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At least 1,063 records · Page 59

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2

Motion-activated wildlife cameras (or “camera traps”) are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the “species model,” and one that determines if an image is empty or if it contains an animal, the “empty-animal model.” Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%–91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%–94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

59 BASIC BIOLOGICAL SCIENCES↗

Large-Scale Classification of Urban Structural Units From Remote Sensing Imagery

Remote sensing in combination with deep learning has become instrumental for efficiently and accurately classifying land-use and land-cover across large geographic areas. These technologies have also been successful in characterizing urban environments in terms of their structural units, structure types, or morphological regions. In these approaches, an urban area is partitioned into regions that exhibit homogeneous physical characteristics. However, existing approaches are typically limited to a single city, use inconsistent typologies, and lack scalability and generalization capacity. In this article, we propose an urban structural units categorization scheme and demonstrate its utility by applying it to 13 cities. Inspired by the lack of scalability and generalization capacity in urban structural units mapping, we extend the reach of deep learning and conduct a set of classification experiments in all 13 cities. These experiments offer insights into the strengths and limitations of deep neural networks for classifying urban structural units over diverse geographic regions and on heterogeneous collections of satellite imagery. The efficacy of the proposed deep learning approach is compared to a baseline method of multiscale image features and support vector machines. Our validation on five cities shows that better performance is achieved with deep neural networks. Additionally, we evaluate the impact of input size, model depth, and spatial pyramid pooling to assess the generalization capacity of deep neural networks.

47 OTHER INSTRUMENTATION↗

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Abstract Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited. Here, we report ECNet (evolutionary context-integrated neural network), a deep-learning algorithm that exploits evolutionary contexts to predict functional fitness for protein engineering. This algorithm integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe. As such, it enables accurate mapping from sequence to function and provides generalization from low-order mutants to higher-order mutants. We show that ECNet predicts the sequence-function relationship more accurately as compared to existing machine learning algorithms by using ~50 deep mutational scanning and random mutagenesis datasets. Moreover, we used ECNet to guide the engineering of TEM-1 β-lactamase and identified variants with improved ampicillin resistance with high success rates.

59 BASIC BIOLOGICAL SCIENCES↗

Extracting low energy signals from raw LArTPC waveforms using deep learning techniques — A proof of concept

Here, we investigate the feasibility of using deep learning techniques, in the form of a one-dimensional convolutional neural network (1D-CNN), for the extraction of signals from the raw waveforms produced by the individual channels of liquid argon time projection chamber (LArTPC) detectors. A minimal generic LArTPC detector model is developed to generate realistic noise and signal waveforms used to train and test the 1D-CNN, and evaluate its performance on low-level signals. We demonstrate that our approach overcomes the inherent shortcomings of traditional cut-based methods by extending sensitivity to signals with ADC values below their imposed thresholds. This approach exhibits great promise in enhancing the capabilities of future generation neutrino experiments like DUNE to carry out their low-energy neutrino physics programs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Evaluation of Machine Learning and Deep Learning Algorithms for Fire Prediction in Southeast Asia

Vegetation fires are prevalent in South/Southeast Asian countries, making fire prediction crucial due to their potential environmental, economic, and social impacts. Accurate predictions of fires facilitate timely interventions, helping to mitigate uncontrolled fires that can lead to biodiversity loss and air quality issues. In this study, we utilize VIIRS satellite-derived fire data alongside six machine learning and deep learning models—Simple Persistence, Multi-Layer Perceptron (MLP), Convolutional Neural Network (CNN), Long Short-Term Memory (LSTM), CNN-LSTM, and ConvLSTM—to determine the most effective fire prediction model, using Root Mean Square Error (RMSE) as the metric. Our results indicate that the CNN model is the most reliable in regions with spatial dependencies, such as Brunei, Indonesia, Malaysia, the Philippines, Timor-Leste, and Thailand. Conversely, the ConvLSTM model excels in countries with complex spatiotemporal dynamics like Laos, Myanmar, and Vietnam. The CNN-LSTM hybrid model also performed well in Cambodia, suggesting a need for a balanced approach in areas requiring both spatial and temporal feature extraction. Furthermore, simpler models like Persistence and MLP showed limitations in capturing dynamic patterns and temporal dependencies. Our findings highlight the importance of evaluating models before implementing any decision support systems (DSS) in fire management. By tailoring models to specific regional fire data, we can enhance prediction accuracy and responsiveness, ultimately improving fire risk management in Southeast Asia and beyond.

Deep learning↗

Constraining chaos: Enforcing dynamical invariants in the training of reservoir computers

Drawing on ergodic theory, we introduce a novel training method for machine learning based forecasting methods for chaotic dynamical systems. The training enforces dynamical invariants—such as the Lyapunov exponent spectrum and the fractal dimension—in the systems of interest, enabling longer and more stable forecasts when operating with limited data. The technique is demonstrated in detail using reservoir computing, a specific kind of recurrent neural network. Finally, results are given for the Lorenz 1996 chaotic dynamical system and a spectral quasi-geostrophic model of the atmosphere, both typical test cases for numerical weather prediction.

97 MATHEMATICS AND COMPUTING↗

Application of a Physics-Informed Convolutional Neural Network for Monitoring the Temperature Fields in High-Temperature Gas Reactors

Here, this work presents current advances in applying a physics-informed convolutional neural network (CNN) to evaluate temperature distributions in advanced reactors. Our goal is to demonstrate that the CNN can reconstruct temperature fields within the solid region of a prismatic fuel assembly in a high-temperature gas reactor (HTGR) with sensor data available in only a few cooling channels. Before that, we showcase the superior performance of the physics-informed CNN in comparison to a purely data-driven multilayer perceptron (MLP), considering a canonical heated channel setup. This analysis shows the advantages of our approach and justifies its choice. The datasets employed here are obtained upon numerical simulations performed with codes under the Nuclear Energy Advanced Modeling and Simulation program. This work is important, as industry experience indicates that the assembly material in HTGR concepts is prone to large thermal-mechanical loads nearing operational limits. This makes it crucial to characterize peak temperatures and their distributions near hot spots. Modern thermocouples are unreliable in these types of harsh environments because of the high neutron fluxes and elevated temperatures involved. The CNN-based field reconstruction represents an attractive solution, enabling sensor arrays in less aggressive locations and augmenting indirect predictions for less accessible regions. The results show that the CNN reduces prediction errors by orders of magnitude in comparison to the MLP, considering the simple yet well-representative heated channel case. In the case of the HTGR fuel assembly, the CNN can successfully reconstruct temperature fields over various cooling regimes. Furthermore, we also explore the algorithm’s ability to detect abnormalities. Interestingly, the CNN proves it has the capacity to detect blockage in one of the noninstrumented cooling channels.

Machine learning↗

Ising-CF: A Pathbreaking Collaborative Filtering Method Through Efficient Ising Machine Learning

Due to Ising models’ strong expressivity and Ising machines’ unique computational power, it is highly desired if Ising-based learning can be used in real-world applications. Unfortunately, the challenges in learning Ising models and gaps between the practical accuracy of Ising machines and the theoretical accuracy of Ising models impede the realization of Ising machines’ potential. Hence, we propose an Ising Machine Learning framework, Ising-CF, for collaborative filtering, a widely-used recommendation method. Specifically, Ising-CF uses Linear Neural Networks with Besag’s pseudo-likelihood and voltage polarization for fast, accurate Ising model learning and an Ising-specific logarithmic quantization for ns-level Ising machine inference with near-theoretical accuracy, 7.3% over SOTA.

Liu, Zhuo↗

Application of Quantum Machine Learning to High Energy Physics Analysis at LHC using IBM Quantum Computer Simulators and IBM Quantum Computer Hardware

Our group pioneers the use of Quantum Machine Learning (QML) on High Energy Physics analysis at LHC. We have successfully employed several QML classification algorithms in the ttH (Higgs production in association with a top quark pair) and Higgs to two muons (Higgs coupling to second generation fermions), two recent LHC flagship physics analysis, on gate-model quantum computer simulators and hardware. The simulation studies have been performed with the IBM Quantum Framework, Google Tensorflow Quantum Framework, and Amazon Braket Framework, and we have achieved good classification performance that is similar to the performances of the classical machine learning methods currently used in LHC physics analyses, classical SVM, classical BDT, and classical deep neural network for example. We have also performed our studies using IBM superconducting quantum computer hardware and the performance is promising and is approaching the performance from IBM quantum simulators. Moreover, we extend our studies to other QML areas such as quantum anomaly detection and quantum generative adversarial, and some preliminary results have been obtained. Also, we have overcome the challenges of intensive computing resources in the cases of large qubits (25 qubits or more) and large numbers of events using NVIDIA cuQuantum with NERSC Perlmutter HPC. Our studies give an example that Quantum Machine Learning performs as well as its classical counterpart for realistic High Energy Physics analysis datasets. Furthermore, our result on noisy quantum hardware provides important validation for the result on noiseless quantum simulators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A deep potential model with long-range electrostatic interactions

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make molecular simulations with the accuracy of quantum mechanical density functional theory possible at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation, we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei + core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the DP long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples: the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Machine-learning based prediction of injection rate and solenoid voltage characteristics in GDI injectors

We report that current state-of-the-art gasoline direct-injection (GDI) engines use multiple injections as one of the key technologies to improve exhaust emissions and fuel efficiency. For this technology to be successful, secured adequate control of fuel quantity for each injection is mandatory. However, nonlinearity and variations in the injection quantity can deteriorate the accuracy of fuel control, especially with small fuel injections. Therefore, it is necessary to understand the complex injection behavior and to develop a predictive model to be utilized in the development process. This study presents a methodology for rate of injection (ROI) and solenoid voltage modeling using artificial neural networks (ANNs) constructed from a set of Zeuch-style hydraulic experimental measurements conducted over a wide range of conditions. A quantitative comparison between the ANN model and the experimental data shows that the model is capable of predicting not only general features of the ROI trend, but also transient and non-linear behaviors at particular conditions. In addition, the end of injection (EOI) could be detected precisely with a virtually generated solenoid voltage signal and the signal processing method, which applies to an actual engine control unit. A correlation between the detected EOI timings calculated from the modeled signal and the measurement results showed a high coefficient of determination.

42 ENGINEERING↗

PPINN: Parareal physics-informed neural network for time-dependent PDEs

Physics-informed neural networks (PINNs) encode physical conservation laws and prior physical knowledge into the neural networks, ensuring the correct physics is represented accurately while alleviating the need for supervised learning to a great degree. While effective for relatively short-term time integration, when long time integration of the time-dependent PDEs is sought, the time–space domain may become arbitrarily large and hence training of the neural network may become prohibitively expensive. To this end, we develop a parareal physics-informed neural network (PPINN), hence decomposing a long-time problem into many independent short-time problems supervised by an inexpensive/fast coarse-grained (CG) solver. In particular, the serial CG solver is designed to provide approximate predictions of the solution at discrete times, while initiate many fine PINNs simultaneously to correct the solution iteratively. There is a two-fold benefit from training PINNs with small-data sets rather than working on a large-data set directly, i.e., training of individual PINNs with small-data is much faster, while training the fine PINNs can be readily parallelized. Consequently, compared to the original PINN approach, the proposed PPINN approach may achieve a significant speed-up for long-time integration of PDEs, assuming that the CG solver is fast and can provide reasonable predictions of the solution, hence aiding the PPINN solution to converge in just a few iterations. To investigate the PPINN performance on solving time-dependent PDEs, we first apply the PPINN to solve the Burgers equation, and subsequently we apply the PPINN to solve a two-dimensional nonlinear diffusion–reaction equation. Furthermore, our results demonstrate that PPINNs converge in a few iterations with significant speed-ups proportional to the number of time-subdomains employed.

42 ENGINEERING↗

Benchmarking universal machine learning interatomic potentials for rapid analysis of inelastic neutron scattering data

The accurate calculation of phonons and vibrational spectra remains a significant challenge, requiring highly precise evaluations of interatomic forces. Traditional methods based on the quantum description of the electronic structure, while widely used, are computationally expensive and demand substantial expertise. Emerging universal machine learning interatomic potentials (uMLIPs) offer a transformative alternative by employing pre-trained neural network surrogates to predict interatomic forces directly from atomic coordinates. This approach dramatically reduces computation time and minimizes the need for technical knowledge. In this paper, we produce a phonon database comprising nearly 5000 inorganic crystals to benchmark the performance of several leading uMLIPs. We further assess these models in real-world applications by using them to analyze experimental inelastic neutron scattering data collected on a variety of materials. Through detailed comparisons, we identify the strengths and limitations of these uMLIPs, providing insights into their accuracy and suitability for fast calculations of phonons and related properties, as well as the potential for real-time interpretation of neutron scattering spectra. Our findings highlight how the rapid advancement of AI in science is revolutionizing experimental research and data analysis.

inelastic neutron scattering↗

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗

Dynamic machine learning-based optimization algorithm to improve boiler efficiency

With decreasing computational costs, improvement in algorithms, and the aggregation of large industrial and commercial datasets, machine learning is becoming a ubiquitous tool for process and business innovations. Machine learning is still lacking applications in the field of dynamic optimization for real-time control. This work presents a novel framework for performing constrained dynamic optimization using a recurrent neural network model combined with a metaheuristic optimizer. The framework is designed to augment an existing control system and is purely data-driven, like most industrial Model Predictive Control applications. Several recurrent neural network models are compared as well as several metaheuristic optimizers. Hyperparameters and optimizer parameters are tuned with parameter sweeps, and the resulting values are reported. Further, the best parameters for each optimizer and model combination are demonstrated in closed-loop control of a dynamic simulation, and several recommendations are made for generalizing this framework to other systems. Up to 0.953% improvement is realized over the non-optimized case for a simulated coal-fired boiler. While this is not a large improvement in percentage, the total economic impact is $991,000 per year, and this study builds a foundation for future machine learning with dynamic optimization.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Development of a plug-and-play anti-noise module for fault diagnosis of rotating machines in nuclear power plants

The health of rotating machines is crucial to the stable operation and safety of nuclear power plants. However, research on machine learning-based fault diagnosis of rotating machines in the nuclear industry is still in its infancy. The signal noise generated in the plant may negatively affect the effectiveness of the analysis. In this paper, a plug-and-play anti-noise machine learning module is proposed to fill the knowledge and capability gap. The modules are loaded into a convolutional neural network called deep residual network (ResNet) to obtain a new model with noise reduction capability. The basic idea is that the module is able to identify noise features and include them in the subsequent analysis, effectively filtering noise at the feature level of the network. Nine variants of the new model are compared with the original ResNet as well as four classical machine learning models to test the effectiveness of the module and to examine the impact of the module's loading modes on the performance of the new model. Finally, this research helps facilitate the application of machine learning in the plant noise environment.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Deep Learning for In-Situ Layer Quality Monitoring during Laser-Based Directed Energy Deposition (LB-DED) Additive Manufacturing Process

Defects are a leading issue for the rejection of parts manufactured through the Directed Energy Deposition (DED) Additive Manufacturing (AM) process. In an attempt to illuminate and advance in situ quality monitoring and control of workpieces, we present an innovative data-driven method that synchronously collects sensing data and AM process parameters with a low sampling rate during the DED process. The proposed data-driven technique determines the important influences that individual printing parameters and sensing features have on prediction at the inter-layer qualification to perform feature selection. Three Machine Learning (ML) algorithms including Random Forest (RF), Support Vector Machine (SVM), and Convolutional Neural Network (CNN) are used. During post-production, a threshold is applied to detect low-density occurrences such as porosity sizes and quantities from CT scans that render individual layers acceptable or unacceptable. This information is fed to the ML models for training. Training/testing are completed offline on samples deemed “high-quality” and “low-quality”, utilizing only features recorded from the build process. CNN results show that the classification of acceptable/unacceptable layers can reach between 90% accuracy while training/testing on a “high-quality” sample and dip to 65% accuracy when trained/tested on “low-quality”/“high-quality” (respectively), indicating over-fitting but showing CNN as a promising inter-layer classifier.

36 MATERIALS SCIENCE↗

BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task

ABSTRACT Motivation Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model’s performance. Results We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets—BioASQ-7b, BioASQ-8b and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets. Availability and implementation BioADAPT-MRC is freely available as an open-source project at https://github.com/mmahbub/BioADAPT-MRC. Supplementary information Supplementary data are available at Bioinformatics online.

60 APPLIED LIFE SCIENCES↗