pwc-archive/papers-with-abstracts huggingface dataset:
Effective Method for Inverse Ising Problem under Missing Observations in Restricted Boltzmann Machines
Authors: Kaiji Sekimoto, Muneki Yasuda
Date: 2025-04-08 00:00:00

Restricted Boltzmann machines (RBMs) are energy-based models analogous to the Ising model and are widely applied in statistical machine learning. The standard inverse Ising problem with a complete dataset requires computing both data and model expectations and is computationally challenging because model expectations have a combinatorial explosion. Furthermore, in many applications, the available datasets are partially incomplete, making it difficult to compute even data expectations. In this study, we propose a approximation framework for these expectations in the practical inverse Ising problems that integrates mean-field approximation or persistent contrastive divergence to generate refined initial points and spatial Monte Carlo integration to enhance estimator accuracy. We demonstrate that the proposed method effectively and accurately tunes the model parameters in comparison to the conventional method.
Diagrammatic expansion for the mutual-information rate in the realm of limited statistics
Authors: Tobias Kühn, Gabriel Mahuas, Ulisse Ferrari
Date: 2025-04-08 00:00:00

Neurons in sensory systems encode stimulus information into their stochastic spiking response. The Mutual information has been broadly applied to these systems to quantify the neurons' capacity of transmitting such information. Yet, while for discrete stimuli, like flashed images or single tones, its computation is straightforward, for dynamical stimuli it is necessary to compute a (mutual) information rate (MIR), therefore integrating over the multiple temporal correlations which characterize sensory systems. Previous methods are based on extensive sampling of the neuronal response, require large amounts of data, and are therefore prone to biases and inaccuracy. Here, we develop Moba-MIRA (moment-based mutual-information-rate approximation), a computational method to estimate the mutual information rate. To derive Moba-MIRA, we use Feynman diagrams to expand the mutual information in arbitrary orders in the correlations around the corresponding value for the empirical spike count distributions of single binss. As a result, only the empirical estimation of the pairwise correlations between time bins and the single-bin entropies are required, without the need for the whole joint probability distributions. We tested Moba-MIRA on synthetic data generated with generalized linear models, and showed that it requires only a few tens of stimulus repetitions to provide an accurate estimate of the information rate. Finally, we applied it to ex-vivo electrophysiological recordings of rats retina, obtaining rates ranging between 5 to 20 bits per second, consistent with earlier estimates.
The Power of the Pareto Front: Balancing Uncertain Rewards for Adaptive Experimentation in scanning probe microscopy
Authors: Yu Liu, Sergei V. Kalinin
Date: 2025-04-09 00:00:00
Tasks: Bayesian Optimization, Decision Making, scientific discovery

Automated experimentation has the potential to revolutionize scientific discovery, but its effectiveness depends on well-defined optimization targets, which are often uncertain or probabilistic in real-world settings. In this work, we demonstrate the application of Multi-Objective Bayesian Optimization (MOBO) to balance multiple, competing rewards in autonomous experimentation. Using scanning probe microscopy (SPM) imaging, one of the most widely used and foundational SPM modes, we show that MOBO can optimize imaging parameters to enhance measurement quality, reproducibility, and efficiency. A key advantage of this approach is the ability to compute and analyze the Pareto front, which not only guides optimization but also provides physical insights into the trade-offs between different objectives. Additionally, MOBO offers a natural framework for human-in-the-loop decision-making, enabling researchers to fine-tune experimental trade-offs based on domain expertise. By standardizing high-quality, reproducible measurements and integrating human input into AI-driven optimization, this work highlights MOBO as a powerful tool for advancing autonomous scientific discovery.
Data Fusion of Deep Learned Molecular Embeddings for Property Prediction
Authors: Robert J Appleton, Brian C Barnes, Alejandro Strachan
Date: 2025-04-09 00:00:00
Tasks: Multi-Task Learning, Property Prediction, Transfer Learning

Data-driven approaches such as deep learning can result in predictive models for material properties with exceptional accuracy and efficiency. However, in many problems data is sparse, severely limiting their accuracy and applicability. To improve predictions, techniques such as transfer learning and multi-task learning have been used. The performance of multi-task learning models depends on the strength of the underlying correlations between tasks and the completeness of the dataset. We find that standard multi-task models tend to underperform when trained on sparse datasets with weakly correlated properties. To address this gap, we use data fusion techniques to combine the learned molecular embeddings of various single-task models and trained a multi-task model on this combined embedding. We apply this technique to a widely used benchmark dataset of quantum chemistry data for small molecules as well as a newly compiled sparse dataset of experimental data collected from literature and our own quantum chemistry and thermochemical calculations. The results show that the fused, multi-task models outperform standard multi-task models for sparse datasets and can provide enhanced prediction on data-limited properties compared to single-task models.
CRYSIM: Prediction of Symmetric Structures of Large Crystals with GPU-based Ising Machines
Authors: Chen Liang, Diptesh Das, Jiang Guo, Ryo Tamura, Zetian Mao, Koji Tsuda
Date: 2025-04-09 00:00:00
Tasks: Bayesian Optimization, GPU

Solving black-box optimization problems with Ising machines is increasingly common in materials science. However, their application to crystal structure prediction (CSP) is still ineffective due to symmetry agnostic encoding of atomic coordinates. We introduce CRYSIM, an algorithm that encodes the space group, the Wyckoff positions combination, and coordinates of independent atomic sites as separate variables. This encoding reduces the search space substantially by exploiting the symmetry in space groups. When CRYSIM is interfaced to Fixstars Amplify, a GPU-based Ising machine, its prediction performance was competitive with CALYPSO and Bayesian optimization for crystals containing more than 150 atoms in a unit cell. Although it is not realistic to interface CRYSIM to current small-scale quantum devices, it has the potential to become the standard CSP algorithm in the coming quantum age.
Cross-functional transferability in universal machine learning interatomic potentials
Authors: Xu Huang, Bowen Deng, Peichen Zhong, Aaron D. Kaplan, Kristin A. Persson, Gerbrand Ceder
Date: 2025-04-07 00:00:00
Tasks: Benchmarking, Transfer Learning

The rapid development of universal machine learning interatomic potentials (uMLIPs) has demonstrated the possibility for generalizable learning of the universal potential energy surface. In principle, the accuracy of uMLIPs can be further improved by bridging the model from lower-fidelity datasets to high-fidelity ones. In this work, we analyze the challenge of this transfer learning problem within the CHGNet framework. We show that significant energy scale shifts and poor correlations between GGA and r$^2$SCAN pose challenges to cross-functional data transferability in uMLIPs. By benchmarking different transfer learning approaches on the MP-r$^2$SCAN dataset of 0.24 million structures, we demonstrate the importance of elemental energy referencing in the transfer learning of uMLIPs. By comparing the scaling law with and without the pre-training on a low-fidelity dataset, we show that significant data efficiency can still be achieved through transfer learning, even with a target dataset of sub-million structures. We highlight the importance of proper transfer learning and multi-fidelity learning in creating next-generation uMLIPs on high-fidelity data.
Machine learning interatomic potential can infer electrical response
Authors: Peichen Zhong, DongJin Kim, Daniel S. King, Bingqing Cheng
Date: 2025-04-07 00:00:00

Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods but do not by themselves incorporate electrical response. Here, we show that polarization and Born effective charge (BEC) tensors can be directly extracted from long-range MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from energy and force data. Using this approach, we predict the infrared spectra of bulk water under zero or finite external electric fields, ionic conductivities of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric PbTiO$_3$ perovskite. This work thus extends the capability of MLIPs to predict electrical response--without training on charges or polarization or BECs--and enables accurate modeling of electric-field-driven processes in diverse systems at scale.
Machine Learning Reveals Composition Dependent Thermal Stability in Halide Perovskites
Authors: Abigail R. Hering, Mansha Dubey, Elahe Hosseini, Meghna Srivastava, Yu An, Juan-Pablo Correa-Baena, Houman Homayoun, Marina S. Leite
Date: 2025-04-05 00:00:00
Tasks: Data Visualization, Dimensionality Reduction, Feature Importance

Halide perovskites exhibit unpredictable properties in response to environmental stressors, due to several composition-dependent degradation mechanisms. In this work, we apply data visualization and machine learning (ML) techniques to reveal unexpected correlations between composition, temperature, and material properties while using high throughput, in situ environmental photoluminescence (PL) experiments. Correlation heatmaps show the strong influence of Cs content on film degradation, and dimensionality reduction visualization methods uncover clear composition-based data clusters. An extreme gradient boosting algorithm (XGBoost) effectively forecasts PL features for ten perovskite films with both composition-agnostic (>85% accuracy) and composition-dependent (>75% accuracy) model approaches, while elucidating the relative feature importance of composition (up to 99%). This model validates a previously unseen anti-correlation between Cs content and material thermal stability. Our ML-based framework can be expanded to any perovskite family, significantly reducing the analysis time currently employed to identify stable options for photovoltaics.
Structured Extraction of Process Structure Properties Relationships in Materials Science
Authors: Amit K Verma, Zhisong Zhang, Junwon Seo, Robin Kuo, Runbo Jiang, Emma Strubell, Anthony D Rollett
Date: 2025-04-04 00:00:00
Tasks: Uncertainty Quantification, Zero-Shot Learning

With the advent of large language models (LLMs), the vast unstructured text within millions of academic papers is increasingly accessible for materials discovery, although significant challenges remain. While LLMs offer promising few- and zero-shot learning capabilities, particularly valuable in the materials domain where expert annotations are scarce, general-purpose LLMs often fail to address key materials-specific queries without further adaptation. To bridge this gap, fine-tuning LLMs on human-labeled data is essential for effective structured knowledge extraction. In this study, we introduce a novel annotation schema designed to extract generic process-structure-properties relationships from scientific literature. We demonstrate the utility of this approach using a dataset of 128 abstracts, with annotations drawn from two distinct domains: high-temperature materials (Domain I) and uncertainty quantification in simulating materials microstructure (Domain II). Initially, we developed a conditional random field (CRF) model based on MatBERT, a domain-specific BERT variant, and evaluated its performance on Domain I. Subsequently, we compared this model with a fine-tuned LLM (GPT-4o from OpenAI) under identical conditions. Our results indicate that fine-tuning LLMs can significantly improve entity extraction performance over the BERT-CRF baseline on Domain I. However, when additional examples from Domain II were incorporated, the performance of the BERT-CRF model became comparable to that of the GPT-4o model. These findings underscore the potential of our schema for structured knowledge extraction and highlight the complementary strengths of both modeling approaches.
Multi-Variable Batch Bayesian Optimization in Materials Research: Synthetic Data Analysis of Noise Sensitivity and Problem Landscape Effects
Authors: Imon Mia, Armi Tiihonen, Anna Ernst, Anusha Srivastava, Tonio Buonassisi, William Vandenberghe, Julia W. P. Hsu
Date: 2025-04-04 00:00:00
Tasks: Bayesian Optimization, Experimental Design, Sensitivity

Bayesian Optimization (BO) machine learning method is increasingly used to guide experimental optimization tasks in materials science. To emulate the large number of input variables and noise-containing results in experimental materials research, we perform batch BO simulation of six design variables with a range of noise levels. Two test cases relevant for materials science problems are examined: a needle-in-a-haystack case (Ackley function) that may be encountered in, e.g., molecule optimizations, and a smooth landscape with a local optimum in addition to the global optimum (Hartmann function) that may be encountered in, e.g., material composition optimization. We show learning curves, performance metrics, and visualization to effectively track the optimization progression and evaluate how the optimization outcomes are affected by noise, batch-picking method, choice of acquisition function, and exploration hyperparameter values. We find that the effects of noise depend on the problem landscape: noise degrades the optimization results of a needle-in-a-haystack search (Ackley) dramatically more. However, with increasing noise, we observe an increasing probability of landing on the local optimum in Hartmann. Therefore, prior knowledge of the problem domain structure and noise level is essential when designing BO for materials research experiments. Synthetic data studies -- with known ground truth and controlled noise levels -- enable us to isolate and evaluate the impact of different batch BO components, {\it e.g.}, acquisition policy, objective metrics, and hyperparameter values, before transitioning to the inherent uncertainties of real experimental systems. The results and methodology of this study will facilitate a greater utilization of BO in guiding experimental materials research, specifically in settings with a large number of design variables to optimize.
Capturing AI's Attention: Physics of Repetition, Hallucination, Bias and Beyond
Authors: Frank Yingjie Huo, Neil F. Johnson
Date: 2025-04-06 00:00:00
Tasks: Hallucination

We derive a first-principles physics theory of the AI engine at the heart of LLMs' 'magic' (e.g. ChatGPT, Claude): the basic Attention head. The theory allows a quantitative analysis of outstanding AI challenges such as output repetition, hallucination and harmful content, and bias (e.g. from training and fine-tuning). Its predictions are consistent with large-scale LLM outputs. Its 2-body form suggests why LLMs work so well, but hints that a generalized 3-body Attention would make such AI work even better. Its similarity to a spin-bath means that existing Physics expertise could immediately be harnessed to help Society ensure AI is trustworthy and resilient to manipulation.
Variational autoencoders understand knot topology
Authors: Anna Braghetto, Sumanta Kundu, Marco Baiesi, Enzo Orlandini
Date: 2025-04-05 00:00:00
Tasks: Decoder, valid

Supervised machine learning (ML) methods are emerging as valid alternatives to standard mathematical methods for identifying knots in long, collapsed polymers. Here, we introduce a hybrid supervised/unsupervised ML approach for knot classification based on a variational autoencoder enhanced with a knot type classifier (VAEC). The neat organization of knots in its latent representation suggests that the VAEC, only based on an arbitrary labeling of three-dimensional configurations, has grasped complex topological concepts such as chirality, unknotting number, braid index, and the grouping in families such as achiral, torus, and twist knots. The understanding of topological concepts is confirmed by the ability of the VAEC to distinguish the chirality of knots $9_{42}$ and $10_{71}$ not used for its training and with a notoriously undetected chirality to standard tools. The well-organized latent space is also key for generating configurations with the decoder that reliably preserves the topology of the input ones. Our findings demonstrate the ability of a hybrid supervised-generative ML algorithm to capture different topological features of entangled filaments and to exploit this knowledge to faithfully reconstruct or produce new knotted configurations without simulations.
Plastic tensor networks for interpretable generative modeling
Authors: Katsuya O. Akamatsu, Kenji Harada, Tsuyoshi Okubo, Naoki Kawashima
Date: 2025-04-09 00:00:00
Tasks: Tensor Networks

A structural optimization scheme for a single-layer nonnegative adaptive tensor tree (NATT) that models a target probability distribution is proposed. The NATT scheme, by construction, has the advantage that it is interpretable as a probabilistic graphical model. We consider the NATT scheme and a recently proposed Born machine adaptive tensor tree (BMATT) optimization scheme and demonstrate their effectiveness on a variety of generative modeling tasks where the objective is to infer the hidden structure of a provided dataset. Our results show that in terms of minimizing the negative log-likelihood, the single-layer scheme has model performance comparable to the Born machine scheme, though not better. The tasks include deducing the structure of binary bitwise operations, learning the internal structure of random Bayesian networks given only visible sites, and a real-world example related to hierarchical clustering where a cladogram is constructed from mitochondrial DNA sequences. In doing so, we also show the importance of the choice of network topology and the versatility of a least-mutual information criterion in selecting a candidate structure for a tensor tree, as well as discuss aspects of these tensor tree generative models including their information content and interpretability.
PETNet -- Coincident Particle Event Detection using Spiking Neural Networks
Authors: Jan Debus, Charlotte Debus, Günther Dissertori, Markus Götz
Date: 2025-04-09 00:00:00
Tasks: Event Detection

Spiking neural networks (SNN) hold the promise of being a more biologically plausible, low-energy alternative to conventional artificial neural networks. Their time-variant nature makes them particularly suitable for processing time-resolved, sparse binary data. In this paper, we investigate the potential of leveraging SNNs for the detection of photon coincidences in positron emission tomography (PET) data. PET is a medical imaging technique based on injecting a patient with a radioactive tracer and detecting the emitted photons. One central post-processing task for inferring an image of the tracer distribution is the filtering of invalid hits occurring due to e.g. absorption or scattering processes. Our approach, coined PETNet, interprets the detector hits as a binary-valued spike train and learns to identify photon coincidence pairs in a supervised manner. We introduce a dedicated multi-objective loss function and demonstrate the effects of explicitly modeling the detector geometry on simulation data for two use-cases. Our results show that PETNet can outperform the state-of-the-art classical algorithm with a maximal coincidence detection $F_1$ of 95.2%. At the same time, PETNet is able to predict photon coincidences up to 36 times faster than the classical approach, highlighting the great potential of SNNs in particle physics applications.
Learning symmetries in datasets
Authors: Veronica Sanz
Date: 2025-04-07 00:00:00

We investigate how symmetries present in datasets affect the structure of the latent space learned by Variational Autoencoders (VAEs). By training VAEs on data originating from simple mechanical systems and particle collisions, we analyze the organization of the latent space through a relevance measure that identifies the most meaningful latent directions. We show that when symmetries or approximate symmetries are present, the VAE self-organizes its latent space, effectively compressing the data along a reduced number of latent variables. This behavior captures the intrinsic dimensionality determined by the symmetry constraints and reveals hidden relations among the features. Furthermore, we provide a theoretical analysis of a simple toy model, demonstrating how, under idealized conditions, the latent space aligns with the symmetry directions of the data manifold. We illustrate these findings with examples ranging from two-dimensional datasets with $O(2)$ symmetry to realistic datasets from electron-positron and proton-proton collisions. Our results highlight the potential of unsupervised generative models to expose underlying structures in data and offer a novel approach to symmetry discovery without explicit supervision.
Quantum Mechanics and Neural Networks
Authors: Christian Ferko, James Halverson
Date: 2025-04-07 00:00:00

We demonstrate that any Euclidean-time quantum mechanical theory may be represented as a neural network, ensured by the Kosambi-Karhunen-Lo\`eve theorem, mean-square path continuity, and finite two-point functions. The additional constraint of reflection positivity, which is related to unitarity, may be achieved by a number of mechanisms, such as imposing neural network parameter space splitting or the Markov property. Non-differentiability of the networks is related to the appearance of non-trivial commutators. Neural networks acting on Markov processes are no longer Markov, but still reflection positive, which facilitates the definition of deep neural network quantum systems. We illustrate these principles in several examples using numerical implementations, recovering classic quantum mechanical results such as Heisenberg uncertainty, non-trivial commutators, and the spectrum.
On multipolar magnetic anomaly detection: multipolar signal subspaces, an analytical orthonormal basis, multipolar truncature and detection performance
Authors: Clément Chenevas-Paule, Steeve Zozor, Laure-Line Rouve, Olivier J. J. Michel, Olivier Pinaud, Romain Kukla
Date: 2025-04-07 00:00:00
Tasks: Anomaly Detection

In this paper, we consider the magnetic anomaly detection problem which aims to find hidden ferromagnetic masses by estimating the weak perturbation they induce on local Earth's magnetic field. We consider classical detection schemes that rely on signals recorded on a moving sensor, and modeling of the source as a function of unknown parameters. As the usual spherical harmonic decomposition of the anomaly has to be truncated in practice, we study the signal vector subspaces induced by each multipole of the decomposition, proving they are not in direct sum, and discussing the impact it has on the choice of the truncation order. Further, to ease the detection strategy based on generalized likelihood ratio test, we rely on orthogonal polynomials theory to derive an analytical set of orthonormal functions (multipolar orthonormal basis functions) that spans the space of the noise-free measured signal. Finally, based on the subspace structure of the multipole vector spaces, we study the impact of the truncation order on the detection performance, beyond the issue of potential surparametrization, and the behaviour of the information criteria used to choose this order.