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At least 1,171 records · Page 65

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗

ARMing the Edge: Designing Edge Computing–Capable Machine Learning Algorithms to Target ARM Doppler Lidar Processing

Abstract There is a need for long-term observations of cloud and precipitation fall speeds in validating and improving rainfall forecasts from climate models. To this end, the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility Southern Great Plains (SGP) site at Lamont, Oklahoma, hosts five ARM Doppler lidars that can measure cloud and aerosol properties. In particular, the ARM Doppler lidars record Doppler spectra that contain information about the fall speeds of cloud and precipitation particles. However, due to bandwidth and storage constraints, the Doppler spectra are not routinely stored. This calls for the automation of cloud and rain detection in ARM Doppler lidar data so that the spectral data in clouds can be selectively saved and further analyzed. During the ARMing the Edge field experiment, a Waggle node capable of performing machine learning applications in situ was deployed at the ARM SGP site for this purpose. In this paper, we develop and test four algorithms for the Waggle node to automatically classify ARM Doppler lidar data. We demonstrate that supervised learning using a ResNet50-based classifier will classify 97.6% of the clear-air images and 94.7% of cloudy images correctly, outperforming traditional peak detection methods. We also show that a convolutional autoencoder paired with k -means clustering identifies 10 clusters in the ARM Doppler lidar data. Three clusters correspond to mostly clear conditions with scattered high clouds, and seven others correspond to cloudy conditions with varying cloud-base heights.

54 ENVIRONMENTAL SCIENCES↗

Insights into cosmological structure formation with machine learning.

Our modern understanding of cosmological structure formation posits that small matter density fluctuations present in the early Universe, as traced by the cosmic microwave background, grow via gravitational instability to form extended haloes of dark matter. A theoretical understanding of the structure, evolution and formation of dark matter haloes is an essential step towards unravelling the intricate connection between halo and galaxy formation, needed to test our cosmological model against data from upcoming galaxy surveys. Physical understanding of the process of dark matter halo formation is made difficult by the highly non-linear nature of the haloes' evolution. I describe a new approach to gain physical insight into cosmological structure formation based on machine learning. This approach combines the ability of machine learning algorithms to learn non-linear relationships, with techniques that enable us to physically interpret the learnt mapping. I describe applicatio ns of th e method, with the aim of investigating which aspects of the early universe density field impact the later formation of dark matter haloes. First I present a case where the process of halo formation is turned into a binary classification problem; the algorithm predicts whether or not dark matter `particles' in the initial conditions of a simulation will collapse into haloes of a given mass range. Second, I present its generalization to regression, where the algorithm infers the final mass of the halo to which each particle will later belong. I show that the initial tidal shear does not play a significant role compared to the initial density field in establishing final halo masses. Finally, I demonstrate that extending the framework to deep learning algorithms such as convolutional neural networks allows us to explore connections between the early universe and late time haloes beyond those studied by existing analytic approximations of halo collapse.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluating lightweight unsupervised online IDS for masquerade attacks in CAN

Vehicular controller area networks (CANs) are susceptible to masquerade attacks by malicious adversaries. In masquerade attacks, adversaries silence a targeted ID and then send malicious frames with forged content at the expected timing of benign frames. As masquerade attacks could seriously harm vehicle functionality and are the stealthiest attacks to detect in CAN, recent work has devoted attention to compare frameworks for detecting masquerade attacks in CAN. However, most existing works report offline evaluations using CAN logs already collected using simulations that do not comply with the domain’s real-time constraints. Here we contribute to advance the state of the art by presenting a comparative evaluation of four different non-deep learning (DL)-based unsupervised online intrusion detection systems (IDS) for masquerade attacks in CAN. Our approach differs from existing comparative evaluations in that we analyze the effect of controlling streaming data conditions in a sliding window setting. In doing so, we use realistic masquerade attacks being replayed from the ROAD dataset. We show that although evaluated IDS are not effective at detecting every attack type, the method that relies on detecting changes in the hierarchical structure of clusters of time series produces the best results at the expense of higher computational overhead. We discuss limitations, open challenges, and how the evaluated methods can be used for practical unsupervised online CAN IDS for masquerade attacks.

Anomaly detection↗

Limited-angle computed tomography with deep image and physics priors

Computed tomography is a well-established x-ray imaging technique to reconstruct the three-dimensional structure of objects. It has been used extensively in a variety of fields, from diagnostic imaging to materials and biological sciences. One major challenge in some applications, such as in electron or x-ray tomography systems, is that the projections cannot be gathered over all the angles due to the sample holder setup or shape of the sample. This results in an ill-posed problem called the limited angle reconstruction problem. Typical image reconstruction in this setup leads to distortion and artifacts, thereby hindering a quantitative evaluation of the results. To address this challenge, we use a generative model to effectively constrain the solution of a physics-based approach. Our approach is self-training that can iteratively learn the nonlinear mapping from partial projections to the scanned object. Because our approach combines the data likelihood and image prior terms into a single deep network, it is computationally tractable and improves performance through an end-to-end training. We also complement our approach with total-variation regularization to handle high-frequency noise in reconstructions and implement a solver based on alternating direction method of multipliers. We present numerical results for various degrees of missing angle range and noise levels, which demonstrate the effectiveness of the proposed approach.

47 OTHER INSTRUMENTATION↗

Learning and Fast Adaptation for Grid Emergency Control via Deep Meta Reinforcement Learning

As power systems are undergoing a significant transformation with more uncertainties, less inertia and closer to operation limits, there is increasing risk of large outages. Thus, there is an imperative need to enhance grid emergency control to maintain system reliability and security. Towards this end, great progress has been made in developing deep reinforcement learning (DRL) based grid control solutions in recent years. However, existing DRL-based solutions have two main limitations: 1) they cannot handle well with a wide range of grid operation conditions, system parameters, and contingencies; 2) they generally lack the ability to fast adapt to new grid operation conditions, system parameters, and contingencies, limiting their applicability for real-world applications. Here, in this paper, we mitigate these limitations by developing a novel deep meta-reinforcement learning (DMRL) algorithm. The DMRL combines the meta strategy optimization together with DRL, and trains policies modulated by a latent space that can quickly adapt to new scenarios. We test the developed DMRL algorithm on the IEEE 300-bus system. We demonstrate fast adaptation of the meta-trained DRL polices with latent variables to new operating conditions and scenarios using the proposed method, which achieves superior performance compared to the state-of-the-art DRL and model predictive control (MPC) methods.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Unpaired image translation to mitigate domain shift in liquid argon time projection chamber detector responses

Deep learning algorithms often are developed and trained on a training dataset and deployed on test datasets. Any systematic difference between the training and a test dataset may severely degrade the final algorithm performance on the test dataset—what is known as the domain shift problem . This issue is prevalent in many scientific domains where algorithms are trained on simulated data but applied to real-world datasets. Typically, the domain shift problem is solved through various domain adaptation (DA) methods. However, these methods are often tailored for a specific downstream task, such as classification or semantic segmentation, and may not easily generalize to different tasks. This work explores the feasibility of using an alternative way to solve the domain shift problem that is not specific to any downstream algorithm. The proposed approach relies on modern Unpaired Image-to-Image (UI2I) translation techniques, designed to find translations between different image domains in a fully unsupervised fashion. In this study, the approach is applied to a domain shift problem commonly encountered in Liquid Argon Time Projection Chamber (LArTPC) detector research when seeking a way to translate samples between two differently distributed LArTPC detector datasets deterministically. This translation allows for mapping real-world data into the simulated data domain where the downstream algorithms can be run with much less domain-shift-related performance degradation. Conversely, using the translation from the simulated data to a real-world domain can increase the realism of the simulated dataset and reduce the magnitude of any systematic uncertainties. To evaluate the quality of the translations, we use both pixel-wise metrics and a downstream task to measure the effectiveness of UI2I methods for mitigating the domain shift problem. We adapted several popular UI2I translation algorithms to work on scientific data and demonstrated the viability of these techniques for solving the domain shift problem with LArTPC detector data. To facilitate further development of DA techniques for scientific datasets, the ‘Simple Liquid-Argon Track Samples’ dataset used in this study is also published.

97 MATHEMATICS AND COMPUTING↗

Newton-Raphson AC Power Flow Convergence Based on Deep Learning Initialization and Homotopy Continuation

Power flow forms the basis of many power system studies. With the increased penetration of renewable energy, grid planners tend to perform multiple power flow simulations under various operating conditions and not just selected snapshots at peak or light load conditions. Getting a converged AC power flow (ACPF) case remains a significant challenge for grid planners especially in large power grid networks. This paper proposes a two-stage approach to improve Newton-Raphson ACPF convergence and was applied to a 6102 bus Electric Reliability Council of Texas (ERCOT) system. The first stage utilizes a deep learning-based initializer with data re-training. Here a deep neural network (DNN) initializer is developed to provide better initial voltage magnitude and angle guesses to aid in power flow convergence. This is because Newton-Raphson ACPF is quite sensitive to the initial conditions and bad initialization could lead to divergence. The DNN initializer includes a data re-training framework that improves the initializer's performance when faced with limited training data. The DNN initializer successfully solved 3,285 cases out of 3,899 non-converging dispatch and performed better than random forest and DC power flow initialization methods. ACPF cases not solved in this first stage are then passed through a hot-starting algorithm based on homotopy continuation with switched shunt control. The hot-starting algorithm successfully converged 416 cases out of the remaining 614 non-converging ACPF dispatch. In conclusion, the combined two-stage approach achieved a 94.9% success rate, by converging a total of 3,701 cases out of the initial 3,899 unsolved cases.

Deep learning↗

Buyers Collusion in Incentivized Forwarding Networks: A Multi-Agent Reinforcement Learning Study

We present the issue of monetarily incentivized forwarding in a multi-hop mesh network architecture from an economic perspective. It is anticipated that credit-incentivized forwarding and relaying will be a simple method of exchanging transmission power and spectrum for connectivity. However, gateways and forwarding nodes, like any other free market, may create an oligopolistic market for the users they serve. In this study, a coalition scheme between buyers aims to address price control by gateways or nodes closer to gateways. In a Stackelberg competition game, buyer agents (users) and sellers (gateways) make decisions using reinforcement learning (RL), with decentralized Deep Q-Networks to buy and sell forwarding resources. We allow communication links between the buyers with a limited messaging space, without defining a collusion mechanism. The idea is to demonstrate that through messaging, and RL tacit collusion can emerge between agents in a decentralized setup. The multi-agent reinforcement learning (MARL) system is presented and analyzed from a machine-learning perspective. Moreover, MARL dynamics are discussed via mean field analysis to better understand divergence causes and make implementation recommendations for such systems. Finally, the simulation results show the results of coordination among the users.

42 ENGINEERING↗

Uncertainty Aware Deep Learning for Particle Accelerators

Standard deep learning models for classification and regression applications are ideal for capturing complex system dynamics. However, their predictions can be arbitrarily inaccurate when the input samples are not similar to the training data. Implementation of distance aware uncertainty estimation can be used to detect these scenarios and provide a level of confidence associated with their predictions. In this paper, we present results from using Deep Gaussian Process Approximation (DGPA) methods for errant beam prediction at Spallation Neutron Source (SNS) accelerator (classification) and we provide an uncertainty aware surrogate model for the Fermi National Accelerator Lab (FNAL) Booster Accelerator Complex (regression).

Rajput, Kishansingh↗

On the Verification of Deep Reinforcement Learning Solution for Intelligent Operation of Distribution Grids

Capabilities of deep reinforcement learning (DRL) in obtaining fast decision policies in high dimensional and stochastic environments have led to its extensive use in operational research, including the operation of distribution grids with high penetration of distributed energy resources (DER). However, the feasibility and robustness of DRL solutions are not guaranteed for the system operator, and hence, those solutions may be of limited practical value. This paper proposes an analytical method to find feasibility ellipsoids that represent the range of multi-dimensional system states in which the DRL solution is guaranteed to be feasible. Empirical studies and stochastic sampling determine the ratio of the discovered to the actual feasible space as a function of the sample size. In addition, the performance of logarithmic, linear, and exponential penalization of infeasibility during the DRL training are studied and compared in order to reduce the number of infeasible solutions

Hosseini, Mohammad Mehdi↗

Yet Another Discriminant Analysis (YADA): A Probabilistic Model for Machine Learning Applications

This paper presents a probabilistic model for various machine learning (ML) applications. While deep learning (DL) has produced state-of-the-art results in many domains, DL models are complex and over-parameterized, which leads to high uncertainty about what the model has learned, as well as its decision process. Further, DL models are not probabilistic, making reasoning about their output challenging. In contrast, the proposed model, referred to as Yet Another Discriminate Analysis(YADA), is less complex than other methods, is based on a mathematically rigorous foundation, and can be utilized for a wide variety of ML tasks including classification, explainability, and uncertainty quantification. YADA is thus competitive in most cases with many state-of-the-art DL models. Ideally, a probabilistic model would represent the full joint probability distribution of its features, but doing so is often computationally expensive and intractable. Hence, many probabilistic models assume that the features are either normally distributed, mutually independent, or both, which can severely limit their performance. YADA is an intermediate model that (1) captures the marginal distributions of each variable and the pairwise correlations between variables and (2) explicitly maps features to the space of multivariate Gaussian variables. Numerous mathematical properties of the YADA model can be derived, thereby improving the theoretic underpinnings of ML. Validation of the model can be statistically verified on new or held-out data using native properties of YADA. However, there are some engineering and practical challenges that we enumerate to make YADA more useful.

97 MATHEMATICS AND COMPUTING↗

Data Selection Improvement For MicroBooNE

Data selection is an extremely important part of data analysis for any experiment. Finding a physics result is often the result of sifting through a massive amount of data, keeping data that we believe to be signal, and throwing out data we do not. This process is called data selection. Creating a selection algorithm is an intensive process that must balance keeping enough data to have statistics and maximizing the signal purity of that data. We also need to choose the right reconstruction method, a tool to take raw data from the detector and convert it into physics results. In this study, we used three different reconstruction tools, Pandora, WireCell, and LANTERN, for the MicroBooNE experiment in conjunction to improve the selection algorithm for analysis. For the case of this study, we look into the charged current N proton 0 pions (CCNp0$\pi$) interaction channel. This is the dominant channel for the Short Baseline Neutrino (SBN) program and is expected to be a large contributor to the Deep Underground Neutrino Experiment (DUNE). We first investigated each of the three tools to find out more about their strengths and weaknesses as reconstructions, and compared them to the truth information directly from the MicroBooNE simulation pipeline. We then put together a direct comparison of the three methods to find which method or combination of methods would return the best result for us. While the study is ongoing, we have learned a lot about data selection for the experiment and the differences between the reconstruction tools.

Dillon, Brayden [Fermilab]↗

Systems and methods for customizing kernel machines with deep neural networks

A method including receiving an input data set. The input data set can include one of a feature domain set or a kernel matrix. The method also can include constructing dense embeddings using: (i) Nyström approximations on the input data set when the input data set comprises the kernel matrix, and (ii) clustered Nyström approximations on the input data set when the input data set comprises the feature domain set. The method additionally can include performing representation learning on each of the dense embeddings using a multi-layer fully-connected network for each of the dense embeddings to generate latent representations corresponding to each of the dense embeddings. The method further can include applying a fusion layer to the latent representations corresponding to the dense embeddings to generate a combined representation. The method additionally can include performing classification on the combined representation. Other embodiments of related systems and methods are also disclosed.

Song, Huan↗

Evaluating Automated Face Identity-Masking Methods with Human Perception and a Deep Convolutional Neural Network

Face de-identification (or “masking”) algorithms have been developed in response to the prevalent use of video recordings in public places. Here, we evaluated the success of face identity masking for human perceivers and a deep convolutional neural network (DCNN). Eight de-identification algorithms were applied to videos of drivers’ faces, while they actively operated a motor vehicle. These masks were pre-selected to be applicable to low-quality video and to maintain coarse information about facial actions. Humans studied high-resolution images to learn driver identities and were tested on their recognition of active drivers in low-resolution videos. Faces in the videos were either unmasked or were masked by one of the eight algorithms. When participants were tested immediately after learning (Experiment 1), all masks reduced identification, with six of eight masks reducing identification to extremely poor performance. In a second experiment, two of the most effective masks were tested after a delay of 7 or 28 days. The delay did not further reduce identification of the masked faces. In all masked conditions, participants maintained stringent decision criteria, with low confidence in recognition, further indicating the effectiveness of the masks. Next, the DCNN performed an identity-matching task between high-resolution images and masked videos—a task analogous to that done by humans. The pattern of accuracy for the DCNN mirrored some, but not all, aspects of human performance, highlighting the need to test the effectiveness of identity masking for both humans and machines. The DCNN was also tested on its ability to match identity between masked and unmasked versions of the same video, based only on the face. DCNN performance for the eight masks offers insight into the nature of the information in faces that is coded in these networks.

97 MATHEMATICS AND COMPUTING↗

Improving River Routing Using a Differentiable Muskingum‐Cunge Model and Physics‐Informed Machine Learning

Recently, rainfall-runoff simulations in small headwater basins have been improved by methodological advances such as deep neural networks (NNs) and hybrid physics-NN models—particularly, a genre called differentiable modeling that intermingles NNs with physics to learn relationships between variables. However, hydrologic routing simulations, necessary for simulating floods in stem rivers downstream of large heterogeneous basins, had not yet benefited from these advances and it was unclear if the routing process could be improved via coupled NNs. We present a novel differentiable routing method (δMC-Juniata-hydroDL2) that mimics the classical Muskingum-Cunge routing model over a river network but embeds an NN to infer parameterizations for Manning's roughness (n) and channel geometries from raw reach-scale attributes like catchment areas and sinuosity. The NN was trained solely on downstream hydrographs. Synthetic experiments show that while the channel geometry parameter was unidentifiable, n can be identified with moderate precision. With real-world data, the trained differentiable routing model produced more accurate long-term routing results for both the training gage and untrained inner gages for larger subbasins (>2,000 km2) than either a machine learning model assuming homogeneity, or simply using the sum of runoff from subbasins. The n parameterization trained on short periods gave high performance in other periods, despite significant errors in runoff inputs. The learned n pattern was consistent with literature expectations, demonstrating the framework's potential for knowledge discovery, but the absolute values can vary depending on training periods. The trained n parameterization can be coupled with traditional models to improve national-scale hydrologic flood simulations.

54 ENVIRONMENTAL SCIENCES↗

Transition metal impurities in silicon: computational search for a semiconductor qubit

Abstract Semiconductors offer a promising platform for physical implementation of qubits, but their broad adoption is presently hindered by limited scalability and/or very low operating temperatures. Learning from the nitrogen-vacancy centers in diamond, our goal is to find equivalent optically active point defect centers in crystalline silicon, which could be advantageous for their scalability and integration with classical devices. Transition metal (TM) impurities in silicon are common paramagnetic deep defects, but a comprehensive theoretical study of the whole 3 d series that considers generalized Koopmans’ condition is missing. We apply the HSE06(+U) method to examine their potential as optically active spin qubits and identify seven TM impurities that have optically allowed triplet–triplet transitions within the silicon band gap. These results provide the first step toward silicon-based qubits with higher operating temperatures for quantum sensing. Additionally, these point defects could lead to spin-photon interfaces in silicon-based qubits and devices for mid-infrared free-space communications.

36 MATERIALS SCIENCE↗

Deblending galaxies with variational autoencoders: A joint multiband, multi-instrument approach

ABSTRACT Blending of galaxies has a major contribution in the systematic error budget of weak-lensing studies, affecting photometric and shape measurements, particularly for ground-based, deep, photometric galaxy surveys, such as the Rubin Observatory Legacy Survey of Space and Time (LSST). Existing deblenders mostly rely on analytic modelling of galaxy profiles and suffer from the lack of flexible yet accurate models. We propose to use generative models based on deep neural networks, namely variational autoencoders (VAE), to learn probabilistic models directly from data. We train a VAE on images of centred, isolated galaxies, which we reuse, as a prior, in a second VAE-like neural network in charge of deblending galaxies. We train our networks on simulated images including six LSST bandpass filters and the visible and near-infrared bands of the Euclid satellite, as our method naturally generalizes to multiple bands and can incorporate data from multiple instruments. We obtain median reconstruction errors on ellipticities and r-band magnitude between ±0.01 and ±0.05, respectively, in most cases, and ellipticity multiplicative bias of 1.6 per cent for blended objects in the optimal configuration. We also study the impact of decentring and prove the method to be robust. This method only requires the approximate centre of each target galaxy, but no assumptions about the number of surrounding objects, pointing to an iterative detection/deblending procedure we leave for future work. Finally, we discuss future challenges about training on real data and obtain encouraging results when applying transfer learning.

Arcelin, Bastien↗