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DOE OSTI2026

Continental-Scale Controls on Hyporheic Respiration Revealed by Knowledge-Guided Machine Learning

Hyporheic zone sediments regulate organic matter turnover and in-stream respiration, yet controls on sediment respiration remain poorly constrained across heterogeneous river networks, limiting prediction of stream metabolism and carbon processing at continental scales. Here, we integrate observations from ~90 river corridors across the United States in the WHONDRS consortium with a knowledge-guided machine learning (KGML) framework that couples thermodynamic rate theory with machine learning to identify dominant controls on hyporheic respiration. Diagnostic analyses show that organic matter concentration and thermodynamic favorability define an upper bound on respiration potential, whereas biological catalytic capacity and physical accessibility jointly govern realized respiration rates through interaction effects. To represent unmeasurable accessibility constraints, we use the mechanistic model as a scaffold for KGML, allowing machine learning to target residual structure not explained by process theory. This hybrid framework improves predictive skill relative to both the mechanistic model alone and fully data-driven models while preserving interpretability. These results indicate that variability in hyporheic respiration is largely mechanistically structured and demonstrate how integrating process theory with explainable AI enhances predictive performance while enabling scalable synthesis of river corridor observations.

Zheng, Jianqiu↗

DOE OSTI2026

Machine learning method for enforcing variable independence in background estimation with LHC data: ABCDisCoTEC

A novel solution is presented for the problem of estimating the backgrounds of a signal search using observed data while simultaneously maximizing the sensitivity of the search to the signal. The 'ABCD method' provides a reliable framework for background estimation by partitioning events into one signal-enhanced region (A) and three background-enhanced control regions (B, C, and D) via two smoothly varying, statistically independent variables. In practice, even slight correlations between the two variables can significantly undermine the method's performance. Thus, choosing appropriate variables by hand can present a formidable challenge, especially when background and signal differ only subtly. To address this issue, the ABCD with distance correlation (ABCDisCo) method was developed to construct two learned variables via a neural network trained to provide strong signal-background discrimination with small values of the distance correlation (DisCo) measure between the two learned variables. However, relying solely on minimizing the DisCo can result in learned variables that may not have distributions of background events that are smoothly varying and localized at extreme values, as necessary for the validity of the background estimation. The ABCDisCo training enhanced with closure (ABCDisCoTEC) method is introduced to solve this issue by directly minimizing the nonclosure, expressed as a dedicated differentiable loss term. This extended method is applied to a data set of proton-proton collisions at a center-of-mass energy of 13 TeV recorded by the CMS detector at the CERN Large Hadron Collider. Additionally, given the complexity of the minimization problem with constraints on multiple loss terms, the modified differential method of multipliers is applied and shown to greatly improve the stability and robustness of the ABCDisCoTEC method, compared to grid search hyperparameter optimization procedures.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

DOE OSTI2021

Improving deep learning-based protein distance prediction in CASP14

Abstract Motivation Accurate prediction of residue–residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Results Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions [i.e. classifying distances between two residues into two categories: in contact (<8 Angstrom) and not in contact otherwise] and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the precision of distance classification. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps. Availability and implementation The software package, source code and data of DeepDist2 are freely available at https://github.com/multicom-toolbox/deepdist and https://zenodo.org/record/4712084#.YIIM13VKhQM. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

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↗

DOE OSTI2020

Automatic microseismic event picking via unsupervised machine learning

SUMMARY Effective and efficient arrival picking plays an important role in microseismic and earthquake data processing and imaging. Widely used short-term-average long-term-average ratio (STA/LTA) based arrival picking algorithms suffer from the sensitivity to moderate-to-strong random ambient noise. To make the state-of-the-art arrival picking approaches effective, microseismic data need to be first pre-processed, for example, removing sufficient amount of noise, and second analysed by arrival pickers. To conquer the noise issue in arrival picking for weak microseismic or earthquake event, I leverage the machine learning techniques to help recognizing seismic waveforms in microseismic or earthquake data. Because of the dependency of supervised machine learning algorithm on large volume of well-designed training data, I utilize an unsupervised machine learning algorithm to help cluster the time samples into two groups, that is, waveform points and non-waveform points. The fuzzy clustering algorithm has been demonstrated to be effective for such purpose. A group of synthetic, real microseismic and earthquake data sets with different levels of complexity show that the proposed method is much more robust than the state-of-the-art STA/LTA method in picking microseismic events, even in the case of moderately strong background noise.

Chen, Yangkang↗

DOE OSTI2020

The PAU Survey: Photometric redshifts using transfer learning from simulations

In this paper, we introduce the DEEPZ deep learning photometric redshift (photo-z) code. As a test case, we apply the code to the PAU survey (PAUS) data in the COSMOS field. DEEPZ reduces the σ68 scatter statistic by 50 percent at iAB = 22.5 compared to existing algorithms. This improvement is achieved through various methods, including transfer learning from simulations where the training set consists of simulations as well as observations, which reduces the need for training data. The redshift probability distribution is estimated with a mixture density network (MDN), which produces accurate redshift distributions. Our code includes an autoencoder to reduce noise and extract features from the galaxy SEDs. It also benefits from combining multiple networks, which lowers the photo-z scatter by 10 percent. Furthermore, training with randomly constructed coadded fluxes adds information about individual exposures, reducing the impact of photometric outliers. In addition to opening up the route for higher redshift precision with narrow bands, these machine learning techniques can also be valuable for broad-band surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Predicting bulge to total luminosity ratio of galaxies using deep learning

ABSTRACT We present a deep learning model to predict the r-band bulge-to-total luminosity ratio (B/T) of nearby galaxies using their multiband JPEG images alone. Our Convolutional Neural Network (CNN) based regression model is trained on a large sample of galaxies with reliable decomposition into the bulge and disc components. The existing approaches to estimate the B/T ratio use galaxy light-profile modelling to find the best fit. This method is computationally expensive, prohibitively so for large samples of galaxies, and requires a significant amount of human intervention. Machine learning models have the potential to overcome these shortcomings. In our CNN model, for a test set of 20 000 galaxies, 85.7 per cent of the predicted B/T values have absolute error (AE) less than 0.1. We see further improvement to 87.5 per cent if, while testing, we only consider brighter galaxies (with r-band apparent magnitude <17) with no bright neighbours. Our model estimates the B/T ratio for the 20 000 test galaxies in less than a minute. This is a significant improvement in inference time from the conventional fitting pipelines, which manage around 2–3 estimates per minute. Thus, the proposed machine learning approach could potentially save a tremendous amount of time, effort, and computational resources while predicting B/T reliably, particularly in the era of next-generation sky surveys such as the Legacy Survey of Space and Time (LSST) and the Euclid sky survey which will produce extremely large samples of galaxies.

Grover, Harsh (ORCID:0000000321338142)↗

DOE OSTI2021

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗

DOE OSTI2022

Estimating cluster masses from SDSS multiband images with transfer learning

ABSTRACT The total masses of galaxy clusters characterize many aspects of astrophysics and the underlying cosmology. It is crucial to obtain reliable and accurate mass estimates for numerous galaxy clusters over a wide range of redshifts and mass scales. We present a transfer-learning approach to estimate cluster masses using the ugriz-band images in the SDSS Data Release 12. The target masses are derived from X-ray or SZ measurements that are only available for a small subset of the clusters. We designed a semisupervised deep learning model consisting of two convolutional neural networks. In the first network, a feature extractor is trained to classify the SDSS photometric bands. The second network takes the previously trained features as inputs to estimate their total masses. The training and testing processes in this work depend purely on real observational data. Our algorithm reaches a mean absolute error (MAE) of 0.232 dex on average and 0.214 dex for the best fold. The performance is comparable to that given by redMaPPer, 0.192 dex. We have further applied a joint integrated gradient and class activation mapping method to interpret such a two-step neural network. The performance of our algorithm is likely to improve as the size of training data set increases. This proof-of-concept experiment demonstrates the potential of deep learning in maximizing the scientific return of the current and future large cluster surveys.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Exploring the dependence of gas cooling and heating functions on the incident radiation field with machine learning

ABSTRACT Gas cooling and heating functions play a crucial role in galaxy formation. But, it is computationally expensive to exactly compute these functions in the presence of an incident radiation field. These computations can be greatly sped up by using interpolation tables of pre-computed values, at the expense of making significant and sometimes even unjustified approximations. Here, we explore the capacity of machine learning to approximate cooling and heating functions with a generalized radiation field. Specifically, we use the machine learning algorithm XGBoost to predict cooling and heating functions calculated with the photoionization code cloudy at fixed metallicity, using different combinations of photoionization rates as features. We perform a constrained quadratic fit in metallicity to enable a fair comparison with traditional interpolation methods at arbitrary metallicity. We consider the relative importance of various photoionization rates through both a principal component analysis (PCA) and calculation of SHapley Additive exPlanation (shap) values for our XGBoost models. We use feature importance information to select different subsets of rates to use in model training. Our XGBoost models outperform a traditional interpolation approach at each fixed metallicity, regardless of feature selection. At arbitrary metallicity, we are able to reduce the frequency of the largest cooling and heating function errors compared to an interpolation table. We find that the primary bottleneck to increasing accuracy lies in accurately capturing the metallicity dependence. This study demonstrates the potential of machine learning methods such as XGBoost to capture the non-linear behaviour of cooling and heating functions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

CMU DeepLens: deep learning for automatic image-based galaxy–galaxy strong lens finding

Galaxy-scale strong gravitational lensing can not only provide a valuable probe of the dark matter distribution of massive galaxies, but also provide valuable cosmological constraints, either by studying the population of strong lenses or by measuring time delays in lensed quasars. Due to the rarity of galaxy-scale strongly lensed systems, fast and reliable automated lens finding methods will be essential in the era of large surveys such as Large Synoptic Survey Telescope, Euclid and Wide-Field Infrared Survey Telescope. To tackle this challenge, we introduce CMU DeepLens, a new fully automated galaxy-galaxy lens finding method based on deep learning. This supervised machine learning approach does not require any tuning after the training step which only requires realistic image simulations of strongly lensed systems. We train and validate our model on a set of 20 000 LSST-like mock observations including a range of lensed systems of various sizes and signal-to-noise ratios (S/N). We find on our simulated data set that for a rejection rate of non-lenses of 99 per cent, a completeness of 90 per cent can be achieved for lenses with Einstein radii larger than 1.4 arcsec and S/N larger than 20 on individual g-band LSST exposures. Finally, we emphasize the importance of realistically complex simulations for training such machine learning methods by demonstrating that the performance of models of significantly different complexities cannot be distinguished on simpler simulations. We make our code publicly available at https://github.com/McWilliamsCenter/CMUDeepLens.

gravitational lensing: strong↗

DOE OSTI2019

Galaxy morphological classification in deep-wide surveys via unsupervised machine learning

ABSTRACT Galaxy morphology is a fundamental quantity, which is essential not only for the full spectrum of galaxy-evolution studies, but also for a plethora of science in observational cosmology (e.g. as a prior for photometric-redshift measurements and as contextual data for transient light-curve classifications). While a rich literature exists on morphological-classification techniques, the unprecedented data volumes, coupled, in some cases, with the short cadences of forthcoming ‘Big-Data’ surveys (e.g. from the LSST), present novel challenges for this field. Large data volumes make such data sets intractable for visual inspection (even via massively distributed platforms like Galaxy Zoo), while short cadences make it difficult to employ techniques like supervised machine learning, since it may be impractical to repeatedly produce training sets on short time-scales. Unsupervised machine learning, which does not require training sets, is ideally suited to the morphological analysis of new and forthcoming surveys. Here, we employ an algorithm that performs clustering of graph representations, in order to group image patches with similar visual properties and objects constructed from those patches, like galaxies. We implement the algorithm on the Hyper-Suprime-Cam Subaru-Strategic-Program Ultra-Deep survey, to autonomously reduce the galaxy population to a small number (160) of ‘morphological clusters’, populated by galaxies with similar morphologies, which are then benchmarked using visual inspection. The morphological classifications (which we release publicly) exhibit a high level of purity, and reproduce known trends in key galaxy properties as a function of morphological type at z < 1 (e.g. stellar-mass functions, rest-frame colours, and the position of galaxies on the star-formation main sequence). Our study demonstrates the power of unsupervised machine learning in performing accurate morphological analysis, which will become indispensable in this new era of deep-wide surveys.

Martin, G.↗

DOE OSTI2021

Simple, low-cost and accurate data-driven geophysical forecasting with learned kernels

Modelling geophysical processes as low-dimensional dynamical systems and regressing their vector field from data is a promising approach for learning emulators of such systems. We show that when the kernel of these emulators is also learned from data (using kernel flows, a variant of cross-validation), then the resulting data-driven models are not only faster than equation-based models but are easier to train than neural networks such as the long short-term memory neural network. In addition, they are also more accurate and predictive than the latter. When trained on geophysical observational data, for example the weekly averaged global sea-surface temperature, considerable gains are also observed by the proposed technique in comparison with classical partial differential equation-based models in terms of forecast computational cost and accuracy. When trained on publicly available re-analysis data for the daily temperature of the North American continent, we observe significant improvements over classical baselines such as climatology and persistence-based forecast techniques. Although our experiments concern specific examples, the proposed approach is general, and our results support the viability of kernel methods (with learned kernels) for interpretable and computationally efficient geophysical forecasting for a large diversity of processes.

58 GEOSCIENCES↗

DOE OSTI2026

Transformer-based operator learning framework for self-energy in strongly correlated systems

We introduce Σ-Attention, a transformer-based operator-learning framework for approximating the self-energy operator of strongly correlated electronic systems. By creating a batched dataset that combines results from three complementary approaches, i.e., many-body perturbation theory, strong-coupling expansion, and exact diagonalization, each effective in specific parameter regimes, Σ-Attention is applied to learn an accurate approximation for the self-energy operator that is valid across a wide range of parameter regimes. This hybrid strategy leverages the strengths of existing methods while relying on the transformer's ability to generalize beyond individual limitations. More importantly, the scalability of the transformer architecture allows the learned self-energy to be extended to systems with larger sizes, leading to much improved computational scaling. Using the one-dimensional Hubbard model, we demonstrate that Σ-Attention can accurately predict the Matsubara Green's function of large systems with a wide range of coupling strength. Our framework offers a promising and scalable pathway for studying strongly correlated systems with many possible generalizations.

Zhu, Yuanran↗

DOE OSTI2020

Assessing three closed-loop learning algorithms by searching for high-quality quantum control pulses

Designing a high-quality control is crucial for reliable quantum computation. Among the existing approaches, closed-loop leaning control is an effective choice. Its efficiency depends on the learning algorithm employed, thus deserving algorithmic comparisons for its practical applications. Here we assess three representative learning algorithms, including GRadient Ascent Pulse Engineering (GRAPE), improved Nelder-Mead (NMplus), and Differential Evolution (DE), by searching for high-quality control pulses to prepare the Bell state. We first implement each algorithm experimentally in a nuclear magnetic resonance system and then conduct a numerical study considering the impact of some possible significant experimental uncertainties. The experiments report the successful preparation of the high-fidelity target state by the three algorithms, while NMplus converges fastest, and these results coincide with the numerical simulations when potential uncertainties are negligible. However, under certain significant uncertainties, these algorithms possess distinct performance with respect to their resulting precision and efficiency, and DE shows the best robustness. Finally, this study provides insight to aid in the practical application of different closed-loop learning algorithms in realistic physical scenarios.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Uncertainty quantification for deep learning in particle accelerator applications

With the advent of increased computational resources and improved algorithms, machine learning-based models are being increasingly applied to complex problems in particle accelerators. However, such data-driven models may provide overly confident predictions with unknown errors and uncertainties. For reliable deployment of machine learning models in high-regret and safety-critical systems such as particle accelerators, estimates of prediction uncertainty are needed along with accurate point predictions. In this investigation, we evaluate Bayesian neural networks (BNN) as an approach that can provide accurate predictions along with reliably quantified uncertainties for particle accelerator problems, and compare their performance with bootstrapped ensembles of neural networks. We select three accelerator setups for this evaluation: a storage ring, a photoinjector, and a linac. The problems span different data volumes and dimensionalities (e.g., scalar predictions as well as image outputs). It is found that BNN provide accurate predictions of the mean along with reliable estimates of predictive uncertainty across the test cases. In this vein, BNN may offer an attractive alternative to deterministic deep learning tools to generate accurate predictions with quantified uncertainties in particle accelerator applications.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Machine learning surrogate for charged particle beam dynamics with space charge based on a recurrent neural network with aleatoric uncertainty

In this work, we develop a machine learning (ML) model with aleatoric uncertainty for the low energy beam transport (LEBT) region of the LANSCE linear accelerator in which we model the transport of a space-charge-dominated 750 keV proton beam through a lattice of 22 quadrupole magnets. Our ML model is developed based on data generated by a Kapchinsky–Vladimirsky (KV) envelope model of beam transport. We show that a recurrent neural network can be used as a dynamical surrogate model for fast prediction of the LEBT beam envelope. Furthermore, we endow the model with the prediction of aleatoric uncertainty and compare three different approaches. We demonstrate that the ML-based uncertainty quantification models are well calibrated and produce good estimates of the regions where the model is less certain about its predictions. This ML framework is a necessary step in the development of a real-time virtual diagnostic tool with uncertainty quantification that can be integrated into more complex downstream tasks (e.g., adaptive control or learning flexible control policies via reinforcement learning) for improved efficiency in beam operations. In future work, we plan to expand on this preliminary study by considering more realistic envelope models that include longitudinal momentum spread and dispersive effects in bending magnets, as well as particle tracking codes with 3D space charge (such as and ). Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Detection of topological materials with machine learning

Databases compiled using ab initio and symmetry-based calculations now contain tens of thousands of topological insulators and topological semimetals. This makes the application of modern machine learning methods to topological materials possible. Using gradient boosted trees, we show how to construct a machine learning model which can predict the topology of a given existent material with an accuracy of 90%. Such predictions are orders of magnitude faster than actual ab initio calculations. In this work, we use machine learning models to probe how different material properties affect topological features. Notably, we observe that topology is mostly determined by the “coarse-grained” chemical composition and crystal symmetry and depends little on the particular positions of atoms in the crystal lattice. We identify the sources of our model's errors and we discuss approaches to overcome them.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗