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At least 55 records · Page 3

ScaleML: Machine Learning based Heap Memory Object Scaling Prediction

Memory subsystem contributes 28-40% of total energy consumption. Several studies investigated energy prediction and consumption via profiling memory object access patterns. However, such profiling leads to higher energy consumption due to intense memory object-level profiling to achieve high prediction accuracy. Further, memory object access pattern prediction has been considered through analyzing the variation between memory object access patterns, referred to as scaling rate. The existing techniques for scaling rate prediction, such as Linear Scaling Rate (LSR), suffer from a high error rate in prediction with changes in access patterns, which leads to a high error rate of energy consumption prediction. In this paper, we compare and evaluate several memory object access pattern prediction models including LSR and machine learning (ML) models. Further, we propose SCALEML, a heap memory object scaling rate prediction mechanism that employs an ML model to achieve high access pattern prediction accuracy with variations in memory object access patterns. We evaluate SCALEML using various application benchmarks. The experimental results show that SCALEML achieves about 20% higher accuracy than the LSR model for predicting the scaling rate of object access patterns and energy estimation.

Park, Joongeon↗

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗

Accuracy of predictions made by machine learned models for biocrude yields obtained from hydrothermal liquefaction of organic wastes

Hydrothermal liquefaction (HTL) has potential for converting abundant wet organic wastes into renewable fuels. Because HTL consists of a complex reaction network, deterministic, physics-based prediction of its biocrude yield is prohibitively difficult. Data-driven methods provide an alternative to the physics-based approach; however, rigorous testing must be performed to ensure the accuracy of predictions made by data-driven methods. To this end, a data set was assembled consisting of 570 data points appearing in the open literature. The data set was divided into training, validation, and test sub-sets and used for evaluating different machine learning regression approaches to predict biocrude yield. Among the tested algorithms, Random Forest and eXtreme Gradient Boosting (XGBoost) predicted biocrude yields in a test set that had not been used for training with the greatest accuracy, with root mean square errors (RMSE) of 8.34 and 8.57, respectively. Further refinement of the Random Forest model reduced its RMSE to 8.07. In comparison, predictions of a series of literature models resulted in RMSE ranging from 9.16 in the most accurate case to 27.6 in the least accurate; most literature models yielded RMSE values > 10. Using biocrude yield predictions from the most accurate Random Forest model and a probabilistic economic analysis found that the model accuracy is sufficient to prioritize allocation of resources based on projected minimum fuel selling price. In our report the models and analysis represent a major advance in the ability to use readily available data to predict biocrude yields on new feedstocks that have not previously been studied.

42 ENGINEERING↗

Genome‐wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus

Abstract Accelerating biomass improvement is a major goal of Miscanthus breeding. The development and implementation of genomic‐enabled breeding tools, like marker‐assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of Miscanthus breeding. The present study conducted genome‐wide association (GWA) and genomic prediction of biomass yield and 14 yield‐components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across 4 years in one subtropical and three temperate locations and genotyped with 268,109 single‐nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported Miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield‐component traits in M. sacchariflorus that may facilitate marker‐assisted breeding for biomass yield. Genomic prediction accuracy for the yield‐related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia ( N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population‐improvement of M. sacchariflorus .

09 BIOMASS FUELS↗

Data for Genome-Wide Association and Genomic Prediction for Yield and Component Traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus .

Biomass Analytics↗

Predicting the formation of fractionally doped perovskite oxides by a function-confined machine learning method

Abstract Fractionally doped perovskites oxides (FDPOs) have demonstrated ubiquitous applications such as energy conversion, storage and harvesting, catalysis, sensor, superconductor, ferroelectric, piezoelectric, magnetic, and luminescence. Hence, an accurate, cost-effective, and easy-to-use methodology to discover new compositions is much needed. Here, we developed a function-confined machine learning methodology to discover new FDPOs with high prediction accuracy from limited experimental data. By focusing on a specific application, namely solar thermochemical hydrogen production, we collected 632 training data and defined 21 desirable features. Our gradient boosting classifier model achieved a high prediction accuracy of 95.4% and a high F1 score of 0.921. Furthermore, when verified on additional 36 experimental data from existing literature, the model showed a prediction accuracy of 94.4%. With the help of this machine learning approach, we identified and synthesized 11 new FDPO compositions, 7 of which are relevant for solar thermochemical hydrogen production. We believe this confined machine learning methodology can be used to discover, from limited data, FDPOs with other specific application purposes.

08 HYDROGEN↗

Di-CNN: Domain-Knowledge-Informed Convolutional Neural Network for Manufacturing Quality Prediction

In manufacturing, convolutional neural networks (CNNs) are widely used on image sensor data for data-driven process monitoring and quality prediction. However, as purely data-driven models, CNNs do not integrate physical measures or practical considerations into the model structure or training procedure. Consequently, CNNs’ prediction accuracy can be limited, and model outputs may be hard to interpret practically. This study aims to leverage manufacturing domain knowledge to improve the accuracy and interpretability of CNNs in quality prediction. A novel CNN model, named Di-CNN, was developed that learns from both design-stage information (such as working condition and operational mode) and real-time sensor data, and adaptively weighs these data sources during model training. It exploits domain knowledge to guide model training, thus improving prediction accuracy and model interpretability. A case study on resistance spot welding, a popular lightweight metal-joining process for automotive manufacturing, compared the performance of (1) a Di-CNN with adaptive weights (the proposed model), (2) a Di-CNN without adaptive weights, and (3) a conventional CNN. The quality prediction results were measured with the mean squared error (MSE) over sixfold cross-validation. Model (1) achieved a mean MSE of 6.8866 and a median MSE of 6.1916, Model (2) achieved 13.6171 and 13.1343, and Model (3) achieved 27.2935 and 25.6117, demonstrating the superior performance of the proposed model.

47 OTHER INSTRUMENTATION↗

Sub-millisecond keyhole pore detection in laser powder bed fusion using sound and light sensors and machine learning

Laser powder bed fusion is a mainstream additive manufacturing technology widely used to manufacture complex parts in prominent sectors, including aerospace, biomedical, and automotive industries. However, during the printing process, the presence of an unstable vapor depression can lead to a type of defect called keyhole porosity, which is detrimental to the part quality. In this study, we developed an effective approach to locally detect the generation of keyhole pores during the printing process by leveraging machine learning and a suite of optical and acoustic sensors. Simultaneous synchrotron x-ray imaging allows the direct visualization of pore generation events inside the sample, offering high-fidelity ground truth. A neural network model adopting SqueezeNet architecture using single-sensor data was developed to evaluate the fidelity of each sensor for capturing keyhole pore generation events. Our comparative study shows that the near infrared images gave the highest prediction accuracy, followed by 100 kHz and 20 kHz microphones, and the photodiode sensitive to processing laser wavelength had the lowest accuracy. Using a single sensor, over 90% prediction accuracy can be achieved with a temporal resolution as short as 0.1 ms. A data fusion scheme was also developed with features extracted using SqueezeNet neural network architecture and classification using different machine learning algorithms. Our work demonstrates the correlation between the characteristic optical and acoustic emissions and the keyhole oscillation behavior, and thereby provides strong physics support for the machine learning approach.

36 MATERIALS SCIENCE↗

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency and CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding of the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools and network analysis to investigate the transcriptional architecture governing circadian-controlled gene expression. While our approach showed moderate accuracy in predicting individual transcription factor-gene interactions - a common challenge with real expression data - network-level topological analysis successfully revealed the organizational principles of circadian regulation. Our analysis identified distinct regulatory modules coordinating day-night metabolic transitions, with photosynthesis and carbon/nitrogen metabolism controlled by day-phase regulators, while nighttime modules orchestrate glycogen mobilization and redox metabolism. Through network centrality analysis, we identified potentially significant but previously understudied transcriptional regulators: HimA as a putative DNA architecture regulator, and TetR and SrrB as potential coordinators of nighttime metabolism, working alongside established global regulators RpaA and RpaB. This work demonstrates how network-level analysis can extract biologically meaningful insights despite limitations in predicting direct regulatory interactions. The regulatory principles uncovered here advance our understanding of how cyanobacteria coordinate complex metabolic transitions and may inform metabolic engineering strategies for enhanced photosynthetic bioproduction from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Bayesian Optimized Deep Ensemble for Uncertainty Quantification of Deep Neural Networks: a System Safety Case Study on Sodium Fast Reactor Thermal Stratification Modeling

Deep neural networks (DNNs) are increasingly important to scientific computing and engineering system simulations. Accurate uncertainty quantification (UQ) for DNNs is critical in safety-sensitive engineering domains. Traditional Deep Ensemble (DE) methods, while easy to implement, frequently suffer from poorly calibrated uncertainty estimates and limited predictive accuracy due to reliance on fixed architectures with varied weight initializations. To address these issues, we introduce a workflow that combines Bayesian Optimization (BO) and DE. The workflow is modular, scalable, and integrates parallel BO initialized with Sobol sequences to individually optimize the hyperparameters of each ensemble member. This method enhances ensemble diversity, improves predictive accuracy, and provides reliable uncertainty estimates. We evaluate the proposed BODE approach in a sodium fast reactor thermal stratification modeling case study, where we used a densely connected convolutional neural network to predict turbulent viscosity during the reactor transient with consideration of data noise. We benchmark its performance against several optimization approaches, including baseline deep ensemble, evolutionary algorithm-optimized ensemble, ensemble formed via random search combined with greedy selection, and a BO ensemble using random initialization. Here, our results demonstrate superior performance of the developed BODE approach. In noise-free scenarios, BODE notably reduces incorrect aleatoric uncertainty and significantly enhances predictive accuracy. Under conditions of 5% and 10% Gaussian noise, BODE adaptively quantifies uncertainty proportional to data noise, achieving up to an 80% reduction in root mean square error compared to baseline methods and producing well-calibrated prediction intervals.

Bayesian optimization↗

Towards a robust out-of-the-box neural network model for genomic data

The accurate prediction of biological features from genomic data is paramount for precision medicine and sustainable agriculture. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and targeted marketing given their prediction accuracy and their robust performance under big data settings. Yet neural network models have not made a successful transition into the medical and biological world due to the ubiquitous characteristics of biological data such as modest sample sizes, sparsity, and extreme heterogeneity. Here, we investigate the robustness, generalization potential and prediction accuracy of widely used convolutional neural network and natural language processing models with a variety of heterogeneous genomic datasets. Mainly, recurrent neural network models outperform convolutional neural network models in terms of prediction accuracy, overfitting and transferability across the datasets under study. While the perspective of a robust out-of-the-box neural network model is out of reach, we identify certain model characteristics that translate well across datasets and could serve as a baseline model for translational researchers.

59 BASIC BIOLOGICAL SCIENCES↗

Train, Inform, Borrow, or Combine? Approaches to Process–Guided Deep Learning for Groundwater–Influenced Stream Temperature Prediction

Although groundwater discharge is a critical stream temperature control process, it is not explicitly represented in many stream temperature models, an omission that may reduce predictive accuracy, hinder management of aquatic habitat, and decrease user confidence. We assessed the performance of a previously-described process-guided deep learning model of stream temperature in the Delaware River Basin (USA). We found lower accuracy (root mean square error [RMSE] of 1.71 versus 1.35°C) and stronger seasonal bias (absolute mean monthly bias of 1.06 vs. 0.68°C) for reaches primarily influenced by deep groundwater as compared to atmospheric conditions. We then tested four approaches for improving groundwater process representation: (a) a custom loss function leveraging the unique patterns of air and water temperature coupling characteristic of different temperature drivers, (b) inclusion of additional groundwater-relevant catchment attributes, (c) incorporation of additional process model outputs, and (d) a composite model. The custom loss function and the additional attributes significantly improved the predictive accuracy in groundwater-dominated reaches (RMSE of 1.37 and 1.26°C) and reduced the seasonal bias (absolute mean monthly bias of 0.44 and 0.48°C), but neither approach could identify holdout groundwater reaches. Variable importance analysis indicates the custom loss function nudges the model to use the existing inputs more efficiently, whereas with the added features the model relies on a broader suite of inputs. This analysis is a substantial step toward more accurately representing groundwater discharge processes in stream temperature models and will improve predictive accuracy and inform habitat management.

54 ENVIRONMENTAL SCIENCES↗

Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture

Abstract Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li 7 P 3 S 11 , a superionic conductor, and show that resulting Li diffusion coefficient is within 14% of that obtained directly from AIMD. The high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.

Chemistry↗

Surrogate modeling and optimization of the leaching process in a rare earth elements recovery plant

Critical minerals (CMs) and Rare Earth Elements (REEs) play a vital role in crucial infrastructure technologies such as renewable energy generation and batteries. Recovering them from waste materials has recently been found to significantly reduce environmental impact and supply chain costs related to these materials. In this work, we investigate surrogate modeling techniques aimed to simplify the modeling, simulation, and optimization of the leaching processes involved in CM and REE recovery flowsheets. As there is currently a lack of systematic studies on this topic, we perform extensive computational testing to ascertain which surrogate models are easier to construct and offer high predictive accuracy. Further, our results suggest that sparse quadratic models balance predictive accuracy and computational efficiency. Training and using these surrogates for global optimization of the leaching process requires two orders of magnitude fewer measurements and is up to four orders of magnitude faster than optimizing the original simulation using equation-oriented optimization or derivative-free optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A new procedure for implementing the modified inherent strain method with improved accuracy in predicting both residual stress and deformation for laser powder bed fusion

As a metal additive manufacturing (AM) process, laser powder bed fusion (L-PBF) has been widely used to produce parts with complex geometries. The large thermal gradient caused by the fast, intense, and repeated laser scanning induces significant residual deformation and stress to the as-built parts, which increase manufacturing difficulty and geometrical inaccuracy as a result. The modified inherent strain (MIS) method exploiting multiscale process simulations was developed to simulate residual deformation accurately and efficiently. However, the existing procedure of implementing the MIS method is found to give inaccurate residual stress prediction. Here in this work, a new implementation procedure for the MIS method is proposed to improve the simulation accuracy of residual stress without degrading the residual deformation prediction. The new procedure concerns the application of inherent strains to the part-scale layer-by-layer finite element model to obtain residual stress and deformation field. While the existing implementation of the part-scale MIS model involves only mechanical properties at ambient temperature, the new procedure adds one more solution step employing mechanical properties at an elevated temperature determined from the inherent strain extraction step. Both numerical and experimental studies are conducted to validate the proposed new implementation procedure. It shows that by using the new procedure, the MIS-based simulation can predict both residual stress and deformation of as-built L-PBF metal parts with good accuracy.

36 MATERIALS SCIENCE↗

Predicting concrete compressive strength using hybrid ensembling of surrogate machine learning models

This study aims to implement a hybrid ensemble surrogate machine learning technique in predicting the compressive strength (CS) of concrete, an important parameter used for durability design and service life prediction of concrete structures in civil engineering projects. For this purpose, an experimental database consisting of 1030 records has been compiled from the machine learning repository of the University of California, Irvine. The database was used to train and validate four conventional machine learning (CML) models, namely Artificial Neural Network (ANN), Linear and Non-Linear Multivariate Adaptive Regression Splines (MARS-L and MARS-C), Gaussian Process Regression (GPR), and Minimax Probability Machine Regression (MPMR). Subsequently, the predicted outputs of CML models were combined and trained using ANN to construct the Hybrid Ensemble Model (HENSM). It is observed that the proposed HENSM produces higher predictive accuracy compared to the CML models used in the present study. The predictive performance of all models for CS prediction was compared using the testing dataset and it is found that the HENSM model attained the highest predictive accuracy in both phases. Based on the experimental results, the newly constructed HENSM model is very potential to be a new alternative in handling the overfitting issues of CML models and hence, can be used to predict the concrete CS, including the design of less polluting and more sustainable concrete constructions.

36 MATERIALS SCIENCE↗

Hierarchical-embedding autoencoder with a predictor as efficient architecture for learning time-evolution in multi-scale turbulent flows

We introduce a scale-aware, data-driven deep learning modeling framework for accurately predicting the time evolution of multi-scale turbulent plasma and liquid flows. The approach is motivated by the idea of scale separation. Structures of vastly different length scales emerge in these systems, and interactions between these structures occur only locally. To exploit this structure, the flow state is transformed by a hierarchical, fully convolutional autoencoder, not into a single embedding layer as in conventional convolutional surrogate models, but into a series of embedding layers. A stepwise training strategy ensures that fine-scale features are encoded on a high-resolution grid, while larger structures are represented on progressively coarser layers. The time evolution predictor advances all embedding layers in sync, capturing local interactions between features at the same scale as well as between all scales. This approach enables efficient modeling of multi-scale systems since negligible interactions between distant, small-scale structures do not need to be directly modeled. Our hierarchical-embedding autoencoder with a predictor framework is evaluated on canonical examples of multi-scale turbulence: two-dimensional Kolmogorov flow and Hasegawa–Wakatani plasma turbulence. In both cases, the proposed framework significantly improves predictive accuracy relative to conventional convolutional network architectures. A significant improvement in prediction accuracy was observed for crucial statistical characteristics of the Hasegawa–Wakatani plasma as well as for individual trajectories of the Kolmogorov flow turbulence. Importantly, the model's rollout for the Hasegawa–Wakatani problem demonstrates a four-order-of-magnitude speedup compared to traditional numerical solvers.

Khrabry, Alexander I. [Princeton Univ., NJ (United↗

Interpretable machine learning-guided design of Fe-based soft magnetic alloys

Here, we present a machine learning (ML) guided approach to predict saturation magnetization (𝑀 S ) and coercivity (𝐻 C ) in Fe-rich soft magnetic alloys, particularly Fe-Si-B systems. ML models trained on experimental data reveal that increasing Si and B content reduces 𝑀 S from 1.81 T (DFT ≈ 2.04 T) to ≈1.54 T (DFT ≈ 1.56T) in Fe-Si-B, which is attributed to decreased magnetic density and structural modifications. Experimental validation of ML predicted magnetic saturation on Fe-1Si-1B (2.09 T), Fe-5Si-5B (2.01 T), and Fe-10Si-10B (1.54 T) alloy compositions further supports our findings. These trends are consistent with density functional theory predictions, which link increased electronic disorder and band broadening to lower 𝑀 S values. Experimental validation on selected alloys confirms the predictive accuracy of the ML model, with good agreement across compositions. Beyond predictive accuracy, detailed uncertainty quantification and model interpretability including through feature importance and partial dependence analysis reveal that 𝑀 S is governed by a nonlinear interplay between Fe content and early transition metal ratios, while 𝐻 C is more sensitive to processing conditions such as ribbon thickness and thermal treatment windows. The ML framework was further applied to Fe-Si-B/Cr/Cu/Zr/Nb alloys in a pseudoquaternary compositional space, which shows comparable magnetic properties to NANOMET (Fe 84.8 ⁢Si 0.5 ⁢B 9.4 ⁢Cu 0.8⁢ P 3.5 ⁢C 1 ), FINEMET (Fe 73.5 ⁢Si 13.5 ⁢B 9 Cu 1 ⁢Nb 3 ), NANOPERM (Fe 88 ⁢Zr 7⁢ B 4 ⁢Cu 1 ), and HITPERM (Fe 44 ⁢Co 44 ⁢Zr 7⁢ B 4 ⁢Cu 1 . Our findings demonstrate the potential of the ML framework for accelerated search of high-performance soft magnetic materials.

density functional theory↗