Uncertainty Quantification for Deep Learning Models in Protein-Ligand Binding Affinity Prediction
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Here, we develop a backward stochastic differential equation based probabilistic machine learning method, which formulates a class of stochastic neural networks as a stochastic optimal control problem. An efficient stochastic gradient descent algorithm is introduced with the gradient computed through a backward stochastic differential equation. Convergence analysis for stochastic gradient descent optimization and numerical experiments for applications of stochastic neural networks are carried out to validate our methodology in both theory and performance.
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Abstract not provided.
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Abstract Deep optical and near-infrared imaging of the entire Galactic plane is essential for understanding our Galaxy’s stars, gas, and dust. The second data release of the Dark Energy Camera (DECam) Plane Survey extends the five-band optical and near-infrared survey of the southern Galactic plane to cover 6.5% of the sky, ∣ b ∣ ≤ 10°, and 6° > ℓ > −124°, complementary to coverage by Pan-STARRS1. Typical single-exposure effective depths, including crowding effects and other complications, are 23.5, 22.6, 22.1, 21.6, and 20.8 mag in g , r , i , z , and Y bands, respectively, with around 1″ seeing. The survey comprises 3.32 billion objects built from 34 billion detections in 21,400 exposures, totaling 260 hr open shutter time on the DECam at Cerro Tololo. The data reduction pipeline features several improvements, including the addition of synthetic source injection tests to validate photometric solutions across the entire survey footprint. A convenient functional form for the detection bias in the faint limit was derived and leveraged to characterize the photometric pipeline performance. A new postprocessing technique was applied to every detection to debias and improve uncertainty estimates of the flux in the presence of structured backgrounds, specifically targeting nebulosity. The images and source catalogs are publicly available at http://decaps.skymaps.info/ .
Deep learning models are being widely used in the field of combustion. Given the black-box nature of typical neural network based models, uncertainty quantification (UQ) is critical to ensure the reliability of predictions as well as the training datasets, and for a principled quantification of noise and its various sources. Deep learning surrogate models for predicting properties of chemical compounds and mixtures have been recently shown to be promising for enabling data-driven fuel design and optimization, with the ultimate goal of improving efficiency and lowering emissions from combustion engines. In this study, UQ is performed for a multi-task deep learning model that simultaneously predicts the research octane number (RON), Motor Octane Number (MON), and Yield Sooting Index (YSI) of pure components and multicomponent blends. The deep learning model is comprised of three smaller networks: Extractor 1, Extractor 2, and Predictor, and a mixing operator. The molecular fingerprints of individual components are encoded via Extractor 1 and Extractor 2, the mixing operator generates fingerprints for mixtures/blends based on linear mixing operation, and the predictor maps the fingerprint to the target properties. Two different classes of UQ methods, Monte Carlo ensemble methods and Bayesian neural networks (BNNs), are employed for quantifying the epistemic uncertainty. Combinations of Bernoulli and Gaussian distributions with DropConnect and DropOut techniques are explored as ensemble methods. All the DropConnect, DropOut and Bayesian layers are applied to the predictor network. Aleatoric uncertainty is modeled by assuming that each data point has an independent uncertainty associated with it. The results of the UQ study are further analyzed to compare the performance of BNN and ensemble methods. Although this study is confined to UQ of fuel property prediction, the methodologies are applicable to other deep learning frameworks that are being widely used in the combustion community.
Second-order photon correlation measurements [g (2) (τ) functions] are widely used to classify single-photon emission purity in quantum emitters or to measure the multiexciton quantum yield of emitters that can simultaneously host multiple excitations – such as quantum dots – by evaluating the value of g (2) (τ = 0). Accumulating enough photons to accurately calculate this value is time consuming and could be accelerated by fitting of few-shot photon correlations. Here, we develop an uncertainty-aware, deep adversarial autoencoder ensemble (AAE) that reconstructs noise-free g (2) (τ) functions from noise-dominated, few-shot inputs. The model is trained with simulated g (2) (τ) functions that are facilely generated by Poisson sampling time bins. The AAE reconstructions are performed orders-of-magnitude faster, with reconstruction errors and estimates of g (2) (τ = 0) that are lower in variance and similar in accuracy compared to Maximum likelihood estimation and Levenberg-Marquardt least-squares fitting approaches, for simulated and experimentally measured few-shot g (2) (τ) functions (~100 two-photon events) of InP/ZnS/ZnSe and CdS/CdSe/CdS quantum dots. The deep-ensemble model comprises eight individual autoencoders, allowing for probabilistic reconstructions of noise-free g (2) (τ) functions, and we show that the predicted variance scales inversely with number of shots, with comparable uncertainties to computationally intensive Markov chain Monte Carlo sampling. Furthermore, this work demonstrates the advantage of machine learning models to perform uncertainty-aware, fast, and accurate reconstructions of simple Poisson-distributed photon correlation functions, allowing for on-the-fly reconstructions and accelerated materials characterization of solid-state quantum emitters.
Abstract not provided.
We propose a Bayesian physics-informed neural network (B-PINN) to solve both forward and inverse nonlinear problems described by partial differential equations (PDEs) and noisy data. In this Bayesian framework, the Bayesian neural network (BNN) combined with a PINN for PDEs serves as the prior while the Hamiltonian Monte Carlo (HMC) or the variational inference (VI) could serve as an estimator of the posterior. B-PINNs make use of both physical laws and scattered noisy measurements to provide predictions and quantify the aleatoric uncertainty arising from the noisy data in the Bayesian framework. Compared with PINNs, in addition to uncertainty quantification, B-PINNs obtain more accurate predictions in scenarios with large noise due to their capability of avoiding overfitting. We conduct a systematic comparison between the two different approaches for the B-PINNs posterior estimation (i.e., HMC or VI), along with dropout used for quantifying uncertainty in deep neural networks. Our experiments show that HMC is more suitable than VI with mean field Gaussian approximation for the B-PINNs posterior estimation, while dropout employed in PINNs can hardly provide accurate predictions with reasonable uncertainty. Finally, we replace the BNN in the prior with a truncated Karhunen-Loève (KL) expansion combined with HMC or a deep normalizing flow (DNF) model as posterior estimators. The KL is as accurate as BNN and much faster but this framework cannot be easily extended to high-dimensional problems unlike the BNN based framework.
The "Deep Blue" aerosol optical depth (AOD) retrieval algorithm was introduced in Collection 5 of the Moderate Resolution Imaging Spectroradiometer (MODIS) product suite, and complemented the existing "Dark Target" land and ocean algorithms by retrieving AOD over bright arid land surfaces, such as deserts. The forthcoming Collection 6 of MODIS products will include a "second generation" Deep Blue algorithm, expanding coverage to all cloud-free and snow-free land surfaces. The Deep Blue dataset will also provide an estimate of the absolute uncertainty on AOD at 550 nm for each retrieval. This study describes the validation of Deep Blue Collection 6 AOD at 550 nm (Tau(sub M)) from MODIS Aqua against Aerosol Robotic Network (AERONET) data from 60 sites to quantify these uncertainties. The highest quality (denoted quality assurance flag value 3) data are shown to have an absolute uncertainty of approximately (0.086+0.56Tau(sub M))/AMF, where AMF is the geometric air mass factor. For a typical AMF of 2.8, this is approximately 0.03+0.20Tau(sub M), comparable in quality to other satellite AOD datasets. Regional variability of retrieval performance and comparisons against Collection 5 results are also discussed.
DeltaUQ is a PyTorch library for uncertainty quantification with deep neural networks. It is designed to be used transform any deep neural network to produce uncertainties on any task (classification, regression).
Model ensembles are effective tools for estimating prediction uncertainty in deep learning atomistic force fields. However, their widespread adoption is hindered by high computational costs and overconfident error estimates. In this work, we address these challenges by leveraging distributions of per-sample errors obtained during training and employing a distance-based similarity search in the model latent space. Our method, which we call LTAU (Loss Trajectory Analysis for Uncertainty), efficiently estimates the full probability distribution function of errors for any test point using the logged training errors, achieving speeds that are 2–3 orders of magnitudes faster than typical ensemble methods and allowing it to be used for tasks where training or evaluating multiple models would be infeasible. We apply LTAU towards estimating parametric uncertainty in atomistic force fields (LTAU-FF), demonstrating that it produces well-calibrated confidence intervals and predicts errors that correlate strongly with the true errors for data near the training domain. Furthermore, we show that the errors predicted by LTAU-FF can be used in practical applications for detecting out-of-domain data, tuning model performance, and predicting failure during simulations. We believe that LTAU will be a valuable tool for uncertainty quantification in atomistic force fields and is a promising method that should be further explored in other domains of machine learning.
Abstract The effectiveness of Carbon Capture and Storage (CCS) as an imperative decarbonization technology relies on the sealing capacity of a fine‐grained caprock to permanently store CO 2 deep underground. Uncertainties in assessing the caprock sealing capacity increase with the spatial and temporal scales and may delay CCS deployment at the gigatonne scale. We have developed a computationally efficient transport model to capture the dynamics of basin‐wide upward CO 2 migration in a multi‐layered setting over geological time scales. We find that massive capillary breakthrough and viscous flow of CO 2 , even through pervasively fractured caprocks, are unlikely to occur and compromise the storage security. Potential leakage from the injection reservoir is hampered by repetitive layering of overlying caprocks. This finding agrees with geologic intuition and should be understandable by the public, contributing to the development of climate policies around this technology with increased confidence that CO 2 will be indefinitely contained in the subsurface.
Hydropower is a key energy source in the western interconnection of the United States, comprising about 25% of the annual installed nameplate capacity in 2020. However, its generation is increasingly impacted by changing hydrological conditions, operational constraints, environmental factors, water availability, and aging dam infrastructure. Assessing hydropower availability and resource adequacy is valuable for shaping energy policies and infrastructure requirements. In this study we evaluate the sensitivity of resource adequacy in the Western Interconnection to the unavailability of hydropower plants, under a wide-ranging set of 16,384 hydropower loss scenarios derived from a combination of 14 major hydrologic regions. Although a complete loss of hydropower capacity in any region is unlikely, studying such scenarios helps in identifying hydrologic regions most critical for maintaining resource adequacy. So, we identify key hydrologic regions with disproportionately large adequacy impacts relative to their installed hydropower capacity and study compounding effects between regions using classification and regression trees. Even after controlling for total installed capacity, we find that hydropower resources in the Pacific Northwest contribute the most to interconnection-wide adequacy outcomes, with resources in Northern California and the Desert Southwest providing more moderate incremental contributions.
SSA oral presentation