Label-Aware Distance Mitigates Temporal And Spatial Variability For Clustering And Visualization Of Single-Cell Gene Expression Data,
2024
The Texas Medical Center Library
Label-Aware Distance Mitigates Temporal And Spatial Variability For Clustering And Visualization Of Single-Cell Gene Expression Data, Shaoheng Liang, Jinzhuang Dou, Ramiz Iqbal, Ken Chen
Faculty, Staff and Student Publications
Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Label-Aware Distance (LAD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate LAD on simulated data as well as apply it to a mouse retina development dataset and a lung dataset. We also found the utility of our …
An Exposome Atlas Of Serum Reveals The Risk Of Chronic Diseases In The Chinese Population,
2024
The Texas Medical Center Library
An Exposome Atlas Of Serum Reveals The Risk Of Chronic Diseases In The Chinese Population, Xiang Li, Chang Su, Fujian Zheng, Mingye Zhang, Yuting Wang, Tiantian Chen, Ting Li, Lina Zhou, Xianzhe Shi, Chunxia Zhao, Xinyu Liu, Surong Mei, Guowang Xu
Faculty, Staff and Student Publications
Although adverse environmental exposures are considered a major cause of chronic diseases, current studies provide limited information on real-world chemical exposures and related risks. For this study, we collected serum samples from 5696 healthy people and patients, including those with 12 chronic diseases, in China and completed serum biomonitoring including 267 chemicals via gas and liquid chromatography-tandem mass spectrometry. Seventy-four highly frequently detected exposures were used for exposure characterization and risk analysis. The results show that region is the most critical factor influencing human exposure levels, followed by age. Organochlorine pesticides and perfluoroalkyl substances are associated with multiple chronic diseases, …
The Acceptance And Use Of Digital Technologies For Self-Reporting Medication Safety Events After Care Transitions To Home In Patients With Cancer: Survey Study,
2024
The Texas Medical Center Library
The Acceptance And Use Of Digital Technologies For Self-Reporting Medication Safety Events After Care Transitions To Home In Patients With Cancer: Survey Study, Sarah T Hawley, Milisa Manojlovich, John C Krauss, Yang Gong
Faculty, Staff and Student Publications
BACKGROUND: Actively engaging patients with cancer and their families in monitoring and reporting medication safety events during care transitions is indispensable for achieving optimal patient safety outcomes. However, existing patient self-reporting systems often cannot address patients' various experiences and concerns regarding medication safety over time. In addition, these systems are usually not designed for patients' just-in-time reporting. There is a significant knowledge gap in understanding the nature, scope, and causes of medication safety events after patients' transition back home because of a lack of patient engagement in self-monitoring and reporting of safety events. The challenges for patients with cancer in …
Geospatial Analysis Of Agricultural Potential In The United States,
2024
Purdue University
Geospatial Analysis Of Agricultural Potential In The United States, Diana Febrita
Graduate Industrial Research Symposium
Traditionally, the agriculture sector is responsible for providing food and crop products. However, the role of agriculture has expanded beyond its traditional function. It is the main sector that contributes to the provision of food, income, employment, environmental protection, and local economic development. Reflecting on the roles of agriculture, understanding the potential of agriculture in the United States is crucial to discovering the prospects and challenges. This study will briefly discuss the agricultural potential in the United States based on the five assets, including natural capital, financial capital, human capital, physical capital, and social capital. To identify the states with …
Accuracy Of Nitrate Hysteresis And Flushing For Agricultural Watersheds In The Midwest,
2024
Purdue University
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 …
Characterization Of Biological Particles Using An Integrated Hyperspectral Imaging And Machine Learning,
2024
Purdue University
Characterization Of Biological Particles Using An Integrated Hyperspectral Imaging And Machine Learning, Kaeul Lim, Arezoo Ardekani
Graduate Industrial Research Symposium
Hyperspectral imaging (HSI) is a promising modality in medicine with many potential applications. This study focuses on developing a label-free lipid nanoparticle characterization method using a convolutional neural network (CNN) analysis of HSI images. The HSI data, hypercube, consists of a series of images acquired at different wavelengths for the same field of view, providing continuous spectra information for each pixel. Three distinct liposome samples were collected for analysis. Advanced image preprocessing and classification methods for HSI data were developed to differentiate liposomes based on their material compositions. Our machine learning-based classification method was able to distinguish different liposome types …
Sepsis Treatment: Reinforced Sequential Decision-Making For Saving Lives,
2024
Purdue University
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,
2024
Purdue University
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 …
Modelling The "Bottom-Up" Development Pattern Of Tar Spot Disease In Corn,
2024
Purdue University
Modelling The "Bottom-Up" Development Pattern Of Tar Spot Disease In Corn, Brenden Lane, Joaquín Guillermo Ramírez-Gil, Carlos Góngora-Canul, Mariela Sofia Fernandez Campos, Andres Cruz-Sancan, Fidel E. Jiménez-Beitia, Alex G. Acosta-Guatemal, Wily Sic, C. D. Cruz
Graduate Industrial Research Symposium
In 2015, the corn-infecting pathogen Phyllachora maydis (causal agent of tar spot disease) was reported for the first time in the United States. The disease has since spread across the US, causing major yield losses. In 2021 alone, 5.88 million metric tons (231.3 million bushels) of US corn yield were lost to this disease, costing an estimated US$1.25 billion. Though fungicides can protect against these agroeconomic losses, application timing can be difficult to optimize because our understanding of tar spot dynamics is still evolving. The current view is that tar spot typically develops bottom-up through a repeating infection cycle. Because …
A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis,
2024
Purdue University
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 …
Resource Optimization For Air Mobility Under Emergency Situations,
2024
Embry-Riddle Aeronautical University
Resource Optimization For Air Mobility Under Emergency Situations, Yongxin (Jack) Liu
Math Department Colloquium Series
This project aims to improve air traffic management in emergencies. We first developed a GRU neural network to forecast weather-related airport capacity constraints using historical data, underscoring the value of real-time data analysis. We then optimized emergency evacuation air travel using Particle Swarm Optimization, demonstrating the ability to quickly aggregate evacuation flight resources cost-effectively. Finally, we provided a hybrid model combining a genetic algorithm with a neural network for evacuation planning, we show that neural network can be integrated accelerate genetic algorithms for efficient and performance assured system optimization.
Assessing Gait Metrics For Early Parkinson's Disease Prediction: A Preliminary Analysis Of Underfit Models,
2024
The University of Texas Rio Grande Valley
Assessing Gait Metrics For Early Parkinson's Disease Prediction: A Preliminary Analysis Of Underfit Models, Daniel Salinas, Gerardo Medellin, Katherine Bolado, Tomas Gomez, Kelsey Potter-Baker, Nawaz Khan Abdul Hack, Ramu Vadukapuram
Research Symposium
Background: Parkinson's Disease (PD) is characterized by both motor and non-motor symptoms, and its diagnosis primarily relies on clinical presentation. There is a growing need for diagnostic tools to identify the early signs of PD, particularly the initial motor impairments often manifested as gait abnormalities. Here we seek to present preliminary findings to address this need. Our study focuses on using Machine Learning techniques (ML) to predict the PD clinical stage most efficiently and accurately. Specifically, we have sought to evaluate how spatiotemporal characteristics and other locomotor performance variables obtained on a walkway system can be utilized to identify the …
Deep Learning Model For Personalized Prediction Of Positive Mrsa Culture Using Time-Series Electronic Health Records,
2024
The Texas Medical Center Library
Deep Learning Model For Personalized Prediction Of Positive Mrsa Culture Using Time-Series Electronic Health Records, Ziqian Xie, Degui Zhi
Faculty, Staff and Student Publications
Methicillin-resistant Staphylococcus aureus (MRSA) poses significant morbidity and mortality in hospitals. Rapid, accurate risk stratification of MRSA is crucial for optimizing antibiotic therapy. Our study introduced a deep learning model, PyTorch_EHR, which leverages electronic health record (EHR) time-series data, including wide-variety patient specific data, to predict MRSA culture positivity within two weeks. 8,164 MRSA and 22,393 non-MRSA patient events from Memorial Hermann Hospital System, Houston, Texas are used for model development. PyTorch_EHR outperforms logistic regression (LR) and light gradient boost machine (LGBM) models in accuracy (AUROC
Symptom Detection With Text Messag Log Distributions For Holistic Depression And Anxiety Screening,
2024
Bryant University
Symptom Detection With Text Messag Log Distributions For Holistic Depression And Anxiety Screening, Ml Tlachac, Michael Heinz, Miranda Reisch, Samuel S. Ogden
Information Systems and Analytics Department Faculty Journal Articles
Major Depressive Disorder (MDD) and Generalized Anxiety Disorder (GAD) are both heterogeneous in their clinical presentations, manifesting with unique symptom profiles. Despite this, prior digital phenotype research has primarily focused on disorder-level detection rather than symptom-level detection. In this research, we predict the existence of individual symptoms of MDD and GAD with SMS log metadata, and ensemble these symptom-level classifiers to screen for depression and anxiety, thus accounting for disorder heterogeneity. Further, we collect an additional dataset of retrospectively harvested SMS logs to augment an existing dataset collected after COVID-19 altered communication patterns, and propose two new types of distribution …
On Intrinsic Dimensionality Of Data Sets And Neural Networks,
2024
Air Force Institute of Technology
On Intrinsic Dimensionality Of Data Sets And Neural Networks, Ori Chachmo
Theses and Dissertations
The concept of Intrinsic Dimensionality (ID) is of special interest in the field of Neural Networks (NNs) since it promotes both (a) a deeper understanding of the underlying mechanisms, and (b) embraces parsimonious modeling (that is, building the right-sized model for the task) with associated benefits to processing speed and storage requirements. This thesis explores the concept of ID via two separate, but related, questions. First, we study the potential of NN ID prediction by exploiting easily obtained quantities measured on the data. We then explore NN ID as an independent concept by comparing the results of different methods for …
Federated Analysis Of Wearables Data For United States Air Force Mental And Physical Readiness,
2024
Air Force Institute of Technology
Federated Analysis Of Wearables Data For United States Air Force Mental And Physical Readiness, Sung Yong O
Theses and Dissertations
This thesis investigates the use of machine learning and deep learning models within a federated learning framework to predict physical and mental readiness in military personnel, using wearable technology data. The collaboration with the 711th Human Performance Wing’s STRONG Lab highlights the importance of readiness as emphasized by the National Defense and Security Strategies. The study evaluates various predictive models, incorporating federated learning to ensure data privacy and security in healthcare systems. By analyzing a comprehensive dataset, the research aims to contribute to military readiness enhancement through technological advancements, supporting health and wellness initiatives to bolster the effectiveness of military …
A Staged Framework For Llm-Powered Information Extraction In Government Contracts,
2024
Air Force Institute of Technology
A Staged Framework For Llm-Powered Information Extraction In Government Contracts, Jung H. Yae
Theses and Dissertations
The manual extraction of meaningful insights and conversion of content into structured forms to enhance document processing require substantial resources and are susceptible to errors. Despite numerous applications of various Natural Language Processing (NLP) models to streamline the manual process, challenges persist due to domain-specific data constraints and the deficiency of annotated data. This study attempts to address these challenges by leveraging a Large Language Model (LLM) to analyze government contracts. Through rigorous evaluation, we demonstrate the LLM’s effectiveness in information extraction and mitigating hallucinations, achieving a 87.86% accuracy in metadata extraction.
Spec: A Soft Prompt-Based Calibration On Performance Variability Of Large Language Model In Clinical Notes Summarization,
2024
The Texas Medical Center Library
Spec: A Soft Prompt-Based Calibration On Performance Variability Of Large Language Model In Clinical Notes Summarization
Faculty, Staff and Student Publications
Electronic health records (EHRs) store an extensive array of patient information, encompassing medical histories, diagnoses, treatments, and test outcomes. These records are crucial for enabling healthcare providers to make well-informed decisions regarding patient care. Summarizing clinical notes further assists healthcare professionals in pinpointing potential health risks and making better-informed decisions. This process contributes to reducing errors and enhancing patient outcomes by ensuring providers have access to the most pertinent and current patient data. Recent research has shown that incorporating instruction prompts with large language models (LLMs) substantially boosts the efficacy of summarization tasks. However, we show that this approach also …
Automated Image Registration For Titanium Aircraft Components Via Resolution-Robust Parallel Neural Networks,
2024
Air Force Institute of Technology
Automated Image Registration For Titanium Aircraft Components Via Resolution-Robust Parallel Neural Networks, Paige T. Luebbering
Theses and Dissertations
Titanium alloys are vital to the structural integrity of military and commercial aircraft, comprising numerous critical components. These components are composed of microtexture regions (MTRs) that, at a specific size and orientation, can lead to aircraft failure. Existing MTR testing methods, such as Electron Backscatter Diffraction, often fall short in effectively detecting these MTRs without causing damage to the component. Addressing this gap, this thesis develops a Parallel Convolutional Neural Network (CNN) model tailored for multi-resolution image registration of Polarized Light Microscopy (PLM) images to enhance MTR identification in a non-invasive manner. The findings reveal a significant enhancement in the …
Multiple Control Of Azoquinoline Based Molecular Photoswitches,
2024
The Texas Medical Center Library
Multiple Control Of Azoquinoline Based Molecular Photoswitches
Faculty, Staff and Student Publications
Multi-addressable molecular switches with high sophistication are creating intensive interest, but are challenging to control. Herein, we incorporated ring-chain dynamic covalent sites into azoquinoline scaffolds for the construction of multi-responsive and multi-state switching systems. The manipulation of ring-chain equilibrium by acid/base and dynamic covalent reactions with primary/secondary amines allowed the regulation of
