Physical Sciences and Mathematics Commons^™

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age And Alzheimer’S Disease Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Fillipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications and Presentations

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with nonspecific chemical oxidation from reactive oxygen species (ROS) whose chemistries are linked to various disease pathologies including neurodegeneration. Emerging evidence shows MSox site occupancy is in some cases under enzymatic regulatory control mediating cellular signaling including phosphorylation and/or calcium signaling, raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age, sex and disease dependent MSox speciation in mouse hippocampus. In …

Ex-Vivo Hippocampus Segmentation Using Diffusion-Weighted Mri, Haoteng Tang, Siyuan Dai, Eric M. Zou, Guodong Liu, Ryan Ahearn, Ryan Krafty, Michel Modo, Liang Zhan

Computer Science Faculty Publications and Presentations

The hippocampus is a crucial brain structure involved in memory formation, spatial navigation, emotional regulation, and learning. An accurate MRI image segmentation of the human hippocampus plays an important role in multiple neuro-imaging research and clinical practice, such as diagnosing neurological diseases and guiding surgical interventions. While most hippocampus segmentation studies focus on using T1-weighted or T2-weighted MRI scans, we explore the use of diffusion-weighted MRI (dMRI), which offers unique insights into the microstructural properties of the hippocampus. Particularly, we utilize various anisotropy measures derived from diffusion MRI (dMRI), including fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity, for …

Possible Role Of Correlation Coefficients And Network Analysis Of Multiple Intracellular Proteins In Blood Cells Of Patients With Bipolar Disorder In Studying The Mechanism Of Lithium Responsiveness: A Proof-Concept Study, Keming Gao, Marzieh Ayati, Nicholas M. Kaye, Mehmet Koyutürk, Joseph R. Calabrese, Eric Christian, Hillard M. Lazarus, David Kaplan

Computer Science Faculty Publications and Presentations

Background: The mechanism of lithium treatment responsiveness in bipolar disorder (BD) remains unclear. The aim of this study was to explore the utility of correlation coefficients and protein-to-protein interaction (PPI) network analyses of intracellular proteins in monocytes and CD4+ lymphocytes of patients with BD in studying the potential mechanism of lithium treatment responsiveness. Methods: Patients with bipolar I or II disorder who were diagnosed with the MINI for DSM-5 and at any phase of the illness with at least mild symptom severity and received lithium (serum level ≥ 0.6 mEq/L) for 16 weeks were divided into two groups, responders (≥50% …

Efficient High-Resolution Time Series Classification Via Attention Kronecker Decomposition, Aosong Feng, Jialin Chen, Juan Garza, Brooklyn Berry, Francisco Salazar, Yifeng Gao, Rex Ying, Leandros Tassiulas

Computer Science Faculty Publications and Presentations

The high-resolution time series classification problem is essential due to the increasing availability of detailed temporal data in various domains. To tackle this challenge effectively, it is imperative that the state-of-theart attention model is scalable to accommodate the growing sequence lengths typically encountered in highresolution time series data, while also demonstrating robustness in handling the inherent noise prevalent in such datasets. To address this, we propose to hierarchically encode the long time series into multiple levels based on the interaction ranges. By capturing relationships at different levels, we can build more robust, expressive, and efficient models that are capable of …

Constrained Multiview Representation For Self-Supervised Contrastive Learning, Siyuan Dai, Kai Ye, Kun Zhao, Ge Cui, Haoteng Tang, Liang Zhan

Computer Science Faculty Publications and Presentations

Representation learning constitutes a pivotal cornerstone in contemporary deep learning paradigms, offering a conduit to elucidate distinctive features within the latent space and interpret the deep models. Nevertheless, the inherent complexity of anatomical patterns and the random nature of lesion distribution in medical image segmentation pose significant challenges to the disentanglement of representations and the understanding of salient features. Methods guided by the maximization of mutual information, particularly within the framework of contrastive learning, have demonstrated remarkable success and superiority in decoupling densely intertwined representations. However, the effectiveness of contrastive learning highly depends on the quality of the positive and …

A Simple Proof That Ricochet Robots Is Pspace-Complete, Jose Balanza-Martinez, Angel A. Cantu, Robert Schweller, Tim Wylie

Computer Science Faculty Publications and Presentations

In this paper, we seek to provide a simpler proof that the relocation problem in Ricochet Robots (Lunar Lockout with fixed geometry) is PSPACE-complete via a reduction from Finite Function Generation (FFG). Although this result was originally proven in 2003, we give a simpler reduction by utilizing the FFG problem, and put the result in context with recent publications showing that relocation is also PSPACE-complete in related models.

Fledge: Ledger-Based Federated Learning Resilient To Inference And Backdoor Attacks, Jorge Castillo, Phillip Rieger, Hossein Fereidooni, Qian Chen, Ahmad Sadeghi

Informatics and Engineering Systems Faculty Publications and Presentations

Federated learning (FL) is a distributed learning process that uses a trusted aggregation server to allow multiple parties (or clients) to collaboratively train a machine learning model without having them share their private data. Recent research, however, has demonstrated the effectiveness of inference and poisoning attacks on FL. Mitigating both attacks simultaneously is very challenging. State-of-the-art solutions have proposed the use of poisoning defenses with Secure Multi-Party Computation (SMPC) and/or Differential Privacy (DP). However, these techniques are not efficient and fail to address the malicious intent behind the attacks, i.e., adversaries (curious servers and/or compromised clients) seek to exploit a …

Multitasking Scheduling With Shared Processing, Bin Fu, Yumei Huo, Hairong Zhao

Computer Science Faculty Publications and Presentations

Recently, the problem of multitasking scheduling has raised a lot of interest in the service industries. Hall et al. (Discrete Applied Mathematics, 2016) proposed a shared processing multitasking scheduling model which allows a team to continue to work on the primary tasks while processing the routinely scheduled activities as they occur. With a team being modeled as a single machine, the processing sharing of the machine is achieved by allocating a fraction of the processing capacity to routine jobs and the remaining fraction, which we denote as sharing ratio, to the primary jobs. In this paper, we generalize this model …

A Review Of Cyber Attacks On Sensors And Perception Systems In Autonomous Vehicle, Taminul Islam, Md. Alif Sheakh, Anjuman Naher Jui, Omar Sharif, Md Zobaer Hasan

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

Vehicle automation has been in the works for a long time now. Automatic brakes, cruise control, GPS satellite navigation, etc. are all common features seen in today's automobiles. Automation and artificial intelligence breakthroughs are likely to lead to an increase in the usage of automation technologies in cars. Because of this, mankind will be more reliant on computer-controlled equipment and car systems in our daily lives. All major corporations have begun investing in the development of self-driving cars because of the rapid advancement of advanced driver support technologies. However, the level of safety and trustworthiness is still questionable. Imagine what …

A Fast And Responsive Web-Based Framework For Visualizing Hpc Application Usage, Ved Arora, Nayeli Gurrola, Amiya K. Maji, Guangzhen Jin

Computer Science Faculty Publications and Presentations

Insights about applications and user environments can help HPC center staff make data-driven decisions about cluster operations. In this paper, we present a fast and responsive web-based visualization framework for analyzing HPC application usage. By leveraging XALT, a powerful tool for tracking application and library usage, we collected tens of millions of data points on a national supercomputer. The portable visualization framework created with Plotly Dash can be easily launched as a container and accessed from a web browser. The presented visualizations take a deep dive into the XALT data, analyzing application use, compiler usage, library usage, and even user-specific …

A Comprehensive Survey Of Complex Brain Network Representation, Haoteng Tang, Guixiang Ma, Yanfu Zhang, Kai Ye, Lei Guo, Guodong Liu, Qi Huang, Yalin Wang, Olusola Ajilore, Alex D. Leow

Computer Science Faculty Publications and Presentations

Highlights

• Major traditional and deep learning methods on brain network representation are overviewed.

• Brain network datasets and algorithm implementation tools are summarized.

• Promising research directions in brain network analysis are discussed.

Abstract

Recent years have shown great merits in utilizing neuroimaging data to understand brain structural and functional changes, as well as its relationship to different neurodegenerative diseases and other clinical phenotypes. Brain networks, derived from different neuroimaging modalities, have attracted increasing attention due to their potential to gain system-level insights to characterize brain dynamics and abnormalities in neurological conditions. Traditional methods aim to pre-define multiple topological features of brain …

Sublinear Time Motif Discovery From Multiple Sequences, Bin Fu, Yunhui Fu, Yuan Xue

Computer Science Faculty Publications and Presentations

In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 . . . gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 . . . bm of G, every character, bi , is probabilistically generated, such that the probability for bi 6= gi is …

Complexity Of Reconfiguration In Surface Chemical Reaction Networks, Robert M. Alaniz, Josh Brunner, Michael Coulombe, Erik D. Demaine, Yevhenii Diomidov, Ryan Knobel, Timothy Gomez, Elise Grizzell, Jayson Lynch, Andrew Rodriguez, Robert Schweller, Tim Wylie

Computer Science Faculty Publications and Presentations

We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different ordered pair of species according to a predefined set of allowed transition rules (chemical reactions). In particular, two questions that are fundamental to the simulation of sCRNs are whether a given configuration of molecules can ever transform into another given configuration, and whether a given cell can ever contain a given species, given a set of transition rules. We show that these problems can be solved in polynomial time, are NP-complete, …

Streaming Approximation Scheme For Minimizing Total Completion Time On Parallel Machines Subject To Varying Processing Capacity, Bin Fu, Yumei Huo, Hairong Zhao

Computer Science Faculty Publications and Presentations

We study the problem of minimizing total completion time on parallel machines subject to varying processing capacity. In this paper, we develop an approximation scheme for the problem under the data stream model where the input data is massive and cannot fit into memory and thus can only be scanned a few times. Our algorithm can compute an approximate value of the optimal total completion time in one pass and output the schedule with the approximate value in two passes.

Early Integrating Of Industry Certification Domains And Objectives Into A Modern A Cybersecurity Degree Curriculum, Mahmoud K. Quweider, Liyu Zhang, Hangsheng Lei

Informatics and Engineering Systems Faculty Publications and Presentations

We have recently created a new bachelor’s degree in cyber security (B.Sc. CS) [1] to address the national and pressing needs for cybersecurity specialists, cyber-crime analysts, incident and intrusions analysts, IT auditors, and many other cyber security related fields. The new degree addresses not only the technical objective of the degree, but also the legal, corporate, policy, procedure, and human ones as well. To achieve such a wide range of objectives within the cyber security degree, a student is required to obtain two national certifications before they graduate. These certifications are embedded in the curricula and are an integral part …

A Survey On Security Analysis Of Machine Learning-Oriented Hardware And Software Intellectual Property, Ashraful Tauhid, Lei Xu, Mostafizur Rahman, Emmett Tomai

Computer Science Faculty Publications and Presentations

Intellectual Property (IP) includes ideas, innovations, methodologies, works of authorship (viz., literary and artistic works), emblems, brands, images, etc. This property is intangible since it is pertinent to the human intellect. Therefore, IP entities are indisputably vulnerable to infringements and modifications without the owner’s consent. IP protection regulations have been deployed and are still in practice, including patents, copyrights, contracts, trademarks, trade secrets, etc., to address these challenges. Unfortunately, these protections are insufficient to keep IP entities from being changed or stolen without permission. As for this, some IPs require hardware IP protection mechanisms, and others require software …

Differences In Intracellular Protein Levels In Monocytes And Cd4+ Lymphocytes Between Bipolar Depressed Patients And Healthy Controls: A Pilot Study With Tyramine-Based Signal-Amplified Flow Cytometry, Keming Gao, Marzieh Ayati, Nicholas M. Kaye, Mehmet Koyutürk, Joseph R. Calabrese, Stephen J. Ganocy, Hillard M. Lazarus, Eric Christian, David Kaplan

Computer Science Faculty Publications and Presentations

Highlights

• To measure 18 intracellular proteins in blood cells of bipolar depressed patients and healthy controls;

• TFour proteins in monocytes and 2 proteins in CD4+ T Cells were significantly lower in patients than in healthy controls;

• The studied proteins are involved in prolactin, leptin, BDNF, and interleukin-3 signal pathways;

• Studying intracellular proteins with enhanced flow cytometry may find biomarkers differentiating bipolar disorder from healthy controls.

Abstract

Background

Molecular biomarkers for bipolar disorder (BD) that distinguish it from other manifestations of depressive symptoms remain unknown. The aim of this study was to determine if a very sensitive tyramine-based signal-amplification technology for …

Security Attacks And Countermeasures In Smart Homes, Hasibul Alam, Emmett Tomai

Computer Science Faculty Publications and Presentations

The Internet of Things (IoT) application is visible in all aspects of humans’ day-to-day affairs. The demand for IoT is growing at an unprecedented rate, from wearable wristwatches to autopilot cars. The smart home has also seen significant advancements to improve the quality of lifestyle. However, the security and privacy of IoT devices have become primary concerns as data is shared among intelligent devices and over the internet in a smart home network. There are several attacks - node capturing attack, sniffing attack, malware attack, boot phase attack, etc., which are conducted by adversaries to breach the security of smart …

Quadcopter Control Using Single Network Adaptive Critics, Alberto Velazquez, Lei Xu, Tohid Sardarmehni

Mechanical Engineering Faculty Publications and Presentations

In this paper, optimal tracking control is found for an inputaffine nonlinear quadcopter using Single Network Adaptive Critics (SNAC). The quadcopter dynamics consists of twelve states and four controls. The states are defined using two related reference frames: the earth frame, which describes the position and angles, and the body frame, which describes the linear and angular velocities. The quadcopter has six outputs and four controls, so it is an underactuated nonlinear system. The optimal control for the system is derived by solving a discrete-time recursive Hamilton-Jacobi-Bellman equation using a linear in-parameter neural network. The neural network is trained to …

Divergent Directionality Of Immune Cell-Specific Protein Expression Between Bipolar Lithium Responders And Non-Responders Revealed By Enhanced Flow Cytometry, Keming Gao, Nicholas M. Kaye, Marzieh Ayati, Mehmet Koyuturk, Joseph R. Calabrese, Eric Christian, Hillard M. Lazarus, David Kaplan

Computer Science Faculty Publications and Presentations

Background and Objectives: There is no biomarker to predict lithium response. This study used CellPrint™ enhanced flow cytometry to study 28 proteins representing a spectrum of cellular pathways in monocytes and CD4+ lymphocytes before and after lithium treatment in patients with bipolar disorder (BD). Materials and Methods: Symptomatic patients with BD type I or II received lithium (serum level ≥ 0.6 mEq/L) for 16 weeks. Patients were assessed with standard rating scales and divided into two groups, responders (≥50% improvement from baseline) and non-responders. Twenty-eight intracellular proteins in CD4+ lymphocytes and monocytes were analyzed with CellPrint™, an enhanced flow …

Exploring Spectral Bias In Time Series Long Sequence Forecasting, Kofi Nketia Ackaah-Gyasi, Sergio Valdez, Yifeng Gao, Li Zhang

Computer Science Faculty Publications and Presentations

Transformers have achieved great success in the task of time series long sequence forecasting (TLSF) in recent years. However, existing research has pointed out that over-parameterized deep learning models are in favor of low frequency and could be difficult to capture high-frequency information for regression fitting task, named spectral bias. Yet the effect of such bias on TLSF problem, an auto-regressive problem with a long forecasting length, has not been explored. In this work, we take the first step to investigate the spectral bias issues in TLSF task for state-of-the-art models. Specifically, we carefully examine three different existing time series …

Sublinear Approximation Schemes For Scheduling Precedence Graphs Of Bounded Depth, Bin Fu, Yumei Huo, Hairong Zhao

Computer Science Faculty Publications and Presentations

We study the classical scheduling problem on parallel machines %with precedence constraints where the precedence graph has the bounded depth h. Our goal is to minimize the maximum completion time. We focus on developing approximation algorithms that use only sublinear space or sublinear time. We develop the first one-pass streaming approximation schemes using sublinear space when all jobs' processing times differ no more than a constant factor c and the number of machines m is at most 2nϵ3hc. This is so far the best approximation we can have in terms of m, since no polynomial time approximation better than 43 …

Pmp: Privacy-Aware Matrix Profile Against Sensitive Pattern Inference, Li Zhang, Jiahao Ding, Yifeng Gao, Jessica Lin

Computer Science Faculty Publications and Presentations

Recent rapid development of sensor technology has allowed massive fine-grained time series (TS) data to be collected and set the foundation for the development of data-driven services and applications. During the process, data sharing is often involved to allow the third-party modelers to perform specific time series data mining (TSDM) tasks based on the need of data owner. The high resolution of TS brings new challenges in protecting privacy. While meaningful information in high-resolution TS shifts from concrete point values to local shape-based segments, numerous research have found that long shape-based patterns could contain more sensitive information and may potentially …

Covert Computation In The Abstract Tile-Assembly Model, Robert M. Alaniz, Timothy Gomez, Andrew Rodriguez, Tim Wylie, David Caballero, Elize Grizzell, Robert Schweller

Computer Science Faculty Publications and Presentations

There have been many advances in molecular computation that offer benefits such as targeted drug delivery, nanoscale mapping, and improved classification of nanoscale organisms. This power led to recent work exploring privacy in the computation, specifically, covert computation in self-assembling circuits. Here, we prove several important results related to the concept of a hidden computation in the most well-known model of self-assembly, the Abstract Tile-Assembly Model (aTAM). We show that in 2D, surprisingly, the model is capable of covert computation, but only with an exponentialsized assembly. We also show that the model is capable of covert computation with polynomial-sized assemblies …

Prediction Of Kinase-Substrate Associations Using The Functional Landscape Of Kinases And Phosphorylation Sites, Marzieh Ayati, Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Mark R. Chance, Mehmet Koyutürk

Computer Science Faculty Publications and Presentations

Protein phosphorylation is a key post-translational modification that plays a central role in many cellular processes. With recent advances in biotechnology, thousands of phosphorylated sites can be identified and quantified in a given sample, enabling proteome-wide screening of cellular signaling. However, for most (> 90%) of the phosphorylation sites that are identified in these experiments, the kinase(s) that target these sites are unknown. To broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations (KSAs), we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships …

Adaptive Resolution Loss: An Efficient And Effective Loss For Time Series Self-Supervised Learning Framework, Kevin Garcia, Juan Manuel Perez, Yifeng Gao

Computer Science Faculty Publications and Presentations

Time series data is a crucial form of information that has vast opportunities. With the widespread use of sensor networks, largescale time series data has become ubiquitous. One of the most prominent problems in time series data mining is representation learning. Recently, with the introduction of self-supervised learning frameworks (SSL), numerous amounts of research have focused on designing an effective SSL for time series data. One of the current state-of-the-art SSL frameworks in time series is called TS2Vec. TS2Vec specially designs a hierarchical contrastive learning framework that uses loss-based training, which performs outstandingly against benchmark testing. However, the computational cost …

Pmp: Privacy-Aware Matrix Profile Against Sensitive Pattern Inference For Time Series, Li Zhang, Jiahao Ding, Yifeng Gao, Jessica Lin

Computer Science Faculty Publications and Presentations

Recent rapid development of sensor technology has allowed massive time series data to be collected and set foundation for the development of data-driven services and applications. During the process, data sharing is often required to allow modelers to perform specific time series data mining tasks based on the need of data owner. The high resolution of time series data brings new challenges in privacy protection, as meaningful information in high-resolution data shifts from concrete point values to shape-based patterns. Numerous research efforts have found that long shape-based patterns could contain more sensitive information and may potentially be extracted and misused …

Adaptive Multiple Distributed Bidirectional Spiral Path Planning For Foraging Robot Swarms, Qi Lu, Ryan Luna

Computer Science Faculty Publications and Presentations

The Distributed Deterministic Spiral Algorithm (DDSA) has shown great foraging efficiency in robot swarms. However, when the number of robots in the swarm increases, scalability becomes a significant bottleneck due to increased collisions among robots, making it challenging to deploy them in the search space (e.g., 20 robots). To address this issue, we propose an adaptive Multiple-Distributed Bidirectional Spiral Algorithm (MDBSA) that enhances scalability. Our proposed algorithm partitions the squared search arena into multiple identical squared regions and assigns robots to regions dynamically based on the number of regions. In each region, a bidirectional spiral search path is planned, and …

Intellibeehive: An Automated Honey Bee, Pollen, And Varroa Destructor Monitoring System, Christian I. Narcia-Macias, Joselito Guardado, Jocell Rodriguez, Joanne Rampersad, Erik Enriquez, Dong-Chul Kim

Computer Science Faculty Publications and Presentations

Utilizing computer vision and the latest technological advancements, in this study, we developed a honey bee monitoring system that aims to enhance our understanding of Colony Collapse Disorder, honey bee behavior, population decline, and overall hive health. The system is positioned at the hive entrance providing real-time data, enabling beekeepers to closely monitor the hive's activity and health through an account-based website. Using machine learning, our monitoring system can accurately track honey bees, monitor pollen-gathering activity, and detect Varroa mites, all without causing any disruption to the honey bees. Moreover, we have ensured that the development of this monitoring system …

A Survey On Security Analysis Of Amazon Echo Devices, Surendra Pathak, Sheikh Ariful Islam, Honglu Jiang, Lei Xu, Emmett Tomai

Computer Science Faculty Publications and Presentations

Since its launch in 2014, Amazon Echo family of devices has seen a considerable increase in adaptation in consumer homes and offices. With a market worth millions of dollars, Echo is used for diverse tasks such as accessing online information, making phone calls, purchasing items, and controlling the smart home. Echo offers user-friendly voice interaction to automate everyday tasks making it a massive success. Though many people view Amazon Echo as a helpful assistant at home or office, few know its underlying security and privacy implications. In this paper, we present the findings of our research on Amazon Echo’s security …