Physical Sciences and Mathematics 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 …

Accuracy Of Nitrate Hysteresis And Flushing For Agricultural Watersheds In The Midwest, Noah Rudko, Sara K. W. Mcmillian, Jane Frankenberger, François Birgand

Graduate Industrial Research Symposium

Storm event-based metrics, such as hysteresis (HI) and flushing (FI), are used to differentiate nitrate pathways and sources, which is essential for watershed management. Estimations of these event-based metrics typically use high frequency (15-minute – hourly) measurements, but daily data are also used due to their greater availability. To date, there has been no study assessing how using lower frequency samples affect the accuracy of HI and FI, which could skew interpretation of potential nutrient pathways and sources. We used continuous measurements of nitrate collected at 9 watersheds throughout the Midwest spanning 448 storms. HI and FI were estimated from …

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 …

Design, Collaborate, Thrive: The Broad Ripple Avenue Project, Jessica Hawley, Emily Nelson, Ericka Miller

Purdue Road School

Broad Ripple Avenue (College Avenue to Winthrop Avenue) needed large-scale stormwater improvements. With the help of the Lochmueller Group and the Broad Ripple Village Association, Indianapolis DPW perceptively took this opportunity to also improve pedestrian facilities and regional multi-modal connectivity by combining multiple regional projects into one construction contract. This consolidation allowed for a cohesive public message through proactive public involvement. Presenters will share how consensus was built between invested parties through a successful public and private partnership.

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.

Processing Of Plastic Film From Potato Starch: Effect Of Drying Methods, Kourtney Collier, Samantha Goins, Austin Chirgwin, Isabelle Stanfield

The Journal of Purdue Undergraduate Research

Starch-based plastics are biodegradable, compostable compounds made of starch and plasticizers from natural sources. Their fabrication involves the starch-plasticizer reaction at 70–100°C followed by cooling and drying. Th e most common drying method is air drying (natural convection), which is effective but slow. Th e objective of this work is to study the effect of fast drying (forced convection) on the quality of the plastic film. Th is work compares the effects of drying conditions and drying rate on warpage, shrinkage rate, and presence of bubbles. Five drying methods are studied: (1) natural convection with uncovered petri dish, (2) natural …

Climate Justice In Engineering Education, Tyler J. Morgan, Donna Riley, Caroline M. Camfield

Discovery Undergraduate Interdisciplinary Research Internship

The goal of this research is to design a learning module for Purdue first-year engineering (FYE) students to learn climate fundamentals, and the role of engineers in responding to climate justice challenges. There is a lack of climate material within these classes currently, leading to a lack of climate conscious engineers in the future. The project entailed reviewing and synthesizing a wide variety of previous research on climate change education in engineering, including key learning objectives and their assessment. Because one of the key foci of the first-year engineering sequence relates to data analysis and management, we focused our work …

Streamlining Project Development Through Planning & Environmental Linkages, Karen Hadley, Brett Lackey

Purdue Road School

As transportation agencies continue to explore ways to be more efficient in the project development process, they are embracing integrated methodologies like planning and environmental linkages. This tool is practical, yet highly effective and inclusive, and teams across the country are experiencing its value. This presentation will highlight a variety of use cases, discuss lessons learned and best practices, and specifically address how planning and environmental linkages can be applied in Indiana and the Midwest.

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, …

Radiation Effects On Space Solar Cells At Various Earth And Jupiter Orbital Altitudes, Naazneen Rana

Discovery Undergraduate Interdisciplinary Research Internship

Solar cells are used as the primary power source for earth-orbiting satellites and as a primary/secondary power source for various missions within the solar system. However, high energy particles from the sun, planetary magnetospheres, and the galaxy can affect the performance and life expectancy of the space solar cell and associated power systems. As the interests for interplanetary travel and the exploration of planets within our solar system increase, the need to understand a device’s performance within a particular planet’s environment is necessary. Therefore, this study will analyze the performance of space solar cells, particularly the SolAero IMM-α, at various …

Rattle Detection – An Automotive Case Study, Orla Hartley

International Conference on Lean Six Sigma

This case study showcases the use of statistical tools to develop an objective Squeak and Rattle (S&R) measurement and detection test for End Of Line (EOL) sign off in an automotive manufacturing environment. Audio Induced S&R is an unwanted vibration within the vehicle caused by the sound system, impacting on customer perception of vehicle quality. Testing for S&R in an automotive environment has a key challenge; how to robustly detect a rattle at the EOL and thus prevent plant escapes to the customer. The objective test developed used microphones and analysers in order to replace an e subjective listening test. …

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 Survey On Subsurface Signal Propagation, Usman Raza, Abdul Salam

Faculty Publications

Wireless Underground Communication (WUC) is an emerging field that is being developed continuously. It provides secure mechanism of deploying nodes underground which shields them from any outside temperament or harsh weather conditions. This paper works towards introducing WUC and give a detail overview of WUC. It discusses system architecture of WUC along with the anatomy of the underground sensor motes deployed in WUC systems. It also compares Over-the-Air and Underground and highlights the major differences between the both type of channels. Since, UG communication is an evolving field, this paper also presents the evolution of the field along with the …

Global Air Quality Trekkers: Nandi Clean Kitchen Study, Samantha Dykhuis, Stephanie Schiavo, Avalin Senefeld

Purdue Journal of Service-Learning and International Engagement

Indoor air pollution is a widespread environmental health challenge sub-Saharan Africa and is the leading cause of premature death in many sub-Saharan African countries. This pollution is primarily caused by the burning of biomass fuels inside an enclosed kitchen in order to provide heat for cooking. Global Air Quality Trekkers is an undergraduate engineering team within the EPICS department at Purdue that began in fall 2016. Our objective is to create a kitchen design that utilizes natural ventilation to mitigate the amount of air pollutants present in these kitchens, specifically in the Nandi community of Western Kenya. This year, our …

Data Is Personal: We Should Treat It As Such, Kaleb Dunn

Student Papers in Public Policy

The rise of the internet as a fact of daily life is the defining element of the modern age. Widespread use of the internet has fundamentally altered entire industries, and much of American life has migrated online. Dating is augmented by online dating; shopping by online shopping; television by internet streaming.

The digitization of American life has brought with it considerable benefits, including great convenience and innumerable efficiencies, but it has not come without a cost. Although there are many business models used by internet companies, many of the now-largest companies in the world have converged on one entity upon …

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 …

High Wind Alerts: A System Created With Observations From The X-Band Teaching And Research Radar, Lauren Warner

The Journal of Purdue Undergraduate Research

Following the August 13, 2011, Indiana State Fair stage collapse tragedy, caused by a wind gust from an approaching thunderstorm, Purdue University enforced a wind speed restriction of 30 mph (13 m s-1) for tents at outdoor events. During these events, volunteers stand outside with handheld anemometers, measuring and reporting when the wind speeds exceed this limit. In this study, we report testing of a new system to automate high-wind alerts based on observations from a Doppler radar, the X-band Teaching and Research Radar (XTRRA), near Purdue’s campus. XTRRA scans over campus at low elevations approximately every 5 minutes. Using …

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 …

Decision Agriculture, Abdul Salam, Usman Raza

Faculty Publications

In this chapter, the latest developments in the field of decision agriculture are discussed. The practice of management zones in digital agriculture is described for efficient and smart faming. Accordingly, the methodology for delineating management zones is presented. Modeling of decision support systems is explained along with discussion of the issues and challenges in this area. Moreover, the precision agriculture technology is also considered. Moreover, the chapter surveys the state of the decision agriculture technologies in the countries such as Bulgaria, Denmark, France, Israel, Malaysia, Pakistan, United Kingdom, Ukraine, and Sweden. Finally, different field factors such as GPS accuracy and …

Electromagnetic Characteristics Of The Soil, Abdul Salam, Usman Raza

Faculty Publications

The electromagnetic characteristics of the soil are discussed in this chapter. The characteristics of porous bedrock, soil medium, and impacts of rain attenuations are also presented. The models of dielectric soil properties are studied with a rigorous focus on the constitutive parameters of subsurface soil medium. Moreover, the permittivity and wavenumber in soil are explained. In addition, the frequency-dependent dielectric properties such as dispersion in soil, absorption characteristic, and penetration depth versus frequency are reviewed. Furthermore, the effective permittivity of soil–water mixture for through-the soil-propagation mechanism is analyzed thoroughly.

Underground Phased Arrays And Beamforming Applications, Abdul Salam, Usman Raza

Faculty Publications

This chapter presents a framework for adaptive beamforming in underground communication. The wireless propagation is thoroughly analyzed to develop a model using the soil moisture as an input parameter to provide feedback mechanism while enhancing the system performance. The working of array element in the soil is analyzed. Moreover, the effect of soil texture and soil moisture on the resonant frequency and return loss is studied in detail. The wave refraction from the soil–air interface highly degrades the performance of the system. Furthermore, to beam steering is done to achieve high gain for lateral component improving the UG communication. The …

Signals In The Soil: An Introduction To Wireless Underground Communications, Abdul Salam, Usman Raza

Faculty Publications

In this chapter, wireless underground (UG) communications are introduced. A detailed overview of WUC is given. A comprehensive review of research challenges in WUC is presented. The evolution of underground wireless is also discussed. Moreover, different component of UG communications is wireless. The WUC system architecture is explained with a detailed discussion of the anatomy of an underground mote. The examples of UG wireless communication systems are explored. Furthermore, the differences of UG wireless and over-the-air wireless are debated. Different types of wireless underground channel (e.g., In-Soil, Soil-to-Air, and Air-to-Soil) are reported as well.