Computer Sciences Commons^™

Concurrent Identification And Characterization Of Protein Structure And Continuous Internal Dynamics With Redcraft, Hanin Omar, Aaron Hein, Casey A. Cole, Homayoun Valafar

Faculty Publications

Internal dynamics of proteins can play a critical role in the biological function of some proteins. Several well documented instances have been reported such as MBP, DHFR, hTS, DGCR8, and NSP1 of the SARS-CoV family of viruses. Despite the importance of internal dynamics of proteins, there currently are very few approaches that allow for meaningful separation of internal dynamics from structural aspects using experimental data. Here we present a computational approach named REDCRAFT that allows for concurrent characterization of protein structure and dynamics. Here, we have subjected DHFR (PDB-ID 1RX2), a 159-residue protein, to a fictitious, mixed mode model of …

Robust Error Estimation Based On Factor-Graph Models For Non-Line-Of-Sight Localization, O. Arda Vanli, Clark N. Taylor

Faculty Publications

This paper presents a method to estimate the covariances of the inputs in a factor-graph formulation for localization under non-line-of-sight conditions. A general solution based on covariance estimation and M-estimators in linear regression problems, is presented that is shown to give unbiased estimators of multiple variances and are robust against outliers. An iteratively re-weighted least squares algorithm is proposed to jointly compute the proposed variance estimators and the state estimates for the nonlinear factor graph optimization. The efficacy of the method is illustrated in a simulation study using a robot localization problem under various process and measurement models and measurement …

Self-Relabeling For Noise-Tolerant Retina Vessel Segmentation Through Label Reliability Estimation, Jiacheng Li, Ruirui Li, Ruize Han, Song Wang

Faculty Publications

Background Retinal vessel segmentation benefits significantly from deep learning. Its performance relies on sufficient training images with accurate ground-truth segmentation, which are usually manually annotated in the form of binary pixel-wise label maps. Manually annotated ground-truth label maps, more or less, contain errors for part of the pixels. Due to the thin structure of retina vessels, such errors are more frequent and serious in manual annotations, which negatively affect deep learning performance.

Methods In this paper, we develop a new method to automatically and iteratively identify and correct such noisy segmentation labels in the process of network training. We consider …

Machine Learning Land Cover And Land Use Classification Of 4-Band Satellite Imagery, Lorelei Turner, Torrey J. Wagner, Paul Auclair, Brent T. Langhals

Faculty Publications

Land-cover and land-use classification generates categories of terrestrial features, such as water or trees, which can be used to track how land is used. This work applies classical, ensemble and neural network machine learning algorithms to a multispectral remote sensing dataset containing 405,000 28x28 pixel image patches in 4 electromagnetic frequency bands. For each algorithm, model metrics and prediction execution time were evaluated, resulting in two families of models; fast and precise. The prediction time for an 81,000-patch group of predictions wasmodels, and >5s for the precise models, and there was not a significant change in prediction time when a …

Effect Of Connection State & Transport/Application Protocol On The Machine Learning Outlier Detection Of Network Intrusions, George Yuchi, Torrey J. Wagner, Paul Auclair, Brent T. Langhals

Faculty Publications

The majority of cyber infiltration & exfiltration intrusions leave a network footprint, and due to the multi-faceted nature of detecting network intrusions, it is often difficult to detect. In this work a Zeek-processed PCAP dataset containing the metadata of 36,667 network packets was modeled with several machine learning algorithms to classify normal vs. anomalous network activity. Principal component analysis with a 10% contamination factor was used to identify anomalous behavior. Models were created using recursive feature elimination on logistic regression and XGBClassifier algorithms, and also using Bayesian and bandit optimization of neural network hyperparameters. These models were trained on a …

Effect Of Trigonometric Transformations On The Machine Learning Prediction And Quality Control Of Air Temperature, Andrea Fenoglio, Torrey J. Wagner, Paul Auclair, Brent T. Langhals

Faculty Publications

Conducting effective quality control of weather observations in real time is vital to the 14th Weather Squadron’s mission of providing authoritative climate data. This study explored automated quality control of weather observations by applying multiple machine learning techniques to 43,487 surface weather observations from 5 years of data at a single location. Temperature predictors were evaluated using recursive feature elimination on linear regression and XGBoost algorithms, as well as using a neural network hyperparameter sweep. Modeling was repeated after calculating trigonometric transforms of temporal variables to give the models insight into the diurnal heating cycle of the Earth. All models …

Extending The Quality Of Secure Service Model To Multi-Hop Networks, Paul M. Simon, Scott R. Graham

Faculty Publications

Rarely are communications networks point-to-point. In most cases, transceiver relay stations exist between transmitter and receiver end-points. These relay stations, while essential for controlling cost and adding flexibility to network architectures, reduce the overall security of the respective network. In an effort to quantify that reduction, we extend the Quality of Secure Service (QoSS) model to these complex networks, specifically multi-hop networks. In this approach, the quantification of security is based upon probabilities that adversarial listeners and disruptors gain access to or manipulate transmitted data on one or more of these multi-hop channels. Message fragmentation and duplication across available channels …

Evaluation Of Deep Neural Network Prospr For Accurate Protein Distance Predictions On Casp14 Targets, Jacob A. Stern, Bryce Eric Hedelius, Olivia Fisher, Wendy M. Billings, Dennis Della Corte

Faculty Publications

The field of protein structure prediction has recently been revolutionized through the introduction of deep learning. The current state-of-the-art tool AlphaFold2 can predict highly accurate structures; however, it has a prohibitively long inference time for applications that require the folding of hundreds of sequences. The prediction of protein structure annotations, such as amino acid distances, can be achieved at a higher speed with existing tools, such as the ProSPr network. Here, we report on important updates to the ProSPr network, its performance in the recent Critical Assessment of Techniques for Protein Structure Prediction (CASP14) competition, and an evaluation of its …

Traffic Collision Avoidance System: False Injection Viability, John Hannah, Robert F. Mills, Richard Dill, Douglas D. Hodson

Faculty Publications

Safety is a simple concept but an abstract task, specifically with aircraft. One critical safety system, the Traffic Collision Avoidance System II (TCAS), protects against mid-air collisions by predicting the course of other aircraft, determining the possibility of collision, and issuing a resolution advisory for avoidance. Previous research to identify vulnerabilities associated with TCAS’s communication processes discovered that a false injection attack presents the most comprehensive risk to veritable trust in TCAS, allowing for a mid-air collision. This research explores the viability of successfully executing a false injection attack against a target aircraft, triggering a resolution advisory. Monetary constraints precluded …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Intelligent Optimization Algorithm-Based Path Planning For A Mobile Robot, Qisong Song, Shaobo Li, Jing Yang, Qiang Bai, Jianjun Hu, Xingxing Zhang, Ansi Zhang

Faculty Publications

The purpose of mobile robot path planning is to produce the optimal safe path. However, mobile robots have poor real-time obstacle avoidance in local path planning and longer paths in global path planning. In order to improve the accuracy of real-time obstacle avoidance prediction of local path planning, shorten the path length of global path planning, reduce the path planning time, and then obtain a better safe path, we propose a real-time obstacle avoidance decision model based on machine learning (ML) algorithms, an improved smooth rapidly exploring random tree (S-RRT) algorithm, and an improved hybrid genetic algorithm-ant colony optimization (HGA-ACO). …

Cognition-Enhanced Machine Learning For Better Predictions With Limited Data, Florian Sense, Ryan Wood, Michael G. Collins, Joshua Fiechter, Aihua W. Wood, Michael Krusmark, Tiffany Jastrzembski, Christopher W. Myers

Faculty Publications

The fields of machine learning (ML) and cognitive science have developed complementary approaches to computationally modeling human behavior. ML's primary concern is maximizing prediction accuracy; cognitive science's primary concern is explaining the underlying mechanisms. Cross-talk between these disciplines is limited, likely because the tasks and goals usually differ. The domain of e-learning and knowledge acquisition constitutes a fruitful intersection for the two fields’ methodologies to be integrated because accurately tracking learning and forgetting over time and predicting future performance based on learning histories are central to developing effective, personalized learning tools. Here, we show how a state-of-the-art ML model can …

High-Throughput Discovery Of Novel Cubic Crystal Materials Using Deep Generative Neural Networks, Yong Zhao, Mohammed Al-Fahdi, Ming Hu, Edirisuriya M.D. Siriwardane, Yuqi Song, Alireza Nasiri, Jianjun Hu

Faculty Publications

High-throughput screening has become one of the major strategies for the discovery of novel functional materials. However, its effectiveness is severely limited by the lack of sufficient and diverse materials in current materials repositories such as the open quantum materials database (OQMD). Recent progress in deep learning have enabled generative strategies that learn implicit chemical rules for creating hypothetical materials with new compositions and structures. However, current materials generative models have difficulty in generating structurally diverse, chemically valid, and stable materials. Here we propose CubicGAN, a generative adversarial network (GAN) based deep neural network model for large scale generative design …

Strengthening Criteria Independence Through Optimization Of Alternative Value Ratio Comparisons, Joseph P. Kristbaum, Frank W. Ciarallo

Faculty Publications

Every decision maker’s internal scale is different based on a myriad of possible factors unique to that decision maker. Conflicting criteria within and between alternatives in multicriteria decision making can create negative effects within the weighting schemes and amplify preference biases and scale disparities between decision makers in a group decision context. Additionally, the weighting of group decision-making frameworks can intensify the already skewed criteria values. When making judgments against requirements, it may be preferable to reduce scale trend distortions between decision makers as much as possible. Previous research supports that certain information presentation modes can significantly reduce preference bias …

Loosening Control—A Hybrid Approach To Controlling Heterogeneous Swarms, Lukas Esterle, David W. King

Faculty Publications

Large pervasive systems, deployed in dynamic environments, require flexible control mechanisms to meet the demands of chaotic state changes while accomplishing system goals. As centralized control approaches may falter in environments where centralized communication and knowledge may be impossible to implement, researchers have proposed decentralized control methods that leverage agent-driven, self-organizing behaviors, to achieve reliable, flexible systems. This article presents and compares the performance of three decentralized control approaches in the online multi-object k-assignment problem. In this domain, a set of sensors is tasked to detect and track an unknown and changing set of targets. Results show that a …

St-V-Net: Incorporating Shape Prior Into Convolutional Neural Netwoks For Proximal Femur Segmentation, Chen Zhao, Joyce H. Keyak, Jinshan Tang, Tadashi S. Kaneko, Sundeep Khosla, Shreyasee Amin, Elizabeth J. Atkinson, Lan-Juan Zhao, Michael J. Serou, Chaoyang Zhang, Hui Shen, Hong-Wen Deng, Weihua Zhou

Faculty Publications

We aim to develop a deep-learning-based method for automatic proximal femur segmentation in quantitative computed tomography (QCT) images. We proposed a spatial transformation V-Net (ST-V-Net), which contains a V-Net and a spatial transform network (STN) to extract the proximal femur from QCT images. The STN incorporates a shape prior into the segmentation network as a constraint and guidance for model training, which improves model performance and accelerates model convergence. Meanwhile, a multi-stage training strategy is adopted to fine-tune the weights of the ST-V-Net. We performed experiments using a QCT dataset which included 397 QCT subjects. During the experiments for the …

Synthetic Aperture Radar Image Recognition Of Armored Vehicles, Christopher Szul, Torrey J. Wagner, Brent T. Langhals

Faculty Publications

Synthetic Aperture Radar (SAR) imagery is not affected by weather and allows for day-and-night observations, however it can be difficult to interpret. This work applies classical and neural network machine learning techniques to perform image classification of SAR imagery. The Moving and Stationary Target Acquisition and Recognition dataset from the Air Force Research Laboratory was used, which contained 2,987 total observations of the BMP-2, BTR-70, and T-72 vehicles. Using a 75%/25% train/test split, the classical model achieved an average multi-class image recognition accuracy of 70%, while a convolutional neural network was able to achieve a 97% accuracy with lower model …

Per-Pixel Cloud Cover Classification Of Multispectral Landsat-8 Data, Salome E. Carrasco, Torrey J. Wagner, Brent T. Langhals

Faculty Publications

Random forest and neural network algorithms are applied to identify cloud cover using 10 of the wavelength bands available in Landsat 8 imagery. The methods classify each pixel into 4 different classes: clear, cloud shadow, light cloud, or cloud. The first method is based on a fully connected neural network with ten input neurons, two hidden layers of 8 and 10 neurons respectively, and a single-neuron output for each class. This type of model is considered with and without L2 regularization applied to the kernel weighting. The final model type is a random forest classifier created from an ensemble of …

Year-Independent Prediction Of Food Insecurity Using Classical & Neural Network Machine Learning Methods, Caleb Christiansen, Torrey J. Wagner, Brent Langhals

Faculty Publications

Current food crisis predictions are developed by the Famine Early Warning System Network, but they fail to classify the majority of food crisis outbreaks with model metrics of recall (0.23), precision (0.42), and f1 (0.30). In this work, using a World Bank dataset, classical and neural network (NN) machine learning algorithms were developed to predict food crises in 21 countries. The best classical logistic regression algorithm achieved a high level of significance (p < 0.001) and precision (0.75) but was deficient in recall (0.20) and f1 (0.32). Of particular interest, the classical algorithm indicated that the vegetation index and the food price index were both positively correlated with food crises. A novel method for performing an iterative multidimensional hyperparameter search is presented, which resulted in significantly improved performance when applied to this dataset. Four iterations were conducted, which resulted in excellent 0.96 for metrics of precision, recall, and f1. Due to this strong performance, the food crisis year was removed from the dataset to prevent immediate extrapolation when used on future data, and the modeling process was repeated. The best “no year” model metrics remained strong, achieving ≥0.92 for recall, precision, and f1 while meeting a 10% f1 overfitting threshold on the test (0.84) and holdout (0.83) datasets. The year-agnostic neural network model represents a novel approach to classify food crises and outperforms current food crisis prediction efforts.

Model For Quantifying The Quality Of Secure Service, Paul M. Simon, Scott R. Graham, Christopher Talbot, Micah J. Hayden

Faculty Publications

Although not common today, communications networks could adjust security postures based on changing mission security requirements, environmental conditions, or adversarial capability, through the coordinated use of multiple channels. This will require the ability to measure the security of communications networks in a meaningful way. To address this need, in this paper, we introduce the Quality of Secure Service (QoSS) model, a methodology to evaluate how well a system meets its security requirements. This construct enables a repeatable and quantifiable measure of security in a single- or multi-channel network under static configurations. In this approach, the quantification of security is based …

Real-Time Motion Tracking Of Cognitive Baxter Robot Based On Differential Inverse Kinematics, Shaobo Li, Xingxing Zhang, Jing Yang, Qiang Bai, Jianjun Hu, Qisong Song, Zhiang Li

Faculty Publications

The tracking motion of the robot is realized based on a specific robot or relying on an expensive movement acquisition system. It has the problems of complex control procedures, lack of real-time performance, and difficulty in achieving secondary development. We propose a robot real-time tracking control method based on the control principle of differential inverse kinematics, which fuses the position and joint angle information of the robot’s actuators to realize the real-time estimation of the user’s movement during the tracking process. The motion coordinates of each joint of the robot are calculated and the coordinate conversion between man and machine …

Defect Detection In Atomic Resolution Transmission Electron Microscopy Images Using Machine Learning, Philip Cho, Aihua W. Wood, Krishnamurthy Mahalingam, Kurt Eyink

Faculty Publications

Point defects play a fundamental role in the discovery of new materials due to their strong influence on material properties and behavior. At present, imaging techniques based on transmission electron microscopy (TEM) are widely employed for characterizing point defects in materials. However, current methods for defect detection predominantly involve visual inspection of TEM images, which is laborious and poses difficulties in materials where defect related contrast is weak or ambiguous. Recent efforts to develop machine learning methods for the detection of point defects in TEM images have focused on supervised methods that require labeled training data that is generated via …

Mlatticeabc: Generic Lattice Constant Prediction Of Crystal Materials Using Machine Learning, Yuxin Li, Wenhui Yang, Rongzhi Dong, Jianjun Hu

Faculty Publications

Lattice constants such as unit cell edge lengths and plane angles are important parameters of the periodic structures of crystal materials. Predicting crystal lattice constants has wide applications in crystal structure prediction and materials property prediction. Previous work has used machine learning models such as neural networks and support vector machines combined with composition features for lattice constant prediction and has achieved a maximum performance for cubic structures with an average coefficient of determination (R2) of 0.82. Other models tailored for special materials family of a fixed form such as ABX3 perovskites can achieve much higher performance due …

Unified Multi-Objective Genetic Algorithm For Energy Efficient Job Shop Scheduling, Hongjong Wei, Shaobo Li, Huageng Quan, Dacheng Liu, Shu Rao, Chuanjiang Li, Jianjun Hu

Faculty Publications

In recent years, people have paid more and more attention to traditional manufacturing’s environmental impact, especially in terms of energy consumption and related emissions of carbon dioxide. Except for adopting new equipment, production scheduling could play an important role in reducing the total energy consumption of a manufacturing plant. Machine tools waste a considerable amount of energy because of their underutilization. Consequently, energy saving can be achieved by switching machines to standby or off when they lay idle for a comparatively long period. Herein, we first introduce the objectives of minimizing non-processing energy consumption, total weighted tardiness and earliness, and …

Implications Of The Quantum Dna Model For Information Sciences, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor, and this model has been supported by pilot research that experimentally demonstrated non-local communication between cells in separated cell cultures. This modeling and pilot research have important implications for information sciences, providing a potential architecture for quantum computing that operates at room temperature and is scalable to millions of qubits, and including the potential for an entanglement communication system based upon the quantum DNA architecture. Such a system could be used to provide non-local quantum key distribution that could not be blocked by any shielding or water depth, would …

The Whole Is Greater Than Its Parts: Ensembling Improves Protein Contact Prediction, Wendy M. Billings, Connor J. Morris, Dennis Della Corte

Faculty Publications

The prediction of amino acid contacts from protein sequence is an important problem, as protein contacts are a vital step towards the prediction of folded protein structures. We propose that a powerful concept from deep learning, called ensembling, can increase the accuracy of protein contact predictions by combining the outputs of different neural network models. We show that ensembling the predictions made by different groups at the recent Critical Assessment of Protein Structure Prediction (CASP13) outperforms all individual groups. Further, we show that contacts derived from the distance predictions of three additional deep neural networks—AlphaFold, trRosetta, and ProSPr—can be substantially …

“When They Say Weed Causes Depression, But It’S Your Fav Antidepressant”: Knowledge-Aware Attention Framework For Relationship Extraction, Shweta Yadav, Usha Lokala, Raminta Daniulaityte, Krishnaprasad Thirunarayan, Francois Lamy, Amit P. Sheth

Faculty Publications

With the increasing legalization of medical and recreational use of cannabis, more research is needed to understand the association between depression and consumer behavior related to cannabis consumption. Big social media data has potential to provide deeper insights about these associations to public health analysts. In this interdisciplinary study, we demonstrate the value of incorporating domain-specific knowledge in the learning process to identify the relationships between cannabis use and depression. We develop an end-to-end knowledge infused deep learning framework (Gated-K-BERT) that leverages the pre-trained BERT language representation model and domain-specific declarative knowledge source (Drug Abuse Ontology) to jointly extract entities …

Zynq System-On-Chip Dma Messaging For Processor Monitoring, Daniel F. Koranek, Douglas D. Hodson, Scott R. Graham

Faculty Publications

Xilinx Zynq-7000 System-on-Chip architectures combine an ARM Cortex-A9 core with an FPGA fabric. One benefit of this hybrid architecture is that it allows fast prototyping of designs where the security of either the processing system (PS) is monitored by the programmable logic (PL) or vice versa. The choice of implementing a design in the PS or PL is driven by cost-to-benefit analysis across many factors. This effort examines the design process required to construct security monitoring designs that use both the PS and PL. For background, this effort reviews similar security monitoring projects. For the effort, a PL peripheral was …

Identify Rna-Associated Subcellular Localizations Based On Multi-Label Learning Using Chou’S 5-Steps Rule, Hao Wang, Yijie Ding, Jijun Tang Ph.D., Quan Zou, Fei Guo

Faculty Publications

Background: Biological functions of biomolecules rely on the cellular compartments where they are located in cells. Importantly, RNAs are assigned in specific locations of a cell, enabling the cell to implement diverse biochemical processes in the way of concurrency. However, lots of existing RNA subcellular localization classifiers only solve the problem of single-label classification. It is of great practical significance to expand RNA subcellular localization into multi-label classification problem.

Results: In this study, we extract multi-label classification datasets about RNA-associated subcellular localizations on various types of RNAs, and then construct subcellular localization datasets on four RNA categories. In order to …

Privacy-Preserving Non-Participatory Surveillance System For Covid-19-Like Pandemics, Mahmoud Nabil, Ahmed Sherif, Mohamed Mahmoud, Waleed Alsmary, Maazen Alsabaan

Faculty Publications

COVID-19 pandemic has revealed a pressing need for an effective surveillance system to control the spread of infection. However, the existing systems are run by the people’s smartphones and without a strong participation from the people, the systems become ineffective. Moreover, these systems can be misused to spy on people and breach their privacy. Due to recent privacy breaches, people became anxious about their privacy, and without privacy reassurance, the people may not accept the systems. In this paper, we propose a non-participatory privacy-preserving surveillance system for COVID-19-like pandemics. The system aims to control the spread of COVID-19 infection without …