Disentangled Multi-Fidelity Deep Bayesian Active Learning

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Other deep learning-based methods use the hierarchical structure, which only supports passing information from low-fidelity to high-fidelity. This approach also leads to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel disentangled deep Bayesian learning framework for multi-fidelity active learning, that learns the surrogate models conditioned on the distribution of functions at multiple fidelities.

Multi-fidelity Hierarchical Neural Processes

Science and engineering fields use computer simulation extensively. These simulations are often run at multiple levels of sophistication to balance accuracy and efficiency. Multi-fidelity surrogate modeling reduces the computational cost by fusing different simulation outputs. Cheap data generated from low-fidelity simulators can be combined with limited high-quality data generated by an expensive high-fidelity simulator. Existing methods based on Gaussian processes rely on strong assumptions of the kernel functions and can hardly scale to high-dimensional settings. We propose Multi-fidelity Hierarchical Neural Processes (MF-HNP), a unified neural latent variable model for multi-fidelity surrogate modeling. MF-HNP inherits the flexibility and scalability of Neural Processes. The latent variables transform the correlations among different fidelity levels from observations to latent space. The predictions across fidelities are conditionally independent given the latent states. It helps alleviate the error propagation issue in existing methods. MF-HNP is flexible enough to handle non-nested high dimensional data at different fidelity levels with varying input and output dimensions. We evaluate MF-HNP on epidemiology and climate modeling tasks, achieving competitive performance in terms of accuracy and uncertainty estimation. In contrast to deep Gaussian Processes with only low-dimensional (< 10) tasks, our method shows great promise for speeding up high-dimensional complex simulations (over 7000 for epidemiology modeling and 45000 for climate modeling).

Multi defect detection and analysis of electron microscopy images with deep learning

Electron microscopy is widely used to explore defects in crystal structures, but human detecting of defects is often time-consuming, error-prone, and unreliable, and is not scalable to large numbers of images or real-time analysis. In this work, we discuss the application of machine learning approaches to find the location and geometry of different defect clusters in irradiated steels. We show that a deep learning based Faster R-CNN analysis system has a performance comparable to human analysis with relatively small training data sets. This study proves the promising ability to apply deep learning to assist the development of automated microscopy data analysis even when multiple features are present and paves the way for fast, scalable, and reliable analysis systems for massive amounts of modern electron microscopy data.

A Deep Learning Based Automatic Defect Analysis Framework for In-situ TEM Ion Irradiations

Videos captured using Transmission Electron Microscopy (TEM) can encode details regarding the morphological and temporal evolution of a material by taking snapshots of the microstructure sequentially. However, manual analysis of such video is tedious, error-prone, unreliable, and prohibitively time-consuming if one wishes to analyze a significant fraction of frames for even videos of modest length. In this work, we developed an automated TEM video analysis system for microstructural features based on the advanced object detection model called YOLO and tested the system on an in-situ ion irradiation TEM video of dislocation loops formed in a FeCrAl alloy. The system provides analysis of features observed in TEM including both static and dynamic properties using the YOLO-based defect detection module coupled to a geometry analysis module and a dynamic tracking module. Results show that the system can achieve human comparable performance with an F1 score of 0.89 for fast, consistent, and scalable frame-level defect analysis. This result is obtained on a real but exceptionally clean and stable data set and more challenging data sets may not achieve this performance. The dynamic tracking also enabled evaluation of individual defect evolution like per defect growth rate at a fidelity never before achieved using common human analysis methods. Our work shows that automatically detecting and tracking interesting microstructures and properties contained in TEM videos is viable and opens new doors for evaluating materials dynamics.

Accelerating Stochastic Simulation with Interactive Neural Processes

Stochastic simulations such as large-scale, spatiotemporal, age-structured epidemic models are computationally expensive at fine-grained resolution. We propose Interactive Neural Process (INP), an interactive framework to continuously learn a deep learning surrogate model and accelerate simulation. Our framework is based on the novel integration of Bayesian active learning, stochastic simulation and deep sequence modeling. In particular, we develop a novel spatiotemporal neural process model to mimic the underlying process dynamics. Our model automatically infers the latent process which describes the intrinsic uncertainty of the simulator. This also gives rise to a new acquisition function that can quantify the uncertainty of deep learning predictions. We design Bayesian active learning algorithms to iteratively query the simulator, gather more data, and continuously improve the model. We perform theoretical analysis and demonstrate that our approach reduces sample complexity compared with random sampling in high dimension. Empirically, we demonstrate our framework can faithfully imitate the behavior of a complex infectious disease simulator with a small number of examples, enabling rapid simulation and scenario exploration.

Quantifying Uncertainty in Deep Spatiotemporal Forecasting

Deep learning is gaining increasing popularity for spatiotemporal forecasting. However, prior works have mostly focused on point estimates without quantifying the uncertainty of the predictions. In high stakes domains, being able to generate probabilistic forecasts with confidence intervals is critical to risk assessment and decision making. Hence, a systematic study of uncertainty quantification (UQ) methods for spatiotemporal forecasting is missing in the community. In this paper, we describe two types of spatiotemporal forecasting problems: regular grid-based and graph-based. Then we analyze UQ methods from both the Bayesian and the frequentist point of view, casting in a unified framework via statistical decision theory. Through extensive experiments on real-world road network traffic, epidemics, and air quality forecasting tasks, we reveal the statistical and computational trade-offs for different UQ methods: Bayesian methods are typically more robust in mean prediction, while confidence levels obtained from frequentist methods provide more extensive coverage over data variations. Computationally, quantile regression type methods are cheaper for a single confidence interval but require re-training for different intervals. Sampling based methods generate samples that can form multiple confidence intervals, albeit at a higher computational cost.

DeepGLEAM: a hybrid mechanistic and deep learning model for COVID-19 forecasting

We introduce DeepGLEAM, a hybrid model for COVID-19 forecasting. DeepGLEAM combines a mechanistic stochastic simulation model GLEAM with deep learning. It uses deep learning to learn the correction terms from GLEAM, which leads to improved performance. We further integrate various uncertainty quantification methods to generate confidence intervals. We demonstrate DeepGLEAM on real-world COVID-19 mortality forecasting tasks.

DeepGLEAM: an hybrid mechanistic and deep learning model for COVID-19 forecasting

We introduce DeepGLEAM, a hybrid model for COVID-19 forecasting. DeepGLEAM combines a mechanistic stochastic simulation model GLEAM with deep learning. It uses deep learning to learn the correction terms from GLEAM, which leads to improved performance. We further integrate various uncertainty quantification methods to generate confidence intervals. We demonstrate DeepGLEAM on real-world COVID-19 mortality forecasting tasks.