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 …

Sepsis Treatment: Reinforced Sequential Decision-Making For Saving Lives, Dipesh Tamboli, Jiayu Chen, Kiran Pranesh Jotheeswaran, Denny Yu, Vaneet Aggarwal

Graduate Industrial Research Symposium

Sepsis, a life-threatening condition triggered by the body's exaggerated response to infection, demands urgent intervention to prevent severe complications. Existing machine learning methods for managing sepsis struggle in offline scenarios, exhibiting suboptimal performance with survival rates below 50%. Our project introduces the "PosNegDM: Reinforcement Learning with Positive and Negative Demonstrations for Sequential Decision-Making" framework utilizing an innovative transformer-based model and a feedback reinforcer to replicate expert actions while considering individual patient characteristics. A mortality classifier with 96.7% accuracy guides treatment decisions towards positive outcomes. The PosNegDM framework significantly improves patient survival, saving 97.39% of patients and outperforming established machine learning …

Online Class-Incremental Learning For Real-World Food Image Classification, Siddeshwar Raghavan, Jiangpeng He, Fengqing Zhu

Graduate Industrial Research Symposium

Food image classification is essential for monitoring health and tracking dietary in image-based dietary assessment methods. However, conventional systems often rely on static datasets with fixed classes and uniform distribution. In contrast, real-world food consumption patterns, shaped by cultural, economic, and personal influences, involve dynamic and evolving data. Thus, it requires the classification system to cope with continuously evolving data. Online Class Incremental Learning (OCIL) addresses the challenge of learning continuously from a single-pass data stream while adapting to the new knowledge and reducing catastrophic forgetting. Experience Replay (ER) based OCIL methods store a small portion of previous data and …

Digitizing Delphi: Educating Audiences Through Virtual Reconstruction, Kate Koury

The Journal of Purdue Undergraduate Research

Implementing a 3D model into a virtual space allows the general public to engage critically with archaeological processes. There are many unseen decisions that go into reconstructing an ancient temple. Analysis of available materials and techniques, predictions of how objects were used, decisions of what sources to reference, puzzle piecing broken remains together, and even educated guesses used to fill gaps in information often go unobserved by the public. This work will educate users about those choices by allowing the side-by-side comparison of conflicting theories on the reconstruction of the Tholos at Delphi, which is an ideal site because of …

Promises And Risks Of Applying Ai Medical Imaging To Early Detection Of Cancers, And Regulation For Ai Medical Imaging, Yiyao Zhang

The Journal of Purdue Undergraduate Research

No abstract provided.

A Computational Profile Of Invasive Lionfish In Belize: A New Insight On A Destructive Species, Joshua E. Balan

The Journal of Purdue Undergraduate Research

Since their discovery in the region in 2009, invasive Indonesian-native lionfish have been taking over the Belize Barrier Reef. As a result, populations of local species have dwindled as they are either eaten or outcompeted by the invaders. This has led to devastating losses ecologically and economically; massive industries in the local nations, such as fisheries and tourism, have suffered greatly. Attempting to combat this, local organizations, from nonprofits to ecotourism companies, have been manually spear-hunting them on scuba dives to cull the population. One such company, Reef Conservation Institute (ReefCI), operating out of Tom Owens Caye outside of Placencia, …

Deep Learning Approaches For Chaotic Dynamics And High-Resolution Weather Simulations In The Us Midwest, Vlada Volyanskaya, Kabir Batra, Shubham Shrivastava

Discovery Undergraduate Interdisciplinary Research Internship

Weather prediction is indispensable across various sectors, from agriculture to disaster forecasting, deeply influencing daily life and work. Recent advancement of AI foundation models for weather and climate predictions makes it possible to perform a large number of predictions in reasonable time to support timesensitive policy- and decision-making. However, the uncertainty quantification, validation, and attribution of these models have not been well explored, and the lack of knowledge can eventually hinder the improvement of their prediction accuracy and precision. Our project is embarking on a two-fold approach leveraging deep learning techniques (LSTM and Transformer) architectures. Firstly, we model the Lorenz …

Les Expositions Turnus, Une Page D’Histoire Transnationale Des Beaux-Arts En Suisse À La Fin Du Xixe Siècle. Et Comment Découvrir Les Humanités Numériques, Béatrice Joyeux-Prunel

Artl@s Bulletin

Cet article présente le travail de la classe d’introduction aux humanités numériques de l’Université de Genève sur les expositions Turnus en Suisse à partir des années 1840. Près de 50 catalogues ont été retranscrits, décrits et structurés à l’aide de scripts Python, puis géolocalisés. Les données ont été ajoutées à BasArt, le répertoire mondial de catalogues d’expositions d’Artl@s (https://artlas.huma-num.fr/map). Elles permettent de mieux comprendre les premières années de ces expositions et leurs dynamiques locales, fédérales et internationales. Le Turnus fut une plaque tournante pour les artistes suisses, voire un tremplin vers le marché européen de l’art.

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 …

Geospatial Data Integration Middleware For Exploratory Analytics Addressing Regional Natural Resource Grand Challenges In The Us Mountain West, Shannon Albeke, Nicholas Case, Samantha Ewers, Jeffrey Hamerlinck, William Kirkpatrick, Jerod Merkle, Luke Todd

I-GUIDE Forum

This paper describes CyberGIS-based research and development aimed at improving geospatial data integration and visual analytics to better understand the impact of regional climate change on water availability in the U.S. Rocky Mountains. Two Web computing applications are presented. DEVISE - Derived Environmental Variability Indices Spatial Extractor, streamlines utilization of environmental data for better-informed wildlife decisions by biologists and game managers. The WY-Adapt platform aims to enhance predictive understanding of climate change impacts on water availability through two modules: “Current Conditions” and “Future Scenarios”. It integrates high-resolution models of the biophysical environment and human interactions, providing a robust framework for …

Graph Transformer Network For Flood Forecasting With Heterogeneous Covariates, Jimeng Shi, Vitalii Stebliankin, Zhaonan Wang, Shaowen Wang, Giri Narasimhan

I-GUIDE Forum

Floods can be very destructive causing heavy damage to life, property, and livelihoods. Global climate change and the consequent sea-level rise have increased the occurrence of extreme weather events, resulting in elevated and frequent flood risk. Therefore, accurate and timely flood forecasting in coastal river systems is critical to facilitate good flood management. However, the computational tools currently used are either slow or inaccurate. In this paper, we propose a Flood prediction tool using Graph Transformer Network (FloodGTN) for river systems. More specifically, FloodGTN learns the spatio-temporal dependencies of water levels at different monitoring stations using Graph Neural Networks (GNNs) …

Solving Geospatial Problems Under Extreme Time Constraints: A Call For Inclusive Geocomputational Education, Coline C. Dony

I-GUIDE Forum

To prepare our next generation to face geospatial problems that have extreme time constraints (e.g., disasters, climate change) we need to create educational pathways that help students develop their geocomputational thinking skills. First, educators are central in helping us create those pathways, therefore, we need to clearly convey to them why and in which contexts this thinking is necessary. For that purpose, a new definition for geocomputational thinking is suggested that makes it clear that this thinking is needed for geospatial problems that have extreme time constraints. Secondly, we can not further burden educators with more demands, rather we should …

Curriculum Design Of Artificial Intelligence And Sustainability In Secondary School, Jinyi Cai, Mei-Po Kwan, Chunyu Hou, Dong Liu, Yeung Yam

I-GUIDE Forum

Artificial Intelligence is revolutionizing numerous sectors with its transformative power, while at the same time, there is an increasing sense of urgency to address sustainability challenges. Despite the significance of both areas, secondary school curriculums still lack comprehensive integration of AI and sustainability education. This paper presents a curriculum designed to bridge this gap. The curriculum integrates progressive objectives, computational thinking competencies and system thinking components across five modules—awareness, knowledge, interaction, empowerment and ethics—to cater to varying learner levels. System thinking components help students understand sustainability in a holistic manner. Computational thinking competencies aim to cultivate computational thinkers to guide …

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 …

The Model 2.0 And Friends: An Interim Report, Garrison W. Cottrell, Martha Gahl, Shubham Kulkarni, Shashank Venkatramani, Yash Shah, Keyu Long, Xuzhe Zhi, Shivaank Agarwal, Cody Li, Jingyuan He, Thomas Fischer

MODVIS Workshop

Last year, I reported on preliminary results of an anatomically-inspired deep learning model of the visual system and its role in explaining the face inversion effect. This year, I will report on new results and some variations on network architectures that we have explored, mainly as a way to generate discussion and get feedback. This is by no means a polished, final presentation!

We look forward to the group’s suggestions for these projects.

Automated Delineation Of Visual Area Boundaries And Eccentricities By A Cnn Using Functional, Anatomical, And Diffusion-Weighted Mri Data, Noah C. Benson, Bogeng Song, Toshikazu Miyata, Hiromasa Takemura, Jonathan Winawer

MODVIS Workshop

Delineating visual field maps and iso-eccentricities from fMRI data is an important but time-consuming task for many neuroimaging studies on the human visual cortex because the traditional methods of doing so using retinotopic mapping experiments require substantial expertise as well as scanner, computer, and human time. Automated methods based on gray-matter anatomy or a combination of anatomy and functional mapping can reduce these requirements but are less accurate than experts. Convolutional Neural Networks (CNNs) are powerful tools for automated medical image segmentation. We hypothesize that CNNs can define visual area boundaries with high accuracy. We trained U-Net CNNs with ResNet18 …

How Object Segmentation And Perceptual Grouping Emerge In Noisy Variational Autoencoders, Ben Lonnqvist, Zhengqing Wu, Michael H. Herzog

MODVIS Workshop

Many animals and humans can recognize and segment objects from their backgrounds. Whether object segmentation is necessary for object recognition has long been a topic of debate. Deep neural networks (DNNs) excel at object recognition, but not at segmentation tasks - this has led to the belief that object recognition and segmentation are separate mechanisms in visual processing. Here, however, we show evidence that in variational autoencoders (VAEs), segmentation and faithful representation of data can be interlinked. VAEs are encoder-decoder models that learn to represent independent generative factors of the data as a distribution in a very small bottleneck layer; …

A Dynamical Model Of Binding In Visual Cortex During Incremental Grouping And Search, Daniel Schmid, Daniel A. Braun, Heiko Neumann

MODVIS Workshop

Binding of visual information is crucial for several perceptual tasks. To incrementally group an object, elements in a space-feature neighborhood need to be bound together starting from an attended location (Roelfsema, TICS, 2005). To perform visual search, candidate locations and cued features must be evaluated conjunctively to retrieve a target (Treisman&Gormican, Psychol Rev, 1988). Despite different requirements on binding, both tasks are solved by the same neural substrate. In a model of perceptual decision-making, we give a mechanistic explanation for how this can be achieved. The architecture consists of a visual cortex module and a higher-order thalamic module. While the …

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. …

On The Use Of Machine Learning For Causal Inference In Extreme Weather Events, Yuzhe Wang

Discovery Undergraduate Interdisciplinary Research Internship

Machine learning has become a helpful tool for analyzing data, and causal Inference is a powerful method in machine learning that can be used to determine the causal relationship in data. In atmospheric and climate science, this technology can also be applied to predicting extreme weather events. One of the causal inference models is Granger causality, which is used in this project. Granger causality is a statistical test for identifying whether one time series is helpful in forecasting the other time series. In granger causality, if a variable X granger-causes Y: it means that by using all information without …

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.

Optimizing Cybersecurity Budgets With Attacksimulation, Alexander Master, George Hamilton, J. Eric Dietz

Faculty Publications

Modern organizations need effective ways to assess cybersecurity risk. Successful cyber attacks can result in data breaches, which may inflict significant loss of money, time, and public trust. Small businesses and non-profit organizations have limited resources to invest in cybersecurity controls and often do not have the in-house expertise to assess their risk. Cyber threat actors also vary in sophistication, motivation, and effectiveness. This paper builds on the previous work of Lerums et al., who presented an AnyLogic model for simulating aspects of a cyber attack and the efficacy of controls in a generic enterprise network. This paper argues that …

Understanding The Influence Of Perceptual Noise On Visual Flanker Effects Through Bayesian Model Fitting, Jordan Deakin, Dietmar Heinke

MODVIS Workshop

No abstract provided.

Hhl Algorithm On The Honeywell H1 Quantum Computer, Adrik B. Herbert, Eric A. F. Reinhardt

Discovery Undergraduate Interdisciplinary Research Internship

The quantum algorithm for linear systems of equations (HHL algorithm) provides an efficient tool for finding solutions to systems of functions with a large number of variables and low sensitivity to changes in inputs (i.e. low error rates). For complex problems, such as matrix inversion, HHL requires exponentially less computational time as compared with classical computation methods. HHL can be adapted to current quantum computing systems with limited numbers of qubits (quantum computation bits) but a high reusability rate such as the Honeywell H1 quantum computer. Some methods for improving HHL have been proposed through the combination of quantum and …

Password Managers: Secure Passwords The Easy Way, Alexander Master

CERIAS Technical Reports

Poor passwords are often the central problem identified when data breaches, ransomware attacks, and identity fraud cases occur. This Purdue Extension publication provides everyday users of Internet websites and computer systems with tools and strategies to protect their online accounts. Securing information access with password managers can be convenient and often free of cost, on a variety of devices and platforms. “Do’s and Don’ts” of password practices are highlighted, as well as the benefits of multi-factor authentication. The content is especially applicable for small businesses or non-profits, where employees often share access to systems or accounts.

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 …