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At least 181 records · Page 10

Emulator-Based Bayesian Calibration of the CISNET Colorectal Cancer Models

Purpose To calibrate Cancer Intervention and Surveillance Modeling Network (CISNET)'s SimCRC, MISCAN-Colon, and CRC-SPIN simulation models of the natural history colorectal cancer (CRC) with an emulator-based Bayesian algorithm and internally validate the model-predicted outcomes to calibration targets.Methods We used Latin hypercube sampling to sample up to 50,000 parameter sets for each CISNET-CRC model and generated the corresponding outputs. We trained multilayer perceptron artificial neural networks (ANNs) as emulators using the input and output samples for each CISNET-CRC model. We selected ANN structures with corresponding hyperparameters (i.e., number of hidden layers, nodes, activation functions, epochs, and optimizer) that minimize the predicted mean square error on the validation sample. We implemented the ANN emulators in a probabilistic programming language and calibrated the input parameters with Hamiltonian Monte Carlo-based algorithms to obtain the joint posterior distributions of the CISNET-CRC models' parameters. We internally validated each calibrated emulator by comparing the model-predicted posterior outputs against the calibration targets.Results The optimal ANN for SimCRC had 4 hidden layers and 360 hidden nodes, MISCAN-Colon had 4 hidden layers and 114 hidden nodes, and CRC-SPIN had 1 hidden layer and 140 hidden nodes. The total time for training and calibrating the emulators was 7.3, 4.0, and 0.66 h for SimCRC, MISCAN-Colon, and CRC-SPIN, respectively. The mean of the model-predicted outputs fell within the 95% confidence intervals of the calibration targets in 98 of 110 for SimCRC, 65 of 93 for MISCAN, and 31 of 41 targets for CRC-SPIN.Conclusions Using ANN emulators is a practical solution to reduce the computational burden and complexity for Bayesian calibration of individual-level simulation models used for policy analysis, such as the CISNET CRC models. In this work, we present a step-by-step guide to constructing emulators for calibrating 3 realistic CRC individual-level models using a Bayesian approach.

artificial neural networks↗

DeepOpt

DeepOpt is a simple and easy-to-use library for performing Bayesian optimization, leveraging the powerful capabilities of BoTorch. Its key feature is the ability to use neural networks as surrogate functions during the optimization process, allowing Bayesian optimization to work smoothly even on large datasets and in many dimensions. DeepOpt also provides simplified wrappers for BoTorch fitting and optimization routines.

Kur, Eugene↗

FlowPM: Distributed TensorFlow implementation of the FastPM cosmological N-body solver

Here, we present FlowPM, a Particle-Mesh (PM) cosmological N-body code implemented in Mesh-TensorFlow for GPU-accelerated, distributed, and differentiable simulations. We implement and validate the accuracy of a novel multi-grid scheme based on multiresolution pyramids to compute large-scale forces efficiently on distributed platforms. We explore the scaling of the simulation on large-scale supercomputers and compare it with corresponding Python based PM code, finding on an average 10x speed-up in terms of wallclock time. We also demonstrate how this novel tool can be used for efficiently solving large scale cosmological inference problems, in particular reconstruction of cosmological fields in a forward model Bayesian framework with hybrid PM and neural network forward model. We provide skeleton code for these examples and the entire code is publicly available at https://github.com/modichirag/flowpm[Formula presented].

79 ASTRONOMY AND ASTROPHYSICS↗

A framework to evaluate machine learning crystal stability predictions

The rapid adoption of machine learning in various scientific domains calls for the development of best practices and community agreed-upon benchmarking tasks and metrics. We present Matbench Discovery as an example evaluation framework for machine learning energy models, here applied as pre-filters to first-principles computed data in a high-throughput search for stable inorganic crystals. We address the disconnect between (1) thermodynamic stability and formation energy and (2) retrospective and prospective benchmarking for materials discovery. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with adaptive user-defined weighting of various performance metrics allowing researchers to prioritize the metrics they value most. To answer the question of which machine learning methodology performs best at materials discovery, our initial release includes random forests, graph neural networks, one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials. We highlight a misalignment between commonly used regression metrics and more task-relevant classification metrics for materials discovery. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV per atom above the convex hull. The benchmark results demonstrate that universal interatomic potentials have advanced sufficiently to effectively and cheaply pre-screen thermodynamic stable hypothetical materials in future expansions of high-throughput materials databases.

Riebesell, Janosh↗

Constraining the Higgs potential with neural simulation-based inference for di-Higgs production

Determining the form of the Higgs potential is one of the most exciting challenges of modern particle physics. Higgs pair production directly probes the Higgs self-coupling and should be observed in the near future at the High-Luminosity LHC. We explore how to improve the sensitivity to physics beyond the Standard Model through per-event kinematics for di-Higgs events. In particular, we employ machine learning through simulation-based inference to estimate per-event likelihood ratios and gauge potential sensitivity gains from including this kinematic information. In terms of the Standard Model Effective Field Theory, we find that adding a limited number of observables can help to remove degeneracies in Wilson coefficient likelihoods and significantly improve the experimental sensitivity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Overview of Algorithms for Using Particle Morphology in Pre-Detonation Nuclear Forensics

A major goal in pre-detonation nuclear forensics is to infer the processing conditions and/or facility type that produced radiological material. This review paper focuses on analyses of particle size, shape, texture (“morphology”) signatures that could provide information on the provenance of interdicted materials. For example, uranium ore concentrates (UOC or yellowcake) include ammonium diuranate (ADU), ammonium uranyl carbonate (AUC), sodium diuranate (SDU), magnesium diuranate (MDU), and others, each prepared using different salts to precipitate U from solution. Once precipitated, UOCs are often dried and calcined to remove adsorbed water. The products can be allowed to react further, forming uranium oxides UO3, U3O8, or UO2 powders, whose surface morphology can be indicative of precipitation and/or calcination conditions used in their production. This review paper describes statistical issues and approaches in using quantitative analyses of measurements such as particle size and shape to infer production conditions. Statistical topics include multivariate t tests (Hotelling’s T 2 ), design of experiments, and several machine learning (ML) options including decision trees, learning vector quantization neural networks, mixture discriminant analysis, and approximate Bayesian computation (ABC). ABC is emphasized as an attractive option to include the effects of model uncertainty in the selected and fitted forward model used for inferring processing conditions.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Use of Soft Computing Technologies for a Qualitative and Reliable Engine Control System for Propulsion Systems

The problem to be addressed in this paper is to explore how the use of Soft Computing Technologies (SCT) could be employed to improve overall vehicle system safety, reliability, and rocket engine performance by development of a qualitative and reliable engine control system (QRECS). Specifically, this will be addressed by enhancing rocket engine control using SCT, innovative data mining tools, and sound software engineering practices used in Marshall's Flight Software Group (FSG). The principle goals for addressing the issue of quality are to improve software management, software development time, software maintenance, processor execution, fault tolerance and mitigation, and nonlinear control in power level transitions. The intent is not to discuss any shortcomings of existing engine control methodologies, but to provide alternative design choices for control, implementation, performance, and sustaining engineering, all relative to addressing the issue of reliability. The approaches outlined in this paper will require knowledge in the fields of rocket engine propulsion (system level), software engineering for embedded flight software systems, and soft computing technologies (i.e., neural networks, fuzzy logic, data mining, and Bayesian belief networks); some of which are briefed in this paper. For this effort, the targeted demonstration rocket engine testbed is the MC-1 engine (formerly FASTRAC) which is simulated with hardware and software in the Marshall Avionics & Software Testbed (MAST) laboratory that currently resides at NASA's Marshall Space Flight Center, building 4476, and is managed by the Avionics Department. A brief plan of action for design, development, implementation, and testing a Phase One effort for QRECS is given, along with expected results. Phase One will focus on development of a Smart Start Engine Module and a Mainstage Engine Module for proper engine start and mainstage engine operations. The overall intent is to demonstrate that by employing soft computing technologies, the quality and reliability of the overall scheme to engine controller development is further improved and vehicle safety is further insured. The final product that this paper proposes is an approach to development of an alternative low cost engine controller that would be capable of performing in unique vision spacecraft vehicles requiring low cost advanced avionics architectures for autonomous operations from engine pre-start to engine shutdown.

Trevino, Luis↗

Support vector machines

Support Vector Machines (SVMs) are a type of supervised learning algorith,, other examples of which are Artificial Neural Networks (ANNs), Decision Trees, and Naive Bayesian Classifiers. Supervised learning algorithms are used to classify objects labled by a 'supervisor' - typically a human 'expert.'.

multiangle↗

A comparison of Gaussian processes and neural networks for computer model emulation and calibration

The Department of Energy relies on complex physics simulations for prediction in domains like cosmology, nuclear theory, and materials science. These simulations are often extremely computationally intensive, with some requiring days or weeks for a single simulation. In order to assure their accuracy, these models are calibrated against observational data in order to estimate inputs and systematic biases. Because of their great computational complexity, this process typically requires the construction of an emulator, a fast approximation to the simulation. In this paper, two emulator approaches are compared: Gaussian process regression and neural networks. Their emulation accuracy and calibration performance on three real problems of Department of Energy interest is considered. On these problems, the Gaussian process emulator tends to be more accurate with narrower, but still well-calibrated uncertainty estimates. The neural network emulator is accurate, but tends to have large uncertainty on its predictions. Finally, as a result, calibration with the Gaussian process emulator produces more constrained posteriors that still perform well in prediction.

97 MATHEMATICS AND COMPUTING↗

Neural network emulation of flow in heavy-ion collisions at intermediate energies

Applications of new techniques in machine learning are speeding up progress in research in various fields. In this work, we construct and evaluate a deep neural network (DNN) to be used within a Bayesian statistical framework as a faster and more reliable alternative to the Gaussian process (GP) emulator of an isospin-dependent Boltzmann-Uehling-Uhlenbeck (IBUU) transport model simulator of heavy-ion reactions at intermediate beam energies. We found strong evidence of the DNN being able to emulate the IBUU simulator's prediction on the strengths of protons' directed and elliptical flow very efficiently even with small training datasets and with accuracy about ten times higher than the GP. Here, limitations of our present work and future improvements are also discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference

Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Leveraging prior mean models for faster Bayesian optimization of particle accelerators

Tuning particle accelerators is a challenging and time-consuming task that can be automated and carried out efficiently using suitable optimization algorithms, such as model-based Bayesian optimization techniques. One of the major advantages of Bayesian algorithms is the ability to incorporate prior information about beam physics and historical behavior into the model used to make control decisions. In this work, we examine incorporating prior accelerator physics information into Bayesian optimization algorithms by utilizing fast executing, neural network models trained on simulated or historical datasets as prior mean functions in Gaussian process models. We show that in ideal cases, this technique substantially increases convergence speed to optimal solutions in high-dimensional tuning parameter spaces. Additionally, we demonstrate that even in non-ideal cases, where prior models of beam dynamics do not exactly match experimental conditions, the use of this technique can still enhance convergence speed. Finally, we demonstrate how these methods can be used to improve optimization in practical applications, such as transferring information gained from beam dynamics simulations to online control of the LCLS injector, and transferring knowledge gained from experimental measurements across different operating modes, such as accelerating different ion species at the ATLAS heavy ion accelerator.

43 PARTICLE ACCELERATORS↗

Adaptive hyperparameter updating for training restricted Boltzmann machines on quantum annealers

Restricted Boltzmann Machines (RBMs) have been proposed for developing neural networks for a variety of unsupervised machine learning applications such as image recognition, drug discovery, and materials design. The Boltzmann probability distribution is used as a model to identify network parameters by optimizing the likelihood of predicting an output given hidden states trained on available data. Training such networks often requires sampling over a large probability space that must be approximated during gradient based optimization. Quantum annealing has been proposed as a means to search this space more efficiently which has been experimentally investigated on D-Wave hardware. D-Wave implementation requires selection of an effective inverse temperature or hyperparameter (β) within the Boltzmann distribution which can strongly influence optimization. Here, we show how this parameter can be estimated as a hyperparameter applied to D-Wave hardware during neural network training by maximizing the likelihood or minimizing the Shannon entropy. We find both methods improve training RBMs based upon D-Wave hardware experimental validation on an image recognition problem. Neural network image reconstruction errors are evaluated using Bayesian uncertainty analysis which illustrate more than an order magnitude lower image reconstruction error using the maximum likelihood over manually optimizing the hyperparameter. The maximum likelihood method is also shown to out-perform minimizing the Shannon entropy for image reconstruction.

97 MATHEMATICS AND COMPUTING↗

Inference, Prediction, & Entropy-Rate Estimation of Continuous-Time, Discrete-Event Processes

Inferring models, predicting the future, and estimating the entropy rate of discrete-time, discrete-event processes is well-worn ground. However, a much broader class of discrete-event processes operates in continuous-time. Here, we provide new methods for inferring, predicting, and estimating them. The methods rely on an extension of Bayesian structural inference that takes advantage of neural network’s universal approximation power. Based on experiments with complex synthetic data, the methods are competitive with the state-of-the-art for prediction and entropy-rate estimation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Random Forest Regressor-Based Approach for Detecting Fault Location and Duration in Power Systems

Power system failures or outages due to short-circuits or “faults” can result in long service interruptions leading to significant socio-economic consequences. It is critical for electrical utilities to quickly ascertain fault characteristics, including location, type, and duration, to reduce the service time of an outage. Existing fault detection mechanisms (relays and digital fault recorders) are slow to communicate the fault characteristics upstream to the substations and control centers for action to be taken quickly. Fortunately, due to availability of high-resolution phasor measurement units (PMUs), more event-driven solutions can be captured in real time. In this paper, we propose a data-driven approach for determining fault characteristics using samples of fault trajectories. A random forest regressor (RFR)-based model is used to detect real-time fault location and its duration simultaneously. This model is based on combining multiple uncorrelated trees with state-of-the-art boosting and aggregating techniques in order to obtain robust generalizations and greater accuracy without overfitting or underfitting. Four cases were studied to evaluate the performance of RFR: 1. Detecting fault location (case 1), 2. Predicting fault duration (case 2), 3. Handling missing data (case 3), and 4. Identifying fault location and length in a real-time streaming environment (case 4). A comparative analysis was conducted between the RFR algorithm and state-of-the-art models, including deep neural network, Hoeffding tree, neural network, support vector machine, decision tree, naive Bayesian, and K-nearest neighborhood. Experiments revealed that RFR consistently outperformed the other models in detection accuracy, prediction error, and processing time.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Probabilistic Classification Using Elemental Abundance Distributions and Lossless Image Compression in Apollo 17 Lunar Dust Samples from Mare Serenitatis

We have previously outlined a strategy for the detection of fossils [Storrie-Lombardi and Hoover, 2004] and extant microbial life [Storrie-Lombaudi and Hoover, 20051 during robotic missions to Mars using co-registered structural and chemical signatures. Data inputs included image lossless compression indices to estimate relative textural complexity and elemental abundance distributions. Two exploratory classification algorithms (principal component analysis and hierarchical cluster analysis) provide an initial tentative classification of all targets. Nonlinear stochastic neural networks are then trained to produce a Bayesian estimate of algorithm classification accuracy. The strategy previously has been successful in distinguishing regions of biotic and abiotic alteration of basalt glass from unaltered samples. [Storrie-Lombardi and Fisk, 2004; Storrie-Lombardi and Fisk, 2004] Such investigations of abiotic versus biotic alteration of terrestrial mineralogy on Earth are compromised by .the difficulty finding mineralogy completely unaffected by the ubiquitous presence of microbial life on the planet. The renewed interest in lunar exploration offers an opportunity to investigate geological materials that may exhibit signs of aqueous alteration, but are highly unlikely to contain contaminating biological weathering signatures. We here present an extension of our earlier data set to include lunar dust samples obtained during the Apollo 17 mission. Apollo 17 landed in the Taurus-Littrow Valley in Mare Serenitatis. Most of the rock samples from this region of the lunar highlands are basalts comprised primarily of plagioclase and pyroxene and selected examples of orange and black volcanic glass. SEM images and elemental abundances (C6, N7, O8, Na11, Mg12, Al13, Si14, P15, S16, Cll7, K19, Ca20, Fe26) for a series of targets in the lunar dust samples are compared to the extant cyanobacteria, fossil trilobites, Orgueil meteorite, and terrestrial basalt targets previously discussed. The data set provides a first step in producing a quantitative probabilistic methodology for geobiological analysis of returned lunar samples or in situ exploration.

Storrie-Lombardi, Michael C.↗

Dark Energy Survey Year 3 results: optimized $w$CDM simulation-based inference with weak lensing map-level hybrid statistics

We present cosmological constraints from the Dark Energy Survey Year 3 (DES Y3) weak lensing data using hierarchical hybrid statistics within a Bayesian simulation-based inference framework that is based on the Gower Street simulations. To maximize the precision of the inference, we have developed a new, information-theory based, data compression of the weak lensing maps to just seven highly informative summary statistics. The hybrid scheme exploits the high information content of the power spectrum, compressing both the power spectrum and neural-based summaries that are designed to extract further information. Our simulation-based approach enables principled forward modelling of all major sources of systematic uncertainty and survey properties into realistic mock observations, including the survey mask, photometric redshift uncertainties, intrinsic galaxy alignments, multiplicative shear calibration bias, source galaxy clustering, non-Gaussian shape noise, and non-linear structure formation. The summary statistics are then used in a Bayesian simulation-based inference pipeline. The inference is validated through coverage tests and checks for robustness against baryonic feedback. Assuming a $w$CDM cosmology, our analysis yields $S_8 = 0.808 \pm 0.017$, $Ω_{\rm m} = 0.325 \pm 0.024$, and $w < -0.766$ (marginalized posterior 68 per cent credible intervals). This rigorous combination of information theory, physics- and neural network-based extreme data compression, and principled Bayesian analysis improves the figure of merit for $(Ω_{\rm m}, S_8, w)$ by 60 per cent over the previous state-of-the-art, and by almost a factor of 3 over two-point analyses of the same data. They are the most precise joint constraints on $(Ω_{\rm m}, S_8, w)$ from weak gravitational lensing data alone of any survey to date. We intend to apply this analysis to the more recent DES Y6 data.

Williamson, J. [University Coll. London]↗