Computer Sciences Commons^™

Enhanced Skin Cancer Diagnosis Through Grid Search Algorithm-Optimized Deep Learning Models For Skin Lesion Analysis, Rudresh Pillai, Neha Sharma, Sheifali Gupta, Deepali Gupta, Sapna Juneja, Saurav Malik, Hong Qin, Mohammed S. Alqahtani, Amel Ksibi

Computer Science Faculty Publications

Skin cancer is a widespread and perilous disease that necessitates prompt and precise detection for successful treatment. This research introduces a thorough method for identifying skin lesions by utilizing sophisticated deep learning (DL) techniques. The study utilizes three convolutional neural networks (CNNs)-CNN1, CNN2, and CNN3-each assigned to a distinct categorization job. Task 1 involves binary classification to determine whether skin lesions are present or absent. Task 2 involves distinguishing between benign and malignant lesions. Task 3 involves multiclass classification of skin lesion images to identify the precise type of skin lesion from a set of seven categories. The most optimal …

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Identifying Patterns For Neurological Disabilities By Integrating Discrete Wavelet Transform And Visualization, Soo Yeon Ji, Sampath Jayarathna, Anne M. Perrotti, Katrina Kardiasmenos, Dong Hyun Jeong

Computer Science Faculty Publications

Neurological disabilities cause diverse health and mental challenges, impacting quality of life and imposing financial burdens on both the individuals diagnosed with these conditions and their caregivers. Abnormal brain activity, stemming from malfunctions in the human nervous system, characterizes neurological disorders. Therefore, the early identification of these abnormalities is crucial for devising suitable treatments and interventions aimed at promoting and sustaining quality of life. Electroencephalogram (EEG), a non-invasive method for monitoring brain activity, is frequently employed to detect abnormal brain activity in neurological and mental disorders. This study introduces an approach that extends the understanding and identification of neurological disabilities …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Use Of Artificial Intelligence In Drug Development, Louise C. Druedahl, Nicholson Price, Timo Minssen, Dipl Jur, Ameet Sarpatwari

Articles

Considerable focus has been placed on the health care applications of artificial intelligence (AI). Already, machine learning, a subset of AI that involves “the use of data and algorithms to imitate the way that humans learn” has been used to predict diseases, while AI-powered smartphone apps have been developed to promote mental health and weight loss. Owing in part to such successes, the market for AI in health care has been forecasted to increase more than 1000% between 2022 and 2029, from $13.8 billion to $164.1 billion. One area of substantial promise is drug development, which is poised to benefit …

A Use Case Of Chatgpt: Summary Of An Expert Panel Discussion On Electronic Health Records And Implementation Science, Seppo T Rinne, Julian Brunner, Timothy P Hogan, Jacqueline M Ferguson, Drew A Helmer, Sylvia J Hysong, Grace Mckee, Amanda Midboe, Megan E Shepherd-Banigan, A Rani Elwy

Center for Medical Ethics and Health Policy Staff Publications

Objective: Artificial intelligence (AI) is revolutionizing healthcare, but less is known about how it may facilitate methodological innovations in research settings. In this manuscript, we describe a novel use of AI in summarizing and reporting qualitative data generated from an expert panel discussion about the role of electronic health records (EHRs) in implementation science.

Materials and methods: 15 implementation scientists participated in an hour-long expert panel discussion addressing how EHRs can support implementation strategies, measure implementation outcomes, and influence implementation science. Notes from the discussion were synthesized by ChatGPT (a large language model-LLM) to generate a manuscript summarizing the discussion, …

Enabling Ai And Robotic Coaches For Physical Rehabilitation Therapy: Iterative Design And Evaluation With Therapists And Post-Stroke Survivors, Min Hun Lee, Daniel Siewiorek, Asim Smailagic, Alexandre Bernardino, Sergi Bermúdez I Badia

Research Collection School Of Computing and Information Systems

Artificial intelligence (AI) and robotic coaches promise the improved engagement of patients on rehabilitation exercises through social interaction. While previous work explored the potential of automatically monitoring exercises for AI and robotic coaches, the deployment of these systems remains a challenge. Previous work described the lack of involving stakeholders to design such functionalities as one of the major causes. In this paper, we present our efforts on eliciting the detailed design specifications on how AI and robotic coaches could interact with and guide patient’s exercises in an effective and acceptable way with four therapists and five post-stroke survivors. Through iterative …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Lesion Detection In Women Breast’S Dynamic Contrast-Enhanced Magnetic Resonance Imaging Using Deep Learning, Sudarshan Saikia, Tapas Si, Darpan Deb, Kangkana Bora, Saurav Mallik, Ujjwal Maulik, Zhongming Zhao

Faculty, Staff and Student Publications

Breast cancer is one of the most common cancers in women and the second foremost cause of cancer death in women after lung cancer. Recent technological advances in breast cancer treatment offer hope to millions of women in the world. Segmentation of the breast's Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) is one of the necessary tasks in the diagnosis and detection of breast cancer. Currently, a popular deep learning model, U-Net is extensively used in biomedical image segmentation. This article aims to advance the state of the art and conduct a more in-depth analysis with a focus on the use …

Deep Learning Uncertainty Quantification For Clinical Text Classification, Alina Peluso, Ioana Danciu, Hong-Jun Yoon, Jamaludin Mohd Yusof, Tanmoy Bhattacharya, Adam Spannaus, Noah Schaefferkoetter, Eric B. Durbin, Xiao-Cheng Wu, Antoinette Stroup, Jennifer Doherty, Stephen Schwartz, Charles Wiggins, Linda Coyle, Lynne Penberthy, Georgia D. Tourassi, Shang Gao

School of Public Health Faculty Publications

INTRODUCTION: Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network's confidence, in-depth analyses are needed to establish whether they are well calibrated. METHOD: In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National …

Cm-Ii Meditation As An Intervention To Reduce Stress And Improve Attention: A Study Of Ml Detection, Spectral Analysis, And Hrv Metrics, Sreekanth Gopi

Master of Science in Computer Science Theses

Students frequently face heightened stress due to academic and social pressures, particularly in de- manding fields like computer science and engineering. These challenges are often associated with serious mental health issues, including ADHD (Attention Deficit Hyperactivity Disorder), depression, and an increased risk of suicide. The average student attention span has notably decreased from 21⁄2 minutes to just 47 seconds, and now it typically takes about 25 minutes to switch attention to a new task (Mark, 2023). Research findings suggest that over 95% of individuals who die by suicide have been diagnosed with depression (Shahtahmasebi, 2013), and almost 20% of students …

Mermaid: A Dataset And Framework For Multimodal Meme Semantic Understanding, Shaun Toh, Adriel Kuek, Wen Haw Chong, Roy Ka Wei Lee

Research Collection School Of Computing and Information Systems

Memes are widely used to convey cultural and societal issues and have a significant impact on public opinion. However, little work has been done on understanding and explaining the semantics expressed in multimodal memes. To fill this research gap, we introduce MERMAID, a dataset consisting of 3,633 memes annotated with their entities and relations, and propose a novel MERF pipeline that extracts entities and their relationships in memes. Our framework combines state-of-the-art techniques from natural language processing and computer vision to extract text and image features and infer relationships between entities in memes. We evaluate the proposed framework on a …

The Use Of Deception In Dementia-Care Robots: Should Robots Tell "White Lies" To Limit Emotional Distress?, Samuel R. Cox, Grace Cheong, Wei Tsang Ooi

ROSA Journal Articles and Publications

With projections of ageing populations and increasing rates of dementia, there is need for professional caregivers. Assistive robots have been proposed as a solution to this, as they can assist people both physically and socially. However, caregivers often need to use acts of deception (such as misdirection or white lies) in order to ensure necessary care is provided while limiting negative impacts on the cared-for such as emotional distress or loss of dignity. We discuss such use of deception, and contextualise their use within robotics.

Deficiency Of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality And Lung Injury In Mice, Ailing Ji, Andrea C. Trumbauer, Victoria P. Noffsinger, Luke W. Meredith, Brittany Dong, Qian Wang, Ling Guo, Xiangan Li, Frederick C. De Beer, Nancy R. Webb, Lisa R. Tannock, Marlene E. Starr, Christopher M. Waters, Preetha Shridas

Saha Cardiovascular Research Center Faculty Publications

Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated …

Exploring Non-Linear Dynamical Structure For Knee Kinematics Using Machine Learning, Liora Mayats-Alpay, Rahul Soangra

Physical Therapy Faculty Articles and Research

Human movement involves complex coordination between multiple limbs during execution. Human gait is cyclic, and the knee's movement inherently follows nonlinear dynamic behavior that linear models cannot adequately capture. In this study, advanced Machine Learning (ML) techniques were employed to combine the Sparse Identification of Nonlinear Dynamics (SINDy) algorithm using Python to reveal governing equations of knee movement during walking. We gathered a single subject's knee motion data using infrared markers during normal walking. We utilized the PySINDy library to determine the governing equations and calculated the coefficient of dynamical systems associated with knee kinematics. Our results emphasize governing equations …

Spatial-Temporal Episodic Memory Modeling For Adls: Encoding, Retrieval, And Prediction, Xinjing Song, Di Wang, Chai Quek, Ah-Hwee Tan, Yanjiang Wang

Research Collection School Of Computing and Information Systems

Activities of daily living (ADLs) relate to people’s daily self-care activities, which reflect their living habits and lifestyle. A prior study presented a neural network model called STADLART for ADL routine learning. In this paper, we propose a cognitive model named Spatial-Temporal Episodic Memory for ADL (STEM-ADL), which extends STADLART to encode event sequences in the form of distributed episodic memory patterns. Specifically, STEM-ADL encodes each ADL and its associated contextual information as an event pattern and encodes all events in a day as an episode pattern. By explicitly encoding the temporal characteristics of events as activity gradient patterns, STEM-ADL …

Responsibility Gaps And Black Box Healthcare Ai: Shared Responsibilization As A Solution, Benjamin H Lang, Sven Nyholm, Jennifer Blumenthal-Barby

Center for Medical Ethics and Health Policy Staff Publications

As sophisticated artificial intelligence software becomes more ubiquitously and more intimately integrated within domains of traditionally human endeavor, many are raising questions over how responsibility (be it moral, legal, or causal) can be understood for an AI’s actions or influence on an outcome. So called “responsibility gaps” occur whenever there exists an apparent chasm in the ordinary attribution of moral blame or responsibility when an AI automates physical or cognitive labor otherwise performed by human beings and commits an error. Healthcare administration is an industry ripe for responsibility gaps produced by these kinds of AI. The moral stakes of healthcare …

Self-Supervised Pseudo Multi-Class Pre-Training For Unsupervised Anomaly Detection And Segmentation In Medical Images, Yu Tian, Fengbei Liu, Guansong Pang, Yuanhong Chen, Yuyuan Liu, Johan W. Verjans, Rajvinder Singh, Gustavo Carneiro

Research Collection School Of Computing and Information Systems

Unsupervised anomaly detection (UAD) methods are trained with normal (or healthy) images only, but during testing, they are able to classify normal and abnormal (or disease) images. UAD is an important medical image analysis (MIA) method to be applied in disease screening problems because the training sets available for those problems usually contain only normal images. However, the exclusive reliance on normal images may result in the learning of ineffective low-dimensional image representations that are not sensitive enough to detect and segment unseen abnormal lesions of varying size, appearance, and shape. Pre-training UAD methods with self-supervised learning, based on computer …

A Reliable And Secure Mobile Cyber-Physical Digital Microfluidic Biochip For Intelligent Healthcare, Yinan Yao, Decheng Qiu, Huangda Liu, Zhongliao Yang, Ximeng Liu, Yang Yang, Chen Dong

Research Collection School Of Computing and Information Systems

Digital microfluidic, as an emerging and potential technology, diversifies the biochemical applications platform, such as protein dilution sewage detection. At present, a vast majority of universal cyberphysical digital microfluidic biochips (DMFBs) transmit data through wires via personal computers and microcontrollers (like Arduino), consequently, susceptible to various security threats and with the popularity of wireless devices, losing competitiveness gradually. On the premise that security be ensured first and foremost, calls for wireless portable, safe, and economical DMFBs are imperative to expand their application fields, engage more users, and cater to the trend of future wireless communication. To this end, a new …

Combat Covid-19 At National Level Using Risk Stratification With Appropriate Intervention, Xuan Jin, Kar Way Tan

Research Collection School Of Computing and Information Systems

In the national battle against COVID-19, harnessing population-level big data is imperative, enabling authorities to devise effective care policies, allocate healthcare resources efficiently, and enact targeted interventions. Singapore adopted the Home Recovery Programme (HRP) in September 2021, diverting low-risk COVID-19 patients to home care to ease hospital burdens amid high vaccination rates and mild symptoms. While a patient's suitability for HRP could be assessed using broad-based criteria, integrating machine learning (ML) model becomes invaluable for identifying high-risk patients prone to severe illness, facilitating early medical assessment. Most prior studies have traditionally depended on clinical and laboratory data, necessitating initial clinic …

A Systematic Collection Of Medical Image Datasets For Deep Learning, Johann Li, Guangming Zhu, Cong Hua, Mingtao Feng, Basheer Bennamoun, Ping Li, Xiaoyuan Lu, Juan Song, Peiyi Shen, Xu Xu, Lin Mei, Liang Zhang, Syed A. A. Shah, Mohammed Bennamoun

Research outputs 2022 to 2026

The astounding success made by artificial intelligence in healthcare and other fields proves that it can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data dependent and require large datasets for training. Many junior researchers face a lack of data for a variety of reasons. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require several other resources, such as professional equipment and expertise. That makes it difficult for novice and non-medical researchers to have access to medical data. Thus, as comprehensively as possible, this article …

Evaluating The Efficacy Of Chatgpt In Navigating The Spanish Medical Residency Entrance Examination (Mir): Promising Horizons For Ai In Clinical Medicine., Francisco Guillen-Grima, Sara Guillen-Aguinaga, Laura Guillen-Aguinaga, Rosa Alas-Brun, Luc Onambele, Wilfrido Ortega, Rocio Montejo, Enrique Aguinaga-Ontoso, Paul Barach, Ines Aguinaga-Ontoso

Department of Medicine Faculty Papers

UNLABELLED: The rapid progress in artificial intelligence, machine learning, and natural language processing has led to increasingly sophisticated large language models (LLMs) for use in healthcare. This study assesses the performance of two LLMs, the GPT-3.5 and GPT-4 models, in passing the MIR medical examination for access to medical specialist training in Spain. Our objectives included gauging the model's overall performance, analyzing discrepancies across different medical specialties, discerning between theoretical and practical questions, estimating error proportions, and assessing the hypothetical severity of errors committed by a physician.

MATERIAL AND METHODS: We studied the 2022 Spanish MIR examination results after excluding …

Data-Driven Decision Support Tool Co-Development With A Primary Health Care Practice Based Learning Network, Jacqueline K. Kueper, Jennifer Rayner, Sara Bhatti, Kelly Angevaare, Sandra Fitzpatrick, Paulino Lucamba, Eric Sutherland, Daniel J. Lizotte

Epidemiology and Biostatistics Publications

Background: The Alliance for Healthier Communities is a learning health system that supports Community Health Centres (CHCs) across Ontario, Canada to provide team-based primary health care to people who otherwise experience barriers to care. This case study describes the ongoing process and lessons learned from the first Alliance for Healthier Communities’ Practice Based Learning Network (PBLN) data-driven decision support tool co-development project.

Methods: We employ an iterative approach to problem identification and methods development for the decision support tool, moving between discussion sessions and case studies with CHC electronic health record (EHR) data. We summarize our work to date in …

Large Language Model Use Cases For Instruction, Plus A Primer On Prompt Engineering, Roy Haggerty, Justin Cochran

LSU Health New Orleans Symposium Series on Artificial Intelligence

AMA Credit Designation Statement: The Louisiana State University School of Medicine, New Orleans designates this live activity for a maximum of 1.0 AMA PRA Category 1 Credit™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

NCPD Credit Designation Statement: Nursing participants may earn 1.0 NCPD contact hours. Each nursing participant must be present for the entire session for which NCPD contact hours are requested and must complete an evaluation of the session to receive credit.

Physics-Informed Neural Networks For Agent-Based Epidemiological Model Calibration, Alvan C. Arulandu, Padmanabhan Seshaiyer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Healthaichain: Improving Security And Safety Using Blockchain Technology Applications In Ai-Based Healthcare Systems, Naresh Kshetri, James Hutson, Revathy G

Faculty Scholarship

Blockchain as a digital ledger for keeping records of digital transactions and other information, it is secure and decentralized technology. The globally growing number of digital population every day possesses a significant threat to online data including the medical and patients’ data. After bitcoin, blockchain technology has emerged into a general-purpose technology with applications in medical industries and healthcare. Blockchain can promote highly configurable openness while retaining the highest security standards for critical data of medical patients. Referred to as distributed record keeping for healthcare systems which makes digital assets unalterable and transparent via a cryptographic hash and decentralized network. …

Delivering Healthcare To The Underserved, Edward Booty

Asian Management Insights

Non-profits, governments, and businesses need to come together and use a data-driven approach to improve local basic healthcare access.

Depaul Digest

DePaul Magazine

College of Education Professor Jason Goulah fosters hope, happiness and global citizenship through DePaul’s Institute for Daisaku Ikeda Studies in Education. Associate Journalism Professor Jill Hopke shares how to talk about climate change. News briefs from DePaul’s 10 colleges and schools: Occupational Therapy Standardized Patient Program, Financial Planning Certificate program, Business Education in Technology and Analytics Hub, Racial Justice Initiative, Teacher Quality Partnership grant, Intimate Partner Violence and Brain Injury collaboration, School of Music Career Closet, Sports Photojournalism course, DePaul Migration Collaborative’s Solutions Lab, Inclusive Screenwriting courses. New appointments: School of Music Dean John Milbauer, College of Education Dean Jennifer …

A Dynamic Online Dashboard For Tracking The Performance Of Division 1 Basketball Athletic Performance, Erica Juliano, Chelsea Thakkar, Christopher B. Taber, Mehul S. Raval, Kaya Tolga, Samah Senbel

School of Computer Science & Engineering Undergraduate Publications

Using Data Analytics is a vital part of sport performance enhancement. We collect data from the Division 1 'Women's basketball athletes and coaches at our university, for use in analysis and prediction. Several data sources are used daily and weekly: WHOOP straps, weekly surveys, polar straps, jump analysis, and training session information. In this paper, we present an online dashboard to visually present the data to the athletes and coaches. R shiny was used to develop the platform, with the data stored on the cloud for instant updates of the dashboard as the data becomes available. The performance of athletes …