Physical Sciences and Mathematics Commons^™

Discrimination Of Leucine And Isoleucine In De Novo Peptide Sequencing Using Deep Neural Networks, Bingran Shen

Electronic Thesis and Dissertation Repository

De novo peptide sequencing from tandem MS data is a key technology in proteomics for understanding the structure of proteins, especially for first seen sequences. Although this technique has advanced rapidly in recent years and become more effective, one crucial problem remained unsolved. Due to the isomerism of leucine and isoleucine, they are practically indistinguishable in de novo sequencing using traditional tandem MS data. Some experimental attempts have been made to resolve this ambiguity such as EThCD fragmentation process. In this study, we took a data focused approach rather than only looking for characteristic satellite ions produced by the EThCD …

Deep Learning To Predict Ocean Seabed Type And Source Parameters, David Franklin Van Komen

Theses and Dissertations

In the ocean, light from the surface dissipates quickly leaving sound the only way to see at a distance. Different sediment types on the ocean floor and water properties like salinity, temperature, and ocean depth all change how sound travels across long distances. Hard sediment types, such as sand and bedrock, are highly reflective while softer sediment types, such as mud, are more absorptive and change the received sound upon arrival. Unfortunately, the vast majority of the ocean floor is not mapped and the expenses involved in creating such a map are far too great. Traditional signal processing methods in …

Exploring The Efficacy Of Transfer Learning In Mining Image‑Based Software Artifacts, Natalie Best, Jordan Ott, Erik J. Linstead

Engineering Faculty Articles and Research

Background

Transfer learning allows us to train deep architectures requiring a large number of learned parameters, even if the amount of available data is limited, by leveraging existing models previously trained for another task. In previous attempts to classify image-based software artifacts in the absence of big data, it was noted that standard off-the-shelf deep architectures such as VGG could not be utilized due to their large parameter space and therefore had to be replaced by customized architectures with fewer layers. This proves to be challenging to empirical software engineers who would like to make use of existing architectures without …

Empirical Studies Of Deep Learning On Information Diffusion On Social Networks And Collective Task Learning For Swarm Robotics, Trung T. Nguyen

Dissertations

Researchers in multiple disciplines have recently adopted deep learning because of its ability of high accuracy representation learning from big and complex data. My research goal in this thesis is developing deep learning models for information diffusion analysis on social networks and collective tasks learning in swarm robotics. Firstly, the information diffusion on social networks is modeled as a multivariate time series in three dimensions with ten features. Then, we applied time-series clustering algorithms with Dynamic Time Warping to discover different patterns of our models. Then, we build a prediction model based on LSTM, which outperforms traditional time-series prediction methods. …

Novel Deep Learning Methods Combined With Static Analysis For Source Code Processing, Duy Quoc Nghi Bui

Dissertations and Theses Collection (Open Access)

It is desirable to combine machine learning and program analysis so that one can leverage the best of both to increase the performance of software analytics. On one side, machine learning can analyze the source code of thousands of well-written software projects that can uncover patterns that partially characterize software that is reliable, easy to read, and easy to maintain. On the other side, the program analysis can be used to define rigorous and unique rules that are only available in programming languages, which enrich the representation of source code and help the machine learning to capture the patterns better. …

Applications Of Artificial Intelligence And Graphy Theory To Cyberbullying, Jesse D. Simpson

MSU Graduate Theses

Cyberbullying is an ongoing and devastating issue in today's online social media. Abusive users engage in cyber-harassment by utilizing social media to send posts, private messages, tweets, or pictures to innocent social media users. Detecting and preventing cases of cyberbullying is crucial. In this work, I analyze multiple machine learning, deep learning, and graph analysis algorithms and explore their applicability and performance in pursuit of a robust system for detecting cyberbullying. First, I evaluate the performance of the machine learning algorithms Support Vector Machine, Naïve Bayes, Random Forest, Decision Tree, and Logistic Regression. This yielded positive results and obtained upwards …

Facial Expression Recognition In The Wild Using Convolutional Neural Networks, Amir Hossein Farzaneh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Facial Expression Recognition (FER) is the task of predicting a specific facial expression given a facial image. FER has demonstrated remarkable progress due to the advancement of deep learning. Generally, a FER system as a prediction model is built using two sub-modules: 1. Facial image representation model that learns a mapping from the input 2D facial image to a compact feature representation in the embedding space, and 2. A classifier module that maps the learned features to the label space comprising seven labels of neutral, happy, sad, surprise, anger, fear, or disgust. Ultimately, …

Improving Convolutional Neural Network Robustness To Adversarial Images Through Image Filtering, Natalie E. Bogda

Masters Theses

The field of computer vision and deep learning is known for its ability to recognize images with extremely high accuracy. Convolutional neural networks exist that can correctly classify 96\% of 1.2 million images of complex scenes. However, with just a few carefully positioned imperceptible changes to the pixels of an input image, an otherwise accurate network will misclassify this almost identical image with high confidence. These perturbed images are known as \textit{adversarial examples} and expose that convolutional neural networks do not necessarily "see" the world in the way that humans do. This work focuses on increasing the robustness of classifiers …

Deep Learning For Remote Sensing Image Processing, Yan Lu

Computational Modeling & Simulation Engineering Theses & Dissertations

Remote sensing images have many applications such as ground object detection, environmental change monitoring, urban growth monitoring and natural disaster damage assessment. As of 2019, there were roughly 700 satellites listing “earth observation” as their primary application. Both spatial and temporal resolutions of satellite images have improved consistently in recent years and provided opportunities in resolving fine details on the Earth's surface. In the past decade, deep learning techniques have revolutionized many applications in the field of computer vision but have not fully been explored in remote sensing image processing. In this dissertation, several state-of-the-art deep learning models have been …

Secure Mobile Computing By Using Convolutional And Capsule Deep Neural Networks, Rui Ning

Electrical & Computer Engineering Theses & Dissertations

Mobile devices are becoming smarter to satisfy modern user's increasing needs better, which is achieved by equipping divers of sensors and integrating the most cutting-edge Deep Learning (DL) techniques. As a sophisticated system, it is often vulnerable to multiple attacks (side-channel attacks, neural backdoor, etc.). This dissertation proposes solutions to maintain the cyber-hygiene of the DL-Based smartphone system by exploring possible vulnerabilities and developing countermeasures.

First, I actively explore possible vulnerabilities on the DL-Based smartphone system to develop proactive defense mechanisms. I discover a new side-channel attack on smartphones using the unrestricted magnetic sensor data. I demonstrate that attackers can …

Facing The Hard Problems In Fgvc, Connor Stanley Anderson

Theses and Dissertations

In fine-grained visual categorization (FGVC), there is a near-singular focus in pursuit of attaining state-of-the-art (SOTA) accuracy. This work carefully analyzes the performance of recent SOTA methods, quantitatively, but more importantly, qualitatively. We show that these models universally struggle with certain "hard" images, while also making complementary mistakes. We underscore the importance of such analysis, and demonstrate that combining complementary models can improve accuracy on the popular CUB-200 dataset by over 5%. In addition to detailed analysis and characterization of the errors made by these SOTA methods, we provide a clear set of recommended directions for future FGVC researchers.

A Survey On Visual Slam Based On Deep Learning, Ruijun Liu, Xiangshang Wang, Zhang Chen, Bohua Zhang

Journal of System Simulation

Abstract: Following the development of computer vision and robotics, visual Simultaneous Localization and Mapping becomes a research focus in the field of unmanned systems. The powerful advantages of deep learning in the image processing offer a huge opportunity to the wide combination of the two fields. The outstanding research achievements of deep learning combined with visual odometry, loop closure detection and semantic Simultaneous Localization and Mapping are summarized. A comparison between the traditional algorithm and method based on deep learning is carried out. The development direction of visual Simultaneous Localization and Mapping based on deep learning is …

Human Depth Maps Restoration Based On Guided Gan, Jingfang Yin, Dengming Zhu, Shi Min, Zhaoqi Wang

Journal of System Simulation

Abstract: The depth maps captured by a small depth camera on mobile devices suffer from the problem of severe holes. The Guided Generative Adversarial Network (Guided GAN) based on deep learning is proposed to restore human depth maps with above problems. The high-precision human segmentation features and depth class features are extracted from the monocular RGB image by the guider based on the stacked hourglass network. The holes in the human depth maps are filled by the special generator under the guidance of the extracted human features. In order to get the more realistic results, the discriminator is introduced …

Deep Learning For Identifying Lung Diseases, Lin Wang

Master of Science in Computer Science Theses

Growing health problems, such as lung diseases, especially for children and the elderly, require better diagnostic methods, such as computer-based solutions, and it is crucial to detect and treat these problems early. The purpose of this article is to design and implement a new computer vision-based algorithm based on lung disease diagnosis, which has better performance in lung disease recognition than previous models to reduce lung-related health problems and costs . In addition, we have improved the accuracy of the five lung diseases detection, which helps doctors and doctors use computers to solve this problem at an early stage.

Deep Learning For Identifying Breast Cancer, Yihong Li

Master of Science in Computer Science Theses

Medical images are playing an increasingly important role in the prevention and diagnosis of diseases. Medical images often contain massive amounts of data. Professional interpretation usually requires a long time of professional study and experience accumulation by doctors. Therefore, the use of super storage and computing power in deep learning as a basis can effectively process a large amount of medical data. Breast cancer brings great harm to female patients, and early diagnosis is the most effective prevention and treatment method, so this project will create a new optimized breast cancer auxiliary diagnosis model based on ResNet. Analyze and process, …

Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of …

Deep Learning Of Facial Embeddings And Facial Landmark Points For The Detection Of Academic Emotions, Hua Leong Fwa

Research Collection School Of Computing and Information Systems

Automatic emotion recognition is an actively researched area as emotion plays a pivotal role in effective human communications. Equipping a computer to understand and respond to human emotions has potential applications in many fields including education, medicine, transport and hospitality. In a classroom or online learning context, the basic emotions do not occur frequently and do not influence the learning process itself. The academic emotions such as engagement, frustration, confusion and boredom are the ones which are pivotal to sustaining the motivation of learners. In this study, we evaluated the use of deep learning on FaceNet embeddings and facial landmark …

How Are Deep Learning Models Similar? An Empirical Study On Clone Analysis Of Deep Learning Software, Xiongfei Wu, Liangyu Qin, Bing Yu, Xiaofei Xie, Lei Ma, Yinxing Xue, Yang Liu, Jianjun Zhao

Research Collection School Of Computing and Information Systems

Deep learning (DL) has been successfully applied to many cutting-edge applications, e.g., image processing, speech recognition, and natural language processing. As more and more DL software is made open-sourced, publicly available, and organized in model repositories and stores (Model Zoo, ModelDepot), there comes a need to understand the relationships of these DL models regarding their maintenance and evolution tasks. Although clone analysis has been extensively studied for traditional software, up to the present, clone analysis has not been investigated for DL software. Since DL software adopts the data-driven development paradigm, it is still not clear whether and to what extent …

Psc2code: Denoising Code Extraction From Programming Screencasts, Lingfeng Bao, Zhenchang Xing, Xin Xia, David Lo, Minghui Wu, Xiaohu Yang

Research Collection School Of Computing and Information Systems

Programming screencasts have become a pervasive resource on the Internet, which help developers learn new programming technologies or skills. The source code in programming screencasts is an important and valuable information for developers. But the streaming nature of programming screencasts (i.e., a sequence of screen-captured images) limits the ways that developers can interact with the source code in the screencasts. Many studies use the Optical Character Recognition (OCR) technique to convert screen images (also referred to as video frames) into textual content, which can then be indexed and searched easily. However, noisy screen images significantly affect the quality of source …

Holiday Highway Traffic Flow Prediction Method Based On Deep Learning, Xiaofeng Ji, Yicheng Ge

Journal of System Simulation

Abstract: Accurately predicting highway traffic holiday flow can provide important data for the emergency management of highway. The LSTM-SVR prediction model is established by using the theoretical framework of deep learning. The BP neural network is used to process the sample data, and the data features captured by LSTM are input into the SVR regression layer to realize the traffic flow prediction. Before and after the “Eleventh” Golden Week, the LSTM-SVR model was verified by using the traffic monitoring data of the intermodulation station in Lijiang City and the prediction results were compared with the others. It is found that …

Action Recognition Using The Motion Taxonomy, Maxat Alibayev

USF Tampa Graduate Theses and Dissertations

In the last years, modern action recognition frameworks with deep architectures have achieved impressive results on the large-scale activity datasets. All state-of-the-art models share one common attribute: two-stream architectures. One deep model takes RGB frames, while the other model is fed with pre-computed optical flow vectors. The outputs of both models are combined to be used as a final probability distribution for the action classes. When comparing the results of individual models with the fused model, it is common to see that that latter method is more superior. Researchers explain that phenomena with the fact that optical flow vectors serve …

Modeling Multi-Targets Sentiment Classification Via Graph Convolutional Networks And Auxiliary Relation, Ao Feng, Zhengjie Gao, Xinyu Song, Ke Ke, Tianhao Xu, Xuelei Zhang

All Faculty Scholarship for the College of the Sciences

Existing solutions do not work well when multi-targets coexist in a sentence. The reason is that the existing solution is usually to separate multiple targets and process them separately. If the original sentence has N target, the original sentence will be repeated for N times, and only one target will be processed each time. To some extent, this approach degenerates the fine-grained sentiment classification task into the sentencelevel sentiment classification task, and the research method of processing the target separately ignores the internal relation and interaction between the targets. Based on the above considerations, we proposes to use Graph Convolutional …

A Cnn Based Cognitive Method To Battlefields Encompassing Situation With Insufficient Samples, Zhu Feng, Xiaofeng Hu, Xiaoyuan He, Yisi Kong, Yang Lu

Journal of System Simulation

Abstract: To research the issue of how to grasp the commander's cognitive experience successfully and effectively facing to battlefields sight map, Convolution Neural Network (CNN) as a kind of the typical algorithm in deep learning can provide the key ways. However, CNN needs the enough samples for running. These samples are hardly to achieve for the time being. Aimed at these problems, some exploring researches were carried out. The issues of battlefields encompassing situation cognition met generally in the warfare and lacking enough samples were discussed. On the basis of analyzing the image characteristics of battlefields encompassing situation and the …

Travel Time Prediction Of Urban Road Based On Deep Learning, Weiwei Zhang, Ruimin Li, Zhongjiao Xie

Journal of System Simulation

Abstract: Travel time prediction of urban road is a significant support for urban intelligent transportation system. Four types of LSTM neural network architecture were selected to predict the urban road travel time. The number of nodes in the LSTM hidden layer was fixed to determine the optimal input length of the model. The input length of the model was fixed and the predictive performance of the four LSTM models under different hidden layer nodes and considering spatial correlation were tested respectively. The performance of spatial LSTM model was compared with four traditional models, for example, BP neural network. The results …

Research Of Air Mission Recognition Method Based On Deep Learning, Qingkai Yao, Shaojun Liu, Xiaoyuan He, Ou Wei

Journal of System Simulation

Abstract: In the large-scale simulation of war game, the air mission is the focus of the commander's attention. The rapid, accurate and automatic recognition of air missions is the prerequisite and basis for intelligent decision making. The rapid development of deep learning technology provided a practical and feasible solution for the extraction of complex battlefield posture features, and provided technical support for studying air mission recognition. The research progress of the traditional mission recognition research method and the mission recognition method based on the deep learning was summarized. The three methods of deep learning of Convolution Neural Network (CNN), Long-short …

Neural Network Models For Nuclear Treaty Monitoring: Enhancing The Seismic Signal Pipeline With Deep Temporal Convolution, Joshua T. Dickey

Theses and Dissertations

Seismic signal processing at the IDC is critical to global security, facilitating the detection and identification of covert nuclear tests in near-real time. This dissertation details three research studies providing substantial enhancements to this pipeline. Study 1 focuses on signal detection, employing a TCN architecture directly against raw real-time data streams and effecting a 4 dB increase in detector sensitivity over the latest operational methods. Study 2 focuses on both event association and source discrimination, utilizing a TCN-based triplet network to extract source-specific features from three-component seismograms, and providing both a complimentary validation measure for event association and a one-shot …

Is Using Deep Learning Frameworks Free?: Characterizing Technical Debt In Deep Learning Frameworks, Jiakun Liu, Qiao Huang, Xin Xia, Emad Shihab, David Lo, Shanping Li

Research Collection School Of Computing and Information Systems

Developers of deep learning applications (shortened as application developers) commonly use deep learning frameworks in their projects. However, due to time pressure, market competition, and cost reduction, developers of deep learning frameworks (shortened as framework developers) often have to sacrifice software quality to satisfy a shorter completion time. This practice leads to technical debt in deep learning frameworks, which results in the increasing burden to both the application developers and the framework developers in future development.In this paper, we analyze the comments indicating technical debt (self-admitted technical debt) in 7 of the most popular open-source deep learning frameworks. Although framework …

Yoga Pose Classification Using Deep Learning, Shruti Kothari

Master's Projects

Human pose estimation is a deep-rooted problem in computer vision that has exposed many challenges in the past. Analyzing human activities is beneficial in many fields like video- surveillance, biometrics, assisted living, at-home health monitoring etc. With our fast-paced lives these days, people usually prefer exercising at home but feel the need of an instructor to evaluate their exercise form. As these resources are not always available, human pose recognition can be used to build a self-instruction exercise system that allows people to learn and practice exercises correctly by themselves. This project lays the foundation for building such a system …

Using Case-Level Context To Classify Cancer Pathology Reports, Shang Gao, Mohammed Alawad, Noah Schaefferkoetter, Lynne Penberthy, Xiao-Cheng Wu, Eric B. Durbin, Linda Coyle, Arvind Ramanathan, Georgia Tourassi

Kentucky Cancer Registry Faculty Publications

Individual electronic health records (EHRs) and clinical reports are often part of a larger sequence-for example, a single patient may generate multiple reports over the trajectory of a disease. In applications such as cancer pathology reports, it is necessary not only to extract information from individual reports, but also to capture aggregate information regarding the entire cancer case based off case-level context from all reports in the sequence. In this paper, we introduce a simple modular add-on for capturing case-level context that is designed to be compatible with most existing deep learning architectures for text classification on individual reports. We …

A Multi-Input Deep Learning Model For C/C++ Source Code Attribution, Richard J. Tindell Ii

Masters Theses, 2020-current

Code stylometry is applying analysis techniques to a collection of source code or binaries to determine variations in style. The variations extracted are often used to identify the author of the text or to differentiate one piece from another.

In this research, we were able to create a multi-input deep learning model that could accurately categorize and group code from multiple projects. The deep learning model took as input word-based tokenization for code comments, character-based tokenization for the source code text, and the metadata features described by A. Caliskan-Islam et al. Using these three inputs, we were able to achieve …