything in 3D Medical Images and Videos
Authors: Jun Ma, Zongxin Yang, Sumin Kim, Bihui Chen, Mohammed Baharoon, Adibvafa Fallahpour, Reza Asakereh, Hongwei Lyu, Bo wang
Date: 2025-04-04 00:00:00
Tasks: Segmentation, Video Segmentation, Video Semantic Segmentation

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.
AdaViT: Adaptive Vision Transformer for Flexible Pretrain and Finetune with Variable 3D Medical Image Modalities
Authors: Badhan Kumar Das, Gengyan Zhao, Han Liu, Thomas J. Re, Dorin Comaniciu, Eli Gibson, Andreas Maier
Date: 2025-04-04 00:00:00
Tasks: Brain Tumor Segmentation, Tumor Segmentation

Pretrain techniques, whether supervised or self-supervised, are widely used in deep learning to enhance model performance. In real-world clinical scenarios, different sets of magnetic resonance (MR) contrasts are often acquired for different subjects/cases, creating challenges for deep learning models assuming consistent input modalities among all the cases and between pretrain and finetune. Existing methods struggle to maintain performance when there is an input modality/contrast set mismatch with the pretrained model, often resulting in degraded accuracy. We propose an adaptive Vision Transformer (AdaViT) framework capable of handling variable set of input modalities for each case. We utilize a dynamic tokenizer to encode different input image modalities to tokens and take advantage of the characteristics of the transformer to build attention mechanism across variable length of tokens. Through extensive experiments, we demonstrate that this architecture effectively transfers supervised pretrained models to new datasets with different input modality/contrast sets, resulting in superior performance on zero-shot testing, few-shot finetuning, and backward transferring in brain infarct and brain tumor segmentation tasks. Additionally, for self-supervised pretrain, the proposed method is able to maximize the pretrain data and facilitate transferring to diverse downstream tasks with variable sets of input modalities.