Cryo‐EM map interpretation and protein model‐building using iterative map segmentation
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59 BASIC BIOLOGICAL SCIENCES↗
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Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
Abstract Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein model-building workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.
59 BASIC BIOLOGICAL SCIENCES↗
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching
Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.
59 BASIC BIOLOGICAL SCIENCES↗
Radiation Mapping UAV [Poster]
The NuMI (Neutrinos at the Main Injector) target system delivers a high-energy flux of muon-neutrinos towards a detector more than 800 km away with the goal of better understanding the origin of the universe and its evolution. The target system becomes radioactive because it is irradiated by a sub-Mega-Watt power proton beam. Radiological hazard is one of critical issues for a radiological worker which limits the iractivities near the target system; however, they often need to quantify the radiation level of the target system manually. Thus, the objective of this project is to reduce their exposure to radiation while improving the accuracy of the measurements. A quadcopter UAV fitted with a radiation dosimeter is ideal to traverse the irradiated environment as it can be deployed in any space and requires minimal hardware integration to the test room. Due to the lack of indoor GPS signal, this UAV utilizes a series of ultrasonic beacons that release several varied-frequency pulses simultaneously in order to localize the drone. The flight controller returns a 3D coordinate tied to the radiation data to understand precisely where radiation spikes are being emitted from the horn. The flight controller stores log data that can be processed into an easily interpretable map of radiation intensities. The radiation map serves as one of the primary references for planning the transportation of the NuMI horn.
43 PARTICLE ACCELERATORS↗
Deep learning-accelerated 3D carbon storage reservoir pressure forecasting based on data assimilation using surface displacement from InSAR
Fast forecasting of the reservoir pressure distribution during geologic carbon storage (GCS) by assimilating monitoring data is a challenging problem. Due to high drilling cost, GCS projects usually have spatially sparse measurements from few wells, leading to high uncertainties in reservoir pressure prediction. To address this challenge, we use low-cost Interferometric Synthetic-Aperture Radar (InSAR) data as monitoring data to infer reservoir pressure build up. We develop a deep learning-accelerated workflow to assimilate surface displacement maps interpreted from InSAR and to forecast dynamic reservoir pressure. Employing an Ensemble Smoother Multiple Data Assimilation (ES-MDA) framework, the workflow updates three-dimensional (3D) geologic properties and predicts reservoir pressure with quantified uncertainties. We use a synthetic commercial-scale GCS model with bimodally distributed permeability and porosity to demonstrate the efficacy of the workflow. A two-step CNN-PCA approach is employed to parameterize the bimodal fields. The computational efficiency of the workflow is boosted by two residual U-Net based surrogate models for surface displacement and reservoir pressure predictions, respectively. The workflow can complete data assimilation and reservoir pressure forecasting in half an hour on a personal computer.
25 ENERGY STORAGE↗
Massive νs through the CNN lens: interpreting the field-level neutrino mass information in weak lensing
Modern cosmological surveys probe the Universe deep into the nonlinear regime, where massive neutrinos suppress cosmic structure. Traditional cosmological analyses, which use the 2-point correlation function to extract information, are no longer optimal in the nonlinear regime, and there is thus much interest in extracting beyond-2-point information to improve constraints on neutrino mass. Quantifying and interpreting the beyond-2-point information is thus a pressing task. We study the field-level information in weak lensing convergence maps using convolution neural networks. We find that the network performance increases as higher source redshifts and smaller scales are considered — investigating up to a source redshift of 2.5 and ℓ max ≃ 10 4 — verifying that massive neutrinos leave a distinct effect on weak lensing. However, the performance of the network significantly drops after scaling out the 2-point information from the maps, implying that most of the field-level information can be found in the 2-point correlation function alone. We quantify these findings in terms of the likelihood ratio and also use Integrated Gradient saliency maps to interpret which parts of the map the network is learning the most from. We find that, in the absence of noise, the network extracts a similar amount of information from the most overdense and underdense regions. However, upon adding noise, the information in underdense regions is distorted as noise disproportionately washes out void-like structures.
Golshan, Malika [University of California, Berkele↗
Interpretable and flexible non-intrusive reduced-order models using reproducing kernel Hilbert spaces
This paper develops an interpretable, non-intrusive reduced-order modeling technique using regularized kernel interpolation. Existing non-intrusive approaches approximate the dynamics of a reduced-order model (ROM) by solving a data-driven least-squares regression problem for low-dimensional matrix operators. Our approach instead leverages regularized kernel interpolation, which yields an optimal approximation of the ROM dynamics from a user-defined reproducing kernel Hilbert space. We show that our kernel-based approach can produce interpretable ROMs whose structure mirrors full-order model structure by embedding judiciously chosen feature maps into the kernel. The approach is flexible and allows a combination of informed structure through feature maps and closure terms via more general nonlinear terms in the kernel. We also derive a computable a posteriori error bound that combines standard error estimates for intrusive projection-based ROMs and kernel interpolants. In conclusion, the approach is demonstrated in several numerical experiments that include comparisons to operator inference using both proper orthogonal decomposition and quadratic manifold dimension reduction.
Data-driven model reduction↗
Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.
59 BASIC BIOLOGICAL SCIENCES↗
Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.
B factors↗
Mapping Stellar Surfaces. II. An Interpretable Gaussian Process Model for Light Curves
The use of Gaussian processes (GPs) as models for astronomical time series data sets has recently become almost ubiquitous, given their ease of use and flexibility. In particular, GPs excel at marginalization over the stellar signal when the variability due to starspots is treated as a nuisance, as in exoplanet transit modeling. However, these effective models are less useful in cases where the starspot signal is of primary interest, since it is not obvious how the parameters of the GP relate to physical parameters like the spot size, contrast, and latitudinal distribution. Instead, it is common practice to explicitly model the effect of individual starspots on the light curve and attempt to infer their properties via optimization or posterior inference. Unfortunately, this process is ill-posed and often computationally intractable when applied to stars with more than a few spots and/or to ensembles of many stars. Here we derive a closed-form expression for a GP that describes the light curve of a rotating, evolving stellar surface conditioned on a given distribution of starspot sizes, contrasts, and latitudes. We demonstrate that this model is correctly calibrated, allowing one to robustly infer physical parameters of interest from one or more light curves, including the typical spot radii and latitudes. Our GP has far-ranging implications for understanding the variability and magnetic activity of stars from light curves and radial velocity measurements, as well as for modeling correlated noise in exoplanet searches. Our implementation is efficient, user-friendly, and open-source, available in the package starry-process.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Laser-driven flash x-ray radiography of a shocked metallic foil
Characterizing hydrodynamic instability evolution in millimeter-scale, high-Z foils is crucial for understanding complex phenomena in high-energy-density physics. Here, we demonstrate a proof-of-concept, laser-driven flash x-ray radiography platform tailored for two-dimensional linear density mapping in shocked high-Z foils. Using chromium (Cr) foils with internal shockwaves (∼100 μm width), our platform achieves a spatial resolution of 59.8 ± 1.4 μm by employing a broadband x-ray source extending into the hundreds of keV range. The setup combines a compound parabolic concentrator cone with a tantalum wire target, a magnetic field to deflect residual transmitted electrons, and a copper casing to shield the sides and rear of the image plate pack. By varying the delay of the short-pulse beam driving the flash x-ray source, we resolve shockwave dynamics, specifically the velocity, position, width, and density profile, within the Cr foil. Reported experimental results are consistent with the corresponding hydrodynamics and radiation transport simulations, which accurately reproduce the measured electron and x-ray source terms. These developments enable the conversion of shockwave radiographs into two-dimensional density maps, enhancing interpretability for hydrodynamic instability evolution applications and validating the simulation approach.
36 MATERIALS SCIENCE↗
Adaptive Graph Learning with Transformer for Multi-Reservoir Inflow Prediction
Reservoir inflow prediction is crucial for water resource management, yet existing approaches mainly focus on single-reservoir models that ignore spatial dependencies among interconnected reservoirs. We introduce AdaTrip as an adaptive, time-varying graph learning framework for multi-reservoir inflow forecasting. AdaTrip constructs dynamic graphs where reservoirs are nodes with directed edges reflecting hydrological connections, employing attention mechanisms to automatically identify crucial spatial and temporal dependencies. Evaluation on thirty reservoirs in the Upper Colorado River Basin demonstrates superiority over existing baselines, with improved performance for reservoirs with limited records through parameter sharing. Additionally, AdaTrip provides interpretable attention maps at edge and time-step levels, offering insights into hydrological controls to support operational decision-making. Our code is available at https://github.com/humphreyhuu/AdaTrip.
Hu, Pengfei [ORNL] (ORCID:0009000367130950)↗
Self-Supervised T-GCN for Detection of Disturbance and Propagation in Power Grid
Urban power systems increasingly rely on dense sensing to monitor grid reliability, yet disturbance labels are scarce and events are rare. We present a self-supervised spatio-temporal method that detects, localizes, and characterizes grid frequency disturbances across urban areas using only unlabeled data. Our approach trains a tiny Temporal Graph Convolutional Network (T-GCN) to forecast per-site frequency residuals (deviation from 60 Hz). The sensor graph is constructed directly from signals using pre-event Pearson correlation with a cross-correlation lag penalty without geocoding. At inference, node-level anomalies are the model's forecast errors; region-level alarms arise from connected components of high-score nodes. We estimate disturbance propagation by computing per-node arrival times (first persistent exceedance), then fit a planar or time-of-arrival model to obtain direction, speed, and an epicenter proxy. With only three real events collected at decisecond resolution across U.S. cities, we evaluate the T-GCN and report time-to-detect, footprint size, and propagation consistency. We further show that short-window embeddings from the T-GCN's hidden states enable few-shot event-vs-background recognition via a simple prototypical classifier. Despite minimal data and no labels, our system yields fast, spatially coherent detection and interpretable propagation maps, offering a practical, lightweight pathway to city-scale grid resilience analytics.
Niu, Haoran [ORNL] (ORCID:0000000155228297)↗
The Trillion Pixel GeoAI Challenge Workshop
Rapid innovations in satellite and airborne remote sensing capabilities holds the promise of collecting high-resolution imagery with daily, even hourly cadence across the entire planet. Availability of such earth observation data streams at varying spatial and temporal scales, coupled with astonishing progress in AI and transformational advances in high performance computing bring into view the possibility of mapping and interpreting the surface of our planet at unprecedented detail. The implications of such capability for science, technology, policy, and security are far reaching. Moreover, even at a modest 5m resolution, 100 trillion pixels will describe the surface of the Earth every day. Consequently, monitoring the pulse of our planet will entail collecting, refining, analyzing, and curating those 100 trillion pixels within a 24-hour period. That is a challenge with unknown solutions as of today’s advances and therefore serves as a key motivation for this workshop. The GEOINT and AI communities have a unique opportunity to enable detailed monitoring the pulse of our planet and obtain new insights into how humans occupy, interact with, and alter the surface of the Earth over time. From a science and technology standpoint, this is a modern-day moonshot that presents numerous challenges particularly related to scaling the analysis to every pixel covering the planet. The challenge of making sense of all these pixels in a timely fashion include image processing at scale, selective analysis of only the pixels that matter, generalizing AI models across heterogeneous locations, computing on hardware that is memory constrained, and deploying automated feature extraction on edge devices. The designing of capable GeoAI workflows and data pipelines will require interdisciplinary efforts and partnerships. The Trillion Pixel Challenge for GeoAI workshop was is promoted as a first community effort to discuss priority research and development directions and to establish the partnerships and collaborations needed to make progress on critical scientific and operational applications from local to regional to planet scale.
97 MATHEMATICS AND COMPUTING↗
We Know Where We Don't Know: 3D Bayesian CNNs for Credible Geometric Uncertainty
Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions.
97 MATHEMATICS AND COMPUTING↗
Floquet dynamics of classical and quantum cavity fields
We show that the time-dependence of electromagnetic field in a periodically modulated cavity can be effectively analyzed using a Floquet map. The map relates the field states separated by one period of the drive; iterative application of the map allows to determine field configuration after arbitrary number of drive periods. For resonant and near-resonant drives, the map has stable and unstable fixed points, which are the loci of infinite energy concentration in the long time limit. The Floquet map method can be applied both to classical and quantum massless field problems, including the dynamical Casimir effect. The stroboscopic time evolution implemented by the map can be interpreted in terms of the wave propagation in a curved space, with the fixed points of the map corresponding to the black hole and white hole horizons. More practically, the map can be used to design protocols for signal compression/decompression, cooling, and sensing.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Explainable deep learning for insights in El Niño and river flows
The El Niño Southern Oscillation (ENSO) is a semi-periodic fluctuation in sea surface temperature (SST) over the tropical central and eastern Pacific Ocean that influences interannual variability in regional hydrology across the world through long-range dependence or teleconnections. Recent research has demonstrated the value of Deep Learning (DL) methods for improving ENSO prediction as well as Complex Networks (CN) for understanding teleconnections. However, gaps in predictive understanding of ENSO-driven river flows include the black box nature of DL, the use of simple ENSO indices to describe a complex phenomenon and translating DL-based ENSO predictions to river flow predictions. Here we show that eXplainable DL (XDL) methods, based on saliency maps, can extract interpretable predictive information contained in global SST and discover SST information regions and dependence structures relevant for river flows which, in tandem with climate network constructions, enable improved predictive understanding. Our results reveal additional information content in global SST beyond ENSO indices, develop understanding of how SSTs influence river flows, and generate improved river flow prediction, including uncertainty estimation. Observations, reanalysis data, and earth system model simulations are used to demonstrate the value of the XDL-CN based methods for future interannual and decadal scale climate projections.
54 ENVIRONMENTAL SCIENCES↗
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 ↗