Physical Sciences and Mathematics Commons^™

Atomlbs: An Atom Based Convolutional Neural Network For Druggable Ligand Binding Site Prediction, Md Ashraful Islam

Theses and Dissertations

Despite advances in drug research and development, there are few and ineffective treatments for a variety of diseases. Virtual screening can drastically reduce costs and accelerate the drug discovery process. Binding site identification is one of the initial and most important steps in structure-based virtual screening. Identifying and defining protein cavities that are likely to bind to a small compound is the objective of this task. In this research, we propose four different convolutional neural networks for predicting ligand-binding sites in proteins. A parallel optimized data pipeline is created to enable faster training of these neural network models on minimal …

Search For Triple-Proton Decay Using Machine Learning With Cuore, Douglas Adams

Theses and Dissertations

A framework to search for a triple-proton decay of ¹³⁰Te in the CUORE detector against a background of muons is presented. We use machine learning to classify different kinds of energy depositing events. We use the classification information to improve our detection or non-detection limits of a triple-proton decay process. We derive and use a methodology of combining Poisson counting statistics with supervised classification machine learning tools. Additionally, a sensitivity calculation is provided which uses the classification counting likelihood. Using our analysis technique, we achieve an lower 2σ half-life bound of 7.43×10²⁴yrs for triple-proton decay of …

Cnn-Based Dendrite Core Detection From Microscopic Images Of Directionally Solidified Ni-Base Alloys, Xiaoguang Li

Theses and Dissertations

Dendrite core is the center point of the dendrite. The information of dendrite core is very helpful for material scientists to analyze the properties of materials. Therefore, detecting the dendrite core is a very important task in the material science field. Meanwhile, because of some special properties of the dendrites, this task is also very challenging. Different from the typical detection problems in the computer vision field, detecting the dendrite core aims to detect a single point location instead of the bounding-box. As a result, the existing regressing bounding-box based detection methods can not work well on this task because …

Enabling Rapid Chemical Analysis Of Plutonium Alloys Via Machine Learning-Enhanced Atomic Spectroscopy Techniques, Ashwin P. Rao

Theses and Dissertations

Analytical atomic spectroscopy methods have the potential to provide solutions for rapid, high fidelity chemical analysis of plutonium alloys. Implementing these methods with advanced analytical techniques can help reduce the chemical analysis time needed for plutonium pit production, directly enabling the 80 pit-per-year by 2030 manufacturing goal outlined in the 2018 Nuclear Posture Review. Two commercial, handheld elemental analyzers were validated for potential in situ analysis of Pu. A handheld XRF device was able to detect gallium in a Pu surrogate matrix with a detection limit of 0.002 wt% and a mean error of 8%. A handheld LIBS device was …

Leveraging Subject Matter Expertise To Optimize Machine Learning Techniques For Air And Space Applications, Philip Y. Cho

Theses and Dissertations

We develop new machine learning and statistical methods that are tailored for Air and Space applications through the incorporation of subject matter expertise. In particular, we focus on three separate research thrusts that each represents a different type of subject matter knowledge, modeling approach, and application. In our first thrust, we incorporate knowledge of natural phenomena to design a neural network algorithm for localizing point defects in transmission electron microscopy (TEM) images of crystalline materials. In our second research thrust, we use Bayesian feature selection and regression to analyze the relationship between fighter pilot attributes and flight mishap rates. We …

Analyzing Microarchitectural Residue In Various Privilege Strata To Identify Computing Tasks, Tor J. Langehaug

Theses and Dissertations

Modern multi-tasking computer systems run numerous applications simultaneously. These applications must share hardware resources including the Central Processing Unit (CPU) and memory while maximizing each application’s performance. Tasks executing in this shared environment leave residue which should not reveal information. This dissertation applies machine learning and statistical analysis to evaluate task residue as footprints which can be correlated to identify tasks. The concept of privilege strata, drawn from an analogy with physical geology, organizes the investigation into the User, Operating System, and Hardware privilege strata. In the User Stratum, an adversary perspective is taken to build an interrogator program that …

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 …

Determining The Effects Of Elevated Carbon Dioxide On Soil Acidification, Cation Depletion, And Soil Inorganic Carbon And Mapping Soil Carbons Using Artificial Intelligence, Jannatul Ferdush

Theses and Dissertations

Soil carbon is the largest sink and source of the global carbon cycle and is disturbed by several natural, anthropogenic, and environmental factors. The global increase of atmospheric CO₂ affects soil carbon cycling through varied biogeochemical processes. The first chapter is a compilation of current information on potential factors triggering soil acidification and weathering mechanisms under elevated CO₂ and their consequences on soil inorganic carbon (SIC) pool and quality. Soil water content and precipitation were critical factors influencing elevated CO₂ effects on the SIC pool. The second chapter examines a detailed column experiment in which six soils …

Using Machine Learning To Classify Volleyball Jumps, Miki Jauhiainen

Theses and Dissertations

In this study, inertial measurement units (IMUs) were used to train a random forest classifier to correctly classify different jump types in volleyball. Athlete motion data were collected in a controlled setting using three IMUs, one on the waist and one on each ankle. There were 11 participants who at the time played volleyball at the collegiate level in the United States, seven male and four female. Each performed the same number of jumps across the eight jump types--five BASIC jumps and three each of the other seven--resulting in 26 jumps per subject for a total of 286. The data …

Reconstructing Historical Earthquake-Induced Tsunamis: Case Study Of 1820 Event Near South Sulawesi, Indonesia, Taylor Jole Paskett

Theses and Dissertations

We build on the method introduced by Ringer, et al., applying it to an 1820 event that happened near South Sulawesi, Indonesia. We utilize other statistical models to aid our Metropolis-Hastings sampler, including a Gaussian process which informs the prior. We apply the method to multiple possible fault zones to determine which fault is the most likely source of the earthquake and tsunami. After collecting nearly 80,000 samples, we find that between the two most likely fault zones, the Walanae fault zone matches the anecdotal accounts much better than Flores. However, to support the anecdotal data, both samplers tend toward …

Image-Based Crack Detection By Extracting Depth Of The Crack Using Machine Learning, Nishat Tabassum

Theses and Dissertations

Concrete structures have been a major aspect of social infrastructure since the ancient Roman times, so they have been used for many centuries. Concrete is used for the durability and support it provides to buildings and bridges. Assessing the state of these structures is important in preserving the longevity of structures and the safety of the public. Detecting cracks in their early stage allows repairs to be made without the need to replace the whole structure, so it reduces the cost. Traditional methods are slowly falling behind as technology advances and an increase in demand for a practical method of …

Language Learning Using Models Of Intentionality In Repeated Games With Cheap Talk, Jonathan Berry Skaggs

Theses and Dissertations

Language is critical to establishing long-term cooperative relationships among intelligent agents (including people), particularly when the agents' preferences are in conflict. In such scenarios, an agent uses speech to coordinate and negotiate behavior with its partner(s). While recent work has shown that neural language modeling can produce effective speech agents, such algorithms typically only accept previous text as input. However, in relationships among intelligent agents, not all relevant context is expressed in conversation. Thus, in this paper, we propose and analyze an algorithm, called Llumi, that incorporates other forms of context to learn to speak in long-term relationships modeled as …

Hardware Isolation Approach To Securely Use Untrusted Gpus In Cloud Environments For Machine Learning, Lucas D. Hall

Theses and Dissertations

Machine Learning (ML) is now a primary method for getting useful information out of the immense volumes of data being generated and stored in society today. Useful data is a commodity for training ML models and those that need data for training are often not the owners of the data leading to a desire to use cloud-based services. Deep learning algorithms are best suited to run on a graphical processing unit (GPU) which presents a specific problem since the GPU is not a secure or trusted piece of hardware in the cloud computing environment.

In this paper, we will analyze …

Physics-Guided Machine Learning In Ocean Acoustics Using Fisher Information, Michael Craig Mortenson

Theses and Dissertations

Waterborne acoustic signals carry information about the ocean environment. Ocean geoacoustic inversion is the task of estimating environmental parameters from received acoustic signals by matching the measured sound with the predictions of a physics-based model. A lower bound on the uncertainty associated with environmental parameter estimates, the Cramér-Rao bound, can be calculated from the Fisher information, which is dependent on derivatives of a physics-based model. Physics-based preconditioners circumvent the need for variable step sizes when computing numerical derivatives. This work explores the feasibility of using a neural network to perform geoacoustic inversion for environmental parameters and their associated uncertainties from …

Using Connections To Make Predictions On Dynamic Networks, Rebecca Dorff Jones

Theses and Dissertations

Networks are sets of objects that are connected in some way and appear abundantly in nature, sociology, and technology. For many centuries, network theory focused on static networks, which are networks that do not change. However, since all networks transform over time, static networks have limited applications. By comparison, dynamic networks model how connections between objects change over time. In this work, we will explore how connections in dynamic networks change and how we can leverage these changes to make predictions about future iterations of networks. We will do this by first considering the link prediction problem, using either Katz …

Improving Anonymized Search Relevance With Natural Language Processing And Machine Learning, Niko A. Petrocelli

Theses and Dissertations

Users often sacrifice personal data for more relevant search results, presenting a problem to communities that desire both search anonymity and relevant results. To balance these priorities, this research examines the impact of using Siamese networks to extend word embeddings into document embeddings and detect similarities between documents. The predicted similarity can locally re-rank search results provided from various sources. This technique is leveraged to limit the amount of information collected from a user by a search engine. A prototype is produced by applying the methodology in a real-world search environment. The prototype yielded an additional function of finding new …

Automated Aircraft Visual Inspection With Artificial Data Generation Enabled Deep Learning, Nathan J. Gaul

Theses and Dissertations

Aircraft visual inspection, which is essential to daily maintenance of an aircraft, is expensive and time-consuming to perform. Augmenting trained maintenance technicians with automated UAVs to collect and analyze images for aircraft inspection is an active research topic and a potential application of CNNs. Training datasets for niche research topics such as aircraft visual inspection are small and challenging to produce, and the manual process of labeling these datasets often produces subjective annotations. Recently, researchers have produced several successful applications of artificially generated datasets with domain randomization for training CNNs for real-world computer vision problems. The research outlined herein builds …

Double Cone Flow Field Reconstruction Between Mach 4 And 12 Using Machine Learning Techniques, Trevor A. Toros

Theses and Dissertations

No abstract provided.

Incorporating Armed Escorts To The Military Medical Evacuation Dispatching Problem Via Stochastic Optimization And Reinforcement Learning, Andrew G. Gelbard

Theses and Dissertations

The military medical evacuation (MEDEVAC) dispatching problem seeks to determine high-quality dispatching policies to maximize the survivability of casualties within contingency operations. This research leverages applied operations research and machine learning techniques to solve the MEDEVAC dispatching problem and evaluate system performance. More specifically, we develop an infinite-horizon, continuous-time Markov decision process (MDP) model and approximate dynamic programming (ADP) solution approach to generate high-quality policies. The ADP solution approach utilizes an approximate value iteration algorithm strategy incorporating gradient descent Q-learning to approximate the value function. A notional, synthetically-generated scenario in Africa based around the capital city of Niger, Niamey is …

Smoothing Of Convolutional Neural Network Classifications, Glen R. Drumm

Theses and Dissertations

Smoothing convolutional neural networks is investigated. When intermittent and random false predictions happen, a technique of average smoothing is applied to smooth out the incorrect predictions. While a simple problem environment shows proof of concept, obstacles remain for applying such a technique to a more operationally complex problem.

Application Of Machine Learning Models With Numerical Simulations Of An Experimental Microwave Induced Plasma Gasification Reactor, Owen D. Sedej

Theses and Dissertations

This thesis aims to contribute to the future development of this technology by providing an in-depth literature review of how this technology physically operates and can be numerically modeled. Additionally, this thesis reviews literature of machine learning models that have been applied to gasification to make accurate predictions regarding the system. Finally, this thesis provides a framework of how to numerically model an experimental plasma gasification reactor in order to inform a variety of machine learning models.

Analysis Of Generalized Artificial Intelligence Potential Through Reinforcement And Deep Reinforcement Learning Approaches, Jonathan Turner

Theses and Dissertations

Artificial Intelligence is the next competitive domain; the first nation to develop human level artificial intelligence will have an impact similar to the development of the atomic bomb. To maintain the security of the United States and her people, the Department of Defense has funded research into the development of artificial intelligence and its applications. This research uses reinforcement learning and deep reinforcement learning methods as proxies for current and future artificial intelligence agents and to assess potential issues in development. Agent performance were compared across two games and one excursion: Cargo Loading, Tower of Hanoi, and Knapsack Problem, respectively. …

Telemetry Data Mining For Unmanned Aircraft Systems, Li Yu

Theses and Dissertations

With ever more data becoming available to the US Air Force, it is vital to develop effective methods to leverage this strategic asset. Machine learning (ML) techniques present a means of meeting this challenge, as these tools have demonstrated successful use in commercial applications. For this research, three ML methods were applied to a unmanned aircraft system (UAS) telemetry dataset with the aim of extracting useful insight related to phases of flight. It was shown that ML provides an advantage in exploratory data analysis and as well as classification of phases. Neural network models demonstrated the best performance with over …

An Empirical Study On The Efficacy Of Evolutionary Algorithms For Automated Neural Architecture Search, Andrew D. Cuccinello

Theses and Dissertations

The configuration and architecture design of neural networks is a time consuming process that has been shown to provide significant training speed and prediction improvements. Traditionally, this process is done manually, but this requires a large amount of expert knowledge and significant investment of labor. As a result it is beneficial to have automated ways to optimize model architectures. In this thesis, we study the use of evolutionary algorithm for neural architecture search (NAS). Moreover, we investigate the effect of integrating evolutionary NAS into deep reinforcement learning to learn control policy for ATARI game playing. Empirical classification results on the …

Incorporating Ontological Information In Biomedical Entity Linking Of Phrases In Clinical Text, Evan French

Theses and Dissertations

Biomedical Entity Linking (BEL) is the task of mapping spans of text within biomedical documents to normalized, unique identifiers within an ontology. Translational application of BEL on clinical notes has enormous potential for augmenting discretely captured data in electronic health records, but the existing paradigm for evaluating BEL systems developed in academia is not well aligned with real-world use cases. In this work, we demonstrate a proof of concept for incorporating ontological similarity into the training and evaluation of BEL systems to begin to rectify this misalignment. This thesis has two primary components: 1) a comprehensive literature review and 2) …

Multi-Modality Automatic Lung Tumor Segmentation Method Using Deep Learning And Radiomics, Siqiu Wang

Theses and Dissertations

Delineation of the tumor volume is the initial and fundamental step in the radiotherapy planning process. The current clinical practice of manual delineation is time-consuming and suffers from observer variability. This work seeks to develop an effective automatic framework to produce clinically usable lung tumor segmentations. First, to facilitate the development and validation of our methodology, an expansive database of planning CTs, diagnostic PETs, and manual tumor segmentations was curated, and an image registration and preprocessing pipeline was established. Then a deep learning neural network was constructed and optimized to utilize dual-modality PET and CT images for lung tumor segmentation. …