Physical Sciences and Mathematics Commons^™

New Methods For Deep Learning Based Real-Valued Inter-Residue Distance Prediction, Jacob Barger

Theses

Background: Much of the recent success in protein structure prediction has been a result of accurate protein contact prediction--a binary classification problem. Dozens of methods, built from various types of machine learning and deep learning algorithms, have been published over the last two decades for predicting contacts. Recently, many groups, including Google DeepMind, have demonstrated that reformulating the problem as a multi-class classification problem is a more promising direction to pursue. As an alternative approach, we recently proposed real-valued distance predictions, formulating the problem as a regression problem. The nuances of protein 3D structures make this formulation appropriate, allowing predictions …

Machine Learning Integrated Design For Additive Manufacturing, Jingchao Jiang, Yi Xiong, Zhiyuan Zhang, David W. Rosen

Research Collection School Of Computing and Information Systems

For improving manufacturing efficiency and minimizing costs, design for additive manufacturing (AM) has been accordingly proposed. The existing design for AM methods are mainly surrogate model based. Due to the increasingly available data nowadays, machine learning (ML) has been applied to medical diagnosis, image processing, prediction, classification, learning association, etc. A variety of studies have also been carried out to use machine learning for optimizing the process parameters of AM with corresponding objectives. In this paper, a ML integrated design for AM framework is proposed, which takes advantage of ML that can learn the complex relationships between the design and …

Experimental Comparison Of Features And Classifiers For Android Malware Detection, Lwin Khin Shar, Biniam Fisseha Demissie, Mariano Ceccato, Wei Minn

Research Collection School Of Computing and Information Systems

Android platform has dominated the smart phone market for years now and, consequently, gained a lot of attention from attackers. Malicious apps (malware) pose a serious threat to the security and privacy of Android smart phone users. Available approaches to detect mobile malware based on machine learning rely on features extracted with static analysis or dynamic analysis techniques. Dif- ferent types of machine learning classi ers (such as support vector machine and random forest) deep learning classi ers (based on deep neural networks) are then trained on extracted features, to produce models that can be used to detect mobile malware. …

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. …

Objsim: Efficient Testing Of Cyber-Physical Systems, Jun Sun, Zijiang Yang

Research Collection School Of Computing and Information Systems

Cyber-physical systems (CPSs) play a critical role in automating public infrastructure and thus attract wide range of attacks. Assessing the effectiveness of defense mechanisms is challenging as realistic sets of attacks to test them against are not always available. In this short paper, we briefly describe smart fuzzing, an automated, machine learning guided technique for systematically producing test suites of CPS network attacks. Our approach uses predictive ma- chine learning models and meta-heuristic search algorithms to guide the fuzzing of actuators so as to drive the CPS into different unsafe physical states. The approach has been proven effective on two …

A Machine Learning Approach For Vulnerability Curation, Yang Chen, Andrew E. Santosa, Ming Yi Ang, Abhishek Sharma, Asankhaya Sharma, David Lo

Research Collection School Of Computing and Information Systems

Software composition analysis depends on database of open-source library vulerabilities, curated by security researchers using various sources, such as bug tracking systems, commits, and mailing lists. We report the design and implementation of a machine learning system to help the curation by by automatically predicting the vulnerability-relatedness of each data item. It supports a complete pipeline from data collection, model training and prediction, to the validation of new models before deployment. It is executed iteratively to generate better models as new input data become available. We use self-training to significantly and automatically increase the size of the training dataset, opportunistically …

Ml-Medic: A Preliminary Study Of An Interactive Visual Analysis Tool Facilitating Clinical Applications Of Machine Learning For Precision Medicine, Laura Stevens, David Kao, Jennifer Hall, Carsten Görg, Kaitlyn Abdo, Erik Linstead

Engineering Faculty Articles and Research

Accessible interactive tools that integrate machine learning methods with clinical research and reduce the programming experience required are needed to move science forward. Here, we present Machine Learning for Medical Exploration and Data-Inspired Care (ML-MEDIC), a point-and-click, interactive tool with a visual interface for facilitating machine learning and statistical analyses in clinical research. We deployed ML-MEDIC in the American Heart Association (AHA) Precision Medicine Platform to provide secure internet access and facilitate collaboration. ML-MEDIC’s efficacy for facilitating the adoption of machine learning was evaluated through two case studies in collaboration with clinical domain experts. A domain expert review was also …

How We Refactor And How We Document It? On The Use Of Supervised Machine Learning Algorithms To Classify Refactoring Documentation, Eman Abdullah Alomar, Anthony Peruma, Mohamed Wiem Mkaouer, Christian D. Newman, Marouane Kessentini, Ali Ouni

Articles

Refactoring is the art of improving the structural design of a software system without altering its external behavior. Today, refactoring has become a well-established and disciplined software engineering practice that has attracted a significant amount of research presuming that refactoring is primarily motivated by the need to improve system structures. However, recent studies have shown that developers may incorporate refactoring strategies in other development-related activities that go beyond improving the design especially with the emerging challenges in contemporary software engineering. Unfortunately, these studies are limited to developer interviews and a reduced set of projects. To cope with the above-mentioned limitations, …

Automated Identification Of Libraries From Vulnerability Data, Chen Yang, Andrew Santosa, Asankhaya Sharma, David Lo

Research Collection School Of Computing and Information Systems

Software Composition Analysis (SCA) has gained traction in recent years with a number of commercial offerings from various companies. SCA involves vulnerability curation process where a group of security researchers, using various data sources, populate a database of open-source library vulnerabilities, which is used by a scanner to inform the end users of vulnerable libraries used by their applications. One of the data sources used is the National Vulnerability Database (NVD). The key challenge faced by the security researchers here is in figuring out which libraries are related to each of the reported vulnerability in NVD. In this article, we …

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

Dissertations & 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 …

Applying Imitation And Reinforcement Learning To Sparse Reward Environments, Haven Brown

Computer Science and Computer Engineering Undergraduate Honors Theses

The focus of this project was to shorten the time it takes to train reinforcement learning agents to perform better than humans in a sparse reward environment. Finding a general purpose solution to this problem is essential to creating agents in the future capable of managing large systems or performing a series of tasks before receiving feedback. The goal of this project was to create a transition function between an imitation learning algorithm (also referred to as a behavioral cloning algorithm) and a reinforcement learning algorithm. The goal of this approach was to allow an agent to first learn to …

Treatment Effects Of Modafinil For Cocaine Use Disorders: A Retrospective Analysis Of Aggregated Clinical Trial Data From Three Cocaine Treatment Studies, Daniel Ruskin

Honors Scholar Theses

Approximately 913,000 individuals in the United States meet the diagnostic criteria for cocaine use disorder (CUD). The widespread usage of cocaine, along with the negative cardiac and neurological effects associated with the drug, has made cocaine one of the top three drugs associated with overdose deaths in the United States. This epidemic has brought cocaine dependency into the public spotlight and has prompted extensive research into treatment strategies. However, at the time of writing, no drugs have been approved by the United States Food and Drug Administration (FDA) for use in treating CUD. The purpose of this study is to …

Graph Classification With Kernels, Embeddings And Convolutional Neural Networks, Monica Golahalli Seenappa, Katerina Potika, Petros Potikas

Faculty Publications, Computer Science

In the graph classification problem, given is a family of graphs and a group of different categories, and we aim to classify all the graphs (of the family) into the given categories. Earlier approaches, such as graph kernels and graph embedding techniques have focused on extracting certain features by processing the entire graph. However, real world graphs are complex and noisy and these traditional approaches are computationally intensive. With the introduction of the deep learning framework, there have been numerous attempts to create more efficient classification approaches. We modify a kernel graph convolutional neural network approach, that extracts subgraphs (patches) …

Are The Code Snippets What We Are Searching For? A Benchmark And An Empirical Study On Code Search With Natural-Language Queries, Shuhan Yan, Hang Yu, Yuting Chen, Beijun Shen

Research Collection School Of Computing and Information Systems

Code search methods, especially those that allow programmers to raise queries in a natural language, plays an important role in software development. It helps to improve programmers' productivity by returning sample code snippets from the Internet and/or source-code repositories for their natural-language queries. Meanwhile, there are many code search methods in the literature that support natural-language queries. Difficulties exist in recognizing the strengths and weaknesses of each method and choosing the right one for different usage scenarios, because (1) the implementations of those methods and the datasets for evaluating them are usually not publicly available, and (2) some methods leverage …

Learning-Guided Network Fuzzing For Testing Cyber-Physical System Defences, Yuqi Chen, Christopher M. Poskitt, Jun Sun, Sridhar Adepu, Fan Zhang

Research Collection School Of Computing and Information Systems

The threat of attack faced by cyber-physical systems (CPSs), especially when they play a critical role in automating public infrastructure, has motivated research into a wide variety of attack defence mechanisms. Assessing their effectiveness is challenging, however, as realistic sets of attacks to test them against are not always available. In this paper, we propose smart fuzzing, an automated, machine learning guided technique for systematically finding 'test suites' of CPS network attacks, without requiring any knowledge of the system's control programs or physical processes. Our approach uses predictive machine learning models and metaheuristic search algorithms to guide the fuzzing of …

Computer Vision Gesture Recognition For Rock Paper Scissors, Nicholas Hunter

Senior Independent Study Theses

This project implements a human versus computer game of rock-paper-scissors using machine learning and computer vision. Player’s hand gestures are detected using single images with the YOLOv3 object detection system. This provides a generalized detection method which can recognize player moves without the need for a special background or lighting setup. Additionally, past moves are examined in context to predict the most probable next move of the system’s opponent. In this way, the system achieves higher win rates against human opponents than by using a purely random strategy.

Renewable Energy Integration In Distribution System With Artificial Intelligence, Yi Gu

Electronic Theses and Dissertations

With the increasing attention of renewable energy development in distribution power system, artificial intelligence (AI) can play an indispensiable role. In this thesis, a series of artificial intelligence based methods are studied and implemented to further enhance the performance of power system operation and control.

Due to the large volume of heterogeneous data provided by both the customer and the grid side, a big data visualization platform is built to feature out the hidden useful knowledge for smart grid (SG) operation, control and situation awareness. An open source cluster calculation framework with Apache Spark is used to discover big data …

Development Of Machine Learning Tutorials For R, John Pintar

All Undergraduate Theses and Capstone Projects

Machine learning (ML) techniques developed in computer science have revolutionized nearly every sector of industry. Despite the prevalence and usefulness of ML, students outside of computer science rarely receive training in ML. Students frequently receive training in statistical analysis, often using the software package R, which is free, open source, and has additional downloadable modules. A popular module is the ML package caret, which contains 238 different ML algorithms, each with 0-9 hyperparameters. caret is powerful, flexible, and provides consistent syntax across algorithms. In the hands of an experienced practitioner, this tunability is welcomed and can increase accuracy. However, when …