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New Methods For Deep Learning Based Real-Valued Inter-Residue Distance Prediction, Jacob Barger
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
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 …
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
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
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, …
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
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
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 …
Computer Vision Gesture Recognition For Rock Paper Scissors, Nicholas Hunter
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.