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GTNet is a neural network capable of identifying the species from which a genomic sequence was derived. Its main use will be in processing metagenomic sequences generated in microbiome research.
The accurate prediction of biological features from genomic data is paramount for precision medicine and sustainable agriculture. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and targeted marketing given their prediction accuracy and their robust performance under big data settings. Yet neural network models have not made a successful transition into the medical and biological world due to the ubiquitous characteristics of biological data such as modest sample sizes, sparsity, and extreme heterogeneity. Here, we investigate the robustness, generalization potential and prediction accuracy of widely used convolutional neural network and natural language processing models with a variety of heterogeneous genomic datasets. Mainly, recurrent neural network models outperform convolutional neural network models in terms of prediction accuracy, overfitting and transferability across the datasets under study. While the perspective of a robust out-of-the-box neural network model is out of reach, we identify certain model characteristics that translate well across datasets and could serve as a baseline model for translational researchers.
On June 5, 2019, the Office of Science (SC) organized a one-day roundtable to focus on enhancing access to high-quality and fully traceable research data, models, and computing resources to increase the value of such resources for artificial intelligence (AI) research and development and the SC mission.1 In this report, we consider AI to be inclusive of, for example, machine learning (ML), deep learning (DL), neural networks (NN), computer vision, and natural language processing (NLP). We consider “data for AI” to mean the digital artifacts used to generate AI models and/or employed in combination with AI models during inference. In part, this roundtable was motivated by the recognition that a large portion of science data currently are not well suited for AI.
Protection is a critical function in power systems to avoid equipment damage, maintain personnel safety, and support system reliability. However, current protective relay technology cannot adequately protect equipment and personnel from effects of some events; these deficiencies are termed protection gaps. In this research, a data-driven approach is proposed to complement traditional protection technology and distinguish fault conditions from transients caused by normal operations. A convolutional neural network (CNN) based fault detection approach is implemented to achieve data translation invariance of the time-series input data. As a result, the data-driven method can accurately detect system faults despite variation and noise in the input data. In addition, using the CNN–based method avoids the complicated manual feature extraction procedure required by many traditional data-driven methods. The effectiveness of the proposed approach is tested on four kinds of protection gaps: high impedance faults, transformer/generator inter-turn faults, distribution system PV circuit faults, and the mis-operation situations of Zone 3 line protection relays operating under system stress. Finally, a transfer learning method is also proposed to address the common issue of data-driven methods for which real-world training data are scarce. Extensive study results demonstrate that the proposed approach can accurately bridge power system protection gaps.
The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.
The proliferation of sensors brings an immense volume of spatio-temporal (ST) data in many domains, including monitoring, diagnostics, and prognostics applications. Data curation is a time-consuming process for a large volume of data, making it challenging and expensive to deploy data analytics platforms in new environments. Transfer learning (TL) mechanisms promise to mitigate data sparsity and model complexity by utilizing pre-trained models for a new task. Despite the triumph of TL in fields like computer vision and natural language processing, efforts on complex ST models for anomaly detection (AD) applications are limited. In this study, we present the potential of TL within the context of high-dimensional ST AD with a hybrid autoencoder architecture, incorporating convolutional, graph, and recurrent neural networks. Motivated by the need for improved model accuracy and robustness, particularly in scenarios with limited training data on systems with thousands of sensors, this research investigates the transferability of models trained on different sections of the Hadron Calorimeter of the Compact Muon Solenoid experiment at CERN. The key contributions of the study include exploring TL’s potential and limitations within the context of encoder and decoder networks, revealing insights into model initialization and training configurations that enhance performance while substantially reducing trainable parameters and mitigating data contamination effects.
The objective of the Gross Motion Control project is to study alternative control approaches that will provide payload invariant high speed trajectory tracking for nonrepetitive motions in free space. The research has concentrated on modifications to the model-based control structure. Development and evaluation is being actively pursued of both adaptive primary (inner loop) and robust secondary (output loop) controllers. In-house developments are compared and contrasted to the techniques proposed by other researchers. The case study for the evaluation is the first three links of a PUMA-560. Incorporating the principals of multiple model adaptive estimation, artificial neural networks, and Lyapunov theory into the model based paradigm has shown the potential for enhanced tracking. Secondary controllers based on Quantitative Feedback Theory, or augmented with auxiliary inputs, significantly improve the robustness to payload variations and unmodeled drive system dynamics. An overview is presented of the different concepts under investigation and a sample is provided of the latest experimental results.
Online event classification is essential to strengthening the reliability of the power transmission system. Recently, deep learning based methods have achieved great success in numerous domains such as computer vision and natural language processing. Researchers began to adopt deep learning based methods to solve the power system event identification problem and achieved effective results. However, these previous works do not consider that deep learning models are vulnerable to adversarial attacks, potentially influencing real-world applications' reliability. In this paper, we adopt several adversarial attack mechanisms by adding tailored noise signal to the input Phasor Measurement Units (PMU) time series and make the deep learning model misclassify the power system event. This numerical study discloses that current state-of-the-art deep learning based power system event classifiers are extremely vulnerable to adversarial attacks, which may jeopardize the reliability of the power transmission system.
We describe the PACE-MAPP algorithm that simultaneously retrieves aerosol and ocean optical parameters using multiangle and multi-channel polarimeter measurements from the SPEXone, Hyper-Angular Rainbow Polarimeter 2 (HARP2), and Ocean Color Instrument (OCI) instruments onboard the NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) observing system PACE-MAPP is adapted from the Research Scanning Polarimeter (RSP) Microphysical Aerosol Properties from Polarimetry (RSP-MAPP) algorithm. A key feature of the MAPP family of algorithms is the use of a coupled vector radiative transfer model such that the atmosphere and ocean are always considered together as one system. Consequently, conservation of energy ensures that negative water-leaving radiances do not occur. PACE-MAPP uses optimal estimation to simultaneously characterize the optical and microphysical properties of aerosol and ocean constituents, find the optimal solution, and reliably account for the uncertainties of each parameter. This coupled approach, together with multiangle, multi-channel polarimeter measurements, will enable retrievals of aerosol and water properties across the Earth’s oceans. The PACE-MAPP algorithm provides aerosol and ocean products for both the open ocean and coastal areas and is designed to be accurate, modular, and efficient by using fast neural networks that replace the time-consuming vector radiative transfer calculations. We provide an overview of the PACE-MAPP framework and also describe its modular components including its aerosol and hydrosol models, ocean bio-optical models, and thin cirrus model.
When learning, the brain modifies individual synaptic connections to reach a desired behavior. Animal and human brains have been shown to be incredibly capable of learning complex and varied functions across a wide variety of tasks. In recent years, artificial neural networks, inspired by human and animal brains, have shown great capabilities in learning a wide variety of difficult tasks. However, artificial neural networks primarily teach themselves through the use of backpropagation, a learning method which has no clear analogue within the brain. Additionally, Artificial Neural Networks primarily use continuous activation functions, which differ significantly from the spiking neuronal behavior present in the brain. In this paper, we discuss and demonstrate a biologically plausible learning method that approximates backpropagation through two techniques on Spiking Neural Networks. First, we show that the local temporal derivatives that are necessary for backpropagation can be approximately recovered through reconstruction using spike timings. Second, we show that through learning during a sleep phase, inspired by neuroscience research into memory replay, the localized parallel feedback path can learn to approximate the derivative through the forward path weight matrix, thus solving the weight transport problem. Lastly, we demonstrate that the combination of these two methods can approach or exceed the accuracy of backpropagation-based methods for a variety of neuromorphic vision tasks while maintaining biological plausibility.
Graph Neural Networks (GNNs) have gained significant attention owing to their ability to handle graph-structured data and the improvement in practical applications. However, many of these models prioritize high utility performance, such as accuracy, with a lack of privacy consideration, which is a major concern in modern society where privacy attacks are rampant. To address this issue, researchers have started to develop privacy-preserving GNNs. Despite this progress, there is a lack of a comprehensive overview of the attacks and the techniques for preserving privacy in the graph domain. In this survey, we aim to address this gap by summarizing the attacks on graph data according to the targeted information, categorizing the privacy preservation techniques in GNNs, and reviewing the datasets and applications that could be used for analyzing/solving privacy issues in GNNs. We also outline potential directions for future research in order to build better privacy-preserving GNNs.
This software is an implementation of the backpropagation algorithm for Intel's neuromorphic research processor, Loihi. The software implements the neural circuit itself and a demonstration application where the MNIST dataset (a standard test problem) is used to train a neural network.
Gamma titanium aluminide (γ-TiAl) is considered a high-performance, low-density replacement for nickel-based superalloys in the aerospace industry due to its high specific strength, which is retained at temperatures above 800 °C. However, low damage tolerance, i.e., brittle material behavior with a propensity to rapid crack propagation, has limited the application of γ-TiAl. Any cracks introduced during manufacturing would dramatically lower the useful (fatigue) life of γ-TiAl components, making the workpiece surface’s quality from finish machining a critical component to product quality and performance. To address this issue and enable more widespread use of γ-TiAl, this research aims to develop a real-time non-destructive evaluation (NDE) quality monitoring technique based on acoustic emission (AE) signals, wavelet transform, and deep neural networks (DNN). Previous efforts have opted for traditional approaches to AE signal analysis, using statistical feature extraction and classification, which face challenges such as the extraction of good/relevant features and low classification accuracy. Hence, this work proposes a novel AI-enabled method that uses a convolutional neural network (CNN) to extract rich and relevant features from a two-dimensional image representation of 1D time-domain AE signals (known as scalograms), subsequently classifying the AE signature based on pedigreed experimental data and finally predicting the process-induced surface quality. The results of the present work show good classification accuracy of 80.83% using scalogram images, in-situ experimental data, and a VGG-19 pre-trained neural network, establishing the significant potential for real-time quality monitoring in manufacturing processes.
This paper describes the development of a planned approach for Autonomous operation of an Unmanned Aerial Vehicle (UAV). A Hybrid approach will seek to provide Knowledge Generation through the application of Artificial Intelligence (AI) and Intelligent Agents (IA) for UAV control. The applications of several different types of AI techniques for flight are explored during this research effort. The research concentration is directed to the application of different AI methods within the UAV arena. By evaluating AI and biological system approaches. which include Expert Systems, Neural Networks. Intelligent Agents, Fuzzy Logic, and Complex Adaptive Systems, a new insight may be gained into the benefits of AI and CAS techniques applied to achieving true autonomous operation of these systems. Although flight systems were explored, the benefits should apply to many Unmanned Vehicles such as: Rovers. Ocean Explorers, Robots, and autonomous operation systems. A portion of the flight system is broken down into control agents that represent the intelligent agent approach used in AI. After the completion of a successful approach, a framework for applying an intelligent agent is presented. The initial results from simulation of a security agent for communication are presented.
Decoding behavior, perception or cognitive state directly from neural signals is critical for brain–computer interface research and an important tool for systems neuroscience. In the last decade, deep learning has become the state-of-the-art method in many machine learning tasks ranging from speech recognition to image segmentation. The success of deep networks in other domains has led to a new wave of applications in neuroscience. In this article, we review deep learning approaches to neural decoding. Here, we describe the architectures used for extracting useful features from neural recording modalities ranging from spikes to functional magnetic resonance imaging. Furthermore, we explore how deep learning has been leveraged to predict common outputs including movement, speech and vision, with a focus on how pretrained deep networks can be incorporated as priors for complex decoding targets like acoustic speech or images. Deep learning has been shown to be a useful tool for improving the accuracy and flexibility of neural decoding across a wide range of tasks, and we point out areas for future scientific development.
We describe a neural network based robotic system. Unlike traditional robotic systems, our approach focussed on non-stationary problems. We indicate that self-organization capability is necessary for any system to operate successfully in a non-stationary environment. We suggest that self-organization should be based on an active exploration process. We investigated neural architectures having novelty sensitivity, selective attention, reinforcement learning, habit formation, flexible criteria categorization properties and analyzed the resulting behavior (consisting of an intelligent initiation of exploration) by computer simulations. While various computer vision researchers acknowledged recently the importance of active processes (Swain and Stricker, 1991), the proposed approaches within the new framework still suffer from a lack of self-organization (Aloimonos and Bandyopadhyay, 1987; Bajcsy, 1988). A self-organizing, neural network based robot (MAVIN) has been recently proposed (Baloch and Waxman, 1991). This robot has the capability of position, size rotation invariant pattern categorization, recognition and pavlovian conditioning. Our robot does not have initially invariant processing properties. The reason for this is the emphasis we put on active exploration. We maintain the point of view that such invariant properties emerge from an internalization of exploratory sensory-motor activity. Rather than coding the equilibria of such mental capabilities, we are seeking to capture its dynamics to understand on the one hand how the emergence of such invariances is possible and on the other hand the dynamics that lead to these invariances. The second point is crucial for an adaptive robot to acquire new invariances in non-stationary environments, as demonstrated by the inverting glass experiments of Helmholtz. We will introduce Pavlovian conditioning circuits in our future work for the precise objective of achieving the generation, coordination, and internalization of sequence of actions.
Significance Water is central across much of the physical and biological sciences and exhibits physical properties that are qualitatively distinct from those of most other liquids. Understanding the microscopic basis of water’s peculiar properties remains an active area of research. One intriguing hypothesis is that liquid water can separate into metastable high- and low-density liquid phases at low temperatures and high pressures, and the existence of this liquid–liquid transition could explain many of water’s anomalous properties. We used state-of-the-art approaches in computational quantum chemistry, statistical mechanics, and machine learning and obtained evidence consistent with a liquid–liquid transition, supporting the argument for the existence of this phenomenon in real water.
Accurate representation of pumping wells is essential for reliable reservoir characterization and simulation of operational scenarios in subsurface flow models. Physics-informed neural networks (PINNs) are emerging as a promising alternative to numerical models for reservoir modeling, offering seamless integration of monitoring data and governing physical equations. However, existing PINN-based studies face major challenges in capturing fluid pressure near wells when using a source/sink term, particularly during the early stages after pumping begins. We address this problem by introducing WellPINN, a workflow in which an initially trained PINN infers fluid pressure across the entire reservoir domain using a large equivalent well radius. This initial PINN solution is then locally refined around the well by a set of subdomain PINNs that are trained for smaller equivalent well radii. Continuity across these subdomain interfaces as well as at the initial condition is ensured by hard-constraining each PINN on its subdomain boundary. Our results demonstrate WellPINN as the first workflow of its kind to focus on accurate inference of fluid pressure from pumping rates throughout the entire injection period, significantly advancing the potential of PINNs for inverse modeling and operational scenario simulations. All data and code for this paper are openly available at https://doi.org/10.20350/DIGITALCSIC/17260.