Research Experience for Undergraduates (REU) Research Projects
Research Experience for Undergraduates (REU) Research Projects
The proposed research projects are subject to change, contingent on new mentors and/or the research interests of the students.
Network analysis of 3D genome organization
Chromosomes are organized into a nonrandom hierarchical structure that consists of two mega-base long compartments called compartments A and B. Compartments A are stretches of transcriptionally active regions which are punctuated by transcriptionally inactive regions called compartments B. These compartments are further segmented into modular units called topologically associated domains (TADs), which exhibit much higher levels of interactions inside the domain compared to interdomain interactions. Genome organization allows the necessary interactions and loops between different regulatory regions to establish the proper gene network for genome function.
This proposed project will use a network analysis approach to understand the topology of the chromosomal contacts that exist in genome organization. Students will perform exploratory network analysis on chromosomal contact network data obtained from Hi-C experiments. The analysis will involve calculating and interpreting network metrics such as the degree of a node, average path length, strong components, clustering coefficients, importance of a node using centrality metrics, etc. Students will also apply different community detection algorithms to detect communities in the network. Subsequent analyses such as association and gene ontology analysis will be performed to interpret these detected communities.
Prerequisites:
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Basic programming skills (Python preferred)
Learning Outcomes:
Undergraduate researchers will:
- Learn and apply different network analysis algorithms.
- Learn how to use different network analysis software tools.
- Exposed to applications of graph theory in biology.
Mentor:
- Benjamin Soibam - Associate Professor, Department of Computer Science and Engineering Technology
Privacy-Preserving Sharing of Correlated Data
Local Differential Privacy (LDP) is a state-of-the-art framework for preserving individual privacy during data sharing with untrusted data collectors, making it a promising technology for privacy-preserving sharing of sensitive data types such as location or graph data. By perturbing data before sharing, LDP provides plausible deniability for individuals, ensuring that private details remain confidential. To date, only a limited set of tasks—such as frequency estimation, heavy hitters, frequent itemset mining, marginal release, and range queries—have been demonstrated using LDP.
This project aims to explore the applicability of existing LDP techniques to graph data, with a focus on enhancing privacy in graph sharing. Graph data, commonly used in domains like social networks, healthcare, and finance, represents entities as nodes (e.g., people, devices) and their interactions or relationships as edges. Sharing these graphs directly can expose sensitive information, so privacy-preserving techniques are critical. Controlled randomness can protect the privacy of individuals while maintaining essential patterns within the graph data. Through this project, students will gain insight into privacy-enhancing technologies and methods for secure data sharing. Additionally, they will acquire hands-on experience in programming by implementing state-of-the-art privacy-preserving techniques.
Prerequisites:
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- Basic programming skills (C++ or Java preferred), Discrete Mathematics, and Probability
Learning Outcomes:
Undergraduate researchers will:
- Be exposed to developing privacy-preserving data sharing techniques
- Learn how to design and conduct experiments and analyze the collected data
- Cross train in data analytics and cybersecurity
Mentors:
- Emre Yilmaz - Assistant Professor, Department of Computer Science and Engineering Technology
Control Loop Performance Monitoring
Control valves play a crucial role in the performance and stability of industrial control loops. However, issues such as valve wear, stiction, hysteresis, improper sizing, or malfunction can significantly degrade control loop performance, leading to inefficiencies, instability, and increased maintenance costs. In addition to traditional methods for diagnosing valve-related issues (that are often labor-intensive, relying on manual inspection and process knowledge), statistical based methods have been proposed over the years.
However, in recent years, machine learning (ML) techniques have emerged as a powerful tool for classification problems. This research aims to use machine learning methods to develop methods to identify issues with control loop performance that are due to valve stiction, hysteresis, and process nonlinearity. It will use large amounts of process data from a control loop (setpoint, process variable, controller output, valve position) to develop models capable of detecting the previously mentioned control valve issues. Case studies from manufacturing industries will be used to demonstrate the effectiveness of methods developed.
Prerequisites:
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- Basic programming skills (Python and MATLAB preferred)
Learning Outcomes:
Undergraduate researchers will:
- Develop research skills by working in an interdisciplinary environment with engineering and computer science professionals.
- Be exposed to process dynamics and control concepts
- Learn how to identify and quantify issues with control systems reliability and performance
- Cross train in computational sciences and engineering
Mentors:
- Vassilios Tzouanas – REU PI, Professor and Chair, Department of Computer Science and Engineering Technology
Understanding Student Behavior While Using Generative AI for Coding
Generative AI tools, such as ChatGPT, have become increasingly popular among students for educational purposes. A recent study reported that approximately 40% of college students have used ChatGPT as part of their higher education experience. Generative AI can be highly beneficial in learning difficult concepts. However, it also poses risks of misuse, such as completing assignments such as essays and writing computer programs. This is particularly concerning in Computer Science, where Generative AI can produce complex code in response to user prompts. This research aims to examine students' physiological responses as they engage with Generative AI for writing computer programs.
In the first phase, the research will focus on designing a study to collect data in a laboratory setting. Study participants will be asked to generate Python programs of varying complexity, both with and without the assistance of Generative AI. Throughout the study, physiological responses - such as eye-gaze movement, body motion, and facial expressions - will be recorded. In the next phase of the research, machine learning algorithms will then be developed to identify physiological patterns associated with the use of Generative AI tools.
Through this project, students will gain exposure to computer science research, including data analysis, algorithm development, model evaluation, and results presentation. Additionally, they will develop soft skills such as teamwork, problem-solving, and adaptability to different approaches.
Prerequisites:
- Basic programming skills (Python preferred)
- Having a background in machine learning is preferred.
Learning Outcomes:
Undergraduate researchers will:
- Be exposed to the human-centered computing research
- Learn how to design and conduct experiments and analyze the collected data
- Cross-train in computational sciences and experimental methods
- Enhance soft skills, such as working in a team, problem-solving skills, and adaptability to different problem-solving approaches.
Mentors:
- Dvijesh Shastri – Professor and Assistant Chair, Department of Computer Science and Engineering Technology
Forensic Engineering
A comprehensive plan for conducting a forensic inspection of property damage attributed to global warming. The primary objectives are to assess the extent of the damage, identify specific climate-related causes, and provide actionable recommendations for remediation and future resilience strategies. Our approach involves a thorough on-site assessment using advanced technologies, analysis of relevant climate data, and interviews with stakeholders to gather qualitative insights. Ultimately, it aims to deliver a detailed report with the application of numerical modeling, thermal assessment, and root cause analysis in this research to classify the types of damage resulting from material degradation, construction defects, global warming, and design deficiencies. The assessment aims to identify the types and extent of damage, underlying causes, and potential mitigation strategies.
This systematic approach allows for a thorough understanding of how these factors contribute to structural vulnerabilities and weak points. By employing advanced modeling techniques and thermal imaging, we can identify specific issues, such as insulation failures and material fatigue, exacerbated by climate change.
Prerequisites:
- Basic programming skills (Microsoft Office, high school physics), writing skills
Learning Outcomes:
Undergraduate researchers will:
- Develop research skills by challenging themselves to find the cause of damages or failures.
- Be exposed to damage measurement technology.
- Learn how to assess and write a technical report.
- Be multi-trained in mathematics, physics, and material science.
Mentors:
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Arash Rahmatian – Associate Professor, Department of Computer Science and Engineering Technology
Utilizing Interpolation Functions to solve Hyperbolic Systems
A shock tube is a device to understand shock waves and other examples of gas dynamics that are waves. These waves can be expressed mathematically by Euler’s equation, which is an example of a hyperbolic system. Hyperbolic systems are a challenge because there are nonlinearities in their boundary conditions and these systems can be solved by various means to include interpolation functions.
I’m working on a book, Fundamentals of Shock Waves, and this work supports the book and also an experimental apparatus I hope to design, build and use for experimentation. This work is also important to further the understanding of gas dynamics around Euler’s equation and the use of interpolation functions in solving differential equations.
Prerequisites:
- Basic programming skills (Python preferred)
Learning Outcomes:
Undergraduate researchers will:
- Provide a foundation in solving numerical differential equations
- Explore various interpolation functions and their applications
- Explore Shock Tubes and Euler’s Equation plus other hyperbolic systems
- Develop computer code to solve a Shock Tube problem
- Discuss Sod’s test cases and other test cases
- Develop a novel interpolation function scheme to solve a given shock tube problem
Mentors:
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Henry Foust – Assistant Professor, Department of Computer Science and Engineering Technology
Understanding Chemical spills of Hazardous Chemicals
Chemical spills are a common problem that industries face. Due to strategic location, Houston and its nearby cities are facing this challenge more than ever due to growing energy demands. Through this research, we want to explore different parameters of spreading of chemicals during spills by using computer simulations. We aim to explore hydrogen sulfide (H2S) chemical spill which is a major problem in Houston as well as cities which deals with petroleum.
The research will provide a deeper understanding of the chemical spills to the REU students as they will go through the learning of computer simulation. The research findings may help mitigation techniques and environmental parameters of dealing with chemical spills.
Prerequisites:
Prerequisites are engineering fluid mechanics, thermodynamics, and an introductory
computer science course
Learning Outcomes:
- What challenges safety professionals faced on dealing with chemical spills?
- What works have been conducted in terms of addressing these challenges?
- What were the financial burdens to address these challenges?
- What numerical techniques researchers used previously?
- What are the environmental parameters and list them to study their ranges?
- Giving alternative solutions to current existing solutions.
Mentors:
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Mahmud Hasan – Assistant Professor, Department of Computer Science and Engineering Technology