Digital Commons Network^™

Deep Learning Methods For Mining Genomic Sequence Patterns, Xin Gao

Dissertations

Nowadays, with the growing availability of large-scale genomic datasets and advanced computational techniques, more and more data-driven computational methods have been developed to analyze genomic data and help to solve incompletely understood biological problems. Among them, deep learning methods, have been proposed to automatically learn and recognize the functional activity of DNA sequences from genomics data. Techniques for efficient mining genomic sequence pattern will help to improve our understanding of gene regulation, and thus accelerate our progress toward using personal genomes in medicine.

This dissertation focuses on the development of deep learning methods for mining genomic sequences. First, we compare …

Computational Intelligence In Steganography: Adaptive Image Watermarking, Xin Zhong

Dissertations

Digital image watermarking, as an extension of traditional steganography, refers to the process of hiding certain messages into cover images. The transport image, called marked-image or stego-image, conveys the hidden messages while appears visibly similar to the cover-image. Therefore, image watermarking enables various applications such as copyright protection and covert communication. In a watermarking scheme, fidelity, capacity and robustness are considered as crucial factors, where fidelity measures the similarity between the cover- and marked-images, capacity measures the maximum amount of watermark that can be embedded, and robustness concerns the watermark extraction under attacks on the marked-image. Watermarking techniques are often …

Discerning Novel Splice Junctions Derived From Rna-Seq Alignment: A Deep Learning Approach, Yi Zhang, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Background: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both possible and widely available. RNA-seq provides unprecedented resolution to identify gene structures and resolve the diversity of splicing variants. However, currently available ab initio aligners are vulnerable to spurious alignments due to random sequence matches and sample-reference genome discordance. As a consequence, a significant set of false positive exon junction predictions would be introduced, which will further confuse downstream analyses of splice variant discovery and abundance estimation.

Results: …

A Microscopic Simulation Laboratory For Evaluation Of Off-Street Parking Systems, Yun Yuan

Theses and Dissertations

The parking industry produces an enormous amount of data every day that, properly analyzed, will change the way the industry operates. The collected data form patterns that, in most cases, would allow parking operators and property owners to better understand how to maximize revenue and decrease operating expenses and support the decisions such as how to set specific parking policies (e.g. electrical charging only parking space) to achieve the sustainable and eco-friendly parking.

However, there lacks an intelligent tool to assess the layout design and operational performance of parking lots to reduce the externalities and increase the revenue. To address …

Sensor-Based Human Activity Recognition Using Bidirectional Lstm For Closely Related Activities, Arumugam Thendramil Pavai

Electronic Theses, Projects, and Dissertations

Recognizing human activities using deep learning methods has significance in many fields such as sports, motion tracking, surveillance, healthcare and robotics. Inertial sensors comprising of accelerometers and gyroscopes are commonly used for sensor based HAR. In this study, a Bidirectional Long Short-Term Memory (BLSTM) approach is explored for human activity recognition and classification for closely related activities on a body worn inertial sensor data that is provided by the UTD-MHAD dataset. The BLSTM model of this study could achieve an overall accuracy of 98.05% for 15 different activities and 90.87% for 27 different activities performed by 8 persons with 4 …

Efficacy Of Deep Learning In Support Of Smart Services, Basheer Mohammed Basheer Qolomany

Dissertations

The massive amount of streaming data generated and captured by smart service appliances, sensors and devices needs to be analyzed by algorithms, transformed into information, and minted to extract knowledge to facilitate timely actions and better decision making. This can lead to new products and services that can dramatically transform our lives. Machine learning and data analytics will undoubtedly play a critical role in enabling the delivery of smart services. Within the machine-learning domain, Deep Learning (DL) is emerging as a superior new approach that is much more effective than any rule or formula used by traditional machine learning. Furthermore, …

Making A Good Thing Better: Enhancing Password/Pin-Based User Authentication With Smartwatch, Bing Chang, Yingjiu Li, Qiongxiao Wang, Wen-Tao Zhu, Robert H. Deng

Research Collection School Of Computing and Information Systems

Wearing smartwatches becomes increasingly popular in people’s lives. This paper shows that a smartwatch can help its bearer authenticate to a login system effectively and securely even if the bearer’s password has already been revealed. This idea is motivated by our observation that a sensor-rich smartwatch is capable of tracking the wrist motions of its bearer typing a password or PIN, which can be used as an authentication factor. The major challenge in this research is that a sophisticated attacker may imitate a user’s typing behavior as shown in previous research on keystroke dynamics based user authentication. We address this …

Transfer Learning With Deep Recurrent Neural Networks For Remaining Useful Life Estimation, Ansi Zhang, Shaobo Li, Yuxin Cui, Zhonghao Liu, Guanci Yang, Jianjun Hu

Faculty Publications

Prognostics, such as remaining useful life (RUL) prediction, is a crucial task in condition-based maintenance. A major challenge in data-driven prognostics is the difficulty of obtaining a sufficient number of samples of failure progression. However, for traditional machine learning methods and deep neural networks, enough training data is a prerequisite to train good prediction models. In this work, we proposed a transfer learning algorithm based on Bi-directional Long Short-Term Memory (BLSTM) recurrent neural networks for RUL estimation, in which the models can be first trained on different but related datasets and then fine-tuned by the target dataset. Extensive experimental results …

Transfer Learning With Deep Recurrent Neural Networks For Remaining Useful Life Estimation, Ansi Zhang, Honglei Wang, Shaobo Li, Yuxin Cui, Guanci Yang, Jianjun Hu

Faculty Publications

Prognostics, such as remaining useful life (RUL) prediction, is a crucial task in condition-based maintenance. A major challenge in data-driven prognostics is the difficulty of obtaining a sufficient number of samples of failure progression. However, for traditional machine learning methods and deep neural networks, enough training data is a prerequisite to train good prediction models. In this work, we proposed a transfer learning algorithm based on Bi-directional Long Short-Term Memory (BLSTM) recurrent neural networks for RUL estimation, in which the models can be first trained on different but related datasets and then fine-tuned by the target dataset. Extensive experimental results …

Improving Knowledge Tracing Model By Integrating Problem Difficulty, Sein Minn, Feida Zhu, Michel C. Desmarais

Research Collection School Of Computing and Information Systems

Intelligent Tutoring Systems (ITS) are designed for providing personalized instructions to students with the needs of their skills. Assessment of student knowledge acquisition dynamically is nontrivial during her learning process with ITS. Knowledge tracing, a popular student modeling technique for student knowledge assessment in adaptive tutoring, which is used for tracing student's knowledge state and detecting student's knowledge acquisition by using decomposed individual skill or problems with a single skill per problem. Unfortunately, recent KT models fail to deal with practices of complex skill composition and variety of concepts included in a problem simultaneously. Our goal is to investigate a …

Learning Generalized Video Memory For Automatic Video Captioning, Poo-Hee Chang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Recent video captioning methods have made great progress by deep learning approaches with convolutional neural networks (CNN) and recurrent neural networks (RNN). While there are techniques that use memory networks for sentence decoding, few work has leveraged on the memory component to learn and generalize the temporal structure in video. In this paper, we propose a new method, namely Generalized Video Memory (GVM), utilizing a memory model for enhancing video description generation. Based on a class of self-organizing neural networks, GVM’s model is able to learn new video features incrementally. The learned generalized memory is further exploited to decode the …

End-To-End Convolutional Neural Network Model For Gear Fault Diagnosis Based On Sound Signals, Yong Yao, Honglei Wang, Shaobo Li, Zhongnhao Liu, Gui Gui, Yabo Dan, Jianjun Hu

Faculty Publications

Currently gear fault diagnosis is mainly based on vibration signals with a few studies on acoustic signal analysis. However, vibration signal acquisition is limited by its contact measuring while traditional acoustic-based gear fault diagnosis relies heavily on prior knowledge of signal processing techniques and diagnostic expertise. In this paper, a novel deep learning-based gear fault diagnosis method is proposed based on sound signal analysis. By establishing an end-to-end convolutional neural network (CNN), the time and frequency domain signals can be fed into the model as raw signals without feature engineering. Moreover, multi-channel information from different microphones can also be fused …

Toward Audio Beehive Monitoring: Deep Learning Vs. Standard Machine Learning In Classifying Beehive Audio Samples, Vladmir Kulyukin, Sarbajit Mukherjee, Prakhar Amlathe

Computer Science Faculty and Staff Publications

Electronic beehive monitoring extracts critical information on colony behavior and phenology without invasive beehive inspections and transportation costs. As an integral component of electronic beehive monitoring, audio beehive monitoring has the potential to automate the identification of various stressors for honeybee colonies from beehive audio samples. In this investigation, we designed several convolutional neural networks and compared their performance with four standard machine learning methods (logistic regression, k-nearest neighbors, support vector machines, and random forests) in classifying audio samples from microphones deployed above landing pads of Langstroth beehives. On a dataset of 10,260 audio samples where the training and testing …

Personality Recognition For Deception Detection, Guozhen An

Dissertations, Theses, and Capstone Projects

Personality aims at capturing stable individual characteristics, typically measurable in quantitative terms, that explain and predict observable behavioral differences. Personality has been proved to be very useful in many life outcomes, and there has been huge interests on predicting personality automatically. Previously, there are tremendous amount of approaches successfully predicting personality. However, most previous research on personality detection has used personality scores assigned by annotators based solely on the text or audio clip, and found that predicting self-reported personality is a much more difficult task than predicting observer-report personality. In our study, we will demonstrate how to accurately detect self-reported …

Product Innovation Design Based On Deep Learning And Kansei Engineering, Huafeng Quan, Shaobo Li, Jianjun Hu

Faculty Publications

Creative product design is becoming critical to the success of many enterprises. However, the conventional product innovation process is hindered by two major challenges: the difficulty to capture users’ preferences and the lack of intuitive approaches to visually inspire the designer, which is especially true in fashion design and form design of many other types of products. In this paper, we propose to combine Kansei engineering and the deep learning for product innovation (KENPI) framework, which can transfer color, pattern, etc. of a style image in real time to a product’s shape automatically. To capture user preferences, we combine Kansei …

A Distributed Semi-Supervised Platform For Dnase-Seq Data Analytics Using Deep Generative Convolutional Networks, Shayan Shams, Richard Platania, Joohyun Kim, Jian Zhang, Kisung Lee, Seungwon Yang, Seung Jong Park

Computer Science Faculty Research & Creative Works

A deep learning approach for analyzing DNase-seq datasets is presented, which has promising potentials for unraveling biological underpinnings on transcription regulation mechanisms. Further understanding of these mechanisms can lead to important advances in life sciences in general and drug, biomarker discovery, and cancer research in particular. Motivated by recent remarkable advances in the field of deep learning, we developed a platform, Deep Semi-Supervised DNase-seq Analytics (DSSDA). Primarily empowered by deep generative Convolutional Networks (ConvNets), the most notable aspect is the capability of semi-supervised learning, which is highly beneficial for common biological settings often plagued with a less sufficient number of …

Deep Learning For Practical Image Recognition: Case Study On Kaggle Competitions, Xulei Yang, Zeng Zeng, Sin G. Teo, Li Wang, Vijay Chandrasekar, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

In past years, deep convolutional neural networks (DCNN) have achieved big successes in image classification and object detection, as demonstrated on ImageNet in academic field. However, There are some unique practical challenges remain for real-world image recognition applications, e.g., small size of the objects, imbalanced data distributions, limited labeled data samples, etc. In this work, we are making efforts to deal with these challenges through a computational framework by incorporating latest developments in deep learning. In terms of two-stage detection scheme, pseudo labeling, data augmentation, cross-validation and ensemble learning, the proposed framework aims to achieve better performances for practical image …

Towards Distributed Cyberinfrastructure For Smart Cities Using Big Data And Deep Learning Technologies, Shayan Shams, Sayan Goswami, Kisung Lee, Seungwon Yang, Seung Jong Park

Computer Science Faculty Research & Creative Works

Recent advances in big data and deep learning technologies have enabled researchers across many disciplines to gain new insight into large and complex data. For example, deep neural networks are being widely used to analyze various types of data including images, videos, texts, and time-series data. In another example, various disciplines such as sociology, social work, and criminology are analyzing crowd-sourced and online social network data using big data technologies to gain new insight from a plethora of data. Even though many different types of data are being generated and analyzed in various domains, the development of distributed city-level cyberinfrastructure …

Human Activity Recognition Based On Transfer Learning, Jinyong Pang

USF Tampa Graduate Theses and Dissertations

Human activity recognition (HAR) based on time series data is the problem of classifying various patterns. Its widely applications in health care owns huge commercial benefit. With the increasing spread of smart devices, people have strong desires of customizing services or product adaptive to their features. Deep learning models could handle HAR tasks with a satisfied result. However, training a deep learning model has to consume lots of time and computation resource. Consequently, developing a HAR system effectively becomes a challenging task. In this study, we develop a solid HAR system using Convolutional Neural Network based on transfer learning, which …

Deep Learning For Segmentation Of 3d Cryo-Em Images, Devin Reid Haslam

Computer Science Theses & Dissertations

Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural determination of protein complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 Å). Most existing methods are image processing methods that do not fully utilize available images in the cryo-EM database. In this paper, we present a deep learning approach to segment secondary structure elements as helices and β-sheets from medium- resolution density maps. The proposed 3D convolutional neural network is shown to detect secondary structure locations with an F1 score between 0.79 and 0.88 for six simulated test cases. …

Deep Learning For Link Prediction In Dynamic Networks Using Weak Estimators, Carter Chiu, Justin Zhan

Computer Science Faculty Research

Link prediction is the task of evaluating the probability that an edge exists in a network, and it has useful applications in many domains. Traditional approaches rely on measuring the similarity between two nodes in a static context. Recent research has focused on extending link prediction to a dynamic setting, predicting the creation and destruction of links in networks that evolve over time. Though a difficult task, the employment of deep learning techniques have shown to make notable improvements to the accuracy of predictions. To this end, we propose the novel application of weak estimators in addition to the utilization …

Exploring The Role Of Semi-Supervised Deep Reinforcement Learning And Ensemble Methods In Support Of The Internet Of Things, Mehdi Mohammadi

Dissertations

Smart services are an important element of the Internet of Things (IoT) ecosystem where insights are drawn from raw data through the use of machine learning techniques. However, the pathway to develop IoT smart services is complicated as IoT data presents several challenges for machine learning, including handling big data, shortage of labeled data, and the need to benefit from the spatio-temporal relations hidden in the training data.

In this dissertation, after reviewing the state-of-the-art deep learning (DL) and deep reinforcement learning (DRL) techniques and their use in support of IoT applications, this study proposes to extend DRL to semi-supervised …

Design And Implementation Of A Domain Specific Language For Deep Learning, Xiao Bing Huang

Theses and Dissertations

\textit {Deep Learning} (DL) has found great success in well-diversified areas such as machine vision, speech recognition, big data analysis, and multimedia understanding recently. However, the existing state-of-the-art DL frameworks, e.g. Caffe2, Theano, TensorFlow, MxNet, Torch7, and CNTK, are programming libraries with fixed user interfaces, internal representations, and execution environments. Modifying the code of DL layers or data structure is very challenging without in-depth understanding of the underlying implementation. The optimization of the code and execution in these tools is often limited and relies on the specific DL computation graph manipulation and scheduling that lack systematic and universal strategies. Furthermore, …

Parameterizing And Aggregating Activation Functions In Deep Neural Networks, Luke Benjamin Godfrey

Graduate Theses and Dissertations

The nonlinear activation functions applied by each neuron in a neural network are essential for making neural networks powerful representational models. If these are omitted, even deep neural networks reduce to simple linear regression due to the fact that a linear combination of linear combinations is still a linear combination. In much of the existing literature on neural networks, just one or two activation functions are selected for the entire network, even though the use of heterogenous activation functions has been shown to produce superior results in some cases. Even less often employed are activation functions that can adapt their …

Ai-Human Collaboration Via Eeg, Adam Noack

All College Thesis Program, 2016-2019

As AI becomes ever more competent and integrated into our lives, the issue of AI-human goal misalignment looms larger. This is partially because there is often a rift between what humans explicitly command and what they actually mean. Most contemporary AI systems cannot bridge this gap. In this study we attempted to reconcile the goals of human and machine by using EEG signals from a human to help a simulated agent complete a task.

Deep Code Comment Generation, Xing Hu, Ge Li, Xin Xia, David Lo, Zhi Jin

Research Collection School Of Computing and Information Systems

During software maintenance, code comments help developerscomprehend programs and reduce additional time spent on readingand navigating source code. Unfortunately, these comments areoften mismatched, missing or outdated in the software projects.Developers have to infer the functionality from the source code.This paper proposes a new approach named DeepCom to automatically generate code comments for Java methods. The generatedcomments aim to help developers understand the functionalityof Java methods. DeepCom applies Natural Language Processing(NLP) techniques to learn from a large code corpus and generatescomments from learned features. We use a deep neural networkthat analyzes structural information of Java methods for bettercomments generation. We conduct …

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 …

A Multi-Step Nonlinear Dimension-Reduction Approach With Applications To Bigdata, R. Krishnan, V. A. Samaranayake, Jagannathan Sarangapani

Mathematics and Statistics Faculty Research & Creative Works

In this paper, a multi-step dimension-reduction approach is proposed for addressing nonlinear relationships within attributes. In this work, the attributes in the data are first organized into groups. In each group, the dimensions are reduced via a parametric mapping that takes into account nonlinear relationships. Mapping parameters are estimated using a low rank singular value decomposition (SVD) of distance covariance. Subsequently, the attributes are reorganized into groups based on the magnitude of their respective singular values. The group-wise organization and the subsequent reduction process is performed for multiple steps until a singular value-based user-defined criterion is satisfied. Simulation analysis is …

Speech Emotion Recognition Using Convolutional Neural Networks, Somayeh Shahsavarani

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Automatic speech recognition is an active field of study in artificial intelligence and machine learning whose aim is to generate machines that communicate with people via speech. Speech is an information-rich signal that contains paralinguistic information as well as linguistic information. Emotion is one key instance of paralinguistic information that is, in part, conveyed by speech. Developing machines that understand paralinguistic information, such as emotion, facilitates the human-machine communication as it makes the communication more clear and natural. In the current study, the efficacy of convolutional neural networks in recognition of speech emotions has been investigated. Wide-band spectrograms of the …

Attributed Social Network Embedding, Lizi Liao, Xiangnan He, Hanwang Zhang, Tat-Seng Chua

Research Collection School Of Computing and Information Systems

Embedding network data into a low-dimensional vector space has shown promising performance for many real-world applications, such as node classification and entity retrieval. However, most existing methods focused only on leveraging network structure. For social networks, besides the network structure, there also exists rich information about social actors, such as user profiles of friendship networks and textual content of citation networks. These rich attribute information of social actors reveal the homophily effect, exerting huge impacts on the formation of social networks. In this paper, we explore the rich evidence source of attributes in social networks to improve network embedding. We …