Physical Sciences and Mathematics Commons^™

Clinical Diagnosis Support With Convolutional Neural Network By Transfer Learning, Spencer Fogleman, Jeremy Otsap, Sangrae Cho

SMU Data Science Review

Breast cancer is prevalent among women in the United States. Breast cancer screening is standard but requires a radiologist to review screening images to make a diagnosis. Diagnosis through the traditional screening method of mammography currently has an accuracy of about 78% for women of all ages and demographics. A more recent and precise technique called Digital Breast Tomosynthesis (DBT) has shown to be more promising but is less well studied. A machine learning model trained on DBT images has the potential to increase the success of identifying breast cancer and reduce the time it takes to diagnose a patient, …

Comparing Machine Learning Techniques With State-Of-The-Art Parametric Prediction Models For Predicting Soybean Traits, Susweta Ray

Department of Statistics: Dissertations, Theses, and Student Work

Soybean is a significant source of protein and oil, and also widely used as animal feed. Thus, developing lines that are superior in terms of yield, protein and oil content is important to feed the ever-growing population. As opposed to the high-cost phenotyping, genotyping is both cost and time efficient for breeders while evaluating new lines in different environments (location-year combinations) can be costly. Several Genomic prediction (GP) methods have been developed to use the marker and environment data effectively to predict the yield or other relevant phenotypic traits of crops. Our study compares a conventional GP method (GBLUP), a …

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 …

The Potential Of Remotely Sensed Vegetation Indices For Monitoring Pasture Condition, Pouria Ramzi, Karen Holmes

Resource management technical reports

The Department of Primary Industries and Regional Development (DPIRD) is developing an integrated monitoring system using remote sensing and on-ground measurements to track pasture condition across Western Australia’s pastoral region. We extended and adapted the methods developed in the Pastoral Lease Assessment Using Geospatial Analysis (PLAGA) project (Robinson et al. 2012), which combined remotely sensed vegetation indices (VIs) with on-ground pasture condition observations to assess the potential of using different vegetation indices in a statewide condition monitoring system.

There were 6 regions in WA’s pastoral rangelands with DPIRD on-ground condition traverse points: Kimberley and Broome, Pilbara, Yalgoo and Sandstone, Goldfields, …

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

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 …

Improving Animal Monitoring Using Small Unmanned Aircraft Systems (Suas) And Deep Learning Networks, Meilun Zhou, Jared A. Elmore, Sathishkumar Samiappan, Kristine O. Evans, Morgan Pfeiffer, Bradley F. Blackwell, Raymond B. Iglay

USDA Wildlife Services: Staff Publications

In recent years, small unmanned aircraft systems (sUAS) have been used widely to monitor animals because of their customizability, ease of operating, ability to access difficult to navigate places, and potential to minimize disturbance to animals. Automatic identification and classification of animals through images acquired using a sUAS may solve critical problems such as monitoring large areas with high vehicle traffic for animals to prevent collisions, such as animal-aircraft collisions on airports. In this research we demonstrate automated identification of four animal species using deep learning animal classification models trained on sUAS collected images. We used a sUAS mounted with …

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 …

Performance Of Openbci Eeg Binary Intent Classification With Laryngeal Imagery, Nathan George, Samuel Kuhn

Regis University Faculty Publications (comprehensive list)

One of the greatest goals of neuroscience in recent decades has been to rehabilitate individuals who no longer have a functional relationship between their mind and their body. Although neuroscience has produced technologies which allow the brains of paralyzed patients to accomplish tasks such as spell words or control a motorized wheelchair, these technologies utilize parts of the brain which may not be optimal for simultaneous use. For example, if you needed to look at flashing lights to spell words for communication, it would be difficult to simultaneously look at where you are moving. To improve upon this issue, this …

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

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 …

Gene Selection And Classification In High-Throughput Biological Data With Integrated Machine Learning Algorithms And Bioinformatics Approaches, Abhijeet R Patil

Open Access Theses & Dissertations

With the rise of high throughput technologies in biomedical research, large volumes of expression profiling, methylation profiling, and RNA-sequencing data are being generated. These high-dimensional data have large number of features with small number of samples, a characteristic called the "curse of dimensionality." The selection of optimal features, which largely affects the performance of classification algorithms in machine learning models, has led to challenging problems in bioinformatics analyses of such high-dimensional datasets. In this work, I focus on the design of two-stage frameworks of feature selection and classification and their applications in multiple sets of colorectal cancer data. The first …

Machine Learning And Bioinformatic Insights Into Key Enzymes For A Bio-Based Circular Economy, Japheth E. Gado

Theses and Dissertations--Chemical and Materials Engineering

The world is presently faced with a sustainability crisis; it is becoming increasingly difficult to meet the energy and material needs of a growing global population without depleting and polluting our planet. Greenhouse gases released from the continuous combustion of fossil fuels engender accelerated climate change, and plastic waste accumulates in the environment. There is need for a circular economy, where energy and materials are renewably derived from waste items, rather than by consuming limited resources. Deconstruction of the recalcitrant linkages in natural and synthetic polymers is crucial for a circular economy, as deconstructed monomers can be used to manufacture …

Estimating Wildlife Strike Costs At Us Airports: A Machine Learning Approach, Levi Altringer, Jordan Navin, Michael J. Begier, Stephanie A. Shwiff, Aaron M. Anderson

USDA Wildlife Services: Staff Publications

Current lower bound estimates of the economic burden of wildlife strikes make use of mean cost assignment to impute missing values in the National Wildlife Strike Database (NWSD). The accuracy of these estimates, however, are undermined by the skewed nature of reported cost data and fail to account for differences in observed strike characteristics—e.g., type of aircraft, size of aircraft, type of damage, size of animal struck, etc. This paper makes use of modern machine learning techniques to provide a more accurate measure of the strike-related costs that accrue to the US civil aviation industry. We estimate that wildlife strikes …

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

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 (∆R_rs) 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), …