Physical Sciences and Mathematics Commons^™

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 …

Recent Advances In Deep Learning For Object Detection, Xiongwei Wu, Doyen Sahoo, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

Object detection is a fundamental visual recognition problem in computer vision and has been widely studied in the past decades. Visual object detection aims to find objects of certain target classes with precise localization in a given image and assign each object instance a corresponding class label. Due to the tremendous successes of deep learning based image classification, object detection techniques using deep learning have been actively studied in recent years. In this paper, we give a comprehensive survey of recent advances in visual object detection with deep learning. By reviewing a large body of recent related work in literature, …

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 …

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 …

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 …

Automatic Delamination Segmentation For Bridge Deck Based On Encoder-Decoder Deep Learning Through Uav-Based Thermography, Chongsheng Cheng, Zhexiong Shang, Zhigang Shen

Department of Construction Engineering and Management: Faculty Publications

Concrete deck delamination often demonstrates strong variations in size, shape, and temperature distribution under the influences of outdoor weather conditions. The strong variations create challenges for pure analytical solutions in infrared image segmentation of delaminated areas. The recently developed supervised deep learning approach demonstrated the potentials in achieving automatic segmentation of RGB images. However, its effectiveness in segmenting thermal images remains under-explored. The main challenge lies in the development of specific models and the generation of a large range of labeled infrared images for training. To address this challenge, a customized deep learning model based on encoder-decoder architecture is proposed …

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 …

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 …

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 …

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 …

Superb: Superior Behavior-Based Anomaly Detection Defining Authorized Users' Traffic Patterns, Daniel Karasek

Master of Science in Computer Science Theses

Network anomalies are correlated to activities that deviate from regular behavior patterns in a network, and they are undetectable until their actions are defined as malicious. Current work in network anomaly detection includes network-based and host-based intrusion detection systems. However, network anomaly detection schemes can suffer from high false detection rates due to the base rate fallacy. When the detection rate is less than the false positive rate, which is found in network anomaly detection schemes working with live data, a high false detection rate can occur. To overcome such a drawback, this paper proposes a superior behavior-based anomaly detection …

Semi-Supervised Deep Learning With Applications In Surgical Video Analysis And Bioinformatics, Sheng Wang

Computer Science and Engineering Dissertations - Archive

In the current era of big data, deep learning has been the state-of-the-art model for various applications. Image-based applications such as image classification, object detection, image segmentation, benefit most from deep learning networks. One reason for the successful applications of deep learning is that there are a large number of labeled training samples for the model to learn from. People are interested in reducing the cost of getting labeled training samples, and there are various research going on with unsupervised, semi-supervised, and self-supervised deep learning. The cost of health-related data is even higher. Labeling the surgical videos with tools being …

Efficient Network Design For High Dimensional Data, Xin Miao

Computer Science and Engineering Dissertations - Archive

Due to the powerful feature representation capabilities, deep learning has became a powerful tool in the field of computer vision. Especially in the aspect of high-dimensional images, deep learning can achieve fast inference compared with most traditional methods. This paper focuses on how to design an efficient neural network and apply it to two high-dimensional images application, video facial landmarks detections and compressive imaging system. In this first part of this paper, we focus on landmarks detection for video facial images. Existing methods for facial landmarks detection mainly rely on cascaded regression. It is an indirect method and progressively estimates …

Stay-At-Home Motor Rehabilitation: Optimizing Spatiotemporal Learning On Low-Cost Capacitive Sensor Arrays, Reid Sutherland

Graduate Theses and Dissertations

Repeated, consistent, and precise gesture performance is a key part of recovery for stroke and other motor-impaired patients. Close professional supervision to these exercises is also essential to ensure proper neuromotor repair, which consumes a large amount of medical resources. Gesture recognition systems are emerging as stay-at-home solutions to this problem, but the best solutions are expensive, and the inexpensive solutions are not universal enough to tackle patient-to-patient variability. While many methods have been studied and implemented, the gesture recognition system designer does not have a strategy to effectively predict the right method to fit the needs of a patient. …

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 …

Development Of Fully Balanced Ssfp And Computer Vision Applications For Mri-Assisted Radiosurgery (Mars), Jeremiah Sanders

Dissertations and Theses (Open Access)

Prostate cancer is the second most common cancer in men and the second-leading cause of cancer death in men. Brachytherapy is a highly effective treatment option for prostate cancer, and is the most cost-effective initial treatment among all other therapeutic options for low to intermediate risk patients of prostate cancer. In low-dose-rate (LDR) brachytherapy, verifying the location of the radioactive seeds within the prostate and in relation to critical normal structures after seed implantation is essential to ensuring positive treatment outcomes.

One current gap in knowledge is how to simultaneously image the prostate, surrounding anatomy, and radioactive seeds within the …

A Framework For Vector-Weighted Deep Neural Networks, Carter Chiu

UNLV Theses, Dissertations, Professional Papers, and Capstones

The vast majority of advances in deep neural network research operate on the basis of a real-valued weight space. Recent work in alternative spaces have challenged and complemented this idea; for instance, the use of complex- or binary-valued weights have yielded promising and fascinating results. We propose a framework for a novel weight space consisting of vector values which we christen VectorNet. We first develop the theoretical foundations of our proposed approach, including formalizing the requisite theory for forward and backpropagating values in a vector-weighted layer. We also introduce the concept of expansion and aggregation functions for conversion between real …

Towards Characterizing Adversarial Defects Of Deep Learning Software From The Lens Of Uncertainty, Xiyue Zhang, Xiaofei Xie, Lei Ma, Xiaoning Du, Qiang Hu, Yang Liu, Jianjun Zhao, Meng Sun

Research Collection School Of Computing and Information Systems

Over the past decade, deep learning (DL) has been successfully applied to many industrial domain-specific tasks. However, the current state-of-the-art DL software still suffers from quality issues, which raises great concern especially in the context of safety- and security-critical scenarios. Adversarial examples (AEs) represent a typical and important type of defects needed to be urgently addressed, on which a DL software makes incorrect decisions. Such defects occur through either intentional attack or physical-world noise perceived by input sensors, potentially hindering further industry deployment. The intrinsic uncertainty nature of deep learning decisions can be a fundamental reason for its incorrect behavior. …

Research On Image Description Method Based On Neural Network, Kong Rui, Xie Wei, Lei Tai

Journal of System Simulation

Abstract: The automatic recognition and automatically describing image content is an important research direction to the artificial intelligence to connect the computer vision and the natural language processing. A method of describing the image content is proposed to generate the natural language by using the deep neural network model. The model consists of a convolutional neural network (CNN) and a recurrent neural network (RNN). The CNN is used to extract features of the input image to generate a fixed-length feature vector, which initializes the RNN to generate the sentences. Experimental results on the MSCOCO image description dataset show the syntactic …

Chaotic Model Prediction With Machine Learning, Yajing Zhao

Theses and Dissertations

Chaos theory is a branch of modern mathematics concerning the non-linear dynamic systems that are highly sensitive to their initial states. It has extensive real-world applications, such as weather forecasting and stock market prediction. The Lorenz system, defined by three ordinary differential equations (ODEs), is one of the simplest and most popular chaotic models. Historically research has focused on understanding the Lorenz system's mathematical characteristics and dynamical evolution including the inherent chaotic features it possesses. In this thesis, we take a data-driven approach and propose the task of predicting future states of the chaotic system from limited observations. We explore …

High Performance And Machine Learning Algorithms For Brain Fmri Data, Taban Eslami

Dissertations

Brain disorders are very difficult to diagnose for reasons such as overlapping nature of symptoms, individual differences in brain structure, lack of medical tests and unknown causes of some disorders. The current psychiatric diagnostic process is based on behavioral observation and may be prone to misdiagnosis.

Noninvasive brain imaging technologies such as Magnetic Resonance Imaging (MRI) and functional Magnetic Resonance Imaging (fMRI) make the process of understanding the structure and function of the brain easier. Quantitative analysis of brain imaging data using machine learning and data mining techniques can be advantageous not only to increase the accuracy of brain disorder …

A Survey Of Feature Extraction And Fusion Of Deep Learning For Detection Of Abnormalities In Video Endoscopy Of Gastrointestinal-Tract, Hussam Ali, Muhammad Sharif, Mussarat Yasmin, Mubashir Husain Rehmani, Farhan Riaz

Publications

A standard screening procedure involves video endoscopy of the Gastrointestinal tract. It is a less invasive method which is practiced for early diagnosis of gastric diseases. Manual inspection of a large number of gastric frames is an exhaustive, time-consuming task, and requires expertise. Conversely, several computer-aided diagnosis systems have been proposed by researchers to cope with the dilemma of manual inspection of the massive volume of frames. This article gives an overview of different available alternatives for automated inspection, detection, and classification of various GI abnormalities. Also, this work elaborates techniques associated with content-based image retrieval and automated systems for …

The Effectiveness Of Transfer Learning Systems On Medical Images, James Boit

Masters Theses & Doctoral Dissertations

Deep neural networks have revolutionized the performances of many machine learning tasks such as medical image classification and segmentation. Current deep learning (DL) algorithms, specifically convolutional neural networks are increasingly becoming the methodological choice for most medical image analysis. However, training these deep neural networks requires high computational resources and very large amounts of labeled data which is often expensive and laborious. Meanwhile, recent studies have shown the transfer learning (TL) paradigm as an attractive choice in providing promising solutions to challenges of shortage in the availability of labeled medical images. Accordingly, TL enables us to leverage the knowledge learned …