Engineering Commons^™

A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes

Graduate Industrial Research Symposium

The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute it into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects, but does not necessarily indicate the initial point of interference within the network. The objective of this project is to take advantage of large scale and genome-wide perturbational datasets by using them to train a tuned machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of …

Closing The Gap: Leveraging Aes-Ni To Balance Adversarial Advantage And Honest User Performance In Argon2i, Nicholas Harrell, Nathaniel Krakauer

CERIAS Technical Reports

The challenge of providing data privacy and integrity while maintaining efficient performance for honest users is a persistent concern in cryptography. Attackers exploit advances in parallel hardware and custom circuit hardware to gain an advantage over regular users. One such method is the use of Application-Specific Integrated Circuits (ASICs) to optimize key derivation function (KDF) algorithms, giving adversaries a significant advantage in password guessing and recovery attacks. Other examples include using graphical processing units (GPUs) and field programmable gate arrays (FPGAs). We propose a focused approach to close the gap between adversarial advantage and honest user performance by leveraging the …

Reducing Uncertainty In Sea-Level Rise Prediction: A Spatial-Variability-Aware Approach, Subhankar Ghosh, Shuai An, Arun Sharma, Jayant Gupta, Shashi Shekhar, Aneesh Subramanian

I-GUIDE Forum

Given multi-model ensemble climate projections, the goal is to accurately and reliably predict future sea-level rise while lowering the uncertainty. This problem is important because sea-level rise affects millions of people in coastal communities and beyond due to climate change's impacts on polar ice sheets and the ocean. This problem is challenging due to spatial variability and unknowns such as possible tipping points (e.g., collapse of Greenland or West Antarctic ice-shelf), climate feedback loops (e.g., clouds, permafrost thawing), future policy decisions, and human actions. Most existing climate modeling approaches use the same set of weights globally, during either regression or …

Improving Developers' Understanding Of Regex Denial Of Service Tools Through Anti-Patterns And Fix Strategies, Sk Adnan Hassan, Zainab Aamir, Dongyoon Lee, James C. Davis, Francisco Servant

Department of Electrical and Computer Engineering Faculty Publications

Regular expressions are used for diverse purposes, including input validation and firewalls. Unfortunately, they can also lead to a security vulnerability called ReDoS (Regular Expression Denial of Service), caused by a super-linear worst-case execution time during regex matching. Due to the severity and prevalence of ReDoS, past work proposed automatic tools to detect and fix regexes. Although these tools were evaluated in automatic experiments, their usability has not yet been studied; usability has not been a focus of prior work. Our insight is that the usability of existing tools to detect and fix regexes will improve if we complement them …

An Empirical Study Of Pre-Trained Model Reuse In The Hugging Face Deep Learning Model Registry, Wenxin Jiang, Nicholas Synovic, Matt Hyatt, Taylor R. Schorlemmer, Rohan Sethi, Yung-Hsiang Lu, George K. Thiruvathukal, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems.

In this work, we present the first empirical investigation of PTM reuse. …

Redefining Research In Nanotechnology Simulations: A New Approach To Data Caching And Analysis, Darin Tsai, Alan Zhang, Aloysius Rebeiro

The Journal of Purdue Undergraduate Research

No abstract provided.

Sok: Analysis Of Software Supply Chain Security By Establishing Secure Design Properties, Chinenye Okafor, Taylor R. Schorlemmer, Santiao Torres-Arias, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

This paper systematizes knowledge about secure software supply chain patterns. It identifies four stages of a software supply chain attack and proposes three security properties crucial for a secured supply chain: transparency, validity, and separation. The paper describes current security approaches and maps them to the proposed security properties, including research ideas and case studies of supply chains in practice. It discusses the strengths and weaknesses of current approaches relative to known attacks and details the various security frameworks put out to ensure the security of the software supply chain. Finally, the paper highlights potential gaps in actor and operation-centered …

Reflecting On Recurring Failures In Iot Development, Dharun Anandayuvaraj, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

As IoT systems are given more responsibility and autonomy, they offer greater benefits, but also carry greater risks. We believe this trend invigorates an old challenge of software engineering: how to develop high-risk software-intensive systems safely and securely under market pressures? As a first step, we conducted a systematic analysis of recent IoT failures to identify engineering challenges. We collected and analyzed 22 news reports and studied the sources, impacts, and repair strategies of failures in IoT systems. We observed failure trends both within and across application domains. We also observed that failure themes have persisted over time. To alleviate …

Exploiting Input Sanitization For Regex Denial Of Service, Efe Barlas, Xin Du, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Web services use server-side input sanitization to guard against harmful input. Some web services publish their sanitization logic to make their client interface more usable, e.g., allowing clients to debug invalid requests locally. However, this usability practice poses a security risk. Specifically, services may share the regexes they use to sanitize input strings — and regex-based denial of service (ReDoS) is an emerging threat. Although prominent service outages caused by ReDoS have spurred interest in this topic, we know little about the degree to which live web services are vulnerable to ReDoS.

In this paper, we conduct the first black-box …

Discrepancies Among Pre-Trained Deep Neural Networks: A New Threat To Model Zoo Reliability, Diego Montes, Pongpatapee Peerapatanapokin, Jeff Schultz, Chengjun Guo, Wenxin Jiang, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Training deep neural networks (DNNs) takes significant time and resources. A practice for expedited deployment is to use pre-trained deep neural networks (PTNNs), often from model zoos.collections of PTNNs; yet, the reliability of model zoos remains unexamined. In the absence of an industry standard for the implementation and performance of PTNNs, engineers cannot confidently incorporate them into production systems. As a first step, discovering potential discrepancies between PTNNs across model zoos would reveal a threat to model zoo reliability. Prior works indicated existing variances in deep learning systems in terms of accuracy. However, broader measures of reliability for PTNNs from …

An Empirical Study On The Impact Of Deep Parameters On Mobile App Energy Usage, Qiang Xu, James C. Davis, Y Charlie Hu, Abhilash Jindal

Department of Electrical and Computer Engineering Faculty Publications

Improving software performance through configuration parameter tuning is a common activity during software maintenance. Beyond traditional performance metrics like latency, mobile app developers are interested in reducing app energy usage. Some mobile apps have centralized locations for parameter tuning, similar to databases and operating systems, but it is common for mobile apps to have hundreds of parameters scattered around the source code. The correlation between these "deep" parameters and app energy usage is unclear. Researchers have studied the energy effects of deep parameters in specific modules, but we lack a systematic understanding of the energy impact of mobile deep parameters. …

Reflections On Software Failure Analysis, Paschal C. Amusuo, Aishwarya Sharma, Siddharth R. Rao, Abbey Vincent, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Failure studies are important in revealing the root causes, behaviors, and life cycle of defects in software systems. These studies either focus on understanding the characteristics of defects in specific classes of systems or the characteristics of a specific type of defect in the systems it manifests in. Failure studies have influenced various software engineering research directions, especially in the area of software evolution, defect detection, and program repair.

In this paper, we reflect on the conduct of failure studies in software engineering. We reviewed a sample of 52 failure study papers. We identified several recurring problems in these studies, …

Characterizing Students’ Engineering Design Strategies Using Energy3d, Jasmine Singh, Viranga Perera, Alejandra Magana, Brittany Newell

Discovery Undergraduate Interdisciplinary Research Internship

The goals of this study are to characterize design actions that students performed when solving a design challenge, and to create a machine learning model to help future students make better engineering design choices. We analyze data from an introductory engineering course where students used Energy3D, an open source computer-aided design software, to design a zero-energy home (i.e. a home that consumes no net energy over a period of a year). Student design actions within the software were recorded into text files. Using a sample of over 300 students, we first identify patterns in the data to assess how students …

A Statistical Impulse Response Model Based On Empirical Characterization Of Wireless Underground Channel, Abdul Salam, Mehmet C. Vuran, Suat Irmak

Faculty Publications

Wireless underground sensor networks (WUSNs) are becoming ubiquitous in many areas. The design of robust systems requires extensive understanding of the underground (UG) channel characteristics. In this paper, an UG channel impulse response is modeled and validated via extensive experiments in indoor and field testbed settings. The three distinct types of soils are selected with sand and clay contents ranging from $13\%$ to $86\%$ and $3\%$ to $32\%$, respectively. The impacts of changes in soil texture and soil moisture are investigated with more than $1,200$ measurements in a novel UG testbed that allows flexibility in soil moisture control. Moreover, the …

Comparison Of Machine Learning Models: Gesture Recognition Using A Multimodal Wrist Orthosis For Tetraplegics, Charlie Martin

The Journal of Purdue Undergraduate Research

Many tetraplegics must wear wrist braces to support paralyzed wrists and hands. However, current wrist orthoses have limited functionality to assist a person’s ability to perform typical activities of daily living other than a small pocket to hold utensils. To enhance the functionality of wrist orthoses, gesture recognition technology can be applied to control mechatronic tools attached to a novel fabricated wrist brace. Gesture recognition is a growing technology for providing touchless human-computer interaction that can be particularly useful for tetraplegics with limited upper-extremity mobility. In this study, three gesture recognition models were compared—two dynamic time-warping models and a hidden …

All You Need To Know About Cybersecurity Ever! In 45 Minutes, Joe Beckman

Purdue Road School

This session will cover the information every local government official needs to know to keep their data safe from hackers.

Wireless Underground Communications In Sewer And Stormwater Overflow Monitoring: Radio Waves Through Soil And Asphalt Medium, Usman Raza, Abdul Salam

Faculty Publications

Storm drains and sanitary sewers are prone to backups and overflows due to extra amount wastewater entering the pipes. To prevent that, it is imperative to efficiently monitor the urban underground infrastructure. The combination of sensors system and wireless underground communication system can be used to realize urban underground IoT applications, e.g., storm water and wastewater overflow monitoring systems. The aim of this article is to establish a feasibility of the use of wireless underground communications techniques, and wave propagation through the subsurface soil and asphalt layers, in an underground pavement system for storm water and sewer overflow monitoring application. …

Urban Underground Infrastructure Monitoring Iot: The Path Loss Analysis, Abdul Salam, Syed Shah

Faculty Publications

The extra quantities of wastewater entering the pipes can cause backups that result in sanitary sewer overflows. Urban underground infrastructure monitoring is important for controlling the flow of extraneous water into the pipelines. By combining the wireless underground communications and sensor solutions, the urban underground IoT applications such as real time wastewater and storm water overflow monitoring can be developed. In this paper, the path loss analysis of wireless underground communications in urban underground IoT for wastewater monitoring has been presented. It has been shown that the communication range of up to 4 kilometers can be achieved from an underground …

An Underground Radio Wave Propagation Prediction Model For Digital Agriculture, Abdul Salam

Faculty Publications

Underground sensing and propagation of Signals in the Soil (SitS) medium is an electromagnetic issue. The path loss prediction with higher accuracy is an open research subject in digital agriculture monitoring applications for sensing and communications. The statistical data are predominantly derived from site-specific empirical measurements, which is considered an impediment to universal application. Nevertheless, in the existing literature, statistical approaches have been applied to the SitS channel modeling, where impulse response analysis and the Friis open space transmission formula are employed as the channel modeling tool in different soil types under varying soil moisture conditions at diverse communication distances …

Underground Environment Aware Mimo Design Using Transmit And Receive Beamforming In Internet Of Underground Things, Abdul Salam

Faculty Publications

In underground (UG) multiple-input and multiple-output (MIMO), the transmit beamforming is used to focus energy in the desired direction. There are three different paths in the underground soil medium through which the waves propagates to reach at the receiver. When the UG receiver receives a desired data stream only from the desired path, then the UG MIMO channel becomes three path (lateral, direct, and reflected) interference channel. Accordingly, the capacity region of the UG MIMO three path interference channel and degrees of freedom (multiplexing gain of this MIMO channel requires careful modeling). Therefore, expressions are required derived the degrees of …

A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak

Faculty Publications

The realization of Internet of Underground Things (IOUT) relies on the establishment of reliable communication links, where the antenna becomes a major design component due to the significant impacts of soil. In this paper, a theoretical model is developed to capture the impacts of change of soil moisture on the return loss, resonant frequency, and bandwidth of a buried dipole antenna. Experiments are conducted in silty clay loam, sandy, and silt loam soil, to characterize the effects of soil, in an indoor testbed and field testbeds. It is shown that at subsurface burial depths (0.1-0.4m), change in soil moisture impacts …

Investigating Dataset Distinctiveness, Andrew Ulmer, Kent W. Gauen, Yung-Hsiang Lu, Zohar R. Kapach, Daniel P. Merrick

The Summer Undergraduate Research Fellowship (SURF) Symposium

Just as a human might struggle to interpret another human’s handwriting, a computer vision program might fail when asked to perform one task in two different domains. To be more specific, visualize a self-driving car as a human driver who had only ever driven on clear, sunny days, during daylight hours. This driver – the self-driving car – would inevitably face a significant challenge when asked to drive when it is violently raining or foggy during the night, putting the safety of its passengers in danger. An extensive understanding of the data we use to teach computer vision models – …

Predict The Failure Of Hydraulic Pumps By Different Machine Learning Algorithms, Yifei Zhou, Monika Ivantysynova, Nathan Keller

The Summer Undergraduate Research Fellowship (SURF) Symposium

Pump failure is a general concerned problem in the hydraulic field. Once happening, it will cause a huge property loss and even the life loss. The common methods to prevent the occurrence of pump failure is by preventative maintenance and breakdown maintenance, however, both of them have significant drawbacks. This research focuses on the axial piston pump and provides a new solution by the prognostic of pump failure using the classification of machine learning. Different kinds of sensors (temperature, acceleration and etc.) were installed into a good condition pump and three different kinds of damaged pumps to measure 10 of …

Deep Neural Network Architectures For Modulation Classification Using Principal Component Analysis, Sharan Ramjee, Shengtai Ju, Diyu Yang, Aly El Gamal

The Summer Undergraduate Research Fellowship (SURF) Symposium

In this work, we investigate the application of Principal Component Analysis to the task of wireless signal modulation recognition using deep neural network architectures. Sampling signals at the Nyquist rate, which is often very high, requires a large amount of energy and space to collect and store the samples. Moreover, the time taken to train neural networks for the task of modulation classification is large due to the large number of samples. These problems can be drastically reduced using Principal Component Analysis, which is a technique that allows us to reduce the dimensionality or number of features of the samples …

Sort Vs. Hash Join On Knights Landing Architecture, Victor L. Pan, Felix Lin

The Summer Undergraduate Research Fellowship (SURF) Symposium

With the increasing amount of information stored, there is a need for efficient database algorithms. One of the most important database operations is “join”. This involves combining columns from two tables and grouping common values in the same row in order to minimize redundant data. The two main algorithms used are hash join and sort merge join. Hash join builds a hash table to allow for faster searching. Sort merge join first sorts the two tables to make it more efficient when comparing values. There has been a lot of debate over which approach is superior. At first, hash join …

Tool For Correlating Ebsd And Afm Data Arrays, Andrew Krawec, Matthew Michie, John Blendell

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ceramic and semiconductor research is limited in its ability to create holistic representations of data in concise, easily-accessible file formats or visual data representations. These materials are used in everyday electronics, and optimizing their electrical and physical properties is important for developing more advanced computational technologies. There is a desire to understand how changing the composition of the ceramic alters the shape and structure of the grown crystals. However, few accessible tools exist to generate a dataset with the proper organization to understand correlations between grain orientation and crystallographic orientation. This paper outlines an approach to analyzing the crystal structure …

Improving The Accuracy For The Long-Term Hydrologic Impact Assessment (L-Thia) Model, Anqi Zhang, Lawrence Theller, Bernard A. Engel

The Summer Undergraduate Research Fellowship (SURF) Symposium

Urbanization increases runoff by changing land use types from less impervious to impervious covers. Improving the accuracy of a runoff assessment model, the Long-Term Hydrologic Impact Assessment (L-THIA) Model, can help us to better evaluate the potential uses of Low Impact Development (LID) practices aimed at reducing runoff, as well as to identify appropriate runoff and water quality mitigation methods. Several versions of the model have been built over time, and inconsistencies have been introduced between the models. To improve the accuracy and consistency of the model, the equations and parameters (primarily curve numbers in the case of this model) …

Web-Based Interactive Social Media Visual Analytics, Diego Rodríguez-Baquero, Jiawei Zhang, David S. Ebert, Sorin A. Matei

The Summer Undergraduate Research Fellowship (SURF) Symposium

Real-time social media platforms enable quick information broadcasting and response during disasters and emergencies. Analyzing the massive amount of generated data to understand the human behavior requires data collection and acquisition, parsing, filtering, augmentation, processing, and representation. Visual analytics approaches allow decision makers to observe trends and abnormalities, correlate them with other variables and gain invaluable insight into these situations. In this paper, we propose a set of visual analytic tools for analyzing and understanding real-time social media data in times of crisis and emergency situations. First, we model the degree of risk of individuals’ movement based on evacuation zones …

Purdue Airsense: An Affordable Way To Measure And Study Air Pollution, Stephane Junior Nouafo Wanko, Shadi Tariq Azouz, Ruihang Du, Brandon Boor, Greg Michalski

The Summer Undergraduate Research Fellowship (SURF) Symposium

Air pollution is a major health hazard worldwide, accounting for one-eighth of all deaths in 2012 (World Health Organization). Globally, there is a severe lack of ground-based spatiotemporal monitoring of gaseous and particulate air pollutants, particularly in Africa, South and Central America, and the Middle East. This is in great part due to the high costs of air quality instrumentation that meet accuracy and reliability criteria set by monitoring agencies. The air quality data that is available is often not presented to the public in a user-friendly manner. Taking advantage of recent developments in low-cost sensing technologies, an integrated sensor …

Optimization And Control Of Production Of Graphene, Atharva Hans, Nimish M. Awalgaonkar, Majed Alrefae, Ilias Bilionis, Timothy S. Fisher

The Summer Undergraduate Research Fellowship (SURF) Symposium

Graphene is a 2-dimensional element of high practical importance. Despite its exceptional properties, graphene’s real applications in industrial or commercial products have been limited. There are many methods to produce graphene, but none has been successful in commercializing its production. Roll-to-roll plasma chemical vapor deposition (CVD) is used to manufacture graphene at large scale. In this research, we present a Bayesian linear regression model to predict the roll-to-roll plasma system’s electrode voltage and current; given a particular set of inputs. The inputs of the plasma system are power, pressure and concentration of gases; hydrogen, methane, oxygen, nitrogen and argon. This …