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An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Chuan Qiu, Kuan-Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong-Wen Deng, Chaoyang Zhang 2022 The Texas Medical Center Library

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

Faculty, Staff and Student 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 …


Enhancing Zero-Shot And Few-Shot Text Classification Using Pre-Trained Language Models, Yanan Chen 2022 Wilfrid Laurier University

Enhancing Zero-Shot And Few-Shot Text Classification Using Pre-Trained Language Models, Yanan Chen

Theses and Dissertations (Comprehensive)

In recent years, the community of natural language processing (NLP) has seen amazing progress in the development of pre-trained language models (PLMs). The novel paradigm of PLMs does not require labeled data, allowing us to experiment with increased training scale through employing freely available colossal online self-training corpus to push the limits. Language models (LMs), such as GPT, BERT and T5, have achieved high performance on a wide range of NLP tasks. Meanwhile, research on zero-shot and few-shot text classification has received increasing attention. As labelling can be costly and time-consuming, how to perform data augmentation (DA) and enhance the …


Perceptions And Needs Of Artificial Intelligence In Health Care To Increase Adoption: Scoping Review, Han Shi Jocelyn CHEW, Palakorn ACHANANUPARP 2022 National University of Singapore

Perceptions And Needs Of Artificial Intelligence In Health Care To Increase Adoption: Scoping Review, Han Shi Jocelyn Chew, Palakorn Achananuparp

Research Collection School Of Computing and Information Systems

Background: Artificial intelligence (AI) has the potential to improve the efficiency and effectiveness of health care service delivery. However, the perceptions and needs of such systems remain elusive, hindering efforts to promote AI adoption in health care. Objective: This study aims to provide an overview of the perceptions and needs of AI to increase its adoption in health care. Methods: A systematic scoping review was conducted according to the 5-stage framework by Arksey and O’Malley. Articles that described the perceptions and needs of AI in health care were searched across nine databases: ACM Library, CINAHL, Cochrane Central, Embase, IEEE Xplore, …


Cross-Modal Food Retrieval: Learning A Joint Embedding Of Food Images And Recipes With Semantic Consistency And Attention Mechanism, Hao WANG, Doyen SAHOO, Chenghao LIU, Ke SHU, Palakorn ACHANANUPARP, Ee-peng LIM, Steven C. H. HOI 2022 Nanyang Technological University

Cross-Modal Food Retrieval: Learning A Joint Embedding Of Food Images And Recipes With Semantic Consistency And Attention Mechanism, Hao Wang, Doyen Sahoo, Chenghao Liu, Ke Shu, Palakorn Achananuparp, Ee-Peng Lim, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

Food retrieval is an important task to perform analysis of food-related information, where we are interested in retrieving relevant information about the queried food item such as ingredients, cooking instructions, etc. In this paper, we investigate cross-modal retrieval between food images and cooking recipes. The goal is to learn an embedding of images and recipes in a common feature space, such that the corresponding image-recipe embeddings lie close to one another. Two major challenges in addressing this problem are 1) large intra-variance and small inter-variance across cross-modal food data; and 2) difficulties in obtaining discriminative recipe representations. To address these …


Highlights Generation For Tennis Matches Using Computer Vision, Natural Language Processing And Audio Analysis, Alon Liberman 2022 The College of Wooster

Highlights Generation For Tennis Matches Using Computer Vision, Natural Language Processing And Audio Analysis, Alon Liberman

Senior Independent Study Theses

This project uses computer vision, natural language processing and audio analysis to automatize the highlights generation task for tennis matches. Computer vision techniques such as camera shot detection, hough transform and neural networks are used to extract the time intervals of the points. To detect the best points, three approaches are used. Point length suggests which points correspond to rallies and aces. The audio waves are analyzed to search for the highest audio peaks, which indicate the moments where the crowd cheers the most. Sentiment analysis, a natural language processing technique, is used to look for points where the commentators …


Private And Federated Deep Learning: System, Theory, And Applications For Social Good, Han Hu 2021 New Jersey Institute of Technology

Private And Federated Deep Learning: System, Theory, And Applications For Social Good, Han Hu

Dissertations

During the past decade, drug abuse continues to accelerate towards becoming the most severe public health problem in the United States. The ability to detect drug­abuse risk behavior at a population scale, such as among the population of Twitter users, can help to monitor the trend of drug­abuse incidents. However, traditional methods do not effectively detect drug­abuse risk behavior in tweets, mainly due to the sparsity of such tweets and the noisy nature of tweets. In the first part of this dissertation work, the task of classifying tweets as containing drug­abuse risk behavior or not, is studied. Millions of public …


A Practical Approach To Automated Software Correctness Enhancement, Aleksandr Zakharchenko 2021 New Jersey Institute of Technology

A Practical Approach To Automated Software Correctness Enhancement, Aleksandr Zakharchenko

Dissertations

To repair an incorrect program does not mean to make it correct; it only means to make it more-correct, in some sense, than it is. In the absence of a concept of relative correctness, i.e. the property of a program to be more-correct than another with respect to a specification, the discipline of program repair has resorted to various approximations of absolute (traditional) correctness, with varying degrees of success. This shortcoming is concealed by the fact that most program repair tools are tested on basic cases, whence making them absolutely correct is not clearly distinguishable from making them relatively more-correct. …


Machine Learning And Computer Vision In Solar Physics, Haodi Jiang 2021 New Jersey Institute of Technology

Machine Learning And Computer Vision In Solar Physics, Haodi Jiang

Dissertations

In the recent decades, the difficult task of understanding and predicting violent solar eruptions and their terrestrial impacts has become a strategic national priority, as it affects the life of human beings, including communication, transportation, the power grid, national defense, space travel, and more. This dissertation explores new machine learning and computer vision techniques to tackle this difficult task. Specifically, the dissertation addresses four interrelated problems in solar physics: magnetic flux tracking, fibril tracing, Stokes inversion and vector magnetogram generation.

First, the dissertation presents a new deep learning method, named SolarUnet, to identify and track solar magnetic flux elements in …


Energy Planning Model Design For Forecasting The Final Energy Consumption Using Artificial Neural Networks, Haidy Eissa 2021 The American University in Cairo AUC

Energy Planning Model Design For Forecasting The Final Energy Consumption Using Artificial Neural Networks, Haidy Eissa

Theses and Dissertations

“Energy Trilemma” has recently received an increasing concern among policy makers. The trilemma conceptual framework is based on three main dimensions: environmental sustainability, energy equity, and energy security. Energy security reflects a nation’s capability to meet current and future energy demand. Rational energy planning is thus a fundamental aspect to articulate energy policies. The energy system is huge and complex, accordingly in order to guarantee the availability of energy supply, it is necessary to implement strategies on the consumption side. Energy modeling is a tool that helps policy makers and researchers understand the fluctuations in the energy system. Over the …


Explaining Deep Learning Models For Tabular Data Using Layer-Wise Relevance Propagation, Ihsan Ullah, Andre Rios, Vaibhov Gala, Susan McKeever 2021 National University of Ireland, Galway

Explaining Deep Learning Models For Tabular Data Using Layer-Wise Relevance Propagation, Ihsan Ullah, Andre Rios, Vaibhov Gala, Susan Mckeever

Articles

Trust and credibility in machine learning models are bolstered by the ability of a model to explain its decisions. While explainability of deep learning models is a well-known challenge, a further challenge is clarity of the explanation itself for relevant stakeholders of the model. Layer-wise Relevance Propagation (LRP), an established explainability technique developed for deep models in computer vision, provides intuitive human-readable heat maps of input images. We present the novel application of LRP with tabular datasets containing mixed data (categorical and numerical) using a deep neural network (1D-CNN), for Credit Card Fraud detection and Telecom Customer Churn prediction use …


Comparative Analysis Of Rgb-Based Eye-Tracking For Large-Scale Human-Machine Applications, Brett Thaman, Trung Cao 2021 Northern Kentucky University

Comparative Analysis Of Rgb-Based Eye-Tracking For Large-Scale Human-Machine Applications, Brett Thaman, Trung Cao

Posters-at-the-Capitol

Gaze tracking has become an established technology that enables using an individual’s gaze as an input signal to support a variety of applications in the context of Human-Computer Interaction. Gaze tracking primarily relies on sensing devices such as infrared (IR) cameras. Nevertheless, in the recent years, several attempts have been realized at detecting gaze by acquiring and processing images acquired from standard RGB cameras. Nowadays, there are only a few publicly available open-source libraries and they have not been tested extensively. In this paper, we present the result of a comparative analysis that studied a commercial eye-tracking device using IR …


Task Classification During Visual Search Using Classic Machine Learning And Deep Learning, Devangi Vilas Chinchankar 2021 San Jose State University

Task Classification During Visual Search Using Classic Machine Learning And Deep Learning, Devangi Vilas Chinchankar

Master's Projects

In an average human life, the eyes not only passively scan visual scenes, but most times end up actively performing tasks including, but not limited to, searching, comparing, and counting. As a result of the advances in technology, we are observing a boost in the average screen time. Humans are now looking at an increasing number of screens and in turn images and videos. Understanding what scene a user is looking at and what type of visual task is being performed can be useful in developing intelligent user interfaces, and in virtual reality and augmented reality devices. In this research, …


Privacy Preserving For Multiple Computer Vision Tasks, Amala Varghese Wilson 2021 San Jose State University

Privacy Preserving For Multiple Computer Vision Tasks, Amala Varghese Wilson

Master's Projects

Privacy-preserving visual recognition is an important area of research that is gaining momentum in the field of computer vision. In a production environment, it is critical to have neural network models learn continually from user data. However, sharing raw user data with a server is less desirable from a regulatory, security and privacy perspective. Federated learning addresses the problem of privacy- preserving visual recognition. More specifically, we closely examine and dissect a framework known as Dual User Adaptation (DUA) presented by Lange et al. at CVPR 2020, due to its novel idea of bringing about user-adaptation on both the server-side …


Nitrogenase Iron Protein Classification Using Cnn Neural Network, Amer Rez 2021 San Jose State University

Nitrogenase Iron Protein Classification Using Cnn Neural Network, Amer Rez

Master's Projects

The nitrogenase iron protein (NifH) is extensively used to study nitrogen fixation, the ecologically vital process of reducing atmospheric nitrogen to a bioavailable form. The discovery rate of novel NifH sequences is high, and there is an ongoing need for software tools to mine NifH records from the GenBank repository. Since record annotations are unreliable, because they contain errors, classifiers based on sequence alone are required. The ARBitrator classifier is highly successful but must be initialized by extensive manual effort. A Deep Learning approach could substantially reduce manual intervention. However, attempts to build a character-based Deep Learning NifH classifier were …


The Impact Of Programming Language’S Type On Probabilistic Machine Learning Models, Sherif Elsaid 2021 San Jose State University

The Impact Of Programming Language’S Type On Probabilistic Machine Learning Models, Sherif Elsaid

Master's Projects

Software development is an expensive and difficult process. Mistakes can be easily made, and without extensive review process, those mistakes can make it to the production code and may have unintended disastrous consequences.

This is why various automated code review services have arisen in the recent years. From AWS’s CodeGuro and Microsoft’s Code Analysis to more integrated code assistants, like IntelliCode and auto completion tools. All of which are designed to help and assist the developers with their work and help catch overlooked bugs.

Thanks to recent advances in machine learning, these services have grown tremen- dously in sophistication to …


An Open Source Direct Messaging And Enhanced Recommendation System For Yioop, Aniruddha Dinesh Mallya 2021 San Jose State University

An Open Source Direct Messaging And Enhanced Recommendation System For Yioop, Aniruddha Dinesh Mallya

Master's Projects

Recommendation systems and direct messaging systems are two popular components of web portals. A recommendation system is an information filtering system that seeks to predict the "rating" or "preference" a user would give to an item and a direct messaging system allows private communication between users of any platform. Yioop, is an open source, PHP search engine and web portal that can be configured to allow users to create discussion groups, blogs, wikis etc.

In this project, we expanded on Yioop’s group system so that every user now has a personal group. Personal groups were then used to add user …


Predicting Stocks With Lstm-Based Drnn And Gan, Duy Ngo 2021 San Jose State University

Predicting Stocks With Lstm-Based Drnn And Gan, Duy Ngo

Master's Projects

Trading equities can be very lucrative for some and a gamble for others. Professional traders and retail traders are constantly amassing information to be a step ahead of the market to profit off the value of stocks on the market. Some of the tools in their arsenal include different types of calculations based on a variety of data collected on a stock. Technical analysis is a technique for traders to analyze the data of equities presented on charts. Often, the way the price changes over time can be used as an indicator for traders to predict how future prices will …


Robotic Olfactory-Based Navigation With Mobile Robots, Lingxiao Wang 2021 Embry-Riddle Aeronautical University

Robotic Olfactory-Based Navigation With Mobile Robots, Lingxiao Wang

Doctoral Dissertations and Master's Theses

Robotic odor source localization (OSL) is a technology that enables mobile robots or autonomous vehicles to find an odor source in unknown environments. It has been viewed as challenging due to the turbulent nature of airflows and the resulting odor plume characteristics. The key to correctly finding an odor source is designing an effective olfactory-based navigation algorithm, which guides the robot to detect emitted odor plumes as cues in finding the source. This dissertation proposes three kinds of olfactory-based navigation methods to improve search efficiency while maintaining a low computational cost, incorporating different machine learning and artificial intelligence methods.

A. …


Identifying Bots On Twitter With Benford’S Law, Sanmesh Bhosale 2021 San Jose State University

Identifying Bots On Twitter With Benford’S Law, Sanmesh Bhosale

Master's Projects

Over time Online Social Networks (OSNs) have grown exponentially in terms of active users and have now become an influential factor in the formation of public opinions. Due to this, the use of bots and botnets for spreading misinformation on OSNs has become a widespread concern. The biggest example of this was during the 2016 American Presidential Elections, where Russian bots on Twitter pumped out fake news to influence the election results.

Identifying bots and botnets on Twitter is not just based on visual analysis and can require complex statistical methods to score a profile based on multiple features and …


Deep Convolutional Neural Networks For Accurate Diagnosis Of Covid-19 Patients Using Chest X-Ray Image Databases From Italy, Canada, And The Usa, Amgad A. Salama, Samy H. Darwish, Samir M. Abdel-Mageed, Radwa A. Meshref, Ehab I. Mohamed 2021 Research and Development Center, Air Defense College

Deep Convolutional Neural Networks For Accurate Diagnosis Of Covid-19 Patients Using Chest X-Ray Image Databases From Italy, Canada, And The Usa, Amgad A. Salama, Samy H. Darwish, Samir M. Abdel-Mageed, Radwa A. Meshref, Ehab I. Mohamed

The University of Louisville Journal of Respiratory Infections

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), famously known as COVID-19, has quickly become a global pandemic. Chest X-ray (CXR) imaging has proven reliable, fast, and cost-effective for identifying COVID-19 infections, which proceeds to display atypical unilateral patchy infiltration in the lungs like typical pneumonia. We employed the deep convolutional neural network (DCNN) ResNet-34 to detect and classify CXR images from patients with COVID-19 and Viral Pneumonia and Normal Controls.

Methods: We created a single database containing 781 source CXR images from four different international sub-databases: the Società Italiana di Radiologia Medica e Interventistica (SIRM), the GitHub Database, the …


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