Theory and Algorithms Commons^™

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu

Computer Science Faculty Publications

We describe our experience porting FUN3D’s CUDA-optimized kernels to Intel oneAPI SYCL.We faced several challenges, including foremost the suboptimal performance of the oneAPI code on Intel’s new data center GPU. Suboptimal performance of the oneAPI code was due primarily to high register spills, memory latency, and poor vectorization. We addressed these issues by implementing the kernels using Intel oneAPI’s Explicit SIMD SYCL extension (ESIMD) API. The ESIMD API enables the writing of explicitly vectorized kernel code, gives more precise control over register usage and prefetching, and better handles thread divergence compared to SYCL. The ESIMD code outperforms the optimized SYCL …

Fast Multiscale Functional Estimation In Optimal Emg Placement For Robotic Prosthesis Controllers, Jin Ren, Guohui Song, Lucia Tabacu, Yuesheng Xu

Mathematics & Statistics Faculty Publications

Electromyogram (EMG) signals play a significant role in decoding muscle contraction information for robotic hand prosthesis controllers. Widely applied decoders require a large amount of EMG signals sensors, resulting in complicated calculations and unsatisfactory predictions. By the biomechanical process of single degree-of-freedom human hand movements, only several EMG signals are essential for accurate predictions. Recently, a novel predictor of hand movements adopted a multistage sequential adaptive functional estimation (SAFE) method based on the historical functional linear model (FLM) to select important EMG signals and provide precise projections.

However, SAFE repeatedly performs matrix-vector multiplications with a dense representation matrix of the …

Machine Learning-Based Jet And Event Classification At The Electron-Ion Collider With Applications To Hadron Structure And Spin Physics, Kyle Lee, James Mulligan, Mateusz Płoskoń, Felix Ringer, Feng Yuan

Physics Faculty Publications

We explore machine learning-based jet and event identification at the future Electron-Ion Collider (EIC). We study the effectiveness of machine learning-based classifiers at relatively low EIC energies, focusing on (i) identifying the flavor of the jet and (ii) identifying the underlying hard process of the event. We propose applications of our machine learning-based jet identification in the key research areas at the future EIC and current Relativistic Heavy Ion Collider program, including enhancing constraints on (transverse momentum dependent) parton distribution functions, improving experimental access to transverse spin asymmetries, studying photon structure, and quantifying the modification of hadrons and jets in …

Machine-Assisted Discovery Of Integrable Symplectic Mappings, T. Zolkin, Y. Kharkov, S. Nagaitsev

Physics Faculty Publications

We present a new automated method for finding integrable symplectic maps of the plane. These dynamical systems possess a hidden symmetry associated with an existence of conserved quantities, i.e., integrals of motion. The core idea of the algorithm is based on the knowledge that the evolution of an integrable system in the phase space is restricted to a lower-dimensional submanifold. Limiting ourselves to polygon invariants of motion, we analyze the shape of individual trajectories thus successfully distinguishing integrable motion from chaotic cases. For example, our method rediscovers some of the famous McMillan-Suris integrable mappings and ultradiscrete Painlevé equations. In total, …

A Survey Of Using Machine Learning In Iot Security And The Challenges Faced By Researchers, Khawlah M. Harahsheh, Chung-Hao Chen

Electrical & Computer Engineering Faculty Publications

The Internet of Things (IoT) has become more popular in the last 15 years as it has significantly improved and gained control in multiple fields. We are nowadays surrounded by billions of IoT devices that directly integrate with our lives, some of them are at the center of our homes, and others control sensitive data such as military fields, healthcare, and datacenters, among others. This popularity makes factories and companies compete to produce and develop many types of those devices without caring about how secure they are. On the other hand, IoT is considered a good insecure environment for cyber …

An Explainable Artificial Intelligence Framework For The Predictive Analysis Of Hypo And Hyper Thyroidism Using Machine Learning Algorithms, Md. Bipul Hossain, Anika Shama, Apurba Adhikary, Avi Deb Raha, K. M. Aslam Uddin, Mohammad Amzad Hossain, Imtia Islam, Saydul Akbar Murad, Md. Shirajum Munir, Anupam Kumur Bairagi

Electrical & Computer Engineering Faculty Publications

The thyroid gland is the crucial organ in the human body, secreting two hormones that help to regulate the human body's metabolism. Thyroid disease is a severe medical complaint that could be developed by high Thyroid Stimulating Hormone (TSH) levels or an infection in the thyroid tissues. Hypothyroidism and hyperthyroidism are two critical conditions caused by insufficient thyroid hormone production and excessive thyroid hormone production, respectively. Machine learning models can be used to precisely process the data generated from different medical sectors and to build a model to predict several diseases. In this paper, we use different machine-learning algorithms to …

Joint Congestion And Contention Avoidance In A Scalable Qos-Aware Opportunistic Routing In Wireless Ad-Hoc Networks, Ali Parsa, Neda Moghim, Sasan Haghani

VMASC Publications

Opportunistic routing (OR) can greatly increase transmission reliability and network throughput in wireless ad-hoc networks by taking advantage of the broadcast nature of the wireless medium. However, network congestion is a barrier in the way of OR's performance improvement, and network congestion control is a challenge in OR algorithms, because only the pure physical channel conditions of the links are considered in forwarding decisions. This paper proposes a new method to control network congestion in OR, considering three types of parameters, namely, the backlogged traffic, the traffic flows' Quality of Service (QoS) level, and the channel occupancy rate. Simulation results …

Efficient Maritime Object Detection And Validation For Enhancing Safety Of Uncrewed Marine Systems, Ahmed Saglam, Yiannis Papelis

VMASC Publications

Safe operation of uncrewed maritime systems is a major concern in the presence of other vehicles or obstacles. Typically, perception algorithms utilize sensor data to identify obstacles that must be avoided, and AI algorithms are used to interpret raw sensor data for use in navigation and object avoidance algorithms. However, perception algorithms are typically computationally expensive. In this paper, we present an efficient method for detecting obstacles using raw lidar data in the form of range or Point Cloud, employing computationally efficient techniques that do not depend on trained models or AI matching. The approach
converts the sensor readings into …

Assessing The Performance Of A Particle Swarm Optimization Mobility Algorithm In A Hybrid Wi-Fi/Lora Flying Ad Hoc Network, William David Paredes

UNF Graduate Theses and Dissertations

Research on Flying Ad-Hoc Networks (FANETs) has increased due to the availability of Unmanned Aerial Vehicles (UAVs) and the electronic components that control and connect them. Many applications, such as 3D mapping, construction inspection, or emergency response operations could benefit from an application and adaptation of swarm intelligence-based deployments of multiple UAVs. Such groups of cooperating UAVs, through the use of local rules, could be seen as network nodes establishing an ad-hoc network for communication purposes.

One FANET application is to provide communication coverage over an area where communication infrastructure is unavailable. A crucial part of a FANET implementation is …

A Diversity-Enhanced Memetic Algorithm For Solving Electric Vehicle Routing Problems With Time Windows And Mixed Backhauls, Jianhua Xiao, Jingguo Du, Zhiguang Cao, Xingyi Zhang, Yunyun Niu

Research Collection School Of Computing and Information Systems

The electric vehicle routing problem (EVRP) has been studied increasingly because of environmental concerns. However, existing studies on the EVRP mainly focus on time windows and sole linehaul customers, which might not be practical as backhaul customers are also ubiquitous in reality. In this study, we investigate an EVRP with time windows and mixed backhauls (EVRPTWMB), where both linehaul and backhaul customers exist and can be served in any order. To address this challenging problem, we propose a diversity-enhanced memetic algorithm (DEMA) that integrates three types of novel operators, including genetic operators based on adaptive selection mechanism, a selection operator …

Apt Adversarial Defence Mechanism For Industrial Iot Enabled Cyber-Physical System, Safdar Hussain Javed, Maaz Bin Ahmad, Muhammad Asif, Waseem Akram, Khalid Mahmood, Ashok Kumar Das, Sachin Shetty

VMASC Publications

The objective of Advanced Persistent Threat (APT) attacks is to exploit Cyber-Physical Systems (CPSs) in combination with the Industrial Internet of Things (I-IoT) by using fast attack methods. Machine learning (ML) techniques have shown potential in identifying APT attacks in autonomous and malware detection systems. However, detecting hidden APT attacks in the I-IoT-enabled CPS domain and achieving real-time accuracy in detection present significant challenges for these techniques. To overcome these issues, a new approach is suggested that is based on the Graph Attention Network (GAN), a multi-dimensional algorithm that captures behavioral features along with the relevant information that other methods …

Patch-Wise Training With Convolutional Neural Networks To Synthetically Upscale Cfd Simulations, John P. Romano, Alec C. Brodeur, Oktay Baysal

Mechanical & Aerospace Engineering Faculty Publications

This paper expands the authors’ prior work[1], which focuses on developing a convolutional neural network (CNN) model capable of mapping time-averaged, unsteady Reynold’s-averaged Navier-Stokes (URANS) simulations to higher resolution results informed by time-averaged detached eddy simulations (DES). The authors present improvements over the prior CNN autoencoder model that result from hyperparameter optimization, increased data set augmentation through the adoption of a patch-wise training approach, and the predictions of primitive variables rather than vorticity magnitude. The training of the CNN model developed in this study uses the same URANS and DES simulations of a transonic flow around several NACA 4-digit airfoils …

The Effect Of The Width Of The Incident Pulse To The Dielectric Transition Layer In The Scattering Of An Electromagnetic Pulse — A Qubit Lattice Algorithm Simulation, George Vahala, Linda Vahala, Abhay K. Ram, Min Soe

Electrical & Computer Engineering Faculty Publications

The effect of the thickness of the dielectric boundary layer that connects a material of refractive index n₁ to another of index n₂is considered for the propagation of an electromagnetic pulse. A qubit lattice algorithm (QLA), which consists of a specially chosen non-commuting sequence of collision and streaming operators acting on a basis set of qubits, is theoretically determined that recovers the Maxwell equations to second-order in a small parameter ϵ. For very thin boundary layer the scattering properties of the pulse mimics that found from the Fresnel jump conditions for a plane wave - except that …

Adaptive Critic Network For Person Tracking Using 3d Skeleton Data, Joseph G. Zalameda, Alex Glandon, Khan M. Iftekharuddin, Mohammad S. Alam (Ed.), Vijayan K. Asari (Ed.)

Electrical & Computer Engineering Faculty Publications

Analysis of human gait using 3-dimensional co-occurrence skeleton joints extracted from Lidar sensor data has been shown a viable method for predicting person identity. The co-occurrence based networks rely on the spatial changes between frames of each joint in the skeleton data sequence. Normally, this data is obtained using a Lidar skeleton extraction method to estimate these co-occurrence features from raw Lidar frames, which can be prone to incorrect joint estimations when part of the body is occluded. These datasets can also be time consuming and expensive to collect and typically offer a small number of samples for training and …

Class Activation Mapping And Uncertainty Estimation In Multi-Organ Segmentation, Md. Shibly Sadique, Walia Farzana, Ahmed Temtam, Khan Iftekharuddin, Khan Iftekharuddin (Ed.), Weijie Chen (Ed.)

Electrical & Computer Engineering Faculty Publications

Deep learning (DL)-based medical imaging and image segmentation algorithms achieve impressive performance on many benchmarks. Yet the efficacy of deep learning methods for future clinical applications may become questionable due to the lack of ability to reason with uncertainty and interpret probable areas of failures in prediction decisions. Therefore, it is desired that such a deep learning model for segmentation classification is able to reliably predict its confidence measure and map back to the original imaging cases to interpret the prediction decisions. In this work, uncertainty estimation for multiorgan segmentation task is evaluated to interpret the predictive modeling in DL …

Intelligent Adaptive Gossip-Based Broadcast Protocol For Uav-Mec Using Multi-Agent Deep Reinforcement Learning, Zen Ren, Xinghua Li, Yinbin Miao, Zhuowen Li, Zihao Wang, Mengyao Zhu, Ximeng Liu, Deng, Robert H.

Research Collection School Of Computing and Information Systems

UAV-assisted mobile edge computing (UAV-MEC) has been proposed to offer computing resources for smart devices and user equipment. UAV cluster aided MEC rather than one UAV-aided MEC as edge pool is the newest edge computing architecture. Unfortunately, the data packet exchange during edge computing within the UAV cluster hasn't received enough attention. UAVs need to collaborate for the wide implementation of MEC, relying on the gossip-based broadcast protocol. However, gossip has the problem of long propagation delay, where the forwarding probability and neighbors are two factors that are difficult to balance. The existing works improve gossip from only one factor, …

I Know What You Are Searching For: Code Snippet Recommendation From Stack Overflow Posts, Zhipeng Gao, Xin Xia, David Lo, John C. Grundy, Xindong Zhang, Zhenchang Xing

Research Collection School Of Computing and Information Systems

Stack Overflow has been heavily used by software developers to seek programming-related information. More and more developers use Community Question and Answer forums, such as Stack Overflow, to search for code examples of how to accomplish a certain coding task. This is often considered to be more efficient than working from source documentation, tutorials, or full worked examples. However, due to the complexity of these online Question and Answer forums and the very large volume of information they contain, developers can be overwhelmed by the sheer volume of available information. This makes it hard to find and/or even be aware …

The History Of The Enigma Machine, Jenna Siobhan Parkinson

History Publications

The history of the Enigma machine begins with the invention of the rotor-based cipher machine in 1915. Various models for rotor-based cipher machines were developed somewhat simultaneously in different parts of the world. However, the first documented rotor machine was developed by Dutch naval officers in 1915. Nonetheless, the Enigma machine was officially invented following the end of World War I by Arthur Scherbius in 1918 (Faint, 2016).

Improving Adjacency List Storage Methods For Polypeptide Similarity Analysis, Arianna Swensen

Honors Theses

Protein design is a complex biomolecular and computational problem. Working on increasingly large protein folding problems requires an improvement in current analysis methods available. This work first discusses various methods of protein design, including de novo protein design, which is the primary focus of this thesis. Then, a new approach utilizing a B+ tree to effectively store and query a graph of keys and vertices is proposed in order to store the number of times two polypeptides are considered to be similar. This approach is found to have a reduction in time complexity from current mapping methods and thus provides …