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Full-Text Articles in Artificial Intelligence and Robotics

Development And Validation Of Venous Thromboembolism-Bidirectional Encoder Representations From Transformers (Vte-Bert) Natural Language Processing Model, Omid Jafari, Shengling Ma, Barbara D Lam, Jun Y Jiang, Emily Zhou, Mrinal Ranjan, Justine Ryu, Raka Bandyo, Arash Maghsoudi, Bo Peng, Christopher I Amos, Abiodun Oluyomi, Nathanael R Fillmore, Jennifer La, Ang Li Aug 2025

Development And Validation Of Venous Thromboembolism-Bidirectional Encoder Representations From Transformers (Vte-Bert) Natural Language Processing Model, Omid Jafari, Shengling Ma, Barbara D Lam, Jun Y Jiang, Emily Zhou, Mrinal Ranjan, Justine Ryu, Raka Bandyo, Arash Maghsoudi, Bo Peng, Christopher I Amos, Abiodun Oluyomi, Nathanael R Fillmore, Jennifer La, Ang Li

Faculty, Staff and Students Publications

Background: Accurate and rapid phenotyping of venous thromboembolism (VTE) in longitudinal studies is important. A natural language processing (NLP) tool externally validated in representative patients is lacking.

Objectives: To train and validate an efficient NLP model to detect incident VTE event.

Methods: We designed a novel NLP platform, NLPMed, to assist thrombosis researchers with data preprocessing, phenotype annotation, language model finetuning, and NLP application. Using clinical notes, discharge summaries, and radiology reports from patients with cancer at 2 healthcare institutions, we finetuned Bio_Clinical Bidirectional Encoder Representations from Transformers (BERT) to develop VTE-BERT. The new model was trained to detect acute …


Computerized Diagnostic Decision Support Systems-Isabel Pro Versus Chatgpt-4 Part Ii, Joe M Bridges, Xiaoqian Jiang, Michael Ige, Oluwatoniloba Toyobo Jun 2025

Computerized Diagnostic Decision Support Systems-Isabel Pro Versus Chatgpt-4 Part Ii, Joe M Bridges, Xiaoqian Jiang, Michael Ige, Oluwatoniloba Toyobo

Faculty, Staff and Student Publications

Objective: Does a Tree-of-Thought prompt and reconsideration of Isabel Pro's differential improve ChatGPT-4's accuracy; does increasing expert panel size improve ChatGPT-4's accuracy; does ChatGPT-4 produce consistent outputs in sequential requests; what is the frequency of fabricated references?

Materials and methods: Isabel Pro, a computerized diagnostic decision support system, and ChatGPT-4, a large language model. Using 201 cases from the New England Journal of Medicine, each system produced a differential diagnosis ranked by likelihood. Statistics were Mean Reciprocal Rank, Recall at Rank, Average Rank, Number of Correct Diagnoses, and Rank Improvement. For reproducibility, the study compared the initial expert panel run …


Should Physicians Take The Rap? Normative Analysis Of Clinician Perspectives On Responsible Use Of 'Black Box' Ai Tools, Ben H Lang, Kristin Kostick-Quenet, Jared N Smith, Meghan Hurley, Rita Dexter, Jennifer Blumenthal-Barby May 2025

Should Physicians Take The Rap? Normative Analysis Of Clinician Perspectives On Responsible Use Of 'Black Box' Ai Tools, Ben H Lang, Kristin Kostick-Quenet, Jared N Smith, Meghan Hurley, Rita Dexter, Jennifer Blumenthal-Barby

Center for Medical Ethics and Health Policy Staff Publications

Background: Increasing interest in deploying artificial intelligence tools in clinical contexts has raised several ethical questions of both normative and empirical interest. One such question in the literature is whether "responsibility gaps" (r-gaps) are created when clinicians utilize or rely on such tools for providing care, and if so, what to do about them. These gaps are particularly likely to arise when using opaque, "black box" AI tools. Compared to normative and legal analysis of AI-generated responsibility gaps in health care, little is known, empirically, about health care providers views on this issue. The present study examines clinician perspectives on …


Ai Model For Predicting Asthma Prognosis In Children, Elham Sagheb, Chung-Il Wi, Katherine S King, Bhavani Singh Agnikula Kshatriya, Euijung Ryu, Hongfang Liu, Miguel A Park, Hee Yun Seol, Shauna M Overgaard, Deepak K Sharma, Young J Juhn, Sunghwan Sohn May 2025

Ai Model For Predicting Asthma Prognosis In Children, Elham Sagheb, Chung-Il Wi, Katherine S King, Bhavani Singh Agnikula Kshatriya, Euijung Ryu, Hongfang Liu, Miguel A Park, Hee Yun Seol, Shauna M Overgaard, Deepak K Sharma, Young J Juhn, Sunghwan Sohn

Faculty, Staff and Student Publications

BACKGROUND: Childhood asthma often continues into adulthood, but some children experience remission. Utilizing electronic health records (EHRs) to predict asthma prognosis can aid health care providers and patients in developing effective prioritized care plans.

OBJECTIVE: We aimed to develop artificial intelligence (AI) models using various clinical variables extracted from EHRs to predict childhood asthma prognosis (remission vs no remission) in different age groups.

METHODS: We developed AI models utilizing patients' EHRs during the first 6, 9, or 12 years of their lives to predict their asthma prognosis status at ages 6 to 9, 9 to 12, or 12 to 15 …


Oculomics: Current Concepts And Evidence, Zhuoting Zhu, Yueye Wang, Ziyi Qi, Wenyi Hu, Xiayin Zhang, Siegfried K Wagner, Yujie Wang, An Ran Ran, Joshua Ong, Ethan Waisberg, Mouayad Masalkhi, Alex Suh, Yih Chung Tham, Carol Y Cheung, Xiaohong Yang, Honghua Yu, Zongyuan Ge, Wei Wang, Bin Sheng, Yun Liu, Andrew G Lee, Alastair K Denniston, Peter Van Wijngaarden, Pearse A Keane, Ching-Yu Cheng, Mingguang He, Tien Yin Wong May 2025

Oculomics: Current Concepts And Evidence, Zhuoting Zhu, Yueye Wang, Ziyi Qi, Wenyi Hu, Xiayin Zhang, Siegfried K Wagner, Yujie Wang, An Ran Ran, Joshua Ong, Ethan Waisberg, Mouayad Masalkhi, Alex Suh, Yih Chung Tham, Carol Y Cheung, Xiaohong Yang, Honghua Yu, Zongyuan Ge, Wei Wang, Bin Sheng, Yun Liu, Andrew G Lee, Alastair K Denniston, Peter Van Wijngaarden, Pearse A Keane, Ching-Yu Cheng, Mingguang He, Tien Yin Wong

Faculty, Staff and Student Publications

The eye provides novel insights into general health, as well as pathogenesis and development of systemic diseases. In the past decade, growing evidence has demonstrated that the eye's structure and function mirror multiple systemic health conditions, especially in cardiovascular diseases, neurodegenerative disorders, and kidney impairments. This has given rise to the field of oculomics-the application of ophthalmic biomarkers to understand mechanisms, detect and predict disease. The development of this field has been accelerated by three major advances: 1) the availability and widespread clinical adoption of high-resolution and non-invasive ophthalmic imaging ("hardware"); 2) the availability of large studies to interrogate associations …


Patient Consent And The Right To Notice And Explanation Of Ai Systems Used In Health Care, Meghan E Hurley, Benjamin H Lang, Kristin Marie Kostick-Quenet, Jared N Smith, Jennifer Blumenthal-Barby Mar 2025

Patient Consent And The Right To Notice And Explanation Of Ai Systems Used In Health Care, Meghan E Hurley, Benjamin H Lang, Kristin Marie Kostick-Quenet, Jared N Smith, Jennifer Blumenthal-Barby

Center for Medical Ethics and Health Policy Staff Publications

Given the need for enforceable guardrails for artificial intelligence (AI) that protect the public and allow for innovation, the U.S. Government recently issued a Blueprint for an AI Bill of Rights which outlines five principles of safe AI design, use, and implementation. One in particular, the right to notice and explanation, requires accurately informing the public about the use of AI that impacts them in ways that are easy to understand. Yet, in the healthcare setting, it is unclear what goal the right to notice and explanation serves, and the moral importance of patient-level disclosure. We propose three normative functions …


Vaxbot-Hpv: A Gpt-Based Chatbot For Answering Hpv Vaccine-Related Questions, Yiming Li, Jianfu Li, Manqi Li, Evan Yu, Danniel Rhee, Muhammad Amith, Lu Tang, Lara S Savas, Licong Cui, Cui Tao Feb 2025

Vaxbot-Hpv: A Gpt-Based Chatbot For Answering Hpv Vaccine-Related Questions, Yiming Li, Jianfu Li, Manqi Li, Evan Yu, Danniel Rhee, Muhammad Amith, Lu Tang, Lara S Savas, Licong Cui, Cui Tao

Faculty, Staff and Student Publications

OBJECTIVE: Human Papillomavirus (HPV) vaccine is an effective measure to prevent and control the diseases caused by HPV. However, widespread misinformation and vaccine hesitancy remain significant barriers to its uptake. This study focuses on the development of VaxBot-HPV, a chatbot aimed at improving health literacy and promoting vaccination uptake by providing information and answering questions about the HPV vaccine.

METHODS: We constructed the knowledge base (KB) for VaxBot-HPV, which consists of 451 documents from biomedical literature and web sources on the HPV vaccine. We extracted 202 question-answer pairs from the KB and 39 questions generated by GPT-4 for training and …


Evaluating The Emotional Accuracy Of Ai-Generated Facial Expressions In Neurotypical Individuals, Antonio Pagán, Katherine A Loveland, Ronald Acierno Jan 2025

Evaluating The Emotional Accuracy Of Ai-Generated Facial Expressions In Neurotypical Individuals, Antonio Pagán, Katherine A Loveland, Ronald Acierno

Faculty, Staff and Student Publications

This study examines the ability of generative artificial intelligence to produce facial expressions representing basic emotions in a neutral context using black-and-white cartoon imagery. Mentalization, the capacity to recognize and interpret one’s own and others’ mental states, is critical for social interaction and emotional regulation. We explored the emotional validation of artificial intelligence (AI)-generated images by assessing the agreement between human interpretations of emotions and those generated by an AI model. Thirty-four participants evaluated images depicting six basic emotions: sadness, anger, happiness, surprise, fear, and disgust. Our findings revealed significant variability in human agreement, with higher concordance for sadness, anger, …


Machine Learning Predicting Acute Pain And Opioid Dose In Radiation Treated Oropharyngeal Cancer Patients, Vivian Salama, Laia Humbert-Vidan, Brandon Godinich, Kareem A Wahid, Dina M Elhabashy, Mohamed A Naser, Renjie He, Abdallah S R Mohamed, Ariana J Sahli, Katherine A Hutcheson, Gary Brandon Gunn, David I Rosenthal, Clifton D Fuller, Amy C Moreno Jan 2025

Machine Learning Predicting Acute Pain And Opioid Dose In Radiation Treated Oropharyngeal Cancer Patients, Vivian Salama, Laia Humbert-Vidan, Brandon Godinich, Kareem A Wahid, Dina M Elhabashy, Mohamed A Naser, Renjie He, Abdallah S R Mohamed, Ariana J Sahli, Katherine A Hutcheson, Gary Brandon Gunn, David I Rosenthal, Clifton D Fuller, Amy C Moreno

Faculty, Staff and Student Publications

Introduction: Acute pain is common among oral cavity/oropharyngeal cancer (OCC/OPC) patients undergoing radiation therapy (RT). This study aimed to predict acute pain severity and opioid doses during RT using machine learning (ML), facilitating risk-stratification models for clinical trials.

Methods: A retrospective study examined 900 OCC/OPC patients treated with RT during 2017-2023. Pain intensity was assessed using NRS (0-none, 10-worst) and total opioid doses were calculated using morphine equivalent daily dose (MEDD) conversion factors. Analgesics efficacy was assessed using combined pain intensity and total MEDD. ML predictive models were developed and validated, including Logistic Regression (LR), Support Vector Machine (SVM), Random …


Artificial Intelligence In Fetal And Pediatric Echocardiography, Alan Wang, Tam T Doan, Charitha Reddy, Pei-Ni Jone Dec 2024

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 …


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 Dec 2024

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 …


Artificial Intelligence And Machine Learning In Cancer Pain: A Systematic Review, Vivian Salama, Brandon Godinich, Yimin Geng, Laia Humbert-Vidan, Laura Maule, Kareem A Wahid, Mohamed A Naser, Renjie He, Abdallah S R Mohamed, Clifton D Fuller, Amy C Moreno Dec 2024

Artificial Intelligence And Machine Learning In Cancer Pain: A Systematic Review, Vivian Salama, Brandon Godinich, Yimin Geng, Laia Humbert-Vidan, Laura Maule, Kareem A Wahid, Mohamed A Naser, Renjie He, Abdallah S R Mohamed, Clifton D Fuller, Amy C Moreno

Faculty, Staff and Student Publications

Background/objectives: Pain is a challenging multifaceted symptom reported by most cancer patients. This systematic review aims to explore applications of artificial intelligence/machine learning (AI/ML) in predicting pain-related outcomes and pain management in cancer.

Methods: A comprehensive search of Ovid MEDLINE, EMBASE and Web of Science databases was conducted using terms: "Cancer," "Pain," "Pain Management," "Analgesics," "Artificial Intelligence," "Machine Learning," and "Neural Networks" published up to September 7, 2023. AI/ML models, their validation and performance were summarized. Quality assessment was conducted using PROBAST risk-of-bias andadherence to TRIPOD guidelines.

Results: Forty four studies from 2006 to 2023 were included. Nineteen studies used …


Toward A Responsible Future: Recommendations For Ai-Enabled Clinical Decision Support, Steven Labkoff, Bilikis Oladimeji, Joseph Kannry, Anthony Solomonides, Russell Leftwich, Eileen Koski, Amanda L Joseph, Monica Lopez-Gonzalez, Lee A Fleisher, Kimberly Nolen, Sayon Dutta, Deborah R Levy, Amy Price, Paul J Barr, Jonathan D Hron, Baihan Lin, Gyana Srivastava, Nuria Pastor, Unai Sanchez Luque, Tien Thi Thuy Bui, Reva Singh, Tayler Williams, Mark G Weiner, Tristan Naumann, Dean F Sittig, Gretchen Purcell Jackson, Yuri Quintana Nov 2024

Toward A Responsible Future: Recommendations For Ai-Enabled Clinical Decision Support, Steven Labkoff, Bilikis Oladimeji, Joseph Kannry, Anthony Solomonides, Russell Leftwich, Eileen Koski, Amanda L Joseph, Monica Lopez-Gonzalez, Lee A Fleisher, Kimberly Nolen, Sayon Dutta, Deborah R Levy, Amy Price, Paul J Barr, Jonathan D Hron, Baihan Lin, Gyana Srivastava, Nuria Pastor, Unai Sanchez Luque, Tien Thi Thuy Bui, Reva Singh, Tayler Williams, Mark G Weiner, Tristan Naumann, Dean F Sittig, Gretchen Purcell Jackson, Yuri Quintana

Faculty, Staff and Student Publications

BACKGROUND: Integrating artificial intelligence (AI) in healthcare settings has the potential to benefit clinical decision-making. Addressing challenges such as ensuring trustworthiness, mitigating bias, and maintaining safety is paramount. The lack of established methodologies for pre- and post-deployment evaluation of AI tools regarding crucial attributes such as transparency, performance monitoring, and adverse event reporting makes this situation challenging.

OBJECTIVES: This paper aims to make practical suggestions for creating methods, rules, and guidelines to ensure that the development, testing, supervision, and use of AI in clinical decision support (CDS) systems are done well and safely for patients.

MATERIALS AND METHODS: In May …


Interpreting The Biological Effects Of Protons As A Function Of Physical Quantity: Linear Energy Transfer Or Microdosimetric Lineal Energy Spectrum?, Fada Guan, Lawrence Bronk, Matthew Kerr, Yuting Li, Leslie A Braby, Mary Sobieski, Xiaochun Wang, Xiaodong Zhang, Clifford Stephan, David R Grosshans, Radhe Mohan Oct 2024

Interpreting The Biological Effects Of Protons As A Function Of Physical Quantity: Linear Energy Transfer Or Microdosimetric Lineal Energy Spectrum?, Fada Guan, Lawrence Bronk, Matthew Kerr, Yuting Li, Leslie A Braby, Mary Sobieski, Xiaochun Wang, Xiaodong Zhang, Clifford Stephan, David R Grosshans, Radhe Mohan

Faculty, Staff and Student Publications

The choice of appropriate physical quantities to characterize the biological effects of ionizing radiation has evolved over time coupled with advances in scientific understanding. The basic hypothesis in radiation dosimetry is that the energy deposited by ionizing radiation initiates all the consequences of exposure in a biological sample (e.g., DNA damage, reproductive cell death). Physical quantities defined to characterize energy deposition have included dose, a measure of the mean energy imparted per unit mass of the target, and linear energy transfer (LET), a measure of the mean energy deposition per unit distance that charged particles traverse in a medium. The …


A Framework For Human Evaluation Of Large Language Models In Healthcare Derived From Literature Review, Thomas Yu Chow Tam, Sonish Sivarajkumar, Sumit Kapoor, Alisa V Stolyar, Katelyn Polanska, Karleigh R Mccarthy, Hunter Osterhoudt, Xizhi Wu, Shyam Visweswaran, Sunyang Fu, Piyush Mathur, Giovanni E Cacciamani, Cong Sun, Yifan Peng, Yanshan Wang Sep 2024

A Framework For Human Evaluation Of Large Language Models In Healthcare Derived From Literature Review, Thomas Yu Chow Tam, Sonish Sivarajkumar, Sumit Kapoor, Alisa V Stolyar, Katelyn Polanska, Karleigh R Mccarthy, Hunter Osterhoudt, Xizhi Wu, Shyam Visweswaran, Sunyang Fu, Piyush Mathur, Giovanni E Cacciamani, Cong Sun, Yifan Peng, Yanshan Wang

Faculty, Staff and Student Publications

With generative artificial intelligence (GenAI), particularly large language models (LLMs), continuing to make inroads in healthcare, assessing LLMs with human evaluations is essential to assuring safety and effectiveness. This study reviews existing literature on human evaluation methodologies for LLMs in healthcare across various medical specialties and addresses factors such as evaluation dimensions, sample types and sizes, selection, and recruitment of evaluators, frameworks and metrics, evaluation process, and statistical analysis type. Our literature review of 142 studies shows gaps in reliability, generalizability, and applicability of current human evaluation practices. To overcome such significant obstacles to healthcare LLM developments and deployments, we …


Diabetes Technology Meeting 2023, Tiffany Tian, Rachel E Aaron, Ashley Y Dunova, Johan H Jendle, David Kerr, Eda Cengiz, Andjela Drincic, John C Pickup, Kong Y Chen, Naomi Schwartz, Douglas B Muchmore, Halis K Akturk, Carol J Levy, Signe Schmidt, Riccardo Bellazzi, Alan H B Wu, Elias K Spanakis, Bijan Najafi, James Geoffrey Chase, Jane Jeffrie Seley, David C Klonoff Sep 2024

Diabetes Technology Meeting 2023, Tiffany Tian, Rachel E Aaron, Ashley Y Dunova, Johan H Jendle, David Kerr, Eda Cengiz, Andjela Drincic, John C Pickup, Kong Y Chen, Naomi Schwartz, Douglas B Muchmore, Halis K Akturk, Carol J Levy, Signe Schmidt, Riccardo Bellazzi, Alan H B Wu, Elias K Spanakis, Bijan Najafi, James Geoffrey Chase, Jane Jeffrie Seley, David C Klonoff

Center on Aging Staff Publications

Diabetes Technology Society hosted its annual Diabetes Technology Meeting from November 1 to November 4, 2023. Meeting topics included digital health; metrics of glycemia; the integration of glucose and insulin data into the electronic health record; technologies for insulin pumps, blood glucose monitors, and continuous glucose monitors; diabetes drugs and analytes; skin physiology; regulation of diabetes devices and drugs; and data science, artificial intelligence, and machine learning. A live demonstration of a personalized carbohydrate dispenser for people with diabetes was presented.


Hyperpolarized Magnetic Resonance Imaging, Nuclear Magnetic Resonance Metabolomics, And Artificial Intelligence To Interrogate The Metabolic Evolution Of Glioblastoma, Kang Lin Hsieh, Qing Chen, Travis C Salzillo, Jian Zhang, Xiaoqian Jiang, Pratip K Bhattacharya, Shyan Shams Aug 2024

Hyperpolarized Magnetic Resonance Imaging, Nuclear Magnetic Resonance Metabolomics, And Artificial Intelligence To Interrogate The Metabolic Evolution Of Glioblastoma, Kang Lin Hsieh, Qing Chen, Travis C Salzillo, Jian Zhang, Xiaoqian Jiang, Pratip K Bhattacharya, Shyan Shams

Faculty, Staff and Student Publications

Glioblastoma (GBM) is a malignant Grade VI cancer type with a median survival duration of only 8-16 months. Earlier detection of GBM could enable more effective treatment. Hyperpolarized magnetic resonance spectroscopy (HPMRS) could detect GBM earlier than conventional anatomical MRI in glioblastoma murine models. We further investigated whether artificial intelligence (A.I.) could detect GBM earlier than HPMRS. We developed a deep learning model that combines multiple modalities of cancer data to predict tumor progression, assess treatment effects, and to reconstruct in vivo metabolomic information from ex vivo data. Our model can detect GBM progression two weeks earlier than conventional MRIs …


Enhancing Clinical Relevance Of Pretrained Language Models Through Integration Of External Knowledge: Case Study On Cardiovascular Diagnosis From Electronic Health Records, Qiuhao Lu, Andrew Wen, Thien Nguyen, Hongfang Liu Aug 2024

Enhancing Clinical Relevance Of Pretrained Language Models Through Integration Of External Knowledge: Case Study On Cardiovascular Diagnosis From Electronic Health Records, Qiuhao Lu, Andrew Wen, Thien Nguyen, Hongfang Liu

Faculty, Staff and Student Publications

Background: Despite their growing use in health care, pretrained language models (PLMs) often lack clinical relevance due to insufficient domain expertise and poor interpretability. A key strategy to overcome these challenges is integrating external knowledge into PLMs, enhancing their adaptability and clinical usefulness. Current biomedical knowledge graphs like UMLS (Unified Medical Language System), SNOMED CT (Systematized Medical Nomenclature for Medicine-Clinical Terminology), and HPO (Human Phenotype Ontology), while comprehensive, fail to effectively connect general biomedical knowledge with physician insights. There is an equally important need for a model that integrates diverse knowledge in a way that is both unified and compartmentalized. …


Missing Wedge Completion Via Unsupervised Learning With Coordinate Networks, Dave Van Veen, Jesús G Galaz-Montoya, Liyue Shen, Philip Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John Pauly May 2024

Missing Wedge Completion Via Unsupervised Learning With Coordinate Networks, Dave Van Veen, Jesús G Galaz-Montoya, Liyue Shen, Philip Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John Pauly

Faculty, Staff and Students Publications

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input …


Evaluation Of An End-To-End Radiotherapy Treatment Planning Pipeline For Prostate Cancer, Mohammad Daniel El Basha, Court Laurence, Carlos Eduardo Cardenas, Julianne Pollard-Larkin, Steven Frank, David T. Fuentes, Falk Poenisch, Zhiqian H. Yu May 2024

Evaluation Of An End-To-End Radiotherapy Treatment Planning Pipeline For Prostate Cancer, Mohammad Daniel El Basha, Court Laurence, Carlos Eduardo Cardenas, Julianne Pollard-Larkin, Steven Frank, David T. Fuentes, Falk Poenisch, Zhiqian H. Yu

Dissertations and Theses (Open Access)

Radiation treatment planning is a crucial and time-intensive process in radiation therapy. This planning involves carefully designing a treatment regimen tailored to a patient’s specific condition, including the type, location, and size of the tumor with reference to surrounding healthy tissues. For prostate cancer, this tumor may be either local, locally advanced with extracapsular involvement, or extend into the pelvic lymph node chain. Automating essential parts of this process would allow for the rapid development of effective treatment plans and better plan optimization to enhance tumor control for better outcomes.

The first objective of this work, to automate the treatment …


Artificial Intelligence-Powered Assessment Of Pathologic Response To Neoadjuvant Atezolizumab In Patients With Nsclc: Results From The Lcmc3 Study, Sanja Dacic, William D Travis, Jennifer M Giltnane, Filip Kos, John Abel, Stephanie Hilz, Junya Fujimoto, Lynette Sholl, Jon Ritter, Farah Khalil, Yi Liu, Amaro Taylor-Weiner, Murray Resnick, Hui Yu, Fred R Hirsch, Paul A Bunn, David P Carbone, Valerie Rusch, David J Kwiatkowski, Bruce E Johnson, Jay M Lee, Stephanie R Hennek, Ilan Wapinski, Alan Nicholas, Ann Johnson, Katja Schulze, Mark G Kris, Ignacio I Wistuba May 2024

Artificial Intelligence-Powered Assessment Of Pathologic Response To Neoadjuvant Atezolizumab In Patients With Nsclc: Results From The Lcmc3 Study, Sanja Dacic, William D Travis, Jennifer M Giltnane, Filip Kos, John Abel, Stephanie Hilz, Junya Fujimoto, Lynette Sholl, Jon Ritter, Farah Khalil, Yi Liu, Amaro Taylor-Weiner, Murray Resnick, Hui Yu, Fred R Hirsch, Paul A Bunn, David P Carbone, Valerie Rusch, David J Kwiatkowski, Bruce E Johnson, Jay M Lee, Stephanie R Hennek, Ilan Wapinski, Alan Nicholas, Ann Johnson, Katja Schulze, Mark G Kris, Ignacio I Wistuba

Faculty, Staff and Student Publications

Introduction: Pathologic response (PathR) by histopathologic assessment of resected specimens may be an early clinical end point associated with long-term outcomes with neoadjuvant therapy. Digital pathology may improve the efficiency and precision of PathR assessment. LCMC3 (NCT02927301) evaluated neoadjuvant atezolizumab in patients with resectable NSCLC and reported a 20% major PathR rate.

Methods: We determined PathR in primary tumor resection specimens using guidelines-based visual techniques and developed a convolutional neural network model using the same criteria to digitally measure the percent viable tumor on whole-slide images. Concordance was evaluated between visual determination of percent viable tumor (n = …


Cancergpt For Few Shot Drug Pair Synergy Prediction Using Large Pretrained Language Models, Tianhao Li, Sandesh Shetty, Advaith Kamath, Ajay Jaiswal, Xiaoqian Jiang, Ying Ding, Yejin Kim Feb 2024

Cancergpt For Few Shot Drug Pair Synergy Prediction Using Large Pretrained Language Models, Tianhao Li, Sandesh Shetty, Advaith Kamath, Ajay Jaiswal, Xiaoqian Jiang, Ying Ding, Yejin Kim

Faculty, Staff and Student Publications

Large language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology and medicine has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Here we report our proposed few-shot learning approach, which uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. …


Artificial Intelligence Model Predicts Sudden Cardiac Arrest Manifesting With Pulseless Electric Activity Versus Ventricular Fibrillation, Lauri Holmstrom, Bryan Bednarski, Harpriya Chugh, Habiba Aziz, Hoang Nhat Pham, Arayik Sargsyan, Audrey Uy-Evanado, Damini Dey, Angelo Salvucci, Jonathan Jui, Kyndaron Reinier, Piotr J Slomka, Sumeet S Chugh Feb 2024

Artificial Intelligence Model Predicts Sudden Cardiac Arrest Manifesting With Pulseless Electric Activity Versus Ventricular Fibrillation, Lauri Holmstrom, Bryan Bednarski, Harpriya Chugh, Habiba Aziz, Hoang Nhat Pham, Arayik Sargsyan, Audrey Uy-Evanado, Damini Dey, Angelo Salvucci, Jonathan Jui, Kyndaron Reinier, Piotr J Slomka, Sumeet S Chugh

Faculty, Staff and Student Publications

BACKGROUND: There is no specific treatment for sudden cardiac arrest (SCA) manifesting as pulseless electric activity (PEA) and survival rates are low; unlike ventricular fibrillation (VF), which is treatable by defibrillation. Development of novel treatments requires fundamental clinical studies, but access to the true initial rhythm has been a limiting factor.

METHODS: Using demographics and detailed clinical variables, we trained and tested an AI model (extreme gradient boosting) to differentiate PEA-SCA versus VF-SCA in a novel setting that provided the true initial rhythm. A subgroup of SCAs are witnessed by emergency medical services personnel, and because the response time is …


Enabling The Clinical Application Of Artificial Intelligence In Genomics: A Perspective Of The Amia Genomics And Translational Bioinformatics Workgroup, Nephi A Walton, Radha Nagarajan, Chen Wang, Murat Sincan, Robert R Freimuth, David B Everman, Derek C Walton, Scott P Mcgrath, Dominick J Lemas, Panayiotis V Benos, Alexander V Alekseyenko, Qianqian Song, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S Williams Jan 2024

Enabling The Clinical Application Of Artificial Intelligence In Genomics: A Perspective Of The Amia Genomics And Translational Bioinformatics Workgroup, Nephi A Walton, Radha Nagarajan, Chen Wang, Murat Sincan, Robert R Freimuth, David B Everman, Derek C Walton, Scott P Mcgrath, Dominick J Lemas, Panayiotis V Benos, Alexander V Alekseyenko, Qianqian Song, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S Williams

Faculty, Staff and Student Publications

OBJECTIVE: Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space.

PROCESS: A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members.

CONCLUSIONS: Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of …


Novel Techniques In Imaging Congenital Heart Disease: Jacc Scientific Statement, Ritu Sachdeva, Aimee K Armstrong, Rima Arnaout, Lars Grosse-Wortmann, B Kelly Han, Luc Mertens, Ryan A Moore, Laura J Olivieri, Anitha Parthiban, Andrew J Powell Jan 2024

Novel Techniques In Imaging Congenital Heart Disease: Jacc Scientific Statement, Ritu Sachdeva, Aimee K Armstrong, Rima Arnaout, Lars Grosse-Wortmann, B Kelly Han, Luc Mertens, Ryan A Moore, Laura J Olivieri, Anitha Parthiban, Andrew J Powell

Faculty, Staff and Students Publications

Recent years have witnessed exponential growth in cardiac imaging technologies, allowing better visualization of complex cardiac anatomy and improved assessment of physiology. These advances have become increasingly important as more complex surgical and catheter-based procedures are evolving to address the needs of a growing congenital heart disease population. This state-of-the-art review presents advances in echocardiography, cardiac magnetic resonance, cardiac computed tomography, invasive angiography, 3-dimensional modeling, and digital twin technology. The paper also highlights the integration of artificial intelligence with imaging technology. While some techniques are in their infancy and need further refinement, others have found their way into clinical workflow …


Preparing Healthcare Education For An Ai-Augmented Future, Jiajie Zhang, Susan H Fenton Jan 2024

Preparing Healthcare Education For An Ai-Augmented Future, Jiajie Zhang, Susan H Fenton

Faculty, Staff and Student Publications

Artificial intelligence (AI) fundamentally transforms healthcare education as a knowledge enterprise, creating a distributed cognitive system composed of the human brain, which remains relatively unchanged, and AI-based knowledge and cognitive functions, which have accelerated exponentially in scale and power. Education must focus on developing skills to collaborate with AI and on achieving outcomes like problems solved and discoveries made. Curriculum and education policies also need to adapt to this transformation.


Computer-Aided Craniofacial Superimposition Validation Study: The Identification Of The Leaders And Participants Of The Polish-Lithuanian January Uprising (1863–1864), Rubén Martos, Rosario Guerra, Fernando Navarro, Michela Peruch, Kevin Neuwirth, Andrea Valsecchi, Rimantas Jankauskas, Oscar Ibáñez Jan 2024

Computer-Aided Craniofacial Superimposition Validation Study: The Identification Of The Leaders And Participants Of The Polish-Lithuanian January Uprising (1863–1864), Rubén Martos, Rosario Guerra, Fernando Navarro, Michela Peruch, Kevin Neuwirth, Andrea Valsecchi, Rimantas Jankauskas, Oscar Ibáñez

Faculty, Staff and Student Publications

In 2017, a series of human remains corresponding to the executed leaders of the "January Uprising" of 1863-1864 were uncovered at the Upper Castle of Vilnius (Lithuania). During the archeological excavations, 14 inhumation pits with the human remains of 21 individuals were found at the site. The subsequent identification process was carried out, including the analysis and cross-comparison of post-mortem data obtained in situ and in the lab with ante-mortem data obtained from historical archives. In parallel, three anthropologists with diverse backgrounds in craniofacial identification and two students without previous experience attempted to identify 11 of these 21 individuals using …


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 Jan 2024

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, …


Responsibility Gaps And Black Box Healthcare Ai: Shared Responsibilization As A Solution, Benjamin H Lang, Sven Nyholm, Jennifer Blumenthal-Barby Dec 2023

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 …


Mpla Case: How Do You Lead As A Lead Physicist?, Patricia Sansourekidou, Leonard Kim, Lee Xu, Mary Gronberg, Cassandra Stambaugh, Dongxu Wang Sep 2023

Mpla Case: How Do You Lead As A Lead Physicist?, Patricia Sansourekidou, Leonard Kim, Lee Xu, Mary Gronberg, Cassandra Stambaugh, Dongxu Wang

Faculty, Staff and Student Publications

This work of fiction is part of a case study series developed by the Medical Physics Leadership Academy (MPLA). It is intended to facilitate the discussion of the managerial and leadership challenges faced by a clinical medical physicist. In this case, a physicist David used to work in a clinic where he thrived and felt like a leader, despite not having the title. After a job change, he is now officially the "Lead Physicist" at a hospital newly affiliated with a large academic healthcare system. He believes he will be equally successful. Yet he struggles to bring about changes and …