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Full-Text Articles in Physical Sciences and Mathematics

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin Dec 2023

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

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Convolution And Autoencoders Applied To Nonlinear Differential Equations, Noah Borquaye Dec 2023

Convolution And Autoencoders Applied To Nonlinear Differential Equations, Noah Borquaye

Electronic Theses and Dissertations

Autoencoders, a type of artificial neural network, have gained recognition by researchers in various fields, especially machine learning due to their vast applications in data representations from inputs. Recently researchers have explored the possibility to extend the application of autoencoders to solve nonlinear differential equations. Algorithms and methods employed in an autoencoder framework include sparse identification of nonlinear dynamics (SINDy), dynamic mode decomposition (DMD), Koopman operator theory and singular value decomposition (SVD). These approaches use matrix multiplication to represent linear transformation. However, machine learning algorithms often use convolution to represent linear transformations. In our work, we modify these approaches to …

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Deep Feature Extraction, Dimensionality Reduction, And Classification Of Medical Images Using Combined Deep Learning Architectures, Autoencoder, And Multiple Machine Learning Models, Ahmet Hi̇dayet Ki̇raz, Fatime Oumar Djibrillah, Mehmet Emi̇n Yüksel Oct 2023

Deep Feature Extraction, Dimensionality Reduction, And Classification Of Medical Images Using Combined Deep Learning Architectures, Autoencoder, And Multiple Machine Learning Models, Ahmet Hi̇dayet Ki̇raz, Fatime Oumar Djibrillah, Mehmet Emi̇n Yüksel

Turkish Journal of Electrical Engineering and Computer Sciences

Accurate analysis and classification of medical images are essential factors in clinical decision-making and patient care. A novel comparative approach for medical image classification is proposed in this study. This new approach involves several steps: deep feature extraction, which extracts the informative features from medical images; concatenation, which concatenates the extracted deep features to form a robust feature vector; dimensionality reduction with autoencoder, which reduces the dimensionality of the feature vector by transforming it into a different feature space with a lower dimension; and finally, these features obtained from all these steps were fed into multiple machine learning classifiers (SVM, …

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Language Modeling Using Image Representations Of Natural Language, Seong Eun Cho Apr 2023

Language Modeling Using Image Representations Of Natural Language, Seong Eun Cho

Theses and Dissertations

This thesis presents training of an end-to-end autoencoder model using the transformer, with an encoder that can encode sentences into fixed-length latent vectors and a decoder that can reconstruct the sentences using image representations. Encoding and decoding sentences to and from these image representations are central to the model design. This method allows new sentences to be generated by traversing the Euclidean space, which makes vector arithmetic possible using sentences. Machines excel in dealing with concrete numbers and calculations, but do not possess an innate infrastructure designed to help them understand abstract concepts like natural language. In order for a …

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A Secure And Efficient Iiot Anomaly Detection Approach Using A Hybrid Deep Learning Technique, Bharath Reedy Konatham Jan 2023

A Secure And Efficient Iiot Anomaly Detection Approach Using A Hybrid Deep Learning Technique, Bharath Reedy Konatham

Browse all Theses and Dissertations

The Industrial Internet of Things (IIoT) refers to a set of smart devices, i.e., actuators, detectors, smart sensors, and autonomous systems connected throughout the Internet to help achieve the purpose of various industrial applications. Unfortunately, IIoT applications are increasingly integrated into insecure physical environments leading to greater exposure to new cyber and physical system attacks. In the current IIoT security realm, effective anomaly detection is crucial for ensuring the integrity and reliability of critical infrastructure. Traditional security solutions may not apply to IIoT due to new dimensions, including extreme energy constraints in IIoT devices. Deep learning (DL) techniques like Convolutional …

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Anomaly Detection Method Of Electrical Power Consumption Based On Deep Autoencoder, Ningke Sun, Yan Wang, Zhicheng Ji Dec 2022

Anomaly Detection Method Of Electrical Power Consumption Based On Deep Autoencoder, Ningke Sun, Yan Wang, Zhicheng Ji

Journal of System Simulation

Abstract: Aiming at the nonlinear and non-stationary characteristics of electrical power consumption data, an abnormal electrical power consumption detection model based on deep autoencoder is proposed. Gated recurrent unit (GRU) network of the deep learning is combined with autoencoder structure, and the encoder and decoder parts of traditional autoencoder are realized by gated recurrent unit network, which gives full play to the data feature extraction capability of gated recurrent unit and the data reconstruction function of autoencoder structure. Based on the reconstruction error between original data and reconstructed data, abnormal data points of the electrical power consumption are detected. By …

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An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong Wen Deng, Chaoyang Zhang Nov 2022

An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong Wen Deng, Chaoyang Zhang

Michigan Tech Publications

Genotype imputation has a wide range of applications in genome-wide association study (GWAS), including increasing the statistical power of association tests, discovering trait-associated loci in meta-analyses, and prioritizing causal variants with fine-mapping. In recent years, deep learning (DL) based methods, such as sparse convolutional denoising autoencoder (SCDA), have been developed for genotype imputation. However, it remains a challenging task to optimize the learning process in DL-based methods to achieve high imputation accuracy. To address this challenge, we have developed a convolutional autoencoder (AE) model for genotype imputation and implemented a customized training loop by modifying the training process with a …

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An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell Iv, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan-Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong-Wen Deng, Chaoyang Zhang Nov 2022

An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell Iv, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan-Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong-Wen Deng, Chaoyang Zhang

Faculty Publications

Genotype imputation has a wide range of applications in genome-wide association study (GWAS), including increasing the statistical power of association tests, discovering trait-associated loci in meta-analyses, and prioritizing causal variants with fine-mapping. In recent years, deep learning (DL) based methods, such as sparse convolutional denoising autoencoder (SCDA), have been developed for genotype imputation. However, it remains a challenging task to optimize the learning process in DL-based methods to achieve high imputation accuracy. To address this challenge, we have developed a convolutional autoencoder (AE) model for genotype imputation and implemented a customized training loop by modifying the training process with a …

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One-Stage Blind Source Separation Via A Sparse Autoencoder Framework, Jason Anthony Dabin May 2022

One-Stage Blind Source Separation Via A Sparse Autoencoder Framework, Jason Anthony Dabin

Dissertations

Blind source separation (BSS) is the process of recovering individual source transmissions from a received mixture of co-channel signals without a priori knowledge of the channel mixing matrix or transmitted source signals. The received co-channel composite signal is considered to be captured across an antenna array or sensor network and is assumed to contain sparse transmissions, as users are active and inactive aperiodically over time. An unsupervised machine learning approach using an artificial feedforward neural network sparse autoencoder with one hidden layer is formulated for blindly recovering the channel matrix and source activity of co-channel transmissions. The BSS sparse autoencoder …

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A Non-Deterministic Deep Learning Based Surrogate For Ice Sheet Modeling, Hannah Jordan Jan 2022

A Non-Deterministic Deep Learning Based Surrogate For Ice Sheet Modeling, Hannah Jordan

Graduate Student Theses, Dissertations, & Professional Papers

Surrogate modeling is a new and expanding field in the world of deep learning, providing a computationally inexpensive way to approximate results from computationally demanding high-fidelity simulations. Ice sheet modeling is one of these computationally expensive models, the model used in this study currently requires between 10 and 20 minutes to complete one simulation. While this process is adequate for certain applications, the ability to use sampling approaches to perform statistical inference becomes infeasible. This issue can be overcome by using a surrogate model to approximate the ice sheet model, bringing the time to produce output down to a tenth …

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Super-Resolution Reconstruction Of Brain Magnetic Resonance Images Via Lightweight Autoencoder, J. Andrew, T.S.R. Mhatesh, Robin D. Sebastin, K. Martin Sagayam, Jennifer Eunice, Marc Pomplun, Helen Dang Jan 2021

Super-Resolution Reconstruction Of Brain Magnetic Resonance Images Via Lightweight Autoencoder, J. Andrew, T.S.R. Mhatesh, Robin D. Sebastin, K. Martin Sagayam, Jennifer Eunice, Marc Pomplun, Helen Dang

Faculty Works: MCS (1984-2023)

Magnetic Resonance Imaging (MRI) is useful to provide detailed anatomical information such as images of tissues and organs within the body that are vital for quantitative image analysis. However, typically the MR images acquired lacks adequate resolution because of the constraints such as patients’ comfort and long sampling duration. Processing the low resolution MRI may lead to an incorrect diagnosis. Therefore, there is a need for super resolution techniques to obtain high resolution MRI images. Single image super resolution (SR) is one of the popular techniques to enhance image quality. Reconstruction based SR technique is a category of single image …

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A Federated Deep Autoencoder For Detecting Iot Cyber Attacks, Christopher M. Regan Dec 2020

A Federated Deep Autoencoder For Detecting Iot Cyber Attacks, Christopher M. Regan

Master of Science in Computer Science Theses

Internet of Things (IoT) devices are mass-produced and rapidly released to the public in a rough state. IoT devices are produced by various companies satisfying various goals, such as monitoring the environment, senor trigger cameras, on-demand electrical switches. These IoT devices are produced by companies to meet a market demand quickly, producing a rough software solution that customers or other enterprises willingly buy with the expectation they will have software updates after production. These IoT devices are often heterogeneous in nature, only to receive updates at infrequently intervals, and can remain out of sight on a home or office network …

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Application Of Autoencoders For Latent Pattern Analysis In Image Time Series, Jiena He Aug 2020

Application Of Autoencoders For Latent Pattern Analysis In Image Time Series, Jiena He

International Development, Community and Environment (IDCE)

The Earth system is considered to possess certain modes - preferred patterns of variability that can represent the latent structure of the climate system, also known as teleconnections. There are approaches to discover these patterns, Principal Components Analysis and Empirical Orthogonal Teleconnection (EOT) analysis. However, while the latter is very effective, it is computationally intensive. An autoencoder is an unsupervised neural network that learns an efficient neural representation of input data. It is considered as a dimensionality reduction tool that is highly similar to PCA and EOT. The hidden layer of an autoencoder represents the most significant information of the …

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Model-Based Deep Siamese Autoencoder For Clustering Single Cell Rna-Seq Data, Zixia Meng May 2020

Model-Based Deep Siamese Autoencoder For Clustering Single Cell Rna-Seq Data, Zixia Meng

Theses

In the biological field, the smallest unit of organisms in most biological systems is the single cell, and the classification of cells is an everlasting problem. A central task for analysis of single-cell RNA-seq data is to identify and characterize novel cell types. Currently, there are several classical methods, such as K-means algorithm, spectral clustering, and Gaussian Mixture Models (GMMs), which are widely used to cluster the cells. Furthermore, typical dimensional reduction methods such as PCA, t-SNE, and ZIDA have been introduced to overcome “the curse of dimensionality”. A more recent method scDeepCluster has demonstrated improved and promising performances in …

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Content Based Image Retrieval (Cbir) For Brand Logos, Enjal Parajuli May 2020

Content Based Image Retrieval (Cbir) For Brand Logos, Enjal Parajuli

Boise State University Theses and Dissertations

This thesis explores the problem of automatically detecting the presence of logos in general images. Brand logos carry the goodwill of a company and are considered to be of high value in the corporate world, and thus automatically determining whether or not a logo is present in an image can be of interest for companies that wish to protect their brand. The problem of automated logo detection is inherently complex, but is further complicated through intentional obfuscation of logo images, for example by color shifting or other slight image modifications that leave the logo intact and easily recognizable by a …

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Representation Learning With Adversarial Latent Autoencoders, Stanislav Pidhorskyi M.S. Jan 2020

Representation Learning With Adversarial Latent Autoencoders, Stanislav Pidhorskyi M.S.

Graduate Theses, Dissertations, and Problem Reports

A large number of deep learning methods applied to computer vision problems require encoder-decoder maps. These methods include, but are not limited to, self-representation learning, generalization, few-shot learning, and novelty detection. Encoder-decoder maps are also useful for photo manipulation, photo editing, superresolution, etc. Encoder-decoder maps are typically learned using autoencoder networks.
Traditionally, autoencoder reciprocity is achieved in the image-space using pixel-wise
similarity loss, which has a widely known flaw of producing non-realistic reconstructions. This flaw is typical for the Variational Autoencoder (VAE) family and is not only limited to pixel-wise similarity losses, but is common to all methods relying upon …

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Optimization Of Real-Time Wireless Sensor Based Big Data With Deep Autoencoder Network: A Tourism Sector Application With Distributed Computing, Beki̇r Aksoy, Utku Kose Jan 2020

Optimization Of Real-Time Wireless Sensor Based Big Data With Deep Autoencoder Network: A Tourism Sector Application With Distributed Computing, Beki̇r Aksoy, Utku Kose

Turkish Journal of Electrical Engineering and Computer Sciences

Internet usage has increased rapidly with the development of information communication technologies. The increase in internet usage led to the growth of data volumes on the internet and the emergence of the big data concept. Therefore, it has become even more important to analyze the data and make it meaningful. In this study, 690 million queries and approximately 5.9 quadrillion data collected daily from different servers were recorded on the Redis servers by using real-time big data analysis method and load balance structure for a company operating in the tourism sector. Here, wireless networks were used as a triggering factor …

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Deep Learning: Edge-Cloud Data Analytics For Iot, Katarina Grolinger, Ananda M. Ghosh Jan 2019

Deep Learning: Edge-Cloud Data Analytics For Iot, Katarina Grolinger, Ananda M. Ghosh

Electrical and Computer Engineering Publications

Sensors, wearables, mobile and other Internet of Thing (IoT) devices are becoming increasingly integrated in all aspects of our lives. They are capable of collecting massive quantities of data that are typically transmitted to the cloud for processing. However, this results in increased network traffic and latencies. Edge computing has a potential to remedy these challenges by moving computation physically closer to the network edge where data are generated. However, edge computing does not have sufficient resources for complex data analytics tasks. Consequently, this paper investigates merging cloud and edge computing for IoT data analytics and presents a deep learning-based …

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Unsupervised Deep Feature Embeddings For Speaker Diarization, Rehan Ahmad, Syed Zubair Jan 2019

Unsupervised Deep Feature Embeddings For Speaker Diarization, Rehan Ahmad, Syed Zubair

Turkish Journal of Electrical Engineering and Computer Sciences

Speaker diarization aims to determine ?who spoke when?? from multispeaker recording environments. In this paper, we propose to learn a set of high-level feature representations, referred to as feature embeddings, from an unsupervised deep architecture for speaker diarization. These sets of embeddings are learned through a deep autoencoder model when trained on mel-frequency cepstral coefficients (MFCCs) of input speech frames. Learned embeddings are then used in Gaussian mixture model based hierarchical clustering for diarization. The results show that these unsupervised embeddings are better compared to MFCCs in reducing the diarization error rate. Experiments conducted on the popular subset of the …

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An Explainable Autoencoder For Collaborative Filtering Recommendation, Pegah Sagheb Haghighi, Olurotimi Seton, Olfa Nasraoui Jan 2019

An Explainable Autoencoder For Collaborative Filtering Recommendation, Pegah Sagheb Haghighi, Olurotimi Seton, Olfa Nasraoui

Faculty Scholarship

Autoencoders are a common building block of Deep Learning architectures, where they are mainly used for representation learning. They have also been successfully used in Collaborative Filtering (CF) recommender systems to predict missing ratings. Unfortunately, like all black box machine learning models, they are unable to explain their outputs. Hence, while predictions from an Autoencoderbased recommender system might be accurate, it might not be clear to the user why a recommendation was generated. In this work, we design an explainable recommendation system using an Autoencoder model whose predictions can be explained using the neighborhood based explanation style. Our preliminary work …

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Comparative Study Of Deep Learning Models For Network Intrusion Detection, Brian Lee, Sandhya Amaresh, Clifford Green, Daniel Engels Apr 2018

Comparative Study Of Deep Learning Models For Network Intrusion Detection, Brian Lee, Sandhya Amaresh, Clifford Green, Daniel Engels

SMU Data Science Review

In this paper, we present a comparative evaluation of deep learning approaches to network intrusion detection. A Network Intrusion Detection System (NIDS) is a critical component of every Internet connected system due to likely attacks from both external and internal sources. A NIDS is used to detect network born attacks such as Denial of Service (DoS) attacks, malware replication, and intruders that are operating within the system. Multiple deep learning approaches have been proposed for intrusion detection systems. We evaluate three models, a vanilla deep neural net (DNN), self-taught learning (STL) approach, and Recurrent Neural Network (RNN) based Long Short …

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A Generalized Deep Learning-Based Diagnostic System For Early Diagnosis Of Various Types Of Pulmonary Nodules, Ahmed Shaffie, Ahmed Soliman, Luay Fraiwan, Mohammed Ghazal, Fatma Taher, Neal Dunlap, Brian Wang, Victor Van Berkel, Robert Keynton, Adel Elmaghraby, Ayman El-Baz Jan 2018

A Generalized Deep Learning-Based Diagnostic System For Early Diagnosis Of Various Types Of Pulmonary Nodules, Ahmed Shaffie, Ahmed Soliman, Luay Fraiwan, Mohammed Ghazal, Fatma Taher, Neal Dunlap, Brian Wang, Victor Van Berkel, Robert Keynton, Adel Elmaghraby, Ayman El-Baz

All Works

© The Author(s) 2018. A novel framework for the classification of lung nodules using computed tomography scans is proposed in this article. To get an accurate diagnosis of the detected lung nodules, the proposed framework integrates the following 2 groups of features: (1) appearance features modeled using the higher order Markov Gibbs random field model that has the ability to describe the spatial inhomogeneities inside the lung nodule and (2) geometric features that describe the shape geometry of the lung nodules. The novelty of this article is to accurately model the appearance of the detected lung nodules using a new …

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Collaborative Topic Regression With Denoising Autoencoder For Content And Community Co-Representation, Trong T. Nguyen, Hady W. Lauw Nov 2017

Collaborative Topic Regression With Denoising Autoencoder For Content And Community Co-Representation, Trong T. Nguyen, Hady W. Lauw

Research Collection School Of Computing and Information Systems

Personalized recommendation of items frequently faces scenarios where we have sparse observations on users' adoption of items. In the literature, there are two promising directions. One is to connect sparse items through similarity in content. The other is to connect sparse users through similarity in social relations. We seek to integrate both types of information, in addition to the adoption information, within a single integrated model. Our proposed method models item content via a topic model, and user communities via an autoencoder model, while bridging a user's community-based preference to her topic-based preference. Experiments on public real-life data showcase the …

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Collective Contextual Anomaly Detection For Building Energy Consumption, Daniel Berhane Araya Aug 2016

Collective Contextual Anomaly Detection For Building Energy Consumption, Daniel Berhane Araya

Electronic Thesis and Dissertation Repository

Commercial and residential buildings are responsible for a substantial portion of total global energy consumption and as a result make a significant contribution to global carbon emissions. Hence, energy-saving goals that target buildings can have a major impact in reducing environmental damage. During building operation, a significant amount of energy is wasted due to equipment and human-related faults. To reduce waste, today's smart buildings monitor energy usage with the aim of identifying abnormal consumption behaviour and notifying the building manager to implement appropriate energy-saving procedures. To this end, this research proposes the \textit{ensemble anomaly detection} (EAD) framework. The EAD is …

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