pwc-archive/papers-with-abstracts huggingface dataset:
A Transformer Model for Predicting Chemical Reaction Products from Generic Templates
Authors: Derin Ozer, Sylvain Lamprier, Thomas Cauchy, Nicolas Gutowski, Benoit Da Mota
Date: 2025-03-04 00:00:00
Tasks: Computational chemistry, Efficient Exploration, valid

The accurate prediction of chemical reaction outcomes is a major challenge in computational chemistry. Current models rely heavily on either highly specific reaction templates or template-free methods, both of which present limitations. To address these limitations, this work proposes the Broad Reaction Set (BRS), a dataset featuring 20 generic reaction templates that allow for the efficient exploration of the chemical space. Additionally, ProPreT5 is introduced, a T5 model tailored to chemistry that achieves a balance between rigid templates and template-free methods. ProPreT5 demonstrates its capability to generate accurate, valid, and realistic reaction products, making it a promising solution that goes beyond the current state-of-the-art on the complex reaction product prediction task.
PIED: Physics-Informed Experimental Design for Inverse Problems
Authors: Apivich Hemachandra, Gregory Kang Ruey Lau, See-Kiong Ng, Bryan Kian Hsiang Low
Date: 2025-03-10 00:00:00
Tasks: Experimental Design, Meta-Learning

In many science and engineering settings, system dynamics are characterized by governing PDEs, and a major challenge is to solve inverse problems (IPs) where unknown PDE parameters are inferred based on observational data gathered under limited budget. Due to the high costs of setting up and running experiments, experimental design (ED) is often done with the help of PDE simulations to optimize for the most informative design parameters to solve such IPs, prior to actual data collection. This process of optimizing design parameters is especially critical when the budget and other practical constraints make it infeasible to adjust the design parameters between trials during the experiments. However, existing experimental design (ED) methods tend to require sequential and frequent design parameter adjustments between trials. Furthermore, they also have significant computational bottlenecks due to the need for complex numerical simulations for PDEs, and do not exploit the advantages provided by physics informed neural networks (PINNs), such as its meshless solutions, differentiability, and amortized training. This work presents PIED, the first ED framework that makes use of PINNs in a fully differentiable architecture to perform continuous optimization of design parameters for IPs for one-shot deployments. PIED overcomes existing methods' computational bottlenecks through parallelized computation and meta-learning of PINN parameter initialization, and proposes novel methods to effectively take into account PINN training dynamics in optimizing the ED parameters. Through experiments based on noisy simulated data and even real world experimental data, we empirically show that given limited observation budget, PIED significantly outperforms existing ED methods in solving IPs, including challenging settings where the inverse parameters are unknown functions rather than just finite-dimensional.
Understanding the role of autoencoders for stiff dynamical systems using information theory
Authors: Vijayamanikandan Vijayarangan, Harshavardhana A. Uranakara, Francisco E. Hernández-Pérez, Hong G. Im
Date: 2025-03-08 00:00:00
Tasks: Decoder

Using the information theory, this study provides insights into how the construction of latent space of autoencoder (AE) using deep neural network (DNN) training finds a smooth low-dimensional manifold in the stiff dynamical system. Our recent study [1] reported that an autoencoder (AE) combined with neural ODE (NODE) as a surrogate reduced order model (ROM) for the integration of stiff chemically reacting systems led to a significant reduction in the temporal stiffness, and the behavior was attributed to the identification of a slow invariant manifold by the nonlinear projection of the AE. The present work offers fundamental understanding of the mechanism by employing concepts from information theory and better mixing. The learning mechanism of both the encoder and decoder are explained by plotting the evolution of mutual information and identifying two different phases. Subsequently, the density distribution is plotted for the physical and latent variables, which shows the transformation of the \emph{rare event} in the physical space to a \emph{highly likely} (more probable) event in the latent space provided by the nonlinear autoencoder. Finally, the nonlinear transformation leading to density redistribution is explained using concepts from information theory and probability.
Learning and discovering multiple solutions using physics-informed neural networks with random initialization and deep ensemble
Authors: Zongren Zou, Zhicheng Wang, George Em Karniadakis
Date: 2025-03-08 00:00:00
Tasks: Uncertainty Quantification

We explore the capability of physics-informed neural networks (PINNs) to discover multiple solutions. Many real-world phenomena governed by nonlinear differential equations (DEs), such as fluid flow, exhibit multiple solutions under the same conditions, yet capturing this solution multiplicity remains a significant challenge. A key difficulty is giving appropriate initial conditions or initial guesses, to which the widely used time-marching schemes and Newton's iteration method are very sensitive in finding solutions for complex computational problems. While machine learning models, particularly PINNs, have shown promise in solving DEs, their ability to capture multiple solutions remains underexplored. In this work, we propose a simple and practical approach using PINNs to learn and discover multiple solutions. We first reveal that PINNs, when combined with random initialization and deep ensemble method -- originally developed for uncertainty quantification -- can effectively uncover multiple solutions to nonlinear ordinary and partial differential equations (ODEs/PDEs). Our approach highlights the critical role of initialization in shaping solution diversity, addressing an often-overlooked aspect of machine learning for scientific computing. Furthermore, we propose utilizing PINN-generated solutions as initial conditions or initial guesses for conventional numerical solvers to enhance accuracy and efficiency in capturing multiple solutions. Extensive numerical experiments, including the Allen-Cahn equation and cavity flow, where our approach successfully identifies both stable and unstable solutions, validate the effectiveness of our method. These findings establish a general and efficient framework for addressing solution multiplicity in nonlinear differential equations.
SODAs: Sparse Optimization for the Discovery of Differential and Algebraic Equations
Authors: Manu Jayadharan, Christina Catlett, Arthur N. Montanari, Niall M. Mangan
Date: 2025-03-08 00:00:00
Tasks: Model Discovery

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by timescale separation, conservation laws, and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods to DAE systems with unknown constraints and time scales. We introduce Sparse Optimization for Differential-Algebraic Systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems and has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves numerical stability when handling high correlations between library terms -- caused by near-perfect algebraic relationships -- by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical, and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.
Multiscale Analysis of Woven Composites Using Hierarchical Physically Recurrent Neural Networks
Authors: Ehsan Ghane, Marina A. Maia, Iuri B. C. M. Rocha, Martin Fagerström, Mohsen Mirakhalaf
Date: 2025-03-06 00:00:00

Multiscale homogenization of woven composites requires detailed micromechanical evaluations, leading to high computational costs. Data-driven surrogate models based on neural networks address this challenge but often suffer from big data requirements, limited interpretability, and poor extrapolation capabilities. This study introduces a Hierarchical Physically Recurrent Neural Network (HPRNN) employing two levels of surrogate modeling. First, Physically Recurrent Neural Networks (PRNNs) are trained to capture the nonlinear elasto-plastic behavior of warp and weft yarns using micromechanical data. In a second scale transition, a physics-encoded meso-to-macroscale model integrates these yarn surrogates with the matrix constitutive model, embedding physical properties directly into the latent space. Adopting HPRNNs for both scale transitions can avoid nonphysical behavior often observed in predictions from pure data-driven recurrent neural networks and transformer networks. This results in better generalization under complex cyclic loading conditions. The framework offers a computationally efficient and explainable solution for multiscale modeling of woven composites.
Machine Learning-based Regional Cooling Demand Prediction with Optimised Dataset Partitioning
Authors: Meng Zhang, Zhihui Li, Zhibin Yu
Date: 2025-03-04 00:00:00
Tasks: Bayesian Optimisation, energy management

In the context of global warming, even relatively cooler countries like the UK are experiencing a rise in cooling demand, particularly in southern regions such as London. This growing demand, especially during the summer months, presents significant challenges for energy management systems. Accurately predicting cooling demand in urban domestic buildings is essential for maintaining energy efficiency. This study introduces a generalised framework for developing high-resolution Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU) networks using physical model-based summer cooling demand data. To maximise the predictive capability and generalisation ability of the models under limited data scenarios, four distinct data partitioning strategies were implemented, including the extrapolation, month-based interpolation, global interpolation, and day-based interpolation. Bayesian Optimisation (BO) was then applied to fine-tune the hyper-parameters, substantially improving the framework predictive accuracy. Results show that the day-based interpolation GRU model demonstrated the best performance due to its ability to retain both the data randomness and the time sequence continuity characteristics. This optimal model achieves a Root Mean Squared Error (RMSE) of 2.22%, a Mean Absolute Error (MAE) of 0.87%, and a coefficient of determination (R square) of 0.9386 on the test set. The generalisation ability of this framework was further evaluated by forecasting.
A Materials Foundation Model via Hybrid Invariant-Equivariant Architectures
Authors: Keqiang Yan, Montgomery Bohde, Andrii Kryvenko, Ziyu Xiang, Kaiji Zhao, Siya Zhu, Saagar Kolachina, Doğuhan Sarıtürk, Jianwen Xie, Raymundo Arroyave, Xiaoning Qian, Xiaofeng Qian, Shuiwang Ji
Date: 2025-02-25 00:00:00
Tasks: Computational Efficiency

Machine learning interatomic potentials (MLIPs) can predict energy, force, and stress of materials and enable a wide range of downstream discovery tasks. A key design choice in MLIPs involves the trade-off between invariant and equivariant architectures. Invariant models offer computational efficiency but may not perform as well, especially when predicting high-order outputs. In contrast, equivariant models can capture high-order symmetries, but are computationally expensive. In this work, we propose HIENet, a hybrid invariant-equivariant materials interatomic potential model that integrates both invariant and equivariant message passing layers, while provably satisfying key physical constraints. HIENet achieves state-of-the-art performance with considerable computational speedups over prior models. Experimental results on both common benchmarks and downstream materials discovery tasks demonstrate the efficiency and effectiveness of HIENet.
Learning conformational ensembles of proteins based on backbone geometry
Authors: Nicolas Wolf, Leif Seute, Vsevolod Viliuga, Simon Wagner, Jan Stühmer, Frauke Gräter
Date: 2025-02-19 00:00:00
Tasks: GPU

Deep generative models have recently been proposed for sampling protein conformations from the Boltzmann distribution, as an alternative to often prohibitively expensive Molecular Dynamics simulations. However, current state-of-the-art approaches rely on fine-tuning pre-trained folding models and evolutionary sequence information, limiting their applicability and efficiency, and introducing potential biases. In this work, we propose a flow matching model for sampling protein conformations based solely on backbone geometry. We introduce a geometric encoding of the backbone equilibrium structure as input and propose to condition not only the flow but also the prior distribution on the respective equilibrium structure, eliminating the need for evolutionary information. The resulting model is orders of magnitudes faster than current state-of-the-art approaches at comparable accuracy and can be trained from scratch in a few GPU days. In our experiments, we demonstrate that the proposed model achieves competitive performance with reduced inference time, across not only an established benchmark of naturally occurring proteins but also de novo proteins, for which evolutionary information is scarce.
Seismic inversion using hybrid quantum neural networks
Authors: Divakar Vashisth, Rohan Sharma, Tapan Mukerji, Mrinal K. Sen
Date: 2025-03-06 00:00:00
Tasks: Decoder, Quantum Machine Learning, Seismic Inversion

Quantum computing leverages qubits, exploiting superposition and entanglement to solve problems intractable for classical computers, offering significant computational advantages. Quantum machine learning (QML), which integrates quantum computing with machine learning, holds immense potential across various fields but remains largely unexplored in geosciences. However, its progress is hindered by the limitations of current NISQ hardware. To address these challenges, hybrid quantum neural networks (HQNNs) have emerged, combining quantum layers within classical neural networks to leverage the strengths of both paradigms. To the best of our knowledge, this study presents the first application of QML to subsurface imaging through the development of hybrid quantum physics-informed neural networks (HQ-PINNs) for seismic inversion. We apply the HQ-PINN framework to invert pre-stack and post-stack seismic datasets, estimating P- and S-impedances. The proposed HQ-PINN architecture follows an encoder-decoder structure, where the encoder (HQNN), processes seismic data to estimate elastic parameters, while the decoder utilizes these parameters to generate the corresponding seismic data based on geophysical relationships. The HQ-PINN model is trained by minimizing the misfit between the input and predicted seismic data generated by the decoder. We systematically evaluate various quantum layer configurations, differentiation methods, and quantum device simulators on the inversion performance, and demonstrate real-world applicability through the individual and simultaneous inversion cases of the Sleipner dataset. The HQ-PINN framework consistently and efficiently estimated accurate subsurface impedances across the synthetic and field case studies, establishing the feasibility of leveraging QML for seismic inversion, thereby paving the way for broader applications of quantum computing in geosciences.
Semi-Supervised Learning for Dose Prediction in Targeted Radionuclide: A Synthetic Data Study
Authors: Jing Zhang, Alexandre Bousse, Laetitia Imbert, Song Xue, Kuangyu Shi, Julien Bert
Date: 2025-03-07 00:00:00
Tasks: Pseudo Label

Targeted Radionuclide Therapy (TRT) is a modern strategy in radiation oncology that aims to administer a potent radiation dose specifically to cancer cells using cancer-targeting radiopharmaceuticals. Accurate radiation dose estimation tailored to individual patients is crucial. Deep learning, particularly with pre-therapy imaging, holds promise for personalizing TRT doses. However, current methods require large time series of SPECT imaging, which is hardly achievable in routine clinical practice, and thus raises issues of data availability. Our objective is to develop a semi-supervised learning (SSL) solution to personalize dosimetry using pre-therapy images. The aim is to develop an approach that achieves accurate results when PET/CT images are available, but are associated with only a few post-therapy dosimetry data provided by SPECT images. In this work, we introduce an SSL method using a pseudo-label generation approach for regression tasks inspired by the FixMatch framework. The feasibility of the proposed solution was preliminarily evaluated through an in-silico study using synthetic data and Monte Carlo simulation. Experimental results for organ dose prediction yielded promising outcomes, showing that the use of pseudo-labeled data provides better accuracy compared to using only labeled data.
Fusion of Various Optimization Based Feature Smoothing Methods for Wearable and Non-invasive Blood Glucose Estimation
Authors: Yiting Wei, Bingo Wing-Kuen Ling, Danni Chen, Yuheng Dai, Qing Liu
Date: 2025-03-06 00:00:00

Recently, the wearable and non-invasive blood glucose estimation approach has been proposed. However, due to the unreliability of the acquisition device, the presence of the noise and the variations of the acquisition environments, the obtained features and the reference blood glucose values are highly unreliable. To address this issue, this paper proposes a polynomial fitting approach to smooth the obtained features or the reference blood glucose values. First, the blood glucose values are estimated based on the individual optimization approaches. Second, the absolute difference values between the estimated blood glucose values and the actual blood glucose values based on each optimization approach are computed. Third, these absolute difference values for each optimization approach are sorted in the ascending order. Fourth, for each sorted blood glucose value, the optimization method corresponding to the minimum absolute difference value is selected. Fifth, the accumulate probability of each selected optimization method is computed. If the accumulate probability of any selected optimization method at a point is greater than a threshold value, then the accumulate probabilities of these three selected optimization methods at that point are reset to zero. A range of the sorted blood glucose values are defined as that with the corresponding boundaries points being the previous reset point and this reset point. Hence, after performing the above procedures for all the sorted reference blood glucose values in the validation set, the regions of the sorted reference blood glucose values and the corresponding optimization methods in these regions are determined. The computer numerical simulation results show that our proposed method yields the mean absolute relative deviation (MARD) at 0.0930 and the percentage of the test data falling in the zone A of the Clarke error grid at 94.1176%.
An artificially intelligent magnetic resonance spectroscopy quantification method: Comparison between QNet and LCModel on the cloud computing platform CloudBrain-MRS
Authors: Meijin Lin, Lin Guo, Dicheng Chen, Jianshu Chen, Zhangren Tu, Xu Huang, Jianhua Wang, Ji Qi, Yuan Long, Zhiguo Huang, Di Guo, Xiaobo Qu, Haiwei Han
Date: 2025-03-06 00:00:00
Tasks: Cloud Computing

Objctives: This work aimed to statistically compare the metabolite quantification of human brain magnetic resonance spectroscopy (MRS) between the deep learning method QNet and the classical method LCModel through an easy-to-use intelligent cloud computing platform CloudBrain-MRS. Materials and Methods: In this retrospective study, two 3 T MRI scanners Philips Ingenia and Achieva collected 61 and 46 in vivo 1H magnetic resonance (MR) spectra of healthy participants, respectively, from the brain region of pregenual anterior cingulate cortex from September to October 2021. The analyses of Bland-Altman, Pearson correlation and reasonability were performed to assess the degree of agreement, linear correlation and reasonability between the two quantification methods. Results: Fifteen healthy volunteers (12 females and 3 males, age range: 21-35 years, mean age/standard deviation = 27.4/3.9 years) were recruited. The analyses of Bland-Altman, Pearson correlation and reasonability showed high to good consistency and very strong to moderate correlation between the two methods for quantification of total N-acetylaspartate (tNAA), total choline (tCho), and inositol (Ins) (relative half interval of limits of agreement = 3.04%, 9.3%, and 18.5%, respectively; Pearson correlation coefficient r = 0.775, 0.927, and 0.469, respectively). In addition, quantification results of QNet are more likely to be closer to the previous reported average values than those of LCModel. Conclusion: There were high or good degrees of consistency between the quantification results of QNet and LCModel for tNAA, tCho, and Ins, and QNet generally has more reasonable quantification than LCModel.
Reproducibility Assessment of Magnetic Resonance Spectroscopy of Pregenual Anterior Cingulate Cortex across Sessions and Vendors via the Cloud Computing Platform CloudBrain-MRS
Authors: Runhan Chen, Meijin Lin, Jianshu Chen, Liangjie Lin, Jiazheng Wang, XiaoQing Li, Jianhua Wang, Xu Huang, Ling Qian, Shaoxing Liu, Yuan Long, Di Guo, Xiaobo Qu, Haiwei Han
Date: 2025-03-06 00:00:00
Tasks: Cloud Computing, Diagnostic

Given the need to elucidate the mechanisms underlying illnesses and their treatment, as well as the lack of harmonization of acquisition and post-processing protocols among different magnetic resonance system vendors, this work is to determine if metabolite concentrations obtained from different sessions, machine models and even different vendors of 3 T scanners can be highly reproducible and be pooled for diagnostic analysis, which is very valuable for the research of rare diseases. Participants underwent magnetic resonance imaging (MRI) scanning once on two separate days within one week (one session per day, each session including two proton magnetic resonance spectroscopy (1H-MRS) scans with no more than a 5-minute interval between scans (no off-bed activity)) on each machine. were analyzed for reliability of within- and between- sessions using the coefficient of variation (CV) and intraclass correlation coefficient (ICC), and for reproducibility of across the machines using correlation coefficient. As for within- and between- session, all CV values for a group of all the first or second scans of a session, or for a session were almost below 20%, and most of the ICCs for metabolites range from moderate (0.4-0.59) to excellent (0.75-1), indicating high data reliability. When it comes to the reproducibility across the three scanners, all Pearson correlation coefficients across the three machines approached 1 with most around 0.9, and majority demonstrated statistical significance (P<0.01). Additionally, the intra-vendor reproducibility was greater than the inter-vendor ones.