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The Methodological Problems Of Incorporating Indigenous Philosophy In Collaborative Research, Luthonliu Gangmei, P. Milan Khangamcha Jan 2025

The Methodological Problems Of Incorporating Indigenous Philosophy In Collaborative Research, Luthonliu Gangmei, P. Milan Khangamcha

Comparative Philosophy

This paper addresses the methodological challenges inherent in collaborative research endeavours focused on the development of Indigenous philosophy. It argues that these challenges persist due to a lack of recognition of the autonomy and intrinsic philosophical value of ethno-philosophy or Indigenous philosophy. Despite the United Nations acknowledging the significance of indigenous worldviews and their philosophical underpinnings, they are still yet to be fully integrated into the global knowledge domain. The paper highlights the tendency to view indigenous philosophy solely as a cultural asset of indigenous peoples rather than recognizing its broader philosophical relevance. It identifies this as a critical interdisciplinary …

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Spartan Daily, January 23, 2025, San Jose State University, School Of Journalism And Mass Communications Jan 2025

Spartan Daily, January 23, 2025, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2025

Volume 164, Issue 1

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Differential Encoding Of Mammalian Proprioception By Voltage-Gated Sodium Channels, Cyrrus M. Espino, Chetan Nagaraja, Serena Ortiz, Jacquelyn R. Dayton, Akash R. Murali, Yanki Ma, Emari L. Mann, Snigdha Garlapalli, Ross P. Wohlgemuth, Sarah E. Brashear, Lucas R. Smith, Katherine A. Wilkinson, Theanne N. Griffith Jan 2025

Differential Encoding Of Mammalian Proprioception By Voltage-Gated Sodium Channels, Cyrrus M. Espino, Chetan Nagaraja, Serena Ortiz, Jacquelyn R. Dayton, Akash R. Murali, Yanki Ma, Emari L. Mann, Snigdha Garlapalli, Ross P. Wohlgemuth, Sarah E. Brashear, Lucas R. Smith, Katherine A. Wilkinson, Theanne N. Griffith

Faculty Research, Scholarly, and Creative Activity

Animals requiring purposeful movement for survival are endowed with mechanoreceptors, called proprioceptors, that provide essential sensory feedback from muscles and joints to spinal cord circuits, which modulates motor output. Despite the essential nature of proprioceptive signaling in daily life, the mechanisms governing proprioceptor activity are poorly understood. Here, we identified nonredundant roles for two voltage-gated sodium channels (NaVs), NaV1.1 and NaV1.6, in mammalian proprioception. Deletion of NaV1.6 in somatosensory neurons (NaV1.6cKO mice) causes severe motor deficits accompanied by loss of proprioceptive transmission, which contrasts with our previous findings using similar mouse models to target NaV1.1 (NaV1.1cKO). In NaV1.6cKO animals, we …

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The Influence Of Maternal Size/Age Effects On The Physiological Responses Of Adult Female Gopher Rockfish (Sebastes Carnatus) To Ocean Acidification And Hypoxia, Dylan H. Sarish Jan 2025

The Influence Of Maternal Size/Age Effects On The Physiological Responses Of Adult Female Gopher Rockfish (Sebastes Carnatus) To Ocean Acidification And Hypoxia, Dylan H. Sarish

Master's Theses

Climate change is rapidly reshaping the chemistry of the ocean. Fishes living in California coastal waters are experiencing increased ocean acidification and hypoxia (OAH) due to more frequent and intense upwelling. Nearshore rockfish may be particularly threatened by these conditions due to their long generational times. However, it is unknown how OAH may impact maternal physiology and reproduction in these viviparous fish. To understand the physiological effects of OAH during gestation, adult female gopher rockfish, Sebastes carnatus, were exposed to a variety of combined OAH stress treatments during different gestational stages. Routine metabolic rate (RMR), maximum metabolic rate (MMR), blood …

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Social Engineering Scenario Generation For Awareness-Based Attack Resilience, Jade Webb Jan 2025

Social Engineering Scenario Generation For Awareness-Based Attack Resilience, Jade Webb

Master's Projects

Social engineering is found in a strong majority of cyberattacks today, as it is a powerful manipulation tactic that does not require the technical skills of hacking. Calculated social engineers utilize simple communication to deceive and exploit their victims, all by capitalizing on the vulnerabilities of human nature: trust and fear. When successful, this inconspicuous technique can lead to millions of dollars in losses. Social engineering is not a one-dimensional technique; criminals often leverage a combination of strategies to craft a robust yet subtle attack. In addition, offenders are continually evolving their methods in efforts to surpass preventive measures. A …

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Cca Analysis Using Computer Vision Techniques, Rahul Thakur Jan 2025

Cca Analysis Using Computer Vision Techniques, Rahul Thakur

Master's Projects

Coral reefs are an essential part of the marine ecosystem. They perform a wide variety of tasks, some directly and others indirectly. They can produce oxygen, absorb carbon dioxide, along with supporting ocean habitat. Crustose Coralline Algae (“CCA”) plays an important role in helping provide structural support to Coral Reef ecosystems. However, global warming is causing ocean water to become more acidic resulting in coral bleaching. This is leading to changes in coral environments and causing coral deaths at alarming rates. Object detection using computer vision techniques, specifically deep learning, can help to monitor coral reef health and identify CCA …

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Retrieval-Augmented Generation For Survival Analysis In Cancers: Methods And Evaluation On The Surveillance, Epidemiology, And End Results Database, Jyothi Vaidyanathan Jan 2025

Retrieval-Augmented Generation For Survival Analysis In Cancers: Methods And Evaluation On The Surveillance, Epidemiology, And End Results Database, Jyothi Vaidyanathan

Master's Projects

Healthcare is one of the most important fields that benefits from advancements in Artificial Intelligence (AI). From classic models like linear regression to cuttingedge transformers, AI is applied across various healthcare subdomains, such as drug discovery, predictive analytics, and personalized medicine, to name a few. These techniques enable medical practitioners to make more informed decisions, significantly improving both the speed and accuracy of diagnoses and treatments. Machine learning has played a transformative role in oncology, especially in areas like early detection, diagnosis, treatment planning, and patient monitoring, by analyzing medical images, clinical information, genomic data, sensor information. Our research aims …

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Conservation Benefits Of A Large Marine Protected Area Network That Spans Multiple Ecosystems, Joshua G. Smith, Cori Lopazanski, Christopher M. Free, Julien Brun, Clarissa Anderson, Mark H. Carr, Joachim Claudet, Jenifer E. Dugan, Jacob G. Eurich, Tessa B. Francis, David A. Gill, Scott L. Hamilton, Kristin Kaschner, David Mouillot, Peter T. Raimondi, Richard M. Starr, Shelby L. Ziegler, Daniel Malone, For Full Author List, See Comments Below Jan 2025

Conservation Benefits Of A Large Marine Protected Area Network That Spans Multiple Ecosystems, Joshua G. Smith, Cori Lopazanski, Christopher M. Free, Julien Brun, Clarissa Anderson, Mark H. Carr, Joachim Claudet, Jenifer E. Dugan, Jacob G. Eurich, Tessa B. Francis, David A. Gill, Scott L. Hamilton, Kristin Kaschner, David Mouillot, Peter T. Raimondi, Richard M. Starr, Shelby L. Ziegler, Daniel Malone, For Full Author List, See Comments Below

Faculty Research, Scholarly, and Creative Activity

Marine protected areas (MPAs) are widely implemented tools for long-term ocean conservation and resource management. Assessments of MPA performance have largely focused on specific ecosystems individually and have rarely evaluated performance across multiple ecosystems either in an individual MPA or across an MPA network. We evaluated the conservation performance of 59 MPAs in California's large MPA network, which encompasses 4 primary ecosystems (surf zone, kelp forest, shallow reef, deep reef) and 4 bioregions, and identified MPA attributes that best explain performance. Using a meta-analytic framework, we evaluated the ability of MPAs to conserve fish biomass, richness, and diversity. At the …

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Examining Equity And Graduation Rates At Two Institutions Using A Course Deficit Model And The Collaborative Learning Through Active Sense-Making In Physics Curriculum, Cassandra A. Paul, David J. Webb Jan 2025

Examining Equity And Graduation Rates At Two Institutions Using A Course Deficit Model And The Collaborative Learning Through Active Sense-Making In Physics Curriculum, Cassandra A. Paul, David J. Webb

Faculty Research, Scholarly, and Creative Activity

We have previously described the reformed introductory physics course, collaborative learning through active sense-making in physics (CLASP), for bioscience students at a large public research one university (Original University) and presented evidence that the course was more successful and more equitable than the course it replaced by several measures. Now we compare the original success of CLASP with an implementation at a second institution. We find that the original results hold at another institution despite some changes to the original curriculum and a somewhat different student population. We find that students who take CLASP are (1) less likely to drop, …

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Advancing The Environmental Dna And Rna Toolkit For Aquatic Ecosystem Monitoring And Management, Xavier Pochon, Holly A. Bowers, Anastasija Zaiko, Susanna A. Wood Jan 2025

Advancing The Environmental Dna And Rna Toolkit For Aquatic Ecosystem Monitoring And Management, Xavier Pochon, Holly A. Bowers, Anastasija Zaiko, Susanna A. Wood

Faculty Research, Scholarly, and Creative Activity

The application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring and management has increased rapidly in the last decade. These methods are providing many new and exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, and species detection. This special issue of PeerJ Life and Environment brings together 20 innovative studies that collectively advance the eDNA toolkit. Four key themes are covered: (i) Methodological advancements, (ii) Ecological health assessments and biomonitoring, (iii) Species detection, and (iv) Application and management. The studies cover a suite of topics including; optimizing sample collection, developing species-specific assays, evaluating bioindicator species, …

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Label-Free Visualization And Segmentation Of Endothelial Cell Mitochondria Using Holotomographic Microscopy And U-Net, Raul Michael, Tallah Modirzadeh, Tahir Bachar Issa, Patrick Jurney Jan 2025

Label-Free Visualization And Segmentation Of Endothelial Cell Mitochondria Using Holotomographic Microscopy And U-Net, Raul Michael, Tallah Modirzadeh, Tahir Bachar Issa, Patrick Jurney

Faculty Research, Scholarly, and Creative Activity

Understanding the physiological processes underlying cardiovascular disease (CVD) requires examination of endothelial cell (EC) mitochondrial networks, because mitochondrial function and adenosine triphosphate production are crucial in EC metabolism, and consequently influence CVD progression. Although current biochemical assays and immunofluorescence microscopy can reveal how mitochondrial function influences cellular metabolism, they cannot achieve live observation and tracking changes in mitochondrial networks through fusion and fission events. Holotomographic microscopy (HTM) has emerged as a promising technique for real-time, label-free visualization of ECs and their organelles, such as mitochondria. This nondestructive, noninterfering live cell imaging method offers unprecedented opportunities to observe mitochondrial network dynamics. …

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Layover Start Timing Predicts Layover Sleep Quantity And Timing On Long-Range And Ultra-Long-Range Trips, Michael J. Rempe, Ian Rasmussen, Kevin Gregory, Cheyenne Johnson, Matthew Hsin, Erin Flynn-Evans, Amanda Lamp, Cassie J. Hilditch Jan 2025

Layover Start Timing Predicts Layover Sleep Quantity And Timing On Long-Range And Ultra-Long-Range Trips, Michael J. Rempe, Ian Rasmussen, Kevin Gregory, Cheyenne Johnson, Matthew Hsin, Erin Flynn-Evans, Amanda Lamp, Cassie J. Hilditch

Faculty Research, Scholarly, and Creative Activity

Study Objectives: Airline transport pilot sleep during layover is an important factor for alertness on subsequent flights. Assessing pilots' sleep on layover is an important first step in helping them obtain the most recuperative sleep possible on layover. Here, we investigate the quantity and timing of sleep during layovers and determine predictors for layover sleep. Methods: Sleep was assessed in 256 pilots flying a total of 473 long-range (LR; flight time 12-16 hours) or ultra-long-range (ULR; flight time > 16 hours) trips. Sleep was assessed using actigraphy. We employed linear mixed-effects models with layover sleep characteristics as the outcomes. The predictor …

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Optogenetic Methods To Stimulate Gamma Motor Neuron Axons Ex Vivo, Apoorva Karekal, Remie Mandawe, Cameron Chun, Sai Kiran Byri, Danitza Cheline, Serena Ortiz, Shawn Hochman, Katherine A. Wilkinson Jan 2025

Optogenetic Methods To Stimulate Gamma Motor Neuron Axons Ex Vivo, Apoorva Karekal, Remie Mandawe, Cameron Chun, Sai Kiran Byri, Danitza Cheline, Serena Ortiz, Shawn Hochman, Katherine A. Wilkinson

Faculty Research, Scholarly, and Creative Activity

It is challenging to stimulate gamma motor neurons, which are important regulators of muscle spindle afferent function, without also recruiting alpha motor neurons. Here, we test the feasibility of stimulating gamma motor neuron axons using optogenetics in two transgenic mouse lines. We used an ex vivo muscle–nerve preparation in adult mice to monitor muscle spindle afferent firing, which should increase in response to gamma motor neuron-induced lengthening of the sensory region of the muscle spindle. A force transducer measured alpha motor neuron-mediated twitch contractions. Blue LED light (470 nm; 1–5 mW) was delivered via a light guide to the sciatic …

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The Chatgpt Fact-Check: Exploiting The Limitations Of Generative Ai To Develop Evidence-Based Reasoning Skills In College Science Courses, Ursula Holzmann, Sulekha Anand, Alexander Y. Payumo Jan 2025

The Chatgpt Fact-Check: Exploiting The Limitations Of Generative Ai To Develop Evidence-Based Reasoning Skills In College Science Courses, Ursula Holzmann, Sulekha Anand, Alexander Y. Payumo

Faculty Research, Scholarly, and Creative Activity

Generative large language models (LLMs) like ChatGPT can quickly produce informative essays on various topics. However, the information generated cannot be fully trusted, as artificial intelligence (AI) can make factual mistakes. This poses challenges for using such tools in college classrooms. To address this, an adaptable assignment called the ChatGPT Fact-Check was developed to teach students in college science courses the benefits of using LLMs for topic exploration while emphasizing the importance of validating their claims based on evidence. The assignment requires students to use ChatGPT to generate essays, evaluate AI-generated sources, and assess the validity of AI-generated scientific claims …

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Reliability And Severity Levels Of The Voice-Related Experiences Of Nonbinary Individuals, Grace Shefcik, Pei Tzu Tsai, Satveer Kler Jan 2025

Reliability And Severity Levels Of The Voice-Related Experiences Of Nonbinary Individuals, Grace Shefcik, Pei Tzu Tsai, Satveer Kler

Faculty Research, Scholarly, and Creative Activity

Objectives: Clinicians providing gender-affirming communication services to nonbinary individuals often utilize client questionnaires. The Voice-related Experiences of Nonbinary Individuals (VENI) is the only published questionnaire exclusively for nonbinary clients. This questionnaire consists of 17 items that gain insight into the client's self-perception of voice and voice-related concerns. According to Shefcik and Tsai (2023), the VENI's content validity is good to excellent. This study evaluated the measure's reliability through internal consistency and test-retest reliability analyses and created impact ratings to support interpretation of scores. Study Design: This study utilized an online survey-based design with test-retest administration. The initial survey was administered …

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Pain For Pain: The Benefits And Challenges Of Bdsm Participation For People With Chronic Pain–An Exploratory Study, Reni Forer, Bryce Westlake Jan 2025

Pain For Pain: The Benefits And Challenges Of Bdsm Participation For People With Chronic Pain–An Exploratory Study, Reni Forer, Bryce Westlake

Faculty Research, Scholarly, and Creative Activity

Research is beginning to find that many BDSM (bondage/discipline, domination/submission, sadism/masochism) practitioners experience benefits beyond sexual pleasure. Additionally, given the relationship between pain and pleasure common in BDSM, there may be certain unanticipated benefits for practitioners reporting chronic pain (PRCP). We conducted an online survey of an international convenience sample of BDSM practitioners (N = 525). Participants were asked about self-perceived benefits and challenges related to participating in BDSM with CP. Using chi-square, independent sample t-test, logistic regression, and linear-by-linear association, responses were combined with demographics, participation timelines, co-participants, motivations, and frequency of activities to identify differences between PRCP and …

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Reinforcement Learning Methods For Assistive And Rehabilitation Robotic Systems: A Survey, Mojtaba Sharifi, Shreesh Tripathi, Yun Chen, Qiang Zhang, Mahdi Tavakoli Jan 2025

Reinforcement Learning Methods For Assistive And Rehabilitation Robotic Systems: A Survey, Mojtaba Sharifi, Shreesh Tripathi, Yun Chen, Qiang Zhang, Mahdi Tavakoli

Faculty Research, Scholarly, and Creative Activity

Advancements in robotic systems aimed at improving mobility for individuals with disabilities have required more sophisticated control and navigation methods. Traditional control approaches often lack the complexity and adaptability needed for the high-dimensional nature of human activities. Consequently, reinforcement learning (RL) has emerged as a dynamic and effective framework for managing robotic actions in complex and unpredictable human environments. This article reviews the integration of RL in robotic systems for enhancing the mobility of individuals with disabilities, addressing the limitations of traditional control methods in complex and unpredictable environments. We critically analyze various RL algorithms, discussing their advantages and challenges …

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Finding Floral And Faunal Species Richness Optima Among Active Fire Regimes, Zachary L. Steel, Alissa M. Fogg, Raphaela Floreani Buzbee, Kate Wilkin, Brandon M. Collins, Ryan Burnett, Marc D. Meyer, Amarina Wuenschel, Scott L. Stephens Jan 2025

Finding Floral And Faunal Species Richness Optima Among Active Fire Regimes, Zachary L. Steel, Alissa M. Fogg, Raphaela Floreani Buzbee, Kate Wilkin, Brandon M. Collins, Ryan Burnett, Marc D. Meyer, Amarina Wuenschel, Scott L. Stephens

Faculty Research, Scholarly, and Creative Activity

Changing fire regimes have important implications for biodiversity and challenge traditional conservation approaches that rely on historical conditions as proxies for ecological integrity. This historical-centric approach becomes increasingly tenuous under climate change, necessitating direct tests of environmental impacts on biodiversity. At the same time, widespread departures from historical fire regimes have limited the ability to sample diverse fire histories. We examined 2 areas in California's Sierra Nevada (USA) with active fire regimes to study the responses of bird, plant, and bat communities to a broad spectrum of temporal, spatial, and severity patterns of fire. Bird and plant species richness peaked …

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Development Of Physics-Based Deterioration Models For Reinforced Soil Retaining Structures, Amr Morsy, Islam Ebo Jan 2025

Development Of Physics-Based Deterioration Models For Reinforced Soil Retaining Structures, Amr Morsy, Islam Ebo

Mineta Transportation Institute

Reinforced soil walls are key earth retention features in the transportation infrastructure. They are used to support and retain soil in a wide variety of crucial structures, such as highways, bridges, and railways, to ensure stability. They also provide solutions for constructing embankments and slopes in constrained spaces, allowing for efficient land use and improved infrastructure planning. This study used advanced numerical modeling to improve the understanding of the behavior and long-term performance of the aging reinforced soil walls from the 1970s for asset management purposes. An asset-scale model was created to simulate the effects of weather on these walls. …

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Family-Level Impacts Of Equine-Assisted Occupational Therapy For Children With Disabilities: An Exploratory Mixed-Methods Pilot Study, Emily Canigiula Jan 2025

Family-Level Impacts Of Equine-Assisted Occupational Therapy For Children With Disabilities: An Exploratory Mixed-Methods Pilot Study, Emily Canigiula

Doctoral Projects

Equine-assisted occupational therapy (EAOT) has been shown to enhance functional, social, and quality-of-life outcomes for children with disabilities (McDaniel Peters & Wood, 2017; Prieto et al., 2022). While child-focused outcomes are well documented, significantly less is known about how EAOT participation may influence caregivers and the broader family unit, as existing research largely prioritizes individual outcomes over family experiences (Peters et al., 2017; Tan & Simmonds, 2018; Trzmiel et al., 2019; Xiao et al., 2023). Emerging qualitative studies suggest potential family-level impacts including family engagement, reduced parental stress, and enhanced feelings of pride, empowerment, and connection (Kalmback et al., 2020; …

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Bridging Gaps With Occupational Therapy: The Unique Role Of Occupational Therapy In Women’S Day Shelters, Alex Sato Jan 2025

Bridging Gaps With Occupational Therapy: The Unique Role Of Occupational Therapy In Women’S Day Shelters, Alex Sato

Doctoral Projects

Homelessness is a multifaceted, complex issue that we face as a society. Mainstream services provided to homeless or vulnerable populations tend to focus on housing and basic services. While these are essential and meaningful, literature suggests there is a lack in trauma and self-care support (Marzana et al., 2023; Milaney et al., 2020). Looking through an Occupational Therapy (OT) lens, there are a multitude of ways the profession can provide holistic care. Current OT service provision within this population most commonly focuses on obtaining and maintaining housing and addressing the survival occupations these individuals may be engaging in (Cunningham & …

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From Silos To Synergies: How To Enhance Interdisciplinary Collaboration Among Graduate Students, Jennifer Jimenez Jan 2025

From Silos To Synergies: How To Enhance Interdisciplinary Collaboration Among Graduate Students, Jennifer Jimenez

Doctoral Projects

Interprofessional education (IPE) is essential for preparing collaborative healthcare practitioners, yet opportunities at San José State University (SJSU) have been limited, inconsistent, and largely dependent on individual faculty initiative. This capstone project aimed to strengthen IPE at SJSU by assessing institutional capacity and developing feasible, sustainable strategies to enhance exposure and participation across health-related programs. Guided by the Person–Environment–Occupation–Performance (PEOP) model and adult learning theory, the project combined a needs assessment, literature review, and partnership with the Healthy Development Community Clinic (HDCC) to create an instructor implementation guide and student introductory modules for HDCC service-learning onboarding. An IRB-approved mixed-methods faculty …

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Multimodal Feature Fusion And Machine Learning For Adhd Detection Using Neuroimaging Data, Isabel Pham Jan 2025

Multimodal Feature Fusion And Machine Learning For Adhd Detection Using Neuroimaging Data, Isabel Pham

Master's Projects

Attention Deficit Hyperactivity Disorder (ADHD) is a common neurodevelopment disorder that can significantly affect a person’s attention, impulse control, and executive function. Currently, the traditional diagnosis method often relies on clinical assessments and observations. However, these methods can be subjective and lead to inconsistencies in diagnosis between individuals. To address this challenge, neuroimaging and machine learning (ML) are promising tools for providing a more objective diagnosis of ADHD. The goal of this project is to apply a multimodal approach in which structural and functional features of specific regions of the brain are used to develop a more accurate and objective …

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Effects Of Data Augmentation On Sponge Identification Using Computer Vision Models, George Ku Jan 2025

Effects Of Data Augmentation On Sponge Identification Using Computer Vision Models, George Ku

Master's Projects

Coral reefs can be primarily found in tropical and sub-tropical regions of our oceans, providing a thriving habitat for millions of species. Marine sponges, which can be frequently found in coral reefs, play a critical role that contributes to the maintenance of these ecosystems, including the recycling of nutrients through water filtration. However, rising ocean temperatures and acidification due to climate change have resulted in the bleaching and death of coral reefs worldwide. In order to preserve these reefs and the sponges that depend on them, scientists have been performing studies on their biodiversity. This includes collecting numerous images of …

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Combining Esm Models With Experimentally Derived Structural Stability To Identify Functional Missense Mutations, Rucha Deo Jan 2025

Combining Esm Models With Experimentally Derived Structural Stability To Identify Functional Missense Mutations, Rucha Deo

Master's Projects

Missense mutations can impact protein function and structure, yet their effects on protein function are difficult to predict. In this study, I compared two deep learning models, ESM1v and ESM1b, by evaluating their mutation predictions against experimental structural stability data. ESM1v showed a stronger correlation with experimental structural stability scores compared to ESM1b. A sigmoid curve was fitted to explore this relationship further. Over 100,000 mutations were identified where experimental stability differed significantly from model predictions. Many mutations that remained structurally stable experimentally but were predicted as harmful by the ESM models were frequently found at known functional sites. Structural …

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Ribomoe: An Application Of Mixture Of Experts On Artificial Riboswitch Classification, Hainian Audrey Long Jan 2025

Ribomoe: An Application Of Mixture Of Experts On Artificial Riboswitch Classification, Hainian Audrey Long

Master's Projects

Urban water sewage is a potential health concern due to its possibility to spread contagious RNA viruses such as Coxsackievirus B3. However, detection of viral particles remains challenging because of low viral concentrations in wastewater and high mutation rates of the RNA virus. To address this, this study proposes a novel viral detection method using synthetic riboswitches that bind to the target virus and trigger a reporter gene, amplifying the detection signals. To support the design of effective riboswitches, we present a machine learning model for classifying riboswitch performance, integrating RNA sequence data with secondary structural features. This model used …

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Identifying Red Sponges On Arms Plates By Preprocessing Images Using Histogram Equalization, Barry Ng Jan 2025

Identifying Red Sponges On Arms Plates By Preprocessing Images Using Histogram Equalization, Barry Ng

Master's Projects

Sponges play a vital role in marine ecosystems, being the only organisms capable of converting dissolved organic matter (DOM) into particulate organic matter (POM). They provide nutrients for coral reefs to thrive in oligotrophic waters. Autonomous reef monitoring structures (ARMS) are used to measure the biodiversity of coral reefs by simulating the complex cavities inside reef structures. Organisms settle on them and scientists can retrieve them after a period of time for analysis. Images are taken of ARMS plates after they are retrieved. Human analysis is unsuitable for the analysis of ARMS plates due to the huge number of images. …

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An Evidence-Based Approach To Predicting Pancreatic Ductal Adenocarcinoma, Surya Teja Nalluri Jan 2025

An Evidence-Based Approach To Predicting Pancreatic Ductal Adenocarcinoma, Surya Teja Nalluri

Master's Projects

Pancreatic ductal adenocarcinoma (PDAC) is a complex disease with hidden clinical indicators, so a reliable diagnosis of PDAC requires high precision and sophisticated analysis. Traditional probabilistic methods often rely on making unwarranted assumptions or undesirable approximations about probabilistic estimates, limiting their ability to provide the precision needed for correct diagnosis and treatment planning. In contrast, Dempster–Shafer Theory offers a formal framework for integrating uncertain and potentially conflicting evidence. This makes it well-suited for analyzing incomplete and ambiguous data typically associated with PDAC. By employing an evidential reasoning (ER) model based on Dempster-Shafer Theory, this approach systematically combines and evaluates imperfect …

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Image-To-Text Transcription: Analyzing And Describing Visual Content, Zixiao Fan Jan 2025

Image-To-Text Transcription: Analyzing And Describing Visual Content, Zixiao Fan

Master's Projects

Image captioning, which provides a textual understanding of visual content, is the fundamental support for the advancement of Human-A.I. Interaction technology. In the hope of exploring the application of such technology, this project focuses on two specific goals. One is to directly explore the application of the image informationretrieving abilities, and the other is to dive into the specifics of the pipeline and components of image captioning models. As a result, this project presents a working app that exploits the text retrieval functionalities to enable image storage with functions like tagging and transcription. It also supports search functionality with a …

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Galora: A Lightweight Graph-Aware Llm Framework For Node Classification On Text-Attributed Graphs, Mayur Choudhary Jan 2025

Galora: A Lightweight Graph-Aware Llm Framework For Node Classification On Text-Attributed Graphs, Mayur Choudhary

Master's Projects

With the exponential rise of language models (LMs) and their potential to understand semantic relationships, large LMs are being used across a wide range of applications. Text-attributed graphs (TAGs) are one notable example where LLMs can be combined with Graph Neural Networks (GNNs) to enhance node classification results. TAGs associate textual content with each node and are commonly seen in various domains such as social networks, citation graphs, recommendation systems, etc. Effectively modeling TAGs would enable deeper insights into different aspects of the graph and improve decision-making in relevant domains. We present GaLoRA, a parameter-efficient framework to integrate structural information …

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