Computer Sciences Commons^™

An Autoencoder-Based Deep Learning Method For Genotype Imputation, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Zhe Luo, Chuan Qiu, Lan Juan Zhao, Kuan-Jui Su, Qing Tian, Hui Shen, Huixiao Hong, Ping Gong, Xinghua Shi, Hong-Wen Deng, Chaoyang Zhang

Faculty, Staff and Student Publications

Genotype imputation has a wide range of applications in genome-wide association study (GWAS), including increasing the statistical power of association tests, discovering trait-associated loci in meta-analyses, and prioritizing causal variants with fine-mapping. In recent years, deep learning (DL) based methods, such as sparse convolutional denoising autoencoder (SCDA), have been developed for genotype imputation. However, it remains a challenging task to optimize the learning process in DL-based methods to achieve high imputation accuracy. To address this challenge, we have developed a convolutional autoencoder (AE) model for genotype imputation and implemented a customized training loop by modifying the training process with a …

Highlights Generation For Tennis Matches Using Computer Vision, Natural Language Processing And Audio Analysis, Alon Liberman

Senior Independent Study Theses

This project uses computer vision, natural language processing and audio analysis to automatize the highlights generation task for tennis matches. Computer vision techniques such as camera shot detection, hough transform and neural networks are used to extract the time intervals of the points. To detect the best points, three approaches are used. Point length suggests which points correspond to rallies and aces. The audio waves are analyzed to search for the highest audio peaks, which indicate the moments where the crowd cheers the most. Sentiment analysis, a natural language processing technique, is used to look for points where the commentators …

Part I - Ai And Data As Medical Devices, W. Nicholson Price Ii

Other Publications

It may seem counterintuitive to open a book on medical devices with chapters on software and data, but these are the frontiers of new medical device regulation and law. Physical devices are still crucial to medicine, but they – and medical practice as a whole – are embedded in and permeated by networks of software and caches of data. Those software systems are often mindbogglingly complex and largely inscrutable, involving artificial intelligence and machine learning. Ensuring that such software works effectively and safely remains a substantial challenge for regulators and policymakers. Each of the three chapters in this part examines …

Towards An Active Foveated Approach To Computer Vision, Dario Dematties, Silvio Rizzi, George K. Thiruvathukal, Alejandro Javier Wainselboim

Computer Science: Faculty Publications and Other Works

In this paper, a series of experimental methods are presented explaining a new approach towards active foveated Computer Vision (CV). This is a collaborative effort between researchers at CONICET Mendoza Technological Scientific Center from Argentina, Argonne National Laboratory (ANL), and Loyola University Chicago from the US. The aim is to advance new CV approaches more in line with those found in biological agents in order to bring novel solutions to the main problems faced by current CV applications. Basically this work enhance Self-supervised (SS) learning, incorporating foveated vision plus saccadic behavior in order to improve training and computational efficiency without …

Application Of Artificial Intelligence To Plasma Metabolomics Profiles To Predict Response To Neoadjuvant Chemotherapy In Triple-Negative Breast Cancer, Ehsan Irajizad, Ranran Wu, Jody Vykoukal, Eunice Murage, Rachelle Spencer, Jennifer B Dennison, Stacy Moulder, Elizabeth Ravenberg, Bora Lim, Jennifer Litton, Debu Tripathym, Vicente Valero, Senthil Damodaran, Gaiane M Rauch, Beatriz Adrada, Rosalind Candelaria, Jason B White, Abenaa Brewster, Banu Arun, James P Long, Kim Anh Do, Sam Hanash, Johannes F Fahrmann

Faculty, Staff and Student Publications

There is a need to identify biomarkers predictive of response to neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC). We previously obtained evidence that a polyamine signature in the blood is associated with TNBC development and progression. In this study, we evaluated whether plasma polyamines and other metabolites may identify TNBC patients who are less likely to respond to NACT. Pre-treatment plasma levels of acetylated polyamines were elevated in TNBC patients that had moderate to extensive tumor burden (RCB-II/III) following NACT compared to those that achieved a complete pathological response (pCR/RCB-0) or had minimal residual disease (RCB-I). We further applied …

Temporal Disambiguation Of Relative Temporal Expressions In Clinical Texts Using Temporally Fine-Tuned Contextual Word Embeddings., Amy L. Olex

Theses and Dissertations

Temporal reasoning is the ability to extract and assimilate temporal information to reconstruct a series of events such that they can be reasoned over to answer questions involving time. Temporal reasoning in the clinical domain is challenging due to specialized medical terms and nomenclature, shorthand notation, fragmented text, a variety of writing styles used by different medical units, redundancy of information that has to be reconciled, and an increased number of temporal references as compared to general domain texts. Work in the area of clinical temporal reasoning has progressed, but the current state-of-the-art still has a ways to go before …

Learning Robot Motion From Creative Human Demonstration, Charles C. Dietzel

Theses and Dissertations

This thesis presents a learning from demonstration framework that enables a robot to learn and perform creative motions from human demonstrations in real-time. In order to satisfy all of the functional requirements for the framework, the developed technique is comprised of two modular components, which integrate together to provide the desired functionality. The first component, called Dancing from Demonstration (DfD), is a kinesthetic learning from demonstration technique. This technique is capable of playing back newly learned motions in real-time, as well as combining multiple learned motions together in a configurable way, either to reduce trajectory error or to generate entirely …

Smart City Management Using Machine Learning Techniques, Mostafa Zaman

Theses and Dissertations

In response to the growing urban population, "smart cities" are designed to improve people's quality of life by implementing cutting-edge technologies. The concept of a "smart city" refers to an effort to enhance a city's residents' economic and environmental well-being via implementing a centralized management system. With the use of sensors and actuators, smart cities can collect massive amounts of data, which can improve people's quality of life and design cities' services. Although smart cities contain vast amounts of data, only a percentage is used due to the noise and variety of the data sources. Information and communication technology (ICT) …

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

A Domain Adaptation Approach For Segmenting Cell Instances In Microscopy Data, Matthew R. Keaton

Graduate Theses, Dissertations, and Problem Reports (ETD)

Automated cellular instance segmentation is a process that has been utilized for accelerating biological research since before the deep learning era, and recent advancements have produced higher quality results with less effort from the biologist. Most current endeavors focus on completely cutting the researcher out of the picture by generating highly generalized models. However, these models invariably fail when faced with novel data and effectively opt to miss out on the full capabilities of deep learning in pursuit of this goal. In our work, we demonstrate how, with even a minimal amount of annotated data, dominant approaches in this space …

An Analysis On Adversarial Machine Learning: Methods And Applications, Ali Dabouei

Graduate Theses, Dissertations, and Problem Reports (ETD)

Deep learning has witnessed astonishing advancement in the last decade and revolutionized many fields ranging from computer vision to natural language processing. A prominent field of research that enabled such achievements is adversarial learning, investigating the behavior and functionality of a learning model in presence of an adversary. Adversarial learning consists of two major trends. The first trend analyzes the susceptibility of machine learning models to manipulation in the decision-making process and aims to improve the robustness to such manipulations. The second trend exploits adversarial games between components of the model to enhance the learning process. This dissertation aims to …

Classifying Blood Glucose Levels Through Noninvasive Features, Rishi Reddy

Graduate Theses, Dissertations, and Problem Reports (ETD)

Blood glucose monitoring is a key process in the prevention and management of certain chronic diseases, such as diabetes. Currently, glucose monitoring for those interested in their blood glucose levels are confronted with options that are primarily invasive and relatively costly. A growing topic of note is the development of non-invasive monitoring methods for blood glucose. This development holds a significant promise for improvement to the quality of life of a significant portion of the population and is overall met with great enthusiasm from the scientific community as well as commercial interest. This work aims to develop a potential pipeline …

Beyond Triplet Loss: Person Re-Identification With Fine-Grained Difference-Aware Pairwise Loss, Cheng Yan, Guansong Pang, Xiao Bai, Changhong Liu, Xin Ning, Jun Zhou

Research Collection School Of Computing and Information Systems

Person Re-IDentification (ReID) aims at re-identifying persons from different viewpoints across multiple cameras. Capturing the fine-grained appearance differences is often the key to accurate person ReID, because many identities can be differentiated only when looking into these fine-grained differences. However, most state-of-the-art person ReID approaches, typically driven by a triplet loss, fail to effectively learn the fine-grained features as they are focused more on differentiating large appearance differences. To address this issue, we introduce a novel pairwise loss function that enables ReID models to learn the fine-grained features by adaptively enforcing an exponential penalization on the images of small differences …

Cross-Modal Food Retrieval: Learning A Joint Embedding Of Food Images And Recipes With Semantic Consistency And Attention Mechanism, Hao Wang, Doyen Sahoo, Chenghao Liu, Ke Shu, Palakorn Achananuparp, Ee-Peng Lim, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

Food retrieval is an important task to perform analysis of food-related information, where we are interested in retrieving relevant information about the queried food item such as ingredients, cooking instructions, etc. In this paper, we investigate cross-modal retrieval between food images and cooking recipes. The goal is to learn an embedding of images and recipes in a common feature space, such that the corresponding image-recipe embeddings lie close to one another. Two major challenges in addressing this problem are 1) large intra-variance and small inter-variance across cross-modal food data; and 2) difficulties in obtaining discriminative recipe representations. To address these …

Advances And Applications In High-Dimensional Heuristic Optimization, Samuel Alexander Vanfossan

Doctoral Dissertations

“Applicable to most real-world decision scenarios, multiobjective optimization is an area of multicriteria decision-making that seeks to simultaneously optimize two or more conflicting objectives. In contrast to single-objective scenarios, nontrivial multiobjective optimization problems are characterized by a set of Pareto optimal solutions wherein no solution unanimously optimizes all objectives. Evolutionary algorithms have emerged as a standard approach to determine a set of these Pareto optimal solutions, from which a decision-maker can select a vetted alternative. While easy to implement and having demonstrated great efficacy, these evolutionary approaches have been criticized for their runtime complexity when dealing with many alternatives or …

Reinforcement Learning: Low Discrepancy Action Selection For Continuous States And Actions, Jedidiah Lindborg

College of Graduate Studies: Theses & Dissertations

In reinforcement learning the process of selecting an action during the exploration or exploitation stage is difficult to optimize. The purpose of this thesis is to create an action selection process for an agent by employing a low discrepancy action selection (LDAS) method. This should allow the agent to quickly determine the utility of its actions by prioritizing actions that are dissimilar to ones that it has already picked. In this way the learning process should be faster for the agent and result in more optimal policies.

Eeg Signals Classification Using Lstm-Based Models And Majority Logic, James A. Orgeron

College of Graduate Studies: Theses & Dissertations

The study of elecroencephalograms (EEGs) has gained enormous interest in the last decade with the increase of computational power and availability of EEG signals collected from various human activities or produced during medical tests. The applicability of analyzing EEG signals ranges from helping impaired people communicate or move (using appropriate medical equipment) to understanding people's feelings and detecting diseases.

We proposed new methodology and models for analyzing and classifying EEG signals collected from individuals observing visual stimuli. Our models rely on powerful Long-Short Term Memory (LSTM) Neural Network models, which are currently the state of the art models for performing …

License Plate Image Quality Enhancement Utilizing Super Resolution Generative Adversarial Networks, Mark Moelter

College of Graduate Studies: Theses & Dissertations

This thesis focuses primarily on enhancing the image quality of blurred license plates through the use of Super-Resolution Generative Adversarial Networks (SRGANs) [1]. We propose a synthetic dataset with SRGAN model to promote blurred image quality enhancement, and allow for model evaluation on a multitude of image input and output size combinations. SRGAN is mainly used for low-resolution image enhancement, but by heavily blurring the input images, the model is tested on its ability to blindly deblur and upsample images to the desired super-resolution (SR) size. The model enhances the image quality to nearly that of the reference images. The …

Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu

Computer Science Faculty Publications

Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in …

Introducing A Real-Time Advanced Eye Movements Analysis Pipeline, Gavindya Jayawardana

Computer Science Faculty Publications

Real-Time Advanced Eye Movements Analysis Pipeline (RAEMAP) is an advanced pipeline to analyze traditional positional gaze measurements as well as advanced eye gaze measurements. The proposed implementation of RAEMAP includes real-time analysis of fixations, saccades, gaze transition entropy, and low/high index of pupillary activity. RAEMAP will also provide visualizations of fixations, fixations on AOIs, heatmaps, and dynamic AOI generation in real-time. This paper outlines the proposed architecture of RAEMAP.

Customer Gaze Estimation In Retail Using Deep Learning, Shashimal Senarath, Primesh Pathirana, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

At present, intelligent computing applications are widely used in different domains, including retail stores. The analysis of customer behaviour has become crucial for the benefit of both customers and retailers. In this regard, the concept of remote gaze estimation using deep learning has shown promising results in analyzing customer behaviour in retail due to its scalability, robustness, low cost, and uninterrupted nature. This study presents a three-stage, three-attention-based deep convolutional neural network for remote gaze estimation in retail using image data. In the first stage, we design a mechanism to estimate the 3D gaze of the subject using image data …

Machine Learning-Based Event Generator For Electron-Proton Scattering, Y. Alanazi, P. Ambrozewicz, M. Battaglieri, A.N. Hiller Blin, M. P. Kuchera, Y. Li, T. Liu, R. E. Mcclellan, W. Melnitchouk, E. Pritchard, M. Robertson, N. Sato, R. Strauss, L. Velasco

Computer Science Faculty Publications

We present a new machine learning-based Monte Carlo event generator using generative adversarial networks (GANs) that can be trained with calibrated detector simulations to construct a vertex-level event generator free of theoretical assumptions about femtometer scale physics. Our framework includes a GAN-based detector folding as a fast-surrogate model that mimics detector simulators. The framework is tested and validated on simulated inclusive deep-inelastic scattering data along with existing parametrizations for detector simulation, with uncertainty quantification based on a statistical bootstrapping technique. Our results provide for the first time a realistic proof of concept to mitigate theory bias in inferring vertex-level event …

Interpretable Design Of Reservoir Computing Networks Using Realization Theory, Wei Miao, Vignesh Narayanan, Jr-Shin Li

Publications

The reservoir computing networks (RCNs) have been successfully employed as a tool in learning and complex decision-making tasks. Despite their efficiency and low training cost, practical applications of RCNs rely heavily on empirical design. In this article, we develop an algorithm to design RCNs using the realization theory of linear dynamical systems. In particular, we introduce the notion of α-stable realization and provide an efficient approach to prune the size of a linear RCN without deteriorating the training accuracy. Furthermore, we derive a necessary and sufficient condition on the irreducibility of the number of hidden nodes in linear RCNs based …

Automatic And Fast Classification Of Barley Grains From Images: A Deep Learning Approach, Syed Afaq Ali Shah, Hao Luo, Putu Dita Pickupana, Alexander Ekeze, Ferdous Sohel, Hamid Laga, Chengdao Li, Blakely Paynter, Penghao Wang

Research outputs 2022 to 2026

Australia has a reputation for producing a reliable supply of high-quality barley in a contaminant-free climate. As a result, Australian barley is highly sought after by malting, brewing, distilling, and feed industries worldwide. Barley is traded as a variety-specific commodity on the international market for food, brewing and distilling end-use, as the intrinsic quality of the variety determines its market value. Manual identification of barley varieties by the naked eye is challenging and time-consuming for all stakeholders, including growers, grain handlers and traders. Current industrial methods for identifying barley varieties include molecular protein weights or DNA based technology, which are …

Perceptions And Needs Of Artificial Intelligence In Health Care To Increase Adoption: Scoping Review, Han Shi Jocelyn Chew, Palakorn Achananuparp

Research Collection School Of Computing and Information Systems

Background: Artificial intelligence (AI) has the potential to improve the efficiency and effectiveness of health care service delivery. However, the perceptions and needs of such systems remain elusive, hindering efforts to promote AI adoption in health care. Objective: This study aims to provide an overview of the perceptions and needs of AI to increase its adoption in health care. Methods: A systematic scoping review was conducted according to the 5-stage framework by Arksey and O’Malley. Articles that described the perceptions and needs of AI in health care were searched across nine databases: ACM Library, CINAHL, Cochrane Central, Embase, IEEE Xplore, …

Artificial Intelligence In The Pediatric Echocardiography Laboratory: Automation, Physiology, And Outcomes, Minh B Nguyen, Olivier Villemain, Mark K Friedberg, Lasse Lovstakken, Craig G Rusin, Luc Mertens

Faculty, Staff and Students Publications

Artificial intelligence (AI) is frequently used in non-medical fields to assist with automation and decision-making. The potential for AI in pediatric cardiology, especially in the echocardiography laboratory, is very high. There are multiple tasks AI is designed to do that could improve the quality, interpretation, and clinical application of echocardiographic data at the level of the sonographer, echocardiographer, and clinician. In this state-of-the-art review, we highlight the pertinent literature on machine learning in echocardiography and discuss its applications in the pediatric echocardiography lab with a focus on automation of the pediatric echocardiogram and the use of echo data to better …

A Drone-Based Application For Scouting Halyomorpha Halys Bugs In Orchards With Multifunctional Nets, Francesco Betti Sorbelli, Federico Coro, Sajal K. Das, Emanuele Di Bella, Lara Maistrello, Lorenzo Palazzetti, Cristina M. Pinotti

Computer Science Faculty Research & Creative Works

In this work, we consider the problem of using a drone to collect information within orchards in order to scout insect pests, i.e., the stink bug Halyomorpha halys. An orchard can be modeled as an aisle-graph, which is a regular and constrained data structure formed by consecutive aisles where trees are arranged in a straight line. For monitoring the presence of bugs, a drone flies close to the trees and takes videos and/or pictures that will be analyzed offline. As the drone's energy is limited, only a subset of locations in the orchard can be visited with a fully charged …

Private And Federated Deep Learning: System, Theory, And Applications For Social Good, Han Hu

Dissertations

During the past decade, drug abuse continues to accelerate towards becoming the most severe public health problem in the United States. The ability to detect drug­abuse risk behavior at a population scale, such as among the population of Twitter users, can help to monitor the trend of drug­abuse incidents. However, traditional methods do not effectively detect drug­abuse risk behavior in tweets, mainly due to the sparsity of such tweets and the noisy nature of tweets. In the first part of this dissertation work, the task of classifying tweets as containing drug­abuse risk behavior or not, is studied. Millions of public …

A Practical Approach To Automated Software Correctness Enhancement, Aleksandr Zakharchenko

Dissertations

To repair an incorrect program does not mean to make it correct; it only means to make it more-correct, in some sense, than it is. In the absence of a concept of relative correctness, i.e. the property of a program to be more-correct than another with respect to a specification, the discipline of program repair has resorted to various approximations of absolute (traditional) correctness, with varying degrees of success. This shortcoming is concealed by the fact that most program repair tools are tested on basic cases, whence making them absolutely correct is not clearly distinguishable from making them relatively more-correct. …

Machine Learning And Computer Vision In Solar Physics, Haodi Jiang

Dissertations

In the recent decades, the difficult task of understanding and predicting violent solar eruptions and their terrestrial impacts has become a strategic national priority, as it affects the life of human beings, including communication, transportation, the power grid, national defense, space travel, and more. This dissertation explores new machine learning and computer vision techniques to tackle this difficult task. Specifically, the dissertation addresses four interrelated problems in solar physics: magnetic flux tracking, fibril tracing, Stokes inversion and vector magnetogram generation.

First, the dissertation presents a new deep learning method, named SolarUnet, to identify and track solar magnetic flux elements in …