Open Access. Powered by Scholars. Published by Universities.®
- Institution
-
- Old Dominion University (9)
- New Jersey Institute of Technology (4)
- University of Kentucky (4)
- Michigan Technological University (2)
- Portland State University (2)
-
- University of Montana (2)
- Boise State University (1)
- City University of New York (CUNY) (1)
- Clemson University (1)
- College of Saint Benedict and Saint John's University (1)
- Illinois Math and Science Academy (1)
- Mississippi State University (1)
- Purdue University (1)
- Sacred Heart University (1)
- San Jose State University (1)
- Selected Works (1)
- Southern Methodist University (1)
- University of Missouri, St. Louis (1)
- University of New Mexico (1)
- University of South Florida (1)
- University of Texas at El Paso (1)
- University of Windsor (1)
- Utah State University (1)
- Washington University in St. Louis (1)
- Wright State University (1)
- Zayed University (1)
- Publication Year
- Publication
-
- Computer Science Theses & Dissertations (4)
- Dissertations (3)
- Computer Science Faculty Publications (2)
- Graduate Student Theses, Dissertations, & Professional Papers (2)
- Systems Science Faculty Publications and Presentations (2)
-
- Theses (2)
- Theses and Dissertations (2)
- All College Thesis Program, 2016-2019 (1)
- All Dissertations (1)
- All Works (1)
- Biological Sciences Faculty Publications (1)
- Biosystems and Agricultural Engineering Faculty Publications (1)
- Boise State University Theses and Dissertations (1)
- Community & Environmental Health Faculty Publications (1)
- Computer Science ETDs (1)
- Computer Science Faculty and Staff Publications (1)
- Dissertations, Master's Theses and Master's Reports (1)
- Electrical & Computer Engineering Theses & Dissertations (1)
- Electronic Theses and Dissertations (1)
- Faculty Research, Scholarly, and Creative Activity (1)
- John E. Sawyer (1)
- Kno.e.sis Publications (1)
- MODVIS Workshop (1)
- Mathematics Faculty Publications (1)
- McKelvey School of Engineering Theses & Dissertations (1)
- Michigan Tech Publications, Part 2 (1)
- Open Access Theses & Dissertations (1)
- Radiology Faculty Publications (1)
- SMU Data Science Review (1)
- School of Computer Science & Engineering Faculty Publications (1)
- Publication Type
Articles 1 - 30 of 43
Full-Text Articles in Life Sciences
Machine Learning As A Tool For Early Detection: A Focus On Late-Stage Colorectal Cancer Across Socioeconomic Spectrums, Hadiza Galadima, Rexford Anson-Dwamena, Ashley Johnson, Ghalib Bello, Georges Adunlin, James Blando
Machine Learning As A Tool For Early Detection: A Focus On Late-Stage Colorectal Cancer Across Socioeconomic Spectrums, Hadiza Galadima, Rexford Anson-Dwamena, Ashley Johnson, Ghalib Bello, Georges Adunlin, James Blando
Community & Environmental Health Faculty Publications
Purpose: To assess the efficacy of various machine learning (ML) algorithms in predicting late-stage colorectal cancer (CRC) diagnoses against the backdrop of socio-economic and regional healthcare disparities. Methods: An innovative theoretical framework was developed to integrate individual- and census tract-level social determinants of health (SDOH) with sociodemographic factors. A comparative analysis of the ML models was conducted using key performance metrics such as AUC-ROC to evaluate their predictive accuracy. Spatio-temporal analysis was used to identify disparities in late-stage CRC diagnosis probabilities. Results: Gradient boosting emerged as the superior model, with the top predictors for late-stage CRC diagnosis being anatomic site, …
Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam
Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam
SMU Data Science Review
Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …
Reconstructing 42 Years (1979–2020) Of Great Lakes Surface Temperature Through A Deep Learning Approach, Miraj Kayastha, Tao Liu, Daniel Titze, Timothy C. Havens, Chenfu Huang, Pengfei Xue
Reconstructing 42 Years (1979–2020) Of Great Lakes Surface Temperature Through A Deep Learning Approach, Miraj Kayastha, Tao Liu, Daniel Titze, Timothy C. Havens, Chenfu Huang, Pengfei Xue
Michigan Tech Publications, Part 2
Accurate estimates for the lake surface temperature (LST) of the Great Lakes are critical to understanding the regional climate. Dedicated lake models of various complexity have been used to simulate LST but they suffer from noticeable biases and can be computationally expensive. Additionally, the available historical LST datasets are limited by either short temporal coverage (<30 >years) or lower spatial resolution (0.25° × 0.25°). Therefore, in this study, we employed a deep learning model based on Long Short-Term Memory (LSTM) neural networks to produce a daily LST dataset for the Great Lakes that spans an unparalleled 42 years (1979–2020) at …30>
Automated Delineation Of Visual Area Boundaries And Eccentricities By A Cnn Using Functional, Anatomical, And Diffusion-Weighted Mri Data, Noah C. Benson, Bogeng Song, Toshikazu Miyata, Hiromasa Takemura, Jonathan Winawer
Automated Delineation Of Visual Area Boundaries And Eccentricities By A Cnn Using Functional, Anatomical, And Diffusion-Weighted Mri Data, Noah C. Benson, Bogeng Song, Toshikazu Miyata, Hiromasa Takemura, Jonathan Winawer
MODVIS Workshop
Delineating visual field maps and iso-eccentricities from fMRI data is an important but time-consuming task for many neuroimaging studies on the human visual cortex because the traditional methods of doing so using retinotopic mapping experiments require substantial expertise as well as scanner, computer, and human time. Automated methods based on gray-matter anatomy or a combination of anatomy and functional mapping can reduce these requirements but are less accurate than experts. Convolutional Neural Networks (CNNs) are powerful tools for automated medical image segmentation. We hypothesize that CNNs can define visual area boundaries with high accuracy. We trained U-Net CNNs with ResNet18 …
Wearable Sensor Gait Analysis For Fall Detection Using Deep Learning Methods, Haben Girmay Yhdego
Wearable Sensor Gait Analysis For Fall Detection Using Deep Learning Methods, Haben Girmay Yhdego
Electrical & Computer Engineering Theses & Dissertations
World Health Organization (WHO) data show that around 684,000 people die from falls yearly, making it the second-highest mortality rate after traffic accidents [1]. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. In light of the recent widespread adoption of wearable sensors, it has become increasingly critical that fall detection models are developed that can effectively process large and sequential sensor signal data. Several researchers have recently developed fall detection algorithms based on wearable sensor data. However, real-time fall detection remains challenging because of the wide …
An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali
An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali
All Works
Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on …
Ambient Electromagnetic Radiation As A Predictor Of Honey Bee (Apis Mellifera) Traffic In Linear And Non-Linear Regression: Numerical Stability, Physical Time And Energy Efficiency, Vladimir Kulyukin, Daniel Coster, Anastasiia Tkachenko, Daniel Hornberger, Aleksey V. Kulyukin
Ambient Electromagnetic Radiation As A Predictor Of Honey Bee (Apis Mellifera) Traffic In Linear And Non-Linear Regression: Numerical Stability, Physical Time And Energy Efficiency, Vladimir Kulyukin, Daniel Coster, Anastasiia Tkachenko, Daniel Hornberger, Aleksey V. Kulyukin
Computer Science Faculty and Staff Publications
Since bee traffic is a contributing factor to hive health and electromagnetic radiation has a growing presence in the urban milieu, we investigate ambient electromagnetic radiation as a predictor of bee traffic in the hive’s vicinity in an urban environment. To that end, we built two multi-sensor stations and deployed them for four and a half months at a private apiary in Logan, Utah, U.S.A. to record ambient weather and electromagnetic radiation. We placed two non-invasive video loggers on two hives at the apiary to extract omnidirectional bee motion counts from videos. The time-aligned datasets were used to evaluate 200 …
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
Computer Science Faculty Publications
More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …
Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa
Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa
Dissertations, Master's Theses and Master's Reports
An Invasive species is a species that is alien or non-native to the ecosystem which causes harm to economic, environmental, or human health (E.O. 13112 of Feb 3, 1999). Invasive species have posed a serious threat to ecosystems across the globe. These invasive species have impacts on the biodiversity and productivity of invaded forests. Remotely sensed data is a valuable resource for understanding and addressing issues related to invasive species. This study presents a novel approach for mapping the distribution of two invasive plant species, Common and Glossy Buckthorn, using unmanned aerial vehicles (UAVs), machine learning algorithms, geographic information systems …
Improved Computational Prediction Of Function And Structural Representation Of Self-Cleaving Ribozymes With Enhanced Parameter Selection And Library Design, James D. Beck
Boise State University Theses and Dissertations
Biomolecules could be engineered to solve many societal challenges, including disease diagnosis and treatment, environmental sustainability, and food security. However, our limited understanding of how mutational variants alter molecular structures and functional performance has constrained the potential of important technological advances, such as high-throughput sequencing and gene editing. Ribonuleic Acid (RNA) sequences are thought to play a central role within many of these challenges. Their continual discovery throughout all domains of life is evidence of their significant biological importance (Weinreb et al., 2016). The self-cleaving ribozyme is a class of noncoding Ribonuleic Acid (ncRNA) that has been useful for …
Classification Models For 2,4-D Formulations In Damaged Enlist Crops Through The Application Of Ftir Spectroscopy And Machine Learning Algorithms, Benjamin Blackburn
Classification Models For 2,4-D Formulations In Damaged Enlist Crops Through The Application Of Ftir Spectroscopy And Machine Learning Algorithms, Benjamin Blackburn
Theses and Dissertations
With new 2,4-Dichlorophenoxyacetic acid (2,4-D) tolerant crops, increases in off-target movement events are expected. New formulations may mitigate these events, but standard lab techniques are ineffective in identifying these 2,4-D formulations. Using Fourier-transform infrared spectroscopy and machine learning algorithms, research was conducted to classify 2,4-D formulations in treated herbicide-tolerant soybeans and cotton and observe the influence of leaf treatment status and collection timing on classification accuracy. Pooled Classification models using k-nearest neighbor classified 2,4-D formulations with over 65% accuracy in cotton and soybean. Tissue collected 14 DAT and 21 DAT for cotton and soybean respectively produced higher accuracies than the …
Impact Of Sleep And Training On Game Performance And Injury In Division-1 Women’S Basketball Amidst The Pandemic, Samah Senbel, S. Sharma, S. M. Raval, Christopher B. Taber, Julie K. Nolan, N. S. Artan, Diala Ezzeddine, Kaya Tolga
Impact Of Sleep And Training On Game Performance And Injury In Division-1 Women’S Basketball Amidst The Pandemic, Samah Senbel, S. Sharma, S. M. Raval, Christopher B. Taber, Julie K. Nolan, N. S. Artan, Diala Ezzeddine, Kaya Tolga
School of Computer Science & Engineering Faculty Publications
We investigated the impact of sleep and training load of Division - 1 women’s basketball players on their game performance and injury prediction using machine learning algorithms. The data was collected during a pandemic-condensed season with unpredictable interruptions to the games and athletic training schedules. We collected data from sleep monitoring devices, training data from coaches, injury reports from medical staff, and weekly survey data from athletes for 22 weeks.With proper data imputation, interpretable feature set, data balancing, and classifiers, we showed that we could predict game performance and injuries with more than 90% accuracy. More importantly, our F1 and …
Intelligent Resource Prediction For Hpc And Scientific Workflows, Benjamin Shealy
Intelligent Resource Prediction For Hpc And Scientific Workflows, Benjamin Shealy
All Dissertations
Scientific workflows and high-performance computing (HPC) platforms are critically important to modern scientific research. In order to perform scientific experiments at scale, domain scientists must have knowledge and expertise in software and hardware systems that are highly complex and rapidly evolving. While computational expertise will be essential for domain scientists going forward, any tools or practices that reduce this burden for domain scientists will greatly increase the rate of scientific discoveries. One challenge that exists for domain scientists today is knowing the resource usage patterns of an application for the purpose of resource provisioning. A tool that accurately estimates these …
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Faculty Research, Scholarly, and Creative Activity
Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.
Deep Learning Applications In Medical Bioinformatics, Ziad Omar
Deep Learning Applications In Medical Bioinformatics, Ziad Omar
Electronic Theses and Dissertations
After a patient’s breast cancer diagnosis, identifying breast cancer lymph node metastases is one of the most important and critical factor that is directly related to the patient’s survival. The traditional way to examine the existence of cancer cells in the breast lymph nodes is through a lymph node procedure, biopsy. The procedure process is time-consuming for the patient and the provider, costly, and lacks accuracy as not every lymph node is examined. The intent of this study is to develop an artificial neural network (ANNs) that would map genetic biomarkers to breast lymph node classes using ANNs. The neural …
Graphical Models In Reconstructability Analysis And Bayesian Networks, Marcus Harris, Martin Zwick
Graphical Models In Reconstructability Analysis And Bayesian Networks, Marcus Harris, Martin Zwick
Systems Science Faculty Publications and Presentations
Reconstructability Analysis (RA) and Bayesian Networks (BN) are both probabilistic graphical modeling methodologies used in machine learning and artificial intelligence. There are RA models that are statistically equivalent to BN models and there are also models unique to RA and models unique to BN. The primary goal of this paper is to unify these two methodologies via a lattice of structures that offers an expanded set of models to represent complex systems more accurately or more simply. The conceptualization of this lattice also offers a framework for additional innovations beyond what is presented here. Specifically, this paper integrates RA and …
A Constitutive-Based Deep Learning Model For The Identification Of Active Contraction Parameters Of The Left Ventricular Myocardium, Igor Augusto Paschoalotte Nobrega
A Constitutive-Based Deep Learning Model For The Identification Of Active Contraction Parameters Of The Left Ventricular Myocardium, Igor Augusto Paschoalotte Nobrega
USF Tampa Graduate Theses and Dissertations
Modern breakthroughs in biomedical engineering, computer science, and data mining have created new opportunities for detecting important mechanical properties of soft tissues that can be employed to identify possible signs of diseases or physiological difficulties. However, the scarcity of different mechanical properties obtained through noninvasive testing emphasizes the importance of incorporating authentic biological data into computer models capable of replicating the behavior of soft tissues.
The field of continuum theory of large deformation hyperactivity permits the formulation of highly descriptive mathematical research and computational models capable of perfectly describing the minute mechanical characteristics of soft materials. By including features about …
Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan
Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan
Mathematics Faculty Publications
The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as …
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Graduate Student Theses, Dissertations, & Professional Papers
The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …
Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė
Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė
Biological Sciences Faculty Publications
Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆Rrs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …
Sensitivity Analysis Of An Agent-Based Simulation Model Using Reconstructability Analysis, Andey M. Nunes, Martin Zwick, Wayne Wakeland
Sensitivity Analysis Of An Agent-Based Simulation Model Using Reconstructability Analysis, Andey M. Nunes, Martin Zwick, Wayne Wakeland
Systems Science Faculty Publications and Presentations
Reconstructability analysis, a methodology based on information theory and graph theory, was used to perform a sensitivity analysis of an agent-based model. The NetLogo BehaviorSpace tool was employed to do a full 2k factorial parameter sweep on Uri Wilensky’s Wealth Distribution NetLogo model, to which a Gini-coefficient convergence condition was added. The analysis identified the most influential predictors (parameters and their interactions) of the Gini coefficient wealth inequality outcome. Implications of this type of analysis for building and testing agent-based simulation models are discussed.
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 …
Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff
Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff
Radiology Faculty Publications
Optimal use of multiparametric magnetic resonance imaging (mpMRI) can identify key MRI parameters and provide unique tissue signatures defining phenotypes of breast cancer. We have developed and implemented a new machine-learning informatic system, termed Informatics Radiomics Integration System (IRIS) that integrates clinical variables, derived from imaging and electronic medical health records (EHR) with multiparametric radiomics (mpRad) for identifying potential risk of local or systemic recurrence in breast cancer patients. We tested the model in patients (n = 80) who had Estrogen Receptor positive disease and underwent OncotypeDX gene testing, radiomic analysis, and breast mpMRI. The IRIS method was trained …
Enrichment Of Ontologies Using Machine Learning And Summarization, Hao Liu
Enrichment Of Ontologies Using Machine Learning And Summarization, Hao Liu
Dissertations
Biomedical ontologies are structured knowledge systems in biomedicine. They play a major role in enabling precise communications in support of healthcare applications, e.g., Electronic Healthcare Records (EHR) systems. Biomedical ontologies are used in many different contexts to facilitate information and knowledge management. The most widely used clinical ontology is the SNOMED CT. Placing a new concept into its proper position in an ontology is a fundamental task in its lifecycle of curation and enrichment.
A large biomedical ontology, which typically consists of many tens of thousands of concepts and relationships, can be viewed as a complex network with concepts as …
Machine Learning Prediction Of Glioblastoma Patient One-Year Survival, Andrew Du '20, Warren Mcgee, Jane Y. Wu
Machine Learning Prediction Of Glioblastoma Patient One-Year Survival, Andrew Du '20, Warren Mcgee, Jane Y. Wu
Student Publications & Research
Glioblastoma (GBM) is a grade IV astrocytoma formed primarily from cancerous astrocytes and sustained by intense angiogenesis. GBM often causes non-specific symptoms, creating difficulty for diagnosis. This study aimed to utilize machine learning techniques to provide an accurate one-year survival prognosis for GBM patients using clinical and genomic data from the Chinese Glioma Genome Atlas. Logistic regression (LR), support vector machines (SVM), random forest (RF), and ensemble models were used to identify and select predictors for GBM survival and to classify patients into those with an overall survival (OS) of less than one year and one year or greater. With …
Outlier Profiles Of Atomic Structures Derived From X-Ray Crystallography And From Cryo-Electron Microscopy, Lin Chen, Jing He, Angelo Facchiano
Outlier Profiles Of Atomic Structures Derived From X-Ray Crystallography And From Cryo-Electron Microscopy, Lin Chen, Jing He, Angelo Facchiano
Computer Science Faculty Publications
Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing …
Cancer Risk Prediction With Whole Exome Sequencing And Machine Learning, Abdulrhman Fahad M Aljouie
Cancer Risk Prediction With Whole Exome Sequencing And Machine Learning, Abdulrhman Fahad M Aljouie
Dissertations
Accurate cancer risk and survival time prediction are important problems in personalized medicine, where disease diagnosis and prognosis are tuned to individuals based on their genetic material. Cancer risk prediction provides an informed decision about making regular screening that helps to detect disease at the early stage and therefore increases the probability of successful treatments. Cancer risk prediction is a challenging problem. Lifestyle, environment, family history, and genetic predisposition are some factors that influence the disease onset. Cancer risk prediction based on predisposing genetic variants has been studied extensively. Most studies have examined the predictive ability of variants in known …
Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan
Statistical And Machine Learning Methods Evaluated For Incorporating Soil And Weather Into Corn Nitrogen Recommendations, Curtis J. Ransom, Newell R. Kitchen, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabián G. Fernández, David W. Franzen, Carrie A. M. Laboski, D. Brenton Myers, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan
John E. Sawyer
Nitrogen (N) fertilizer recommendation tools could be improved for estimating corn (Zea mays L.) N needs by incorporating site-specific soil and weather information. However, an evaluation of analytical methods is needed to determine the success of incorporating this information. The objectives of this research were to evaluate statistical and machine learning (ML) algorithms for utilizing soil and weather information for improving corn N recommendation tools. Eight algorithms [stepwise, ridge regression, least absolute shrinkage and selection operator (Lasso), elastic net regression, principal component regression (PCR), partial least squares regression (PLSR), decision tree, and random forest] were evaluated using a dataset …
Model-Based Deep Autoencoders For Characterizing Discrete Data With Application To Genomic Data Analysis, Tian Tian
Dissertations
Deep learning techniques have achieved tremendous successes in a wide range of real applications in recent years. For dimension reduction, deep neural networks (DNNs) provide a natural choice to parameterize a non-linear transforming function that maps the original high dimensional data to a lower dimensional latent space. Autoencoder is a kind of DNNs used to learn efficient feature representation in an unsupervised manner. Deep autoencoder has been widely explored and applied to analysis of continuous data, while it is understudied for characterizing discrete data. This dissertation focuses on developing model-based deep autoencoders for modeling discrete data. A motivating example of …
Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy
Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy
Computer Science Theses & Dissertations
Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies.
First, we identify a protein structural fragment library (Frag-K) composed of a …