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Articles 331 - 360 of 1803
Full-Text Articles in Computer Sciences
Gamified Mhealth System For Evaluating Upper Limb Motor Performance In Children: Cross-Sectional Feasibility Study, Md Raihan Mia, Sheikh Iqbal Ahamed, Samuel Nemanich
Gamified Mhealth System For Evaluating Upper Limb Motor Performance In Children: Cross-Sectional Feasibility Study, Md Raihan Mia, Sheikh Iqbal Ahamed, Samuel Nemanich
Computer Science Faculty Research and Publications
Background: Approximately 17% of children in the United States have been diagnosed with a developmental or neurological disorder that affects upper limb (UL) movements needed for completing activities of daily living. Gold-standard laboratory assessments of the UL are objective and precise but may not be portable, while clinical assessments can be time-intensive. We developed MoEvGame, a mobile health (mHealth) gamification software system for the iPad, as a potential advanced technology to assess UL motor functions.
Objective: This feasibility study examines whether MoEvGame can assess children’s whole-limb movement, fine motor skills, manual dexterity, and bimanual coordination. The specific aims were to …
Delivery Of Medical Supplies To Remote Locations Via Unmanned Aerial Vehicles: Approaches, Challenges, And Solutions, Meshari Aljohani, Ravi Mukkamala, Stephanie Olariu
Delivery Of Medical Supplies To Remote Locations Via Unmanned Aerial Vehicles: Approaches, Challenges, And Solutions, Meshari Aljohani, Ravi Mukkamala, Stephanie Olariu
Computer Science Faculty Publications
Unmanned Aerial Vehicles (UAVs) are becoming more important in improving healthcare logistics, in particular due to their cost effectiveness, minimized risk, and versatile operational capabilities. This study explores the deployment of autonomous UAVs to deliver medical supplies to remote areas. Advances in ledger technology, smart contracts, and machine learning have transformed tasks previously managed by human teams or manually controlled UAVs into fully autonomous missions. We present a comprehensive analysis of the challenges and initial solutions vital for the effective use of autonomous UAVs in the delivery of medical supplies. In addition, we propose a machine-learning model to optimize UAV …
Gramseq-Dta: A Grammar-Based Drug-Target Affinity Prediction Approach Fusing Gene Expression Information, Kasul Debnath, Pratip Rana, Preetam Ghosh
Gramseq-Dta: A Grammar-Based Drug-Target Affinity Prediction Approach Fusing Gene Expression Information, Kasul Debnath, Pratip Rana, Preetam Ghosh
Computer Science Faculty Publications
Drug–target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common approach that has demonstrated good results in drug–target affinity prediction. However, these approach lacks information on the relative position of the atoms and bonds. To address this limitation, graph-based representations have been used to some extent. However, solely considering the structural aspect of drugs and targets may be insufficient for accurate DTA prediction. Integrating the functional aspect of these drugs at the genetic level can enhance …
Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria
Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria
Computer Science Faculty Publications
Brain metastases (BMs) are the most common adult central nervous system malignancy, affecting 20–40% of cancer patients. Accurate segmentation of metastatic lesions in multi-modal MRI is essential for treatment planning and prognosis however, manual delineation is time consuming and prone to variability. Traditional deep learning models such as U-Net, have improved segmentation accuracy but capture limited long-range dependencies and struggle with variations in metastasis size, shape, and distribution. This study introduces the Adaptive Integrated Multi-modal Segmentation (AIMS) model, an adaptive self-attention framework within a hybrid U-Net and Transformer architecture to enhance BM segmentation by leveraging multi-modal MRI integration. The proposed …
Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang
Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang
Computer Science Faculty Publications
Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …
Optiselect And Enshap: Integrating Machine Learning And Game Theory For Ischemic Stroke Prediction, Pritam Chakraborty, Anjan Bandyopadhyay, Sricheta Parul, Sujata Swain, Partha Sarathy Banerjee, Tapas Si, Hong Qin, Saurav Mallik
Optiselect And Enshap: Integrating Machine Learning And Game Theory For Ischemic Stroke Prediction, Pritam Chakraborty, Anjan Bandyopadhyay, Sricheta Parul, Sujata Swain, Partha Sarathy Banerjee, Tapas Si, Hong Qin, Saurav Mallik
Computer Science Faculty Publications
Stroke analysis using game theory and machine learning techniques. The study investigates the use of the Shapley value in predictive ischemic brain stroke analysis. Initially, preference algorithms identify the most important features in various machine learning models, including logistic regression, K-nearest neighbor, decision tree, support vector machine (linear kernel), support vector machine ( RBF kernel), neural networks, etc. For each sample, the top 3, 4, and 5 features are evaluated and selected to evaluate their performance. The Shapley value method was used to rank the models using their best four features based on their predictive capabilities. As a result, better-performing …
A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh
A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh
Computer Science Faculty Publications
Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …
Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He
Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He
Computer Science Faculty Publications
Accurate quantifying dietary contents, such as calories, proteins, carbohydrates, and fats, from an image of a meal plate is vital for managing diabetes. Recently, Large Multimodal Models (LMMs) have excelled in complex vision-language tasks due to their use of very large, highly diverse data. This study benchmarked the use of seven LMMs that include full and lightweight models of GPT, Gemini, and Llama for nutrition estimation based on Google's Nutrition5k dataset and our own phone-collected DonateAndLearn dataset. We analyzed the performance of LMMs and the RGB-D fusion model, in which the RGB-D model was specifically trained using Nutrition5k data. On …
Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He
Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He
Computer Science Faculty Publications
DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …
Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh
Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh
Computer Science Faculty Publications
Predicting the length of stay (LoS) is important for hospital administration, as it helps allocate proper resources, such as bed management and hospital staffing. Patients' Electronic Health Records (EHRs) contain highly relevant data for LoS prediction; however, their integration and effective use in predictive modeling for accurately estimating LoS remain challenging. To address this, we propose a homogeneous Graph Neural Network (GNN)-based framework for predicting LoS. This method employs a comprehensive data fusion strategy based on the hospital Visit-based Similarity Graph (VSG), which integrates diverse multi-modal clinical features into a coherent, homogeneous graph representation. Next, this VSG is fed into …
Environment Scan Of Generative Ai Infrastructure For Clinical And Translational Science, Hua Xu, Jiang Bian, Chunhua Weng, Yifan Peng, Betina Idnay, Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos, Douglas S. Bell, Cody Bumgardner, Thomas Campion, Mario Castro, James J. Cimino, I. Glenn Cohen, David Dorr, Peter L. Elkin, Jungwei W. Fan, Todd Ferris, David J. Foran, David Hanauer, Mike Hogarth, Kun Huang, Jayashree Kalpathy-Cramer, Manoj Kandpal, Niranjan S. Karnik, Avnish Katoch, Albert M. Lai, Christophe G. Lambert, Lang Li, Christopher Lindsell, Jinze Liu, Zhiyong Lu, Yuan Luo, Peter Mcgarvey, Eneida A. Mendonca, Parsa Mirhaji, Shawn Murphy, John D. Osborne, Ioannis C. Paschalidis, Paul A. Harris, Fred Prior, Nicholas J. Shaheen, Nawar Shara, Ida Sim, Umberto Tachinardi, Lemuel R. Waitman, Rosalind J. Wright, Adrian H. Zai, Kai Zheng, Sandra Soo-Jin Lee, Bradley A. Malin, Karthik Natarajan, Nicholson Price, Rui Zhang, Yiye Zhang
Environment Scan Of Generative Ai Infrastructure For Clinical And Translational Science, Hua Xu, Jiang Bian, Chunhua Weng, Yifan Peng, Betina Idnay, Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos, Douglas S. Bell, Cody Bumgardner, Thomas Campion, Mario Castro, James J. Cimino, I. Glenn Cohen, David Dorr, Peter L. Elkin, Jungwei W. Fan, Todd Ferris, David J. Foran, David Hanauer, Mike Hogarth, Kun Huang, Jayashree Kalpathy-Cramer, Manoj Kandpal, Niranjan S. Karnik, Avnish Katoch, Albert M. Lai, Christophe G. Lambert, Lang Li, Christopher Lindsell, Jinze Liu, Zhiyong Lu, Yuan Luo, Peter Mcgarvey, Eneida A. Mendonca, Parsa Mirhaji, Shawn Murphy, John D. Osborne, Ioannis C. Paschalidis, Paul A. Harris, Fred Prior, Nicholas J. Shaheen, Nawar Shara, Ida Sim, Umberto Tachinardi, Lemuel R. Waitman, Rosalind J. Wright, Adrian H. Zai, Kai Zheng, Sandra Soo-Jin Lee, Bradley A. Malin, Karthik Natarajan, Nicholson Price, Rui Zhang, Yiye Zhang
Articles
This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 institutions supported by the CTSA Program led by the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH) at the United States. Key findings indicate a diverse range of institutional strategies, with most organizations in the experimental phase of GenAI deployment. The results underscore the need for a more coordinated approach to GenAI governance, emphasizing collaboration among senior leaders, clinicians, information technology staff, and researchers. Our analysis reveals that 53% of …
Synthetic Data Generation Of Health And Demographic Surveillance Systems Data: A Case Study In A Low- And Middle-Income Country, Dorcas G. Mwigereri, Nigel T. Kamotho, Akbar K. Waljee, Ryan T. Rego, Eileen M. Weinheimer-Haus, Farhana Alarakhiya, Anthony K. Ngugi, W. Nicholson Price, Ji Zhu, Stephen Peter Wong, Geoffrey H. Siwo
Synthetic Data Generation Of Health And Demographic Surveillance Systems Data: A Case Study In A Low- And Middle-Income Country, Dorcas G. Mwigereri, Nigel T. Kamotho, Akbar K. Waljee, Ryan T. Rego, Eileen M. Weinheimer-Haus, Farhana Alarakhiya, Anthony K. Ngugi, W. Nicholson Price, Ji Zhu, Stephen Peter Wong, Geoffrey H. Siwo
Articles
Objective: To evaluate effectiveness of open-source generative models in producing high-quality tabular synthetic data using a Health and Demographic Surveillance System (HDSS) dataset from rural Kenya, as a proof of concept in a low- and middle-income (LMIC) setting.
Materials and Methods: Three open-source models (CTGAN, TableGAN, and CopulaGAN) were used to generate synthetic data from the Kaloleni/ Rabai HDSS dataset. To assess the quality of the synthetic datasets generated by each model, we performed fidelity, utility, and privacy tests.
Results: CTGAN outperformed the other models, producing synthetic data that closely mirrored the statistical properties of the real dataset while preserving …
Machine Learning Methods For Pattern Recognition Analysis Of Genomic And Molecular Data, Kuang Du
Machine Learning Methods For Pattern Recognition Analysis Of Genomic And Molecular Data, Kuang Du
Dissertations
While immune therapies achieve remarkable success in treating various cancers, only a subset of patients achieves a durable clinical response, and many exhibit innate or acquired resistance. Precision medicine aims to tailor treatments to individual patients based on specific biological markers, ensuring that each patient receives the therapy most likely to be effective. Predictive biomarkers and gene signatures offer potential for more personalized treatment strategies by identifying patients likely to benefit. Recent studies suggest that gene signatures, comprising sets of genes, hold predictive value for certain clinical variables. Typically derived from biological expert knowledge, these signatures demonstrate substantial predictive potential, …
Automated Segmentation Of The Ulnar Nerve In Mri Using Deep Learning Techniques, Akhil Nagulapalli
Automated Segmentation Of The Ulnar Nerve In Mri Using Deep Learning Techniques, Akhil Nagulapalli
Theses
Cubital Tunnel Syndrome (CuTS), a condition caused by compression of the ulnar nerve, results in numbness, tingling, pain, and even muscle atrophy, affecting fine motor skills and diminishing patient quality of life. Accurate diagnosis of CuTS is challenging, as current diagnostic methods—including clinical exams, nerve conduction studies, and unaided MRI—often lack the precision to reliably identify the nerve and detect compression in its early stages. Deep learning-based segmentation offers a promising solution, enabling precise and automated identification of nerve structures in MRI images, which could significantly improve diagnostic accuracy and support timely intervention.
A novel deep learning model for segmenting …
Artificial Intelligence In Fetal And Pediatric Echocardiography, Alan Wang, Tam T Doan, Charitha Reddy, Pei-Ni Jone
Artificial Intelligence In Fetal And Pediatric Echocardiography, Alan Wang, Tam T Doan, Charitha Reddy, Pei-Ni Jone
Faculty, Staff and Students Publications
Echocardiography is the main modality in diagnosing acquired and congenital heart disease (CHD) in fetal and pediatric patients. However, operator variability, complex image interpretation, and lack of experienced sonographers and cardiologists in certain regions are the main limitations existing in fetal and pediatric echocardiography. Advances in artificial intelligence (AI), including machine learning (ML) and deep learning (DL), offer significant potential to overcome these challenges by automating image acquisition, image segmentation, CHD detection, and measurements. Despite these promising advancements, challenges such as small number of datasets, algorithm transparency, physician comfort with AI, and accessibility must be addressed to fully integrate AI …
Measurement Of Breast Artery Calcification Using An Artificial Intelligence Detection Model And Its Association With Major Adverse Cardiovascular Events, Suzanne Rose, Josette Hartnett, Zachary Estep, Daniyal Ameen, Shweta Karki, Edward Schuster, Rebecca Newman, David Hsi
Measurement Of Breast Artery Calcification Using An Artificial Intelligence Detection Model And Its Association With Major Adverse Cardiovascular Events, Suzanne Rose, Josette Hartnett, Zachary Estep, Daniyal Ameen, Shweta Karki, Edward Schuster, Rebecca Newman, David Hsi
Department of Medicine Faculty Papers
Breast artery calcification (BAC) obtained from standard mammographic images is currently under evaluation to stratify risk of major adverse cardiovascular events in women. Measuring BAC using artificial intelligence (AI) technology, we aimed to determine the relationship between BAC and coronary artery calcification (CAC) severity with Major Adverse Cardiac Events (MACE). This retrospective study included women who underwent chest computed tomography (CT) within one year of mammography. T-test assessed the associations between MACE and variables of interest (BAC versus MACE, CAC versus MACE). Risk differences were calculated to capture the difference in observed risk and reference groups. Chi-square tests and/or Fisher's …
Editorial: Artificial Intelligence For Smart Health: Learning, Simulation, And Optimization, Bing Yao, Nathan Gaw, Hyo Kyung Lee
Editorial: Artificial Intelligence For Smart Health: Learning, Simulation, And Optimization, Bing Yao, Nathan Gaw, Hyo Kyung Lee
Faculty Publications
With rapid developments in medical sensing and imaging, we now live in an era of data explosion in which large amounts of data are readily available in clinical environments. The fast-growing biomedical and healthcare data provide unprecedented opportunities for data-driven scientific knowledge discovery and clinical decision support. Our Research Topic aims to catalyze synergies among biomedical informatics, machine learning, computer simulation, operations research, systems engineering, and other related fields with three specific goals: (1) develop cutting-edge data-driven models to accelerate scientific knowledge discovery in biomedicine using healthcare data collected from laboratory systems, imaging systems, and medical and sensing devices; (2) …
Ethical Aspects Of Utilising Artificial Intelligence In Clinical Settings, Jeffrey Byrnes, Michael Robinson
Ethical Aspects Of Utilising Artificial Intelligence In Clinical Settings, Jeffrey Byrnes, Michael Robinson
Philosophy Faculty Articles and Research
In response to recent proposals to utilize artificial intelligence (AI) to automate ethics consultations in healthcare, we raise two main problems for the prospect of having healthcare professionals rely on AI-driven programs to provide ethical guidance in clinical matters. The first cause for concern is that, because these programs would effectively function like black boxes, this approach seems to preclude the kind of transparency that would allow clinical staff to explain and justify treatment decisions to patients, fellow caregivers, and those tasked with providing oversight. The other main problem is that the kind of authority that would need to be …
Transparency And Authority Concerns With Using Ai To Make Ethical Recommendations In Clinical Settings, Jeffrey Byrnes, Michael Robinson
Transparency And Authority Concerns With Using Ai To Make Ethical Recommendations In Clinical Settings, Jeffrey Byrnes, Michael Robinson
Philosophy Faculty Articles and Research
In response to recent proposals to utilize artificial intelligence (AI) to automate ethics consultations in healthcare, we raise two main problems for the prospect of having healthcare professionals rely on AI-driven programs to provide ethical guidance in clinical matters. The first cause for concern is that, because these programs would effectively function like black boxes, this approach seems to preclude the kind of transparency that would allow clinical staff to explain and justify treatment decisions to patients, fellow caregivers, and those tasked with providing oversight. The other main problem is that the kind of authority that would need to be …
Feasibility Of Large Language Models For Ceus Li-Rads Categorization Of Small Liver Nodules In Patients At Risk For Hepatocellular Carcinoma, Jiayan Huang, Rui Yang, Xiaotong Huang, Keyu Zeng, Yan Liu, Jun Luo, Andrej Lyshchik, Qiang Lu
Feasibility Of Large Language Models For Ceus Li-Rads Categorization Of Small Liver Nodules In Patients At Risk For Hepatocellular Carcinoma, Jiayan Huang, Rui Yang, Xiaotong Huang, Keyu Zeng, Yan Liu, Jun Luo, Andrej Lyshchik, Qiang Lu
Department of Radiology Faculty Papers
BACKGROUND: Large language models (LLMs) offer opportunities to enhance radiological applications, but their performance in handling complex tasks remains insufficiently investigated.
PURPOSE: To evaluate the performance of LLMs integrated with Contrast-enhanced Ultrasound Liver Imaging Reporting and Data System (CEUS LI-RADS) in diagnosing small (≤20mm) hepatocellular carcinoma (sHCC) in high-risk patients.
MATERIALS AND METHODS: From November 2014 to December 2023, high-risk HCC patients with untreated small (≤20mm) focal liver lesions (sFLLs), were included in this retrospective study. ChatGPT-4.0, ChatGPT-4o, ChatGPT-4o mini, and Google Gemini were integrated with imaging features from structured CEUS LI-RADS reports to assess their diagnostic performance for sHCC. …
Artificial Intelligence-Based Methodologies For Early Diagnostic Precision And Personalized Therapeutic Strategies In Neuro-Ophthalmic And Neurodegenerative Pathologies, Rahul Kumar, Ethan Waisberg, Joshua Ong, Phani Paladugu, Dylan Amiri, Jeremy Saintyl, Jahnavi Yelamanchi, Robert Nahouraii, Ram Jagadeesan, Alireza Tavakkoli
Artificial Intelligence-Based Methodologies For Early Diagnostic Precision And Personalized Therapeutic Strategies In Neuro-Ophthalmic And Neurodegenerative Pathologies, Rahul Kumar, Ethan Waisberg, Joshua Ong, Phani Paladugu, Dylan Amiri, Jeremy Saintyl, Jahnavi Yelamanchi, Robert Nahouraii, Ram Jagadeesan, Alireza Tavakkoli
SKMC Student Presentations and Publications
Advancements in neuroimaging, particularly diffusion magnetic resonance imaging (MRI) techniques and molecular imaging with positron emission tomography (PET), have significantly enhanced the early detection of biomarkers in neurodegenerative and neuro-ophthalmic disorders. These include Alzheimer's disease, Parkinson's disease, multiple sclerosis, neuromyelitis optica, and myelin oligodendrocyte glycoprotein antibody disease. This review highlights the transformative role of advanced diffusion MRI techniques-Neurite Orientation Dispersion and Density Imaging and Diffusion Kurtosis Imaging-in identifying subtle microstructural changes in the brain and visual pathways that precede clinical symptoms. When integrated with artificial intelligence (AI) algorithms, these techniques achieve unprecedented diagnostic precision, facilitating early detection of neurodegeneration and …
Alphafold2-Based Characterization Of Apo And Holo Protein Structures And Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics And Ligand-Induced Conformational Changes, Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Alphafold2-Based Characterization Of Apo And Holo Protein Structures And Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics And Ligand-Induced Conformational Changes, Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms. Using several well-established datasets of structurally diverse apo-holo protein pairs, the proposed approach enables robust predictions of apo and holo structures and conformational ensembles, …
Screensafefuture: A Parent-Empathetic And Pragmatic Mhealth Application For Toddlers' Brain Development Addressing Screen-Addiction Challenges, Nafisa Anjum, Md. Mehedi Hasan, Syeda Umme Salma, Liang Zhao, Maria Valero, Nazmus Sakib
Screensafefuture: A Parent-Empathetic And Pragmatic Mhealth Application For Toddlers' Brain Development Addressing Screen-Addiction Challenges, Nafisa Anjum, Md. Mehedi Hasan, Syeda Umme Salma, Liang Zhao, Maria Valero, Nazmus Sakib
Faculty Articles
The surging incidents of infants and toddlers screen addiction in the United States are becoming a pressing concern, given its compound impact on cognitive, mental, and physical growth. To address this era's critical child health and development problem, in this paper an innovative mHealth application—ScreenSafeFuture—is proposed. ScreenSafeFuture provides practical solutions that seamlessly fit into parents' busy lifestyles, acknowledging the effectiveness and convenience of smartphones as a healthcare tool. The solution includes essential features designed to enhance the experience between parents and their children under 3 years old encompassing an alternative activity advocator for a personalized parent-offspring scenario, screen time tracking …
Safeguarding Virtual Healthcare: A Novel Attacker-Centric Model For Data Security And Privacy, Suvineetha Herath, Haywood Gelman, John Hastings, Yong Wang
Safeguarding Virtual Healthcare: A Novel Attacker-Centric Model For Data Security And Privacy, Suvineetha Herath, Haywood Gelman, John Hastings, Yong Wang
Research & Publications
The rapid growth of remote healthcare delivery has introduced significant security and privacy risks to protected health information (PHI). Analysis of a comprehensive healthcare security breach dataset covering 2009-2023 reveals their significant prevalence and impact. This study investigates the root causes of such security incidents and introduces the Attacker-Centric Approach (ACA), a novel threat model tailored to protect PHI. ACA addresses limitations in existing threat models and regulatory frameworks by adopting a holistic attacker-focused perspective, examining threats from the viewpoint of cyber adversaries, their motivations, tactics, and potential attack vectors. Leveraging established risk management frameworks, ACA provides a multi-layered approach …
A Machine Learning Approach To Multifactorial Modeling Of Episodic Memory Performance, Evan Fletcher, Marianne Chanti-Ketterl, Emily Hokett, Yi Lor, Umesh Venkatesan, Paola Gilsanz, Rachel Whitmer, Ruijia Chen, Kristen George, Zvinka Zlatar
A Machine Learning Approach To Multifactorial Modeling Of Episodic Memory Performance, Evan Fletcher, Marianne Chanti-Ketterl, Emily Hokett, Yi Lor, Umesh Venkatesan, Paola Gilsanz, Rachel Whitmer, Ruijia Chen, Kristen George, Zvinka Zlatar
Moss-Magee Rehabilitation Papers
BACKGROUND: Neurocognitive health is influenced by multiple modifiable and non-modifiable lifestyle factors. Machine learning tools offer a promising approach to better understand complex models of cognitive function. We used extreme gradient boosting (XG Boost), an algorithm of decision-tree modeling, to analyze the association between 15 late-life lifestyle and demographic factors with episodic memory performance. METHOD: Our dataset consisted of 2247 participants from the KHANDLE and STAR cohorts. Participants included 841 men and 1406 women, an ethnoracial diversity of 413 Asian, 987 Black, 349 Latinx, and 496 White adults with age range 54-90 (mean = 74). XG Boost models of continuous …
Prevalence Of Autism Spectrum Characteristics In Students Taking Undergraduate Computing Courses, Rachel Michaela Mettenbrink
Prevalence Of Autism Spectrum Characteristics In Students Taking Undergraduate Computing Courses, Rachel Michaela Mettenbrink
School of Computing: Dissertations, Theses, and Student Research
The incidence rate of autism spectrum condition (ASC) has increased significantly in recent decades, as awareness of the condition and its impacts increases amongst clinicians, parents, and the general population. Medical literature has proposed that there may be a relationship between ASC and participation in the computing field. This study tests for the prevalence of autism spectrum condition traits measured by delivering the Autism Spectrum Quotient (AQ) to a population of undergraduate computer science students. We examine the relationships between AQ scores and students taking undergraduate computer science classes, sex, socioeconomic status, and parents in the computing industry. Additionally, we …
Addressing Ethical Issues In Healthcare Artificial Intelligence Using A Lifecycle-Informed Process, Benjamin X Collins, Jean-Christophe Bélisle-Pipon, Barbara J Evans, Kadija Ferryman, Xiaoqian Jiang, Camille Nebeker, Laurie Novak, Kirk Roberts, Martin Were, Zhijun Yin, Vardit Ravitsky, Joseph Coco, Rachele Hendricks-Sturrup, Ishan Williams, Ellen W Clayton, Bradley A Malin, Bridge2ai Ethics And Trustworthy Ai Working Group
Addressing Ethical Issues In Healthcare Artificial Intelligence Using A Lifecycle-Informed Process, Benjamin X Collins, Jean-Christophe Bélisle-Pipon, Barbara J Evans, Kadija Ferryman, Xiaoqian Jiang, Camille Nebeker, Laurie Novak, Kirk Roberts, Martin Were, Zhijun Yin, Vardit Ravitsky, Joseph Coco, Rachele Hendricks-Sturrup, Ishan Williams, Ellen W Clayton, Bradley A Malin, Bridge2ai Ethics And Trustworthy Ai Working Group
Faculty, Staff and Student Publications
OBJECTIVES: Artificial intelligence (AI) proceeds through an iterative and evaluative process of development, use, and refinement which may be characterized as a lifecycle. Within this context, stakeholders can vary in their interests and perceptions of the ethical issues associated with this rapidly evolving technology in ways that can fail to identify and avert adverse outcomes. Identifying issues throughout the AI lifecycle in a systematic manner can facilitate better-informed ethical deliberation.
MATERIALS AND METHODS: We analyzed existing lifecycles from within the current literature for ethical issues of AI in healthcare to identify themes, which we relied upon to create a lifecycle …
From A Timeline Contact Graph To Close Contact Tracing And Infection Diffusion Intervention, Yipeng Zhang, Zhifeng Bao, Yuchen Li, Baihua Zheng, Xiaoli Wang
From A Timeline Contact Graph To Close Contact Tracing And Infection Diffusion Intervention, Yipeng Zhang, Zhifeng Bao, Yuchen Li, Baihua Zheng, Xiaoli Wang
Research Collection School Of Computing and Information Systems
This paper proposes a novel graph structure to address the problems of information spreading in a real-world, frequently updating graph, with two main contributions at hand: accurately tracing infection diffusion according to fine-grained user movements and finding vulnerable vertices under the virus immunization scenario to mitigate infection diffusion. Unlike previous work that primarily predicts the long-term epidemic trend at the census level, this study aims to intervene in the short-term at the individual level. Therefore, two downstream tasks are formulated to illustrate practicalities: Epidemic Mitigating in Public Area problem (EMA) and Epidemic Maximized Spread in Public Area problem (ESA), where …
A Hybrid Approach Of Vision Transformers And Cnns For Detection Of Ulcerative Colitis, Syed Abdullah Shah, Imran Taj, Syed Muhammad Usman, Syed Nehal Hassan Shah, Ali Shariq Imran, Shehzad Khalid
A Hybrid Approach Of Vision Transformers And Cnns For Detection Of Ulcerative Colitis, Syed Abdullah Shah, Imran Taj, Syed Muhammad Usman, Syed Nehal Hassan Shah, Ali Shariq Imran, Shehzad Khalid
All Works
Ulcerative Colitis is an Inflammatory Bowel disease caused by a variety of factors that lead to a serious impact on the quality of life of the patients if left untreated. Due to complexities in the identification procedures of this disease, the treatment timeline and quality can be severely affected, leading to further consequences for the sufferer. The difficulties in identification are due to high patients to healthcare professionals ratio. Researchers have proposed variety of machine/deep learning methods for automated detection of ulcerative colitis, however, several challenges exists including class imbalance problem, comprehensive feature extraction and accurate classification. We propose a …
Exploring Post-Covid-19 Health Effects And Features With Advanced Machine Learning Techniques, Muhammad N. Islam, Md S. Islam, Nahid H. Shourav, Iftiaqur Rahman, Faiz A. Faisal, Md M. Islam, Iqbal H. Sarker
Exploring Post-Covid-19 Health Effects And Features With Advanced Machine Learning Techniques, Muhammad N. Islam, Md S. Islam, Nahid H. Shourav, Iftiaqur Rahman, Faiz A. Faisal, Md M. Islam, Iqbal H. Sarker
Research outputs 2022 to 2026
COVID-19 is an infectious respiratory disease that has had a significant impact, resulting in a range of outcomes including recovery, continued health issues, and the loss of life. Among those who have recovered, many experience negative health effects, particularly influenced by demographic factors such as gender and age, as well as physiological and neurological factors like sleep patterns, emotional states, anxiety, and memory. This research aims to explore various health factors affecting different demographic profiles and establish significant correlations among physiological and neurological factors in the post-COVID-19 state. To achieve these objectives, we have identified the post-COVID-19 health factors and …