Physical Sciences and Mathematics Commons^™

Npgreat: Assembly Of The Human Subtelomere Regions With The Use Of Ultralong Nanopore Reads And Linked Reads, Eleni Adam, Desh Ranjan, Harold Riethman

Computer Science Faculty Publications

Background: Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function.

Results: We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with mapped ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets of DNA sequences identified …

Hydrological Drought Forecasting Using A Deep Transformer Model, Amobichukwu C. Amanambu, Joann Mossa, Yin-Hsuen Chen

University Administration Publications

Hydrological drought forecasting is essential for effective water resource management planning. Innovations in computer science and artificial intelligence (AI) have been incorporated into Earth science research domains to improve predictive performance for water resource planning and disaster management. Forecasting of future hydrological drought can assist with mitigation strategies for various stakeholders. This study uses the transformer deep learning model to forecast hydrological drought, with a benchmark comparison with the long short-term memory (LSTM) model. These models were applied to the Apalachicola River, Florida, with two gauging stations located at Chattahoochee and Blountstown. Daily stage-height data from the period 1928–2022 were …

Applications Of Blockchain In Business Processes: A Comprehensive Review, Wattana Viriyasitavat, Li Xu, Dusit Niyato, Zhuming Bi, Danupol Hoonsopon

Information Technology & Decision Sciences Faculty Publications

Blockchain (BC), as an emerging technology, is revolutionizing Business Process Management (BPM) in multiple ways. The main adoption is to serve as a trusted infrastructure to guarantee the trust of collaborations among multiple partners in trustless environments. Especially, BC enables trust of information by using Distributed Ledger Technology (DLT). With the power of smart contracts, BC enforces the obligations of counterparties that transact in a business process (BP) by programming the contracts as transactions. This paper aims to study the state-of-the-art of BC technologies by (1) exploring its applications in BPM with the focus on how BC provides the trust …

Smart Manufacturing—Theories, Methods, And Applications, Zhuming Bi, Lida Xu, Puren Ouyang

Information Technology & Decision Sciences Faculty Publications

(First paragraph) Smart manufacturing (SM) distinguishes itself from other system paradigms by introducing ‘smartness’ as a measure to a manufacturing system; however, researchers in different domains have different expectations of system smartness from their own perspectives. In this Special Issue (SI), SM refers to a system paradigm where digital technologies are deployed to enhance system smartness by (1) empowering physical resources in production, (2) utilizing virtual and dynamic assets over the internet to expand system capabilities, (3) supporting data-driven decision making at all domains and levels of businesses, or (4) reconfiguring systems to adapt changes and uncertainties in dynamic environments. …

Runtime Energy Savings Based On Machine Learning Models For Multicore Applications, Vaibhav Sundriyal, Masha Sosonkina

Electrical & Computer Engineering Faculty Publications

To improve the power consumption of parallel applications at the runtime, modern processors provide frequency scaling and power limiting capabilities. In this work, a runtime strategy is proposed to maximize energy savings under a given performance degradation. Machine learning techniques were utilized to develop performance models which would provide accurate performance prediction with change in operating core-uncore frequency. Experiments, performed on a node (28 cores) of a modern computing platform showed significant energy savings of as much as 26% with performance degradation of as low as 5% under the proposed strategy compared with the execution in the unlimited power case.

A Super Fast Algorithm For Estimating Sample Entropy, Weifeng Liu, Ying Jiang, Yuesheng Xu

Mathematics & Statistics Faculty Publications

: Sample entropy, an approximation of the Kolmogorov entropy, was proposed to characterize complexity of a time series, which is essentially defined as − log(B/A), where B denotes the number of matched template pairs with length m and A denotes the number of matched template pairs with m + 1, for a predetermined positive integer m. It has been widely used to analyze physiological signals. As computing sample entropy is time consuming, the box-assisted, bucket-assisted, x-sort, assisted sliding box, and kd-tree-based algorithms were proposed to accelerate its computation. These algorithms require O(N²) or …

Understanding The Mechanism Of Deep Learning Frameworks In Lesion Detection For Pathological Images With Breast Cancer, Wei-Wen Hsu, Chung-Hao Chen, Chang Hao, Yu-Ling Hou, Xiang Gao, Yun Shao, Xueli Zhang, Jingjing Wang, Tao He, Yanhong Tai

Electrical & Computer Engineering Faculty Publications

With the advances of scanning sensors and deep learning algorithms, computational pathology has drawn much attention in recent years and started to play an important role in the clinical workflow. Computer-aided detection (CADe) systems have been developed to assist pathologists in slide assessment, increasing diagnosis efficiency and reducing misdetections. In this study, we conducted four experiments to demonstrate that the features learned by deep learning models are interpretable from a pathological perspective. In addition, classifiers such as the support vector machine (SVM) and random forests (RF) were used in experiments to replace the fully connected layers and decompose the end-to-end …

Formal Modeling And Verification Of A Blockchain-Based Crowdsourcing Consensus Protocol, Hamra Afzaal, Muhammad Imran, Muhammad Umar Janjua, Sarada Prasad Gochhayat

VMASC Publications

Crowdsourcing is an effective technique that allows humans to solve complex problems that are hard to accomplish by automated tools. Some significant challenges in crowdsourcing systems include avoiding security attacks, effective trust management, and ensuring the system’s correctness. Blockchain is a promising technology that can be efficiently exploited to address security and trust issues. The consensus protocol is a core component of a blockchain network through which all the blockchain peers achieve an agreement about the state of the distributed ledger. Therefore, its security, trustworthiness, and correctness have vital importance. This work proposes a Secure and Trustworthy Blockchain-based Crowdsourcing (STBC) …

Ascp-Iomt: Ai-Enabled Lightweight Secure Communication Protocol For Internet Of Medical Things, Mohammad Wazid, Jaskaran Singh, Ashok Kumar Das, Sachin Shetty, Muhammad Khurram Khan, Joel J.P.C. Rodrigues

VMASC Publications

The Internet of Medical Things (IoMT) is a unification of smart healthcare devices, tools, and software, which connect various patients and other users to the healthcare information system through the networking technology. It further reduces unnecessary hospital visits and the burden on healthcare systems by connecting the patients to their healthcare experts (i.e., doctors) and allows secure transmission of healthcare data over an insecure channel (e.g., the Internet). Since Artificial Intelligence (AI) has a great impact on the performance and usability of an information system, it is important to include its modules in a healthcare information system, which will be …

Module 3: Technology Foresight And Insurtech, Michael Mcshane, C. Ariel Pinto, Hesamoddin Tahami, Hengameh Fakhravar

Developing Technology Foresight: Case Study of AI in InsurTech

Instructional Module 3 for course, Developing Technology Foresight: Case Study of AI in InsurTech.

Insurtech And Distribution, Michael Mcshane, C. Ariel Pinto, Hesamoddin Tahami, Hengameh Fakhravar

Developing Technology Foresight: Case Study of AI in InsurTech

Questions regarding InsurTech and distribution.

D-Lib Magazine Pioneered Web-Based Scholarly Communication, Michael L. Nelson, Herbert Van De Sompel

Computer Science Faculty Publications

The web began with a vision of, as stated by Tim Berners-Lee in 1991, “that much academic information should be freely available to anyone”. For many years, the development of the web and the development of digital libraries and other scholarly communications infrastructure proceeded in tandem. A milestone occurred in July, 1995, when the first issue of D-Lib Magazine was published as an online, HTML-only, open access magazine, serving as the focal point for the then emerging digital library research community. In 2017 it ceased publication, in part due to the maturity of the community it served as well as …

Spaghetti Tracer: A Framework For Tracing Semiregular Filamentous Densities In 3d Tomograms, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D …

Scholarly Big Data Quality Assessment: A Case Study Of Document Linking And Conflation With S2orc, Jian Wu, Ryan Hiltabrand, Dominik Soós, C. Lee Giles

Computer Science Faculty Publications

Recently, the Allen Institute for Artificial Intelligence released the Semantic Scholar Open Research Corpus (S2ORC), one of the largest open-access scholarly big datasets with more than 130 million scholarly paper records. S2ORC contains a significant portion of automatically generated metadata. The metadata quality could impact downstream tasks such as citation analysis, citation prediction, and link analysis. In this project, we assess the document linking quality and estimate the document conflation rate for the S2ORC dataset. Using semi-automatically curated ground truth corpora, we estimated that the overall document linking quality is high, with 92.6% of documents correctly linking to six major …

Post-Quantum Secure Identity-Based Encryption Scheme Using Random Integer Lattices For Iot-Enabled Ai Applications, Dharminder Dharminder, Ashok Kumar Das, Sourav Saha, Basudeb Bera, Athanasios V. Vasilakos

VMASC Publications

Identity-based encryption is an important cryptographic system that is employed to ensure confidentiality of a message in communication. This article presents a provably secure identity based encryption based on post quantum security assumption. The security of the proposed encryption is based on the hard problem, namely Learning with Errors on integer lattices. This construction is anonymous and produces pseudo random ciphers. Both public-key size and ciphertext-size have been reduced in the proposed encryption as compared to those for other relevant schemes without compromising the security. Next, we incorporate the constructed identity based encryption (IBE) for Internet of Things (IoT) applications, …

Runtime Power Allocation Based On Multi-Gpu Utilization In Gamess, Masha Sosonkina, Vaibhav Sundriyal, Jorge Luis Galvez Vallejo

Electrical & Computer Engineering Faculty Publications

To improve the power consumption of parallel applications at the runtime, modern processors provide frequency scaling and power limiting capabilities. In this work, a runtime strategy is proposed to maximize performance under a given power budget by distributing the available power according to the relative GPU utilization. Time series forecasting methods were used to develop workload prediction models that provide accurate prediction of GPU utilization during application execution. Experiments were performed on a multi-GPU computing platform DGX-1 equipped with eight NVIDIA V100 GPUs used for quantum chemistry calculations in the GAMESS package. For a limited power budget, the proposed strategy …

An Exploration On Apts In Biocybersecurity And Cyberbiosecurity, Xavier-Lewis Palmer, Lucas Potter, Saltuk Karahan

School of Cybersecurity Faculty Publications

Novel and complex digital threats that are increasingly interwoven with means and products of biology that can affect society. Much work in Biocybersecurity/Cyberbiosecurity (BCS/CBS) discuss vulnerabilities, but few deeply address malicious actor varieties as attacks at this intersection are new. The path to those attacks remains mostly theoretical, presenting considerable difficulty to accomplish in practical scenarios. In terms of advanced persistent threats (APTs) this of course needs to change as biomanufacturing facilities are at risk, considering Covid-19 and other potential pandemics. Further attacks are not out of reach and thus we must start to imagine how BCS APTs may appear. …

A Channel State Information Based Virtual Mac Spoofing Detector, Peng Jiang, Hongyi Wu, Chunsheng Xin

Electrical & Computer Engineering Faculty Publications

Physical layer security has attracted lots of attention with the expansion of wireless devices to the edge networks in recent years. Due to limited authentication mechanisms, MAC spoofing attack, also known as the identity attack, threatens wireless systems. In this paper, we study a new type of MAC spoofing attack, the virtual MAC spoofing attack, in a tight environment with strong spatial similarities, which can create multiple counterfeits entities powered by the virtualization technologies to interrupt regular services. We develop a system to effectively detect such virtual MAC spoofing attacks via the deep learning method as a countermeasure. …

Arithfusion: An Arithmetic Deep Model For Temporal Remote Sensing Image Fusion, Md Reshad Ul Hoque, Jian Wu, Chiman Kwan, Krzysztof Koperski, Jiang Li

Electrical & Computer Engineering Faculty Publications

Different satellite images may consist of variable numbers of channels which have different resolutions, and each satellite has a unique revisit period. For example, the Landsat-8 satellite images have 30 m resolution in their multispectral channels, the Sentinel-2 satellite images have 10 m resolution in the pan-sharp channel, and the National Agriculture Imagery Program (NAIP) aerial images have 1 m resolution. In this study, we propose a simple yet effective arithmetic deep model for multimodal temporal remote sensing image fusion. The proposed model takes both low- and high-resolution remote sensing images at t₁ together with low-resolution images at a …

Qu-Brats: Miccai Brats 2020 Challenge On Quantifying Uncertainty In Brain Tumor Segmentation - Analysis Of Ranking Scores And Benchmarking Results, Raghav Mehta, Angelos Filos, Ujjwal Baid, Chiharu Sako, Richard Mckinley, Michael Rebsamen, Katrin Dätwyler, Raphael Meier, Piotr Radojewski, Gowtham Krishnan Murugesan, Sahil Nalawade, Chandan Ganesh, Ben Wagner, Fang F. Yu, Baowei Fei, Ananth J. Madhuranthakam, Joseph A. Maldjian, Laura Daza, Catalina Gómez, Pablo Arbeláez, Chengliang Dai, Shuo Wang, Hadrien Reynaud, Yuan-Han Mo, Elsa Angelini, Yike Guo, Wenjia Bai, Subhashis Banerjee, Lin-Min Pei, Murat Ak, Sarahi Rosas-González, Ilyess Zemmoura, Clovis Tauber, Minh H. Vu, Tufve Nyholm, Tommy Löfstedt, Laura Mora Ballestar, Veronica Vilaplana, Hugh Mchugh, Gonzalo Maso Talou, Alan Wang, Jay Patel, Ken Chang, Katharina Hoebel, Mishka Gidwani, Nishanth Arun, Sharut Gupta, Mehak Aggarwal, Praveer Singh, Elizabeth R. Gerstner, Jayashree Kalpathy-Cramer, Nicholas Boutry, Alexis Huard, Lasitha Vidyaratne, Md. Monibor Rahman, Khan M. Iftekharuddin, Joseph Chazalon, Elodie Puybareau, Guillaume Tochon, Jun Ma, Mariano Cabezas, Xavier Llado, Arnau Oliver, Liliana Valencia, Sergi Valverde, Mehdi Amian, Mohammadreza Soltaninejad, Andriy Myronenko, Ali Hatamizadeh, Xue Feng, Quan Dou, Nicholas Tustison, Craig Meyer, Nisarg A. Shah, Sanjay Talbar, Marc-André Weber, Abhishek Mahajan, Andras Jakab, Roland Wiest, Hassan M. Fathallah-Shaykh, Arash Nazeri, Mikhail Milchenko1, Daniel Marcus, Aikaterini Kotrotsou, Rivka Colen, John Freymann, Justin Kirby, Christos Davatzikos, Bjoern Menze, Spyridon Bakas, Yarin Gal, Tal Arbel

Electrical & Computer Engineering Faculty Publications

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. …

Segmenting Technical Drawing Figures In Us Patents, Md Reshad Ul Hoque, Xin Wei, Muntabir Hasan Choudhury, Kehinde Ajayi, Martin Gryder, Jian Wu, Diane Oyen

Computer Science Faculty Publications

Image segmentation is the core computer vision problem for identifying objects within a scene. Segmentation is a challenging task because the prediction for each pixel label requires contextual information. Most recent research deals with the segmentation of natural images rather than drawings. However, there is very little research on sketched image segmentation. In this study, we introduce heuristic (point-shooting) and deep learning-based methods (U-Net, HR-Net, MedT, DETR) to segment technical drawings in US patent documents. Our proposed methods on the US Patent dataset achieved over 90% accuracy where transformer performs well with 97% segmentation accuracy, which is promising and computationally …

Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu

Computer Science Faculty Publications

Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in …

Healthcare 5.0 Security Framework: Applications, Issues And Future Research Directions, Mohammad Wazid, Ashok Kumar Das, Noor Mohd, Youngho Park

VMASC Publications

Healthcare 5.0 is a system that can be deployed to provide various healthcare services. It does these services by utilising a new generation of information technologies, such as Internet of Things (IoT), Artificial Intelligence (AI), Big data analytics, blockchain and cloud computing. Due to the introduction of healthcare 5.0, the paradigm has been now changed. It is disease-centered to patient-centered care where it provides healthcare services and supports to the people. However, there are several security issues and challenges in healthcare 5.0 which may cause the leakage or alteration of sensitive healthcare data. This demands that we need a robust …

Development Of A Framework To Support Informed Shipbuilding Based On Supply Chain Disruptions, Katherine Smith, Rafael Diaz, Yuzhong Shen

VMASC Publications

In addition to stresses induced by the Covid-19 pandemic, supply chains worldwide have been growing more complex while facing a continuous onslaught of disruptions. This paper presents an analysis and extension of a graph based model for modeling and simulating the effects of such disruptions. The graph based model combines a Bayesian network approach for simulating risks with a network dependency analysis approach for simulating the propagation of disruptions through the network over time. The initial analysis provides evidence supporting extension to for using a multi-layered approach allowing for the inclusion of cyclic features in supply chain models. Initial results …

Human Ergonomic Simulation To Support The Design Of An Exoskeleton For Lashing/De-Lashing Operations Of Containers Cargo, Francesco Longo, Antonio Padovano, Vittorio Solina, Virginia D' Augusta, Stefan Venzl, Roberto Calbi, Michele Bartuni, Ornella Anastasi, Rafael Diaz

VMASC Publications

Lashing and de-lashing operations of containers cargo on board containerships are considered as quite strenuous activities in which operators are required to work continuously over a 6 or 8 hours shift with very limited break. This is mostly because containerships need to leave the port as soon as possible and containers loading and unloading operations must be executed with very high productivity (stay moored in a port is a totally unproductive time for a ship and a loss-making business for a shipping company). Operators performing lashing and de-lashing operations are subjected to intense ergonomic stress and uncomfortable working postures. To …

Coupled Dynamics Of Spin Qubits In Optical Dipole Microtraps: Application To The Error Analysis Of A Rydberg-Blockade Gate, L. V. Gerasimov, R. R. Yusupov, A. D. Moiseevsky, I. Vybornyi, K. S. Tikhonov, S. P. Kulik, S. S. Straupe, Charles I. Sukenik, D. V. Kupriyanov

Physics Faculty Publications

Single atoms in dipole microtraps or optical tweezers have recently become a promising platform for quantum computing and simulation. Here we report a detailed theoretical analysis of the physics underlying an implementation of a Rydberg two-qubit gate in such a system—a cornerstone protocol in quantum computing with single atoms. We focus on a blockade-type entangling gate and consider various decoherence processes limiting its performance in a real system. We provide numerical estimates for the limits on fidelity of the maximally entangled states and predict the full process matrix corresponding to the noisy two-qubit gate. We consider different excitation geometries and …

Security Concerns On Machine Learning Solutions For 6g Networks In Mmwave Beam Prediction, Ferhat Ozgur Catak, Murat Kuzlu, Evren Catak, Umit Cali, Devrim Unal

Engineering Technology Faculty Publications

6G – sixth generation – is the latest cellular technology currently under development for wireless communication systems. In recent years, machine learning (ML) algorithms have been applied widely in various fields, such as healthcare, transportation, energy, autonomous cars, and many more. Those algorithms have also been used in communication technologies to improve the system performance in terms of frequency spectrum usage, latency, and security. With the rapid developments of ML techniques, especially deep learning (DL), it is critical to consider the security concern when applying the algorithms. While ML algorithms offer significant advantages for 6G networks, security concerns on artificial …

Multi-User Eye-Tracking, Bhanuka Mahanama

Computer Science Faculty Publications

The human gaze characteristics provide informative cues on human behavior during various activities. Using traditional eye trackers, assessing gaze characteristics in the wild requires a dedicated device per participant and therefore is not feasible for large-scale experiments. In this study, we propose a commodity hardware-based multi-user eye-tracking system. We leverage the recent advancements in Deep Neural Networks and large-scale datasets for implementing our system. Our preliminary studies provide promising results for multi-user eye-tracking on commodity hardware, providing a cost-effective solution for large-scale studies.

Module 1: Introduction To Technology Foresight, Risk Management, And Insurtech, Michael Mcshane, C. Ariel Pinto, Hesamoddin Tahami, Hengameh Fakhravar

Developing Technology Foresight: Case Study of AI in InsurTech

Instructional Module 1 for course, Developing Technology Foresight: Case Study of AI in InsurTech.

Module 2: Case Studies Of Ai And Insurtech, Michael Mcshane, C. Ariel Pinto, Hesamoddin Tahami, Hengameh Fakhravar

Developing Technology Foresight: Case Study of AI in InsurTech

Instructional Module 2 for course, Developing Technology Foresight: Case Study of AI in InsurTech.