Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design
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97 MATHEMATICS AND COMPUTING↗
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Results for “deep generative models”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Report on the AAPM grand challenge on deep generative modeling for learning medical image statistics
Abstract Background The findings of the 2023 AAPM Grand Challenge on Deep Generative Modeling for Learning Medical Image Statistics are reported in this Special Report. Purpose The goal of this challenge was to promote the development of deep generative models for medical imaging and to emphasize the need for their domain‐relevant assessments via the analysis of relevant image statistics. Methods As part of this Grand Challenge, a common training dataset and an evaluation procedure was developed for benchmarking deep generative models for medical image synthesis. To create the training dataset, an established 3D virtual breast phantom was adapted. The resulting dataset comprised about 108 000 images of size 512 512. For the evaluation of submissions to the Challenge, an ensemble of 10 000 DGM‐generated images from each submission was employed. The evaluation procedure consisted of two stages. In the first stage, a preliminary check for memorization and image quality (via the Fréchet Inception Distance [FID]) was performed. Submissions that passed the first stage were then evaluated for the reproducibility of image statistics corresponding to several feature families including texture, morphology, image moments, fractal statistics, and skeleton statistics. A summary measure in this feature space was employed to rank the submissions. Additional analyses of submissions was performed to assess DGM performance specific to individual feature families, the four classes in the training data, and also to identify various artifacts. Results Fifty‐eight submissions from 12 unique users were received for this Challenge. Out of these 12 submissions, 9 submissions passed the first stage of evaluation and were eligible for ranking. The top‐ranked submission employed a conditional latent diffusion model, whereas the joint runners‐up employed a generative adversarial network, followed by another network for image superresolution. In general, we observed that the overall ranking of the top 9 submissions according to our evaluation method (i) did not match the FID‐based ranking, and (ii) differed with respect to individual feature families. Another important finding from our additional analyses was that different DGMs demonstrated similar kinds of artifacts. Conclusions This Grand Challenge highlighted the need for domain‐specific evaluation to further DGM design as well as deployment. It also demonstrated that the specification of a DGM may differ depending on its intended use.
Radiology, Nuclear Medicine & Medical Imaging↗
CO 2 storage site characterization using ensemble-based approaches with deep generative models
Estimating spatially distributed properties such as permeability from available sparse measurements is a great challenge in efficient subsurface CO 2 storage operations. In this paper, a deep generative model that can accurately capture complex subsurface structure is tested with an ensemble-based inversion method for accurate and accelerated characterization of CO 2 storage sites. We chose Wasserstein Generative Adversarial Network with Gradient Penalty (WGAN-GP) for its realistic reservoir property representation and Ensemble Smoother with Multiple Data Assimilation (ES-MDA) for its robust data fitting and uncertainty quantification capability. WGAN-GP are trained to generate high-dimensional permeability fields from a low-dimensional latent space and ES-MDA then updates the latent variables by assimilating available measurements. Several subsurface site characterization examples including Gaussian, channelized, and fractured reservoirs are used to evaluate the accuracy and computational efficiency of the proposed method and the main features of the unknown permeability fields are characterized accurately with reliable uncertainty quantification. Furthermore, the estimation performance is compared with a widely-used variational, i.e., optimization-based, inversion approach, and the proposed approach outperforms the variational inversion method in several benchmark cases. We explain such superior performance by visualizing the objective function in the latent space: because of nonlinear and aggressive dimension reduction via generative modeling, the objective function surface becomes extremely complex while the ensemble approximation can smooth out the multi-modal surface during the minimization. This suggests that the ensemble-based approach works well over the variational approach when combined with deep generative models at the cost of forward model runs unless convergence-ensuring modifications are implemented in the variational inversion.
42 ENGINEERING↗
VFR Trajectory Forecasting using Deep Generative Model for Autonomous Airspace Operations
To enable the airspace integration of autonomous operations, such as uncrewed aircraft conducting cargo deliveries, there is a need to forecast the positions of the surrounding traffic with which they may interact. This paper focuses on forecasting Visual Flight Rules traffic, a significant source of uncertainty and risk in the airspace, especially around small regional airports, due to the unplanned and often untracked nature of such flights. A deep generative model is developed, trained on historical traffic data at example towered and non-towered airports, and used to predict flight trajectories. Experimental results are presented comparing the performance of variational autoencoder and classical machine learning forecasting when applied to both the towered and non-towered airports over varying time horizons. The results show the advantages of the variational autoencoder in producing accurate probabilistic forecasts over varying time horizons.
uncrewed aircraft↗
VFR Trajectory Forecasting using Deep Generative Model for Autonomous Airspace Operations
To enable the airspace integration of autonomous operations, such as uncrewed aircraft conducting cargo deliveries, there is a need to forecast the positions of the surrounding traffic with which they may interact. This paper focuses on forecasting Visual Flight Rules traffic, a significant source of uncertainty and risk in the airspace, especially around small regional airports, due to the unplanned and often untracked nature of such flights. A deep generative model is developed, trained on historical traffic data at example towered and non-towered airports, and used to predict flight trajectories. Experimental results are presented comparing the performance of variational autoencoder and classical machine learning forecasting when applied to both the towered and non-towered airports over varying time horizons. The results show the advantages of the variational autoencoder in producing accurate probabilistic forecasts over varying time horizons.
uncrewed aircraft↗
A Path Towards Quantum Advantage in Training Deep Generative Models with Quantum Annealing
A class of quantum-classical hybrid machine-learning algorithms can be obtained by integrating classical deep generative models with quantum probability distributions as 'priors' over their latent variables. We introduce a hybrid implementation of variational autoencoders (QVAE) and also present a technique to hybridize flow-based invertible generative models. We demonstrate the use of D-Wave quantum annealers as physical simulators of quantum Boltzmann machines (QBM) to perform quantum-assisted training of QVAE. Latent-space QBM develop slowly mixing modes, opening a path to obtain quantum advantage in generative modeling with available quantum devices.
Vinci, Walter↗
Deep Generative Models in Energy System Applications: Review, Challenges, and Future Directions
In recent years, with the advent of mature machine learning products like ChatGPT, Stable Diffusion, and Sora, the world has witnessed tremendous changes driven by the rapid development of generative artificial intelligence (GAI). Beyond applications in text, speech, image, and video creation, deep generative models (DGMs) underpinning these cutting-edge technologies have also been employed by domain researchers to address scientific and engineering challenges. This paper aims to fill a gap in the research community by providing a systematic review of how DGMs have been utilized in energy system applications. After introducing four most popular DGMs, we review and categorize 196 research articles into five focus areas: data generation, forecasting, situational awareness, modeling, and optimal decision-making. Through this classification, we uncover trends in how DGMs are employed for each type of problem, highlighting GAI techniques that contribute to breakthroughs over traditional methods. We discuss limitations in existing literature, engineering challenges, and propose future directions, all tailored to the unique nature of problems in energy system engineering. Our goal is to offer insights for energy system domain researchers, providing a comprehensive view of existing studies and potential future opportunities.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Deep generative models for vehicle speed trajectories
Generating realistic vehicle speed trajectories is a crucial component in evaluating vehicle fuel economy and in predictive control of self-driving cars. Traditional generative models rely on Markov chain methods and can produce accurate synthetic trajectories but are subject to the curse of dimensionality. They do not allow to include conditional input variables into the generation process. In this paper, we show how extensions to deep generative models allow accurate and scalable generation. Proposed architectures involve recurrent and feed-forward layers and are trained using adversarial techniques. Our models are shown to perform well on generating vehicle trajectories using a model trained on GPS data from Chicago metropolitan area.
33 ADVANCED PROPULSION SYSTEMS↗
Data-driven prediction of α IIb β 3 integrin activation paths using manifold learning and deep generative modeling
The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αI I b β3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. Furthermore, this work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multi-scale technique to predict transition pathways for biomolecular systems.
97 MATHEMATICS AND COMPUTING↗
Deep Generative Models for Fast Photon Shower Simulation in ATLAS
The need for large-scale production of highly accurate simulated event samples for the extensive physics programme of the ATLAS experiment at the Large Hadron Collider motivates the development of new simulation techniques. Building on the recent success of deep learning algorithms, variational autoencoders and generative adversarial networks are investigated for modelling the response of the central region of the ATLAS electromagnetic calorimeter to photons of various energies. The properties of synthesised showers are compared with showers from a full detector simulation using GEANT4 . Both variational autoencoders and generative adversarial networks are capable of quickly simulating electromagnetic showers with correct total energies and stochasticity, though the modelling of some shower shape distributions requires more refinement. This feasibility study demonstrates the potential of using such algorithms for ATLAS fast calorimeter simulation in the future and shows a possible way to complement current simulation techniques.
97 MATHEMATICS AND COMPUTING↗
A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases
Human diseases are characterized by intricate cellular dynamics. Single-cell transcriptomics provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in silico drug interventions. Here we introduce UNAGI, a deep generative neural network tailored to analyse time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modelling and screening. When applied to a dataset from patients with idiopathic pulmonary fibrosis, UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation using proteomics reveals the accuracy of UNAGI’s cellular dynamics analysis, and the use of the fibrotic cocktail-treated human precision-cut lung slices confirms UNAGI’s predictions that nifedipine, an antihypertensive drug, may have anti-fibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including COVID, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond idiopathic pulmonary fibrosis, amplifying its use in the quest for therapeutic solutions across diverse pathological landscapes.
Neural Network↗
Conditional deep generative models for simultaneous simulation and reconstruction of entire events
We extend the particle-flow neural assisted simulations (arnassus) framework of fast simulation and reconstruction to entire collider events. In particular, we use two generative artificial intelligence tools, continuous normalizing flows and diffusion models, to create a set of reconstructed particle-flow objects conditioned on truth-level particles from CMS Open Simulations. While previous work focused on jets, our updated methods now can accommodate all particle-flow objects in an event along with particle-level attributes like particle type and production vertex coordinates. This approach is fully automated, entirely written in Python, and GPU-compatible. Using a variety of physics processes at the LHC, we show that the extended arnassus is able to generalize beyond the training dataset and outperforms the standard, public tool elphes.
Dreyer, Etienne [Weizmann Institute of Science, Re↗
Designing Large Datasets: Data-Scarce and Stable Deep Generative Models for Turning Sparse Experiments into Big Datasets in Materials Science
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Robertson, Andreas Euan↗
Physics-informed Deep Generative Models to Quantify Uncertainties in Geophysical Full-waveform Inversion
SSA oral presentation
Elmeliegy, Abdelrahman M↗
Local-Global Decompositions: Data-scarce and Stable Deep Generative Models for Turning Sparse Experiments into Big Datasets in Materials Science
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Robertson, Andreas Euan↗
Generative models on phase space
Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be concentrated on a submanifold of the data embedding space. For high-energy physics data, consisting of collections of relativistic energy-momentum 4-vectors, this submanifold can enforce extremely strong physically-motivated priors, such as energy and momentum conservation. If these constraints are learned only approximately, rather than exactly, this can inhibit the interpretability and reliability of such generative models. To remedy this deficiency, we introduce generative models which are, by construction, confined at every step of their sampling trajectory to the manifold of massless N-particle Lorentz-invariant phase space in the center-of-momentum frame. In the case of diffusion models, the "pure noise" forward process endpoint corresponds to the uniform distribution on phase space, which provides a clear starting point from which to identify how correlations among the particles emerge during the reverse (de-noising) process. We demonstrate that our models are able to learn both few-particle and many-particle distributions with various singularity structures, paving the way for future interpretability studies using generative models trained on simulated jet data.
Bogorad, Zachary [Fermilab]↗
Enabling Interoperability in Earth System Digital Twins (ESDT): Integrating Observations, Models, and AI for Actionable Insights Through NASA'S Intelligent Systems Technology Program
NASA’s Intelligent Systems Technology Program (IST) is driving a paradigm shift in Earth science through the development of Earth System Digital Twins (ESDT). These integrated information systems create a dynamic "digital replica" of the Earth by harmonizing continuous, multi-source observations with high-fidelity models and state-of-the-art artificial intelligence (AI) that enable “What now?”, “What next?”, and “What if?” scenario building. These scenarios are reflected in NASA IST’s series of ESDTs, from the Coastal Zone Digital Twin that integrates complex data on the current state of the Chesapeake Bay to the Terrestrial Environmental Rapid-Replication and Assimilation Hydrometeorological (TerraHydro) AI-based ESDT that forecasts water movement across Earth’s surface, to the Agriculture Land Information System (AgLIS) which can be used to assess optimal planting dates and crop yield estimates. By bridging the gap between vast data archives and actionable insights, these projects enable a system-of-systems approach to understanding complex, interacting Earth processes. This poster will highlight recent innovations and future directions from NASA’s ESDT initiatives: Continuous Data Assimilation & Multi-Source Fusion. A core requirement of the ESDT work is the transition from static models to dynamic "living" replicas. This involves creating frameworks for the continual assimilation of near-real-time data from uncoordinated, heterogeneous sources, including satellite observations and airborne assets, and ground-based Internet of Things (IoT) sensors. These systems link design, operational status, and environmental data, ensuring the digital twin accurately reflects the current state of the physical Earth system. High-Fidelity Hybrid Modeling & Computational Acceleration to enable interactive "what-if" explorations, programs are moving beyond traditional, slow physical solvers by developing fast surrogate machine learning models and Deep Generative Models (DGMs). These hybrid approaches use neural networks to emulate complex physics, such as cloud feedback or ocean dynamics, at a fraction of the original computing cost, often leveraging advanced hardware like Graphics Processing Units (GPUs) to achieve the necessary scale. Federated Ecosystems & Interoperable Frameworks rather than building isolated tools, NASA IST is moving toward federated ESDTs and reusable analytic collaborative frameworks. This theme focuses on interoperability standards and common ontologies that allow specialized digital twins to interact and share data. This system-of-systems architecture supports multi-discipline investigations, such as analyzing how upstream watershed changes impact downstream urban flooding or how wildfire emissions affect regional air quality. By leveraging these advancements, ESDTs empower researchers and decision-makers to conduct real-time analysis and run complex hypothetical scenarios, ultimately improving our understanding of Earth’s evolving systems and informing critical real-world applications.
Earth System↗