Data Science Commons^™

Deep Learning Model For Personalized Prediction Of Positive Mrsa Culture Using Time-Series Electronic Health Records, Masayuki Nigo, Laila Rasmy, Bingyu Mao, Bijun Sai Kannadath, Ziqian Xie, Degui Zhi

Faculty, Staff and Student Publications

Methicillin-resistant Staphylococcus aureus (MRSA) poses significant morbidity and mortality in hospitals. Rapid, accurate risk stratification of MRSA is crucial for optimizing antibiotic therapy. Our study introduced a deep learning model, PyTorch_EHR, which leverages electronic health record (EHR) time-series data, including wide-variety patient specific data, to predict MRSA culture positivity within two weeks. 8,164 MRSA and 22,393 non-MRSA patient events from Memorial Hermann Hospital System, Houston, Texas are used for model development. PyTorch_EHR outperforms logistic regression (LR) and light gradient boost machine (LGBM) models in accuracy (AUROC

The Hsp90-Myc-Cdk9 Network Drives Therapeutic Resistance In Mantle Cell Lymphoma, Fangfang Yan, Vivian Jiang, Alexa Jordan, Yuxuan Che, Yang Liu, Qingsong Cai, Yu Xue, Yijing Li, Joseph Mcintosh, Zhihong Chen, Jovanny Vargas, Lei Nie, Yixin Yao, Heng-Huan Lee, Wei Wang, Johnnelson R Bigcal, Maria Badillo, Jitendra Meena, Christopher Flowers, Jia Zhou, Zhongming Zhao, Lukas M Simon, Michael Wang

Faculty, Staff and Student Publications

Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton's tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 …

Leveraging Machine Learning & Deep Learning Methodologies To Detect Deepfakes, Aniruddha Tiwari

All Graduate Theses, Dissertations, and Other Capstone Projects

The rapid evolution of deep learning (DL) and machine learning (ML) techniques has facilitated the rise of highly convincing synthetic media, commonly referred to as deepfakes. These manipulative media artifacts, generated through advanced artificial intelligence algorithms, pose significant challenges in distinguishing them from authentic content. Given their potential to be disseminated widely across various online platforms, the imperative for robust detection methodologies becomes apparent. Accordingly, this study explores the efficacy of existing ML/DL-based approaches and aims to compare which type of methodology performs better in identifying deepfake content. In response to the escalating threat posed by deepfakes, previous research efforts …

Disentangling Accelerated Cognitive Decline From The Normal Aging Process And Unraveling Its Genetic Components: A Neuroimaging-Based Deep Learning Approach, Yulin Dai, Yu-Chun Hsu, Brisa S Fernandes, Kai Zhang, Xiaoyang Li, Nitesh Enduru, Andi Liu, Astrid M Manuel, Xiaoqian Jiang, Zhongming Zhao, Alzheimer’S Disease Neuroimaging Initiative

Faculty, Staff and Student Publications

BACKGROUND: The progressive cognitive decline, an integral component of Alzheimer's disease (AD), unfolds in tandem with the natural aging process. Neuroimaging features have demonstrated the capacity to distinguish cognitive decline changes stemming from typical brain aging and AD between different chronological points.

OBJECTIVE: To disentangle the normal aging effect from the AD-related accelerated cognitive decline and unravel its genetic components using a neuroimaging-based deep learning approach.

METHODS: We developed a deep-learning framework based on a dual-loss Siamese ResNet network to extract fine-grained information from the longitudinal structural magnetic resonance imaging (MRI) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. …

A Transformer-Based Deep Learning Approach For Fairly Predicting Post-Liver Transplant Risk Factors, Can Li, Xiaoqian Jiang, Kai Zhang

Faculty, Staff and Student Publications

Liver transplantation is a life-saving procedure for patients with end-stage liver disease. There are two main challenges in liver transplant: finding the best matching patient for a donor and ensuring transplant equity among different subpopulations. The current MELD scoring system evaluates a patient's mortality risk if not receiving an organ within 90 days. However, the donor-patient matching should also consider post-transplant risk factors, such as cardiovascular disease, chronic rejection, etc., which are all common complications after transplant. Accurate prediction of these risk scores remains a significant challenge. In this study, we used predictive models to solve the above challenges. Specifically, …

Lesion Detection In Women Breast’S Dynamic Contrast-Enhanced Magnetic Resonance Imaging Using Deep Learning, Sudarshan Saikia, Tapas Si, Darpan Deb, Kangkana Bora, Saurav Mallik, Ujjwal Maulik, Zhongming Zhao

Faculty, Staff and Student Publications

Breast cancer is one of the most common cancers in women and the second foremost cause of cancer death in women after lung cancer. Recent technological advances in breast cancer treatment offer hope to millions of women in the world. Segmentation of the breast's Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) is one of the necessary tasks in the diagnosis and detection of breast cancer. Currently, a popular deep learning model, U-Net is extensively used in biomedical image segmentation. This article aims to advance the state of the art and conduct a more in-depth analysis with a focus on the use …

Utilizing Multitask Transfer Learning For Sonographic Rheumatoid Arthritis Synovitis Grading, Jordan Marie Claire Sanders

Doctoral Dissertations and Master's Theses

Classifying the four sonographic Rheumatoid Arthritis (RA) synovitis grades (Grade 0, Grade 1, Grade 2, and Grade 3) is a difficult problem due to the complexity of the relevant markers. Therefore, the current research proposes a Multitask Transfer Learning (MTL) framework for sonographic RA synovitis grading of Ultrasound (US) images in Brightness mode (B-Mode) and Power Doppler mode.

In the medical community, the lack of reliability of scoring these images has been an issue and reason for concern for doctors and other medical practitioners. The human/machine variability across the acquisition procedure of these US images creates an additional challenge that …

Deep Learning Approaches With Optimum Alpha For Energy Usage Forecasting, Aji Prasetya Wibawa, Agung Bella Putra Utama, Ade Kurnia Ganesh Akbari, Akhmad Fanny Fadhilla, Alfiansyah Putra Pertama Triono, Andien Khansa’A Iffat Paramarta, Faradini Usha Setyaputri, Leonel Hernandez

Knowledge Engineering and Data Science

Energy use is an essential aspect of many human activities, from individual to industrial scale. However, increasing global energy demand and the challenges posed by environmental change make understanding energy use patterns crucial. Accurate predictions of future energy consumption can greatly influence decision-making, supply-demand stability and energy efficiency. Energy use data often exhibits time-series patterns, which creates complexity in forecasting. To address this complexity, this research utilizes Deep Learning (DL), Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN), Long Short-term Memory (LSTM), Bidirectional LSTM (Bi-LSTM), and Gated Recurrent Unit (GRU) models. The main objective is to improve the accuracy of …

Single-Cell Analysis Of Chromatin Accessibility In The Adult Mouse Brain, Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren

Faculty, Staff and Student Publications

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are …

Domain Specific Feature Representation Learning For Diverse Temporal Data, Farhan Asif Chowdhury

Computer Science ETDs

Humans can leverage domain context to recognize novel patterns and categories based on limited known examples. In contrast, computational learning methods are not adept at exploiting context and require sufficient labeled examples to achieve similar accuracy. Many temporal data domain, for example, seismic signals and oil mining sensor data, requires domain expert annotation, which is both costly and time-consuming. The dependency on training data limits the applicability of machine learning algorithms for domains with limited labeled data. This dissertation aims to address this gap by developing temporal mining algorithms that exploit domain context to learn discriminative feature representation from limited …

Improving Semantic Document Classification Accuracy By Integrating Human-Crafted Knowledge, Zachary Weinfeld, Lubomir Stanchev

College of Engineering Summer Undergraduate Research Program

Document classification is a pivotal task in various domains, warranting the development of robust algorithms. Among these, the Bidirectional Encoder Representations from Transformers (BERT) algorithm, introduced by Google, has proven to perform well when fine-tuned for the task at hand. Leveraging transformer architecture, BERT demonstrates stellar language understanding capabilities. However, the integration of BERT with a range of techniques has shown potential for further enhancing classification accuracy. This work investigates several techniques that leverage semantic understanding to improve the performance of document classification models trained with BERT. Specifically, we explore three methods. First, we will balance corpuses afflicted by imbalanced …

The Impacts Of Transfer Learning For Ungulate Recognition At Sevilleta National Wildlife Refuge, Michael Gurule

Geography ETDs

As camera traps have grown in popularity, their utilization has expanded to numerous fields, including wildlife research, conservation, and ecological studies. The information gathered using this equipment gives researchers a precise and comprehensive understanding about the activities of animals in their natural environments. For this type of data to be useful, camera trap images must be labeled so that the species in the images can be classified and counted. This has typically been done by teams of researchers and volunteers, and it can be said that the process is at best time-consuming. With recent developments in deep learning, the process …

Non-Invasive Arterial Blood Pressure Measurement And Spo2 Estimation Using Ppg Signal: A Deep Learning Framework, Yan Chu, Kaichen Tang, Yu-Chun Hsu, Tongtong Huang, Dulin Wang, Wentao Li, Sean I Savitz, Xiaoqian Jiang, Shayan Shams

Faculty, Staff and Student Publications

BACKGROUND: Monitoring blood pressure and peripheral capillary oxygen saturation plays a crucial role in healthcare management for patients with chronic diseases, especially hypertension and vascular disease. However, current blood pressure measurement methods have intrinsic limitations; for instance, arterial blood pressure is measured by inserting a catheter in the artery causing discomfort and infection.

METHOD: Photoplethysmogram (PPG) signals can be collected via non-invasive devices, and therefore have stimulated researchers' interest in exploring blood pressure estimation using machine learning and PPG signals as a non-invasive alternative. In this paper, we propose a Transformer-based deep learning architecture that utilizes PPG signals to conduct …

Automated Classification Of Pectinodon Bakkeri Teeth Images Using Machine Learning, Jacob A. Bahn

MS in Computer Science Project Reports

Microfossil dinosaur teeth are studied by paleontologists in order to better under- stand dinosaurs. Currently, tooth classification is a long, manual, error-ridden process. Deep learning offers a solution that allows for an automated way of classifying images of these microfossil teeth. In this thesis, we aimed to use deep learning in order to develop an automated approach for classifying images of Pectinodon bakkeri teeth. The proposed model was trained using a custom topology and it classified the images based on clusters created via K-Means. The model had an accuracy of 71%, a precision of 71%, a recall of 70.5%, and …

Deep Learning For Online Fashion: A Novel Solution For The Retail E-Commerce Industry, Zachary O. Harris, Gowtham G. Katta, Robert Slater, Joseph L. Woodall Iv

SMU Data Science Review

The online shopping experience for clothing can be further enhanced by implementing Deep Learning techniques, such as Computer Vision and personalized recommendation systems. Automation, as a principle, can be applied to solving problems surrounding efficacy, efficiency, and security. It also provides a layer of abstraction for the user during the online shopping experience. This research aims to apply Deep Learning methods and principles of automation to augment the e-commerce fashion market in a novel way. After using these methods, it was found that Convolutional Autoencoders and Item-to-Item Based Recommenders may be used to accurately and precisely recommend articles of clothing …

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …

Integrated Mrna Sequence Optimization Using Deep Learning, Haoran Gong, Jianguo Wen, Ruihan Luo, Yuzhou Feng, Jingjing Guo, Hongguang Fu, Xiaobo Zhou

Faculty, Staff and Student Publications

The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation. In ORF optimization, BiLSTM-CRF (bidirectional long-short-term memory with conditional random …

Classification Of Darknet Traffic By Application Type, Shruti Sharma

Master's Projects

The darknet is frequently exploited for illegal purposes and activities, which makes darknet traffic detection an important security topic. Previous research has focused on various classification techniques for darknet traffic using machine learning and deep learning. We extend previous work by considering the effectiveness of a wide range of machine learning and deep learning technique for the classification of darknet traffic by application type. We consider the CICDarknet2020 dataset, which has been used in many previous studies, thus enabling a direct comparison of our results to previous work. We find that XGBoost performs the best among the classifiers that we …

Practical Ai Value Alignment Using Stories, Md Sultan Al Nahian

Theses and Dissertations--Computer Science

As more machine learning agents interact with humans, it is increasingly a prospect that an agent trained to perform a task optimally - using only a measure of task performance as feedback--can violate societal norms for acceptable behavior or cause harm. Consequently, it becomes necessary to prioritize task performance and ensure that AI actions do not have detrimental effects. Value alignment is a property of intelligent agents, wherein they solely pursue goals and activities that are non-harmful and beneficial to humans. Current approaches to value alignment largely depend on imitation learning or learning from demonstration methods. However, the dynamic nature …

Split Learning For Distributed Collaborative Training Of Deep Learning Models In Health Informatics, Zhuohang Li, Chao Yan, Xinmeng Zhang, Gharib Gharibi, Zhijun Yin, Xiaoqian Jiang, Bradley A Malin

Faculty, Staff and Student Publications

Deep learning continues to rapidly evolve and is now demonstrating remarkable potential for numerous medical prediction tasks. However, realizing deep learning models that generalize across healthcare organizations is challenging. This is due, in part, to the inherent siloed nature of these organizations and patient privacy requirements. To address this problem, we illustrate how split learning can enable collaborative training of deep learning models across disparate and privately maintained health datasets, while keeping the original records and model parameters private. We introduce a new privacy-preserving distributed learning framework that offers a higher level of privacy compared to conventional federated learning. We …

Dynamic Predictions Of Thermal Heating And Cooling Of Silicon Wafer, Hitesh Kumar

Master's Projects

Neural Networks are now emerging in every industry. All the industries are trying their best to exploit the benefits of neural networks and deep learning to make predictions or simulate their ongoing process with the use of their generated data. The purpose of this report is to study the heating pattern of a silicon wafer and make predictions using various machine learning techniques. The heating of the silicon wafer involves various factors ranging from number of lamps, wafer properties and points taken in consideration to capture the heating temperature. This process involves dynamic inputs which facilitates the heating of the …

Breast Density Classification Using Deep Learning, Conrad Thomas Testagrose

UNF Graduate Theses and Dissertations

Breast density screenings are an accepted means to determine a patient's predisposed risk of breast cancer development. Although the direct correlation is not fully understood, breast cancer risk increases with higher levels of mammographic breast density. Radiologists visually assess a patient's breast density using mammogram images and assign a density score based on four breast density categories outlined by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts to develop automated tools that assist radiologists with increasing workloads and to help reduce the intra- and inter-rater variability between radiologists. In this thesis, I explored two deep-learning-based approaches …

Remote Sensing Approach For Terramechanics Applications Utilizing Machine And Deep Learning, Jordan J. Ewing

Dissertations, Master's Theses and Master's Reports

Terrain traversability is critical for developing Go/No Go maps, significantly impacting a mission's success. To predict the mobility of a vehicle over a terrain, one must understand the soil characteristics. In situ measurements performed by soldiers in the field are the current method of collecting this information, which is time-consuming, are only point measurements, and can put soldiers in harm's way. Therefore, this study investigates using remote sensing as an alternative approach to characterize terrain properties.

This approach will explore the relationships between electromagnetic radiation and soil types with varying properties. Optical, thermal, and hyperspectral sensors will be used to …

Investigating Applications Of Deep Learning For Diagnosis Of Post Traumatic Elbow Disease, Hugh James

McKelvey School of Engineering Graduate Student Theses & Dissertations

Traumatic events such as dislocation, breaks, and arthritis of musculoskeletal joints can cause the development of post-traumatic joint contracture (PTJC). Clinically, noninvasive techniques such as Magnetic Resonance Imaging (MRI) scans are used to analyze the disease. Such procedures require a patient to sit sedentary for long periods of time and can be expensive as well. Additionally, years of practice and experience are required for clinicians to accurately recognize the diseased anterior capsule region and make an accurate diagnosis. Manual tracing of the anterior capsule is done to help with diagnosis but is subjective and timely. As a result, there is …

Classification Of Breast Cancer Histopathological Images Using Semi-Supervised Gans, Balaji Avvaru, Nibhrat Lohia, Sowmya Mani, Vijayasrikanth Kaniti

SMU Data Science Review

Breast cancer is diagnosed more frequently than skin cancer in women in the United States. Most breast cancer cases are diagnosed in women, while children and men are less likely to develop the disease. Various tissues in the breast grow uncontrollably, resulting in breast cancer. Different treatments analyze microscopic histopathology images for diagnosis that help accurately detect cancer cells. Deep learning is one of the evolving techniques to classify images where accuracy depends on the volume and quality of labeled images. This study used various pre-trained models to train the histopathological images and analyze these models to create a new …

Classification Of Pixel Tracks To Improve Track Reconstruction From Proton-Proton Collisions, Kebur Fantahun, Jobin Joseph, Halle Purdom, Nibhrat Lohia

SMU Data Science Review

In this paper, machine learning techniques are used to reconstruct particle collision pathways. CERN (Conseil européen pour la recherche nucléaire) uses a massive underground particle collider, called the Large Hadron Collider or LHC, to produce particle collisions at extremely high speeds. There are several layers of detectors in the collider that track the pathways of particles as they collide. The data produced from collisions contains an extraneous amount of background noise, i.e., decays from known particle collisions produce fake signal. Particularly, in the first layer of the detector, the pixel tracker, there is an overwhelming amount of background noise that …

Cov-Inception: Covid-19 Detection Tool Using Chest X-Ray, Aswini Thota, Ololade Awodipe, Rashmi Patel

SMU Data Science Review

Since the pandemic started, researchers have been trying to find a way to detect COVID-19 which is a cost-effective, fast, and reliable way to keep the economy viable and running. This research details how chest X-ray radiography can be utilized to detect the infection. This can be for implementation in Airports, Schools, and places of business. Currently, Chest imaging is not a first-line test for COVID-19 due to low diagnostic accuracy and confounding with other viral pneumonia. Different pre-trained algorithms were fine-tuned and applied to the images to train the model and the best model obtained was fine-tuned InceptionV3 model …

Deep Learning For Detecting Trees In The Urban Environment From Lidar, Julian R. Rice

Master's Theses

Cataloguing and classifying trees in the urban environment is a crucial step in urban and environmental planning. However, manual collection and maintenance of this data is expensive and time-consuming. Algorithmic approaches that rely on remote sensing data have been developed for tree detection in forests, though they generally struggle in the more varied urban environment. This work proposes a novel method for the detection of trees in the urban environment that applies deep learning to remote sensing data. Specifically, we train a PointNet-based neural network to predict tree locations directly from LIDAR data augmented with multi-spectral imaging. We compare this …

Human Facial Expressions Identification Using Convolutionalneural Network With Vgg16 Architecture, Luther Alexander Latumakulita, Sandy Laurentius Lumintang, Deiby Tineke Salaki, Steven R. Sentinuwo, Alwin Melkie Sambul, Noorul Islam

Knowledge Engineering and Data Science

The human facial expression identification system is essential in developing human interaction and technology. The development of Artificial Intelligence for monitoring human emotions can be helpful in the workplace. Commonly, there are six basic human expressions, namely anger, disgust, fear, happiness, sadness, and surprise, that the system can identify. This study aims to create a facial expression identification system based on basic human expressions using the Convolutional Neural Network (CNN) with a 16-layer VGG architecture. Two thousand one hundred thirty-seven facial expression images were selected from the FER2013, JAFFE, and MUG datasets. By implementing image augmentation and setting up the …

Quadratic Neural Network Architecture As Evaluated Relative To Conventional Neural Network Architecture, Reid Taylor

Senior Theses

Current work in the field of deep learning and neural networks revolves around several variations of the same mathematical model for associative learning. These variations, while significant and exceptionally applicable in the real world, fail to push the limits of modern computational prowess. This research does just that: by leveraging high order tensors in place of 2nd order tensors, quadratic neural networks can be developed and can allow for substantially more complex machine learning models which allow for self-interactions of collected and analyzed data. This research shows the theorization and development of mathematical model necessary for such an idea to …