Scott T. Doyle PhD
Scott T. Doyle
PhD
Associate Professor
Department of Pathology and Anatomical Sciences
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Bioinformatics; Biomedical Image Analysis; Biomedical Imaging; Digital Pathology; Image Analysis; Quantitative Histology
Professional Summary:
Our group specializes in building quantitative image and data analysis algorithms for biomedical datasets. For the past 9 years, I have been developing computerized methods to quantify and analyze large medical imaging datasets. These methods include data processing, object detection / segmentation, feature extraction and selection, dimensionality reduction, and classification (supervised and unsupervised).
I strongly believe in translating academic research into real-world products and services. To that end, along with my colleagues, I have worked at a start-up company to bring my work into the marketplace -- an experience that has given me great insight into the business side of academia. This experience broadened my understanding of how basic research is translated into a profitable enterprise, and I believe these lessons have made me a better engineer.
I am currently working as an Assistant Professor in the Department of Pathology & Anatomical Sciences at the University at Buffalo, where I am focused on building a teaching and research program for quantitative modeling of anatomy and cell biology. This program will introduce students of both medicine and engineering to pattern classification approaches developed in recent years, applying them to real-world clinical problems.
Education and Training:
- Other, R Bioconductor Training Sessions, Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute (2016)
- Other, hES Stem Cell Culture Training Program, WNYSTEM Stem Cell Culture, Banking, and Training Facility (2014)
- Other, Optical Microscopy & Imaging in the Biomedical Sciences, Marine Biological Laboratory (2014)
- PhD, Biomedical Engineering, Rutgers, The State University of New Jersey (2011)
- BS, Biomedical Engineering, Rutgers, The State University of New Jersey (2006)
Employment:
- Associate Professor, Pathology and Anatomical Sciences, The University at Buffalo Jacobs School of Medicine and Biomedical Sciences (2022-present)
- Assistant Professor, Pathology and Anatomical Sciences, The University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2014–2022)
- Technical Liason, Imaging Research Scientist, Veterans Affairs Hospital (2017–2018)
- Director of Research, Ibris, Inc. (2011–2014)
- Graduate Student, Biomedical Engineering, Rutgers, The State University of New Jersey Graduate School - New Brunswick (2006–2011)
Research Centers:
- Center for Computational Research (CCR)
UB 2020 Strategic Strengths:
- Information and Computing Technology
Grants and Sponsored Research:
- July 2023–June 2026
The Effect of WTC Exposure on Thyroid Cancer in the Survivor Population
NIH
Role: Co-Investigator
$100,297 - January 2024–December 2024
Initiative for Private and Secure Collaborative AI Training in Computational Pathology
Clinical and Translational Science Institute (CTSI)
Role: Principal Investigator
$50,000 - April 2020–March 2024
Quantitative Risk Model for Predicting Likelihood of Recurrence for Oral Cavity Cancer
NIH
Role: Principal Investigator
$2,003,024 - August 2021–July 2023
Improving Virtual Gross Anatomy: Enhancing the Information Content of Cadaveric CT Scans
National Institutes of Health (NIBIB)
$30,805 - May 2017–May 2021
Integration of Physical and Virtual Cadavers in a Hybrid Gross Anatomy Curriculum
Center for Educational Innovation
Role: Co-Investigator
$10,000 - September 2011–August 2012
Decision Support System for Predicting Outcome of ER+ Breast Cancers
National Institutes of Health
Role: Co-Investigator
$207,067 - September 2007–May 2010
Accurate and Reproducible Computerized Detection and Grading of Prostate Cancer from Histopathology
Department of Defense
Role: Principal Investigator
$92,500
Patents:
- Malignancy Diagnosis Using Content-based Image Retrieval of Tissue Histopat This invention relates to computer-aided diagnostics using content-based retrieval of histopathological image features. Specifically, the invention relates to the extraction of image features from a histopathological image based on predetermined criteria and their analysis for malignancy determination. (2012)
Journal Articles:
- Kapustin DA, Yun J, Su V, Rubin SJ, Modica I, Chung D, Fan J, Khan MN, Chai RL, Karasick M, Doyle S, Brandwein-Weber M, Urken ML. (2024) Frozen Section Timeout: Pilot Study to Reconcile Margins Using 3D Resected Specimen and Defect Scans. The Laryngoscope (Feb), 134(2): 725-731.
- Finkelstein S, Timmaraju VA, Samankan S, O'Malley Q, Kapustin D, Spaulding S, Xing M, Matloob A, Beute J, Seo G, Saturno M, Greenberg L, Wein L, Gonzalez-Velazquez C, Doyle S, Levine J, Urken M, Brandwein-Weber M. (2023) Functional loss of tumor suppressor genes detected by loss of heterozygosity, but not driver mutations, predicts aggressive lymph node status in papillary thyroid carcinoma. Pathology, research and practice (Nov), 251: 154842.
- Kapustin D, Su V, Yun J, Rubin SJ, Chung D, Modica I, Khan MN, Chai RL, Karasick M, Doyle S, Brandwein-Weber M, Urken ML. (2023) iPad Annotation of 3D Surgical Models Using Procreate®: Novel Documentation of Supplemental Margins. The Laryngoscope (Nov).
- Yun J, Su V, Kapustin D, Rubin SJ, Brandwein-Weber M, Khan MN, Chai R, Doyle S, Karasick M, Urken ML. (2023) Intraoperative three-dimensional scanning of head and neck surgical defects: Enhanced communication and documentation of harvested supplemental margins. Head & neck (Oct), 45(10): 2690-2699.
- Lewis S, Inglis S, Doyle S. (2023) The role of anatomical context in soft-tissue multi-organ segmentation of cadaveric non-contrast-enhanced whole body CT. Medical physics (Aug), 50(8): 5061-5074. doi:10.1002/mp.16330
- DeRosa A, Ablove T, Doyle S, Lewis S. (2023) Comparison of Bony Pelvic Dimensions and Demographic Risk Factors in Individuals With and Without Pelvic Organ Prolapse. Obstetrics & Gynecology (May), 141(5S) doi:10.1097/01.AOG.0000930008.01080.64
- Ablove T, DeRosa A, Lewis S, Benson K, Mendel F, Doyle S. (2023) Pelvic Floor Pressures Differ Based on Location in the Pelvis and Body Position: A Cadaver Mode. Bioengineering (Basel, Switzerland) (Mar), 10(3). doi:10.3390/bioengineering10030329
- Wysocki MA, Doyle ST. (2023) Advancing Osteoporosis Evaluation Procedures: Detailed Computational Analysis of Regional Structural Vulnerabilities in Osteoporotic Bone. Journal of personalized medicine (Feb), 13(2). doi:10.3390/jpm13020321
- Wysocki MA, Lewis SA, Doyle ST. (2023) Developing Patient-Specific Statistical Reconstructions of Healthy Anatomical Structures to Improve Patient Outcomes. Bioengineering (Basel, Switzerland) (Jan), 10(2). doi:10.3390/bioengineering10020123
- Samankan S, Militello L, Seo G, Everest S, O'Malley Q, Spaulding SL, Xing M, Matloob A, Beute J, Chai R, Doyle S, Urken ML, Brandwein-Weber M. (2022) Tall cell variant papillary thyroid carcinoma impacts disease-free survival at the 10 % cut-point on multivariate analysis. Pathology, research and practice (Aug), 236: 154012.
- Wysocki MA, Doyle S. (2022) Enhancing biomedical data validity with standardized segmentation finite element analysis. Scientific reports (Jun), 12(1): 9860. doi:10.1038/s41598-022-13961-0
- Folmsbee J, Zhang L, Lu X, Rahman J, Gentry J, Conn B, Vered M, Roy P, Gupta R, Lin D, Samankan S, Dhorajiva P, Peter A, Wang M, Israel A, Brandwein-Weber M, Doyle S. (2022) Histology segmentation using active learning on regions of interest in oral cavity squamous cell carcinoma. Journal of pathology informatics (Jan), 13: 100146. doi:10.1016/j.jpi.2022.100146
- Whitney J, Corredor G, Janowczyk A, Ganesan S, Doyle ST, Tomaszewski J, Feldman M, Gilmore H, Madabhushi A. (2018) Quantitative nuclear histomorphometry predicts oncotype DX risk categories for early stage ER+ breast cancer. BMC Cancer (May), 18(1)
- Gurcan, MN, Tomaszewski JE, Overton, JA, Doyle ST, Ruttenberg, A, Smith, B. (2016) Developing the Quantitative Histopathology Image Onetology(QHIO): A Case study using the hot spot detection problem. J. Biomed Inform (Dec), 66
- Janowczyk A, Doyle S, Gilmore H, Madabhushi A, Doyle ST. (2016) A resolution adaptive deep hierarchical (RADHicaL) learning scheme applied to nuclear segmentation of digital pathology images. Comput Methods Biomech Biomed Eng Imaging Vis (Apr), 6(3)
- Doyle ST, Brandwein-Gensler MS, Tomaszewski JE. (2016) Quantification of tumor morphology via 3D histology; application to oral cavity cancers. SPIE (Jan)
- Sridhar A, Doyle S, Madabhushi A, Doyle ST. (2015) Content-based image retrieval of digitized histopathology in boosted spectrally embedded spaces. J Pathol Inform (Jun), 6
- Smith B, Arabandi S, Brochhausen M, Calhoun M, Ciccarese P, Doyle S, Gibaud B, Goldberg I, Kahn CE, Overton J, Tomaszewski J, Gurcan M, Doyle ST. (2015) Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform (Jun), 6
- Smith B., Arabandi S., Brochhasen M., Calhoun M., Ciccarese P., Doyle ST, Gibaud B., Goldberg I., Kahn CE Jr., Overton J., Tomaszewski JE, Gurcan M. (2015) Biomedical imaging ontologies: A summary and proposal for future work. J Pathol Inform (Jun), 23(6:37)
- Doyle ST, Feldman MD, Shih N, Tomaszewski JE, Madabhushi A. (2012) Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer. BMC Bioinformatics (Oct), 13
- Doyle ST, Feldman MD, Tomaszewski JE, Madabhushi A. (2012) A boosted Bayesian multiresolution classifier for prostate cancer detection from digitized needle biopsies. IEEE Transactions on Biomedical Engineering (May), 59(5)
- Doyle ST, Monaco JP, Feldman MD, Tomaszewski JE, Madabhushi A. (2011) An Active Learning Based Classification Strategy for the Minority Class Problem: Application to Histopathology Annotation. BMC Bioinformatics (Oct), 12
- Madabhushi A, Agner S, Basavanhally A, Doyle ST, Lee G. (2011) Computer-aided prognosis: predicting patient and disease outcome via quantitative fusion of multi-scale, multi-modal data. Computerized Medical Imaging and Graphics (Oct), 35(7-8)
- Madabhushi A, Doyle ST, Lee G, Basavanhally A, Monaco J, Masters S, Tomaszewski JE, Feldman M. (2010) Integrated diagnostics: a conceptual framework with examples. Clinical Chemistry and Laboratory Medicine (Jan), 48(7)
- Alexe G, Monaco J, Doyle ST, Basavanhally A, Reddy A, Seiler M, Ganesan S, Bhanot G, Madabhushi A. (2009) Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging. Experimental Biology and Medicine (Jan), 234(8)
Abstracts:
- Balachandran D, Folmsbee J, Brandwein-Weber M, and Doyle ST. (2021) Quantitative tissue architecture features are statistically similar between human-annotated and AI-generated tumor label maps in early-stage oral cavity cancer. Modern Pathology, United States and Canadian Academy of Pathology. (Feb) 889-926, (638) Poster
- Folmsbee J, Brandwein-Weber M, Doyle ST. (2021) Whole slide analysis of oral cavity cancer: Large scale active learning. Modern Pathology, (Feb) 889-926, (642) Poster
- Lewis S, Folmsbee J, Inglis SD, Doyle ST. (2018) Building a Hybrid Gross Anatomy Curriculum: Integration of Virtual & Cadaveric Models. The FASEB Journal, (Apr)
- Folmsbee J, Doyle ST. (2018) Active Deep Learning: Improved Training Efficiency of Convolutional Neural Networks for Tissue Classification in Oral Cavity Cancer. 2018 15th IEEE International Symposium on Biomedical Imaging, (Apr)
- Johnson S, Brandwein M, Doyle ST. (2018) Registration parameter optimization for 3d tissue modeling from resected tumors cut into serial H&E slides. Proc. SPIE 10581, Medical Imaging 2018: Digital Pathology, 105810T, (Mar)
- Therrien R, Doyle ST. (2018) Role of training data variability on classifier performance and generalizability. Proc. SPIE 10581, Medical Imaging 2018: Digital Pathology; 1058109, (Mar)
- Johnson S, Ablove TS, Doyle ST. (2017) Macroscopic Anatomy at Microscopic Scale: Registration of Serial Sections of Histopathology for 3d. 15th Annual Meeting of Imaging Network Ontario, (Mar)
- Therrien R, Mangione W, Doyle ST. (2017) Quantitative Dataset Similarity for Fusing Multi-Institutional Image Collections. 15th Annual Meeting of Imaging Network Ontario, (Mar)
- Salunke SU, Ablove TS, Danforth TL, Tomaszewski JE, Doyle ST. (2017) Data-driven sampling method for building 3d anatomical models from serial histology. Proc. SPIE 10140, Medical Imaging 2017: Digital Pathology; 1014005, (Feb)
- Doyle ST, Brandwein-Gensler MS, Tomaszewski JE. (2016) Quantification of tumor morphology via 3d histology: Application to oral cavity cancers. Proc. SPIE 9791, Medical Imaging 2016: Digital Pathology; 979112, (Feb)
- Doyle ST, Feldman MD, Tomaszewski JE, Shih N, Madabhushi A. (2011) Cascaded multi-class pairwise classifier (CascaMPa) for normal, cancerous, and cancer confounder classes in prostate histology. 2011 IEEE International Symposium on Biomedical Imaging (ISBI), (Apr)
- Sridhar A, Doyle ST, Madabhushi A. (2011) Boosted Spectral Embedding (BoSE): Applications to Content-Based Image Retrieval of Histopathology. 2011 8th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Madabhushi A, Basavanhally A, Doyle ST, Agner S, Lee G. (2010) Computer-Aided Prognosis: Predicting Patient and Disease Outcome Via Multi-Modal Image Analysis. 2010 7th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Doyle ST, Monaco J, Madabhushi A, Lindholm S, Ljung P, Ladic L, Tomaszewski JE, Feldman M. (2010) Evaluation of effects of JPEG2000 compression on a computer-aided detection system for prostate cancer on digitized histopathology. 2010 7th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Basavanhally A, Doyle ST, Madabhushi A. (2010) Predicting Classifier Performance with a Small Training Set: Applications to Computer-Aided Diagnosis and Prognosis. 2010 7th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Lee G, Doyle ST, Monaco J, Master SR, Feldman MD, Tomaszewski JE, Madabhushi A. (2009) A Knowledge Representation Framework for Integration, Classification of Multi-Scale Imaging and Non-Imaging Data: Preliminary Results in Predicting Prostate Cancer Recurrence by Fusing Mass Spectrometry and Histology. 2009 6th IEEE International Syposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Naik S, Doyle ST, Agner S, Madabhushi A, Feldman MD, Tomaszewski JE. (2008) Automated gland and nuclei segmentation for grading of prostate and breast cancer histopathology. 2008 5th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Doyle ST, Agner S, Madabhushi A, Feldman MD, Tomaszewski JE. (2008) Automated grading of breast cancer histopathology using spectral clustering with textural and architectural image features. 2008 5th IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, (Jan)
- Doyle ST, Rodriguez C, Madabhushi A, Tomaszeweski J, Feldman M. (2006) Detecting prostatic adenocarcinoma from digitized histology using a multi-scale hierarchical classification approach. Conf Proc IEEE Eng Med Biol Soc, (Jan)
- Doyle ST, Madabhushi A, Feldman MD, Tomaszewski JE. (2006) A boosting cascade for automated detection of prostate cancer from digitized histology. MICCAI, Lecture Notes in Computer Science, (Jan)
Evaluative Studies and Case Reports:
- Lewis S, Inglis S, Doyle ST. (2021) Seckel Syndrome & Skull Morphology: Quantifying Characteristics. International Journal of Case Reports (Feb), 202(5): 1-13. doi:10.28933/ijcr-2021-02-1205
Professional Memberships:
- United States & Canadian Association of Pathologists; USCAP Academic Member (2018–present)
- RIS2E Faculty Member; Structural Sciences Learning Center (SSLC) faculty member, University at Buffalo, Buffalo, NY (2018–present)
- Society of Photonics and Imaging Engineers (SPIE) (2014–present)
Presentations:
- "Computational Pathology Tools for Head and Neck Pathology" Head and Neck MDT Lifehouse Meeting (2023)
- "SUNYCell: A Collaborative Computational Pathology Framework" ITU/WHO AI-4-Health Meeting (2023)
- "Computational Pathology in Practice: Analyzing Oral Cavity Cancer" Pathology & Laboratory Medicine Departmental Seminar (AI Interest Group), University of California, Irvine, Orange, CA (2021)
- "Why – And What – Can We Do?" Histology Image Analysis (HIMA) Imaging Science Workshop (2021)
- "Hands-on ‘0 to AI’ (Part I) – Classical ML" PathLAKE Masterclass: AI for Pathologists, University of Warwick, PathLAKE Center of Excellence (2021)
- "How to Solve a Cpath Problem: Steps and Workflow" PathLAKE Masterclass: AI for Pathologists, University of Warwick, PathLAKE Center of Excellence (2021)
- "Predicting Early Stage Oral Cavity Cancer Recurrence Using Computational Pathology and Artificial Intelligence" City-Wide Grand Rounds Lecture; Department of Medicine; University at Buffalo (2021)
- "Building an AI School for Pathology" PathLAKE Masterclass: Data Science for Computational Pathology; PathLAKE Center of Excellence, University of Warwick (2020)
- "Building and Deploying Machine Learning and Deep Learning Solutions for Computational Pathology" Microcredit Course: Computational Pathology Introduction; Indian Institute of Technology Kharagpur (2020)
- "Introduction to Machine Learning (AKA Artificial Intelligence)" Resident Lecture; Department of Pathology & Anatomical Sciences; University at Buffalo (2019)
- "Biomedical Imaging Ontologies to Promote Interoperability of Heterogeneous Data" American Society of Nephrology (ASN) National Meeting: Kidney Week (2019)
- "Basic Principles of Image Analysis, Segmentation, Feature Extraction" American Society of Nephrology (ASN) GlomCon Series; Computational Nephropathology: From Basics to Applications (2019)
- "Building an AI School for Pathology: Workflow for Human-AI Interfaces" 31st European Congress of Pathology (ECP): Computational Pathology Symposium (2019)
- "AI and Pathology in Training: Building and Explaining Algorithms to Medical Students" Histology Image Analysis (HIMA) Pathology Informatics Summit (2019)
- "Computational Pathology and Anatomy using Traditional and Deep Machine Learning Methods" Grand Rounds; Department of Biomedical Informatics; University at Buffalo (2019)
- "Machine Learning for the Practicing Pathologist" USCAP Workshop for Clinical Pathology (2019)
- "Artificial Intelligence School for Pathology: Understanding Deep and Traditional Machine Learning for Oral Cavity Cancer Risk Prediction" Grand Rounds; Department of Pathology & Anatomical Sciences; University at Buffalo (2018)
- "Computational Pathology for Risk Prediction" Seminar Series; Department of Pathology; Ichan School of Medicine, Mount Sinai Hospital (2018)
- "Image Analysis, Graph Theory, and Machine Learning for 2D & 3D Modelling of Oral Cavity Cancer" Seminar Series; Department of Pathology; Ichan School of Medicine, Mount Sinai Hospital (2017)
- "HistoCAD in the Prediction of Outcomes" ASIP Bioimaging Workshop; American Society for Investigative Pathology (2014)
Service Activities:
- NIH SPORE Grant Reviewer: Responsible for reviewing large multi-center grants as part of the NIH SPORE Mechanism, providing scores and participating in grant center discussions.; Reviewer (2021)
- Prepare for and participate in LCME Accreditation Site Visits. Responsible for providing junior faculty input on medical school curriculum, education, and environment.; LCME Group Junior Faculty Representative (2019)
- Mentor undergraduate students from under-represented groups (first-generation and low-income backgrounds) on their path to a PhD.; McNair Scholarship Program Mentor (2019–present)
- Served as departmental representative from Pathology & Anatomical Sciences for the Ph.D. Program in Biomedical Sciences. Responsible for reviewing and leading discussions on applicants to the PPBS program. Developed PPBS curriculum changes as mandated by external reviewers.; PPBS Graduate Admissions and Steering Committee Member (2018–present)
- Develop and implement the “Atoms to Anatomy” research direction in JSMBS and the Department of Pathology and Anatomical Sciences.; Structural Sciences Learning Center (SSLC) (2018–present)
- March for Babies Raised over $1,000 for March of Dimes in Buffalo, NY; participated in the "March for Babies" event; Volunteer (2018–present)
- Develop JSMBS strategic plan for research direction and school basic science policies and focus. Advertise the efforts of the strategic planning committee.; JSMBS Research Strategic Planning Committee (2017–present)
- Responsible for reviewing, scoring, and interviewing applicants to the Department of Pathology & Anatomical Sciences.; Graduate Admissions Committee Member (Pathology & Anatomical Sciences) (2016–present)
- Responsible for working with PAS administration to ensure that the departmental website is transitioned and maintained to new JSMBS formatting.; Website Transition Committee Member (Pathology & Anatomical Sciences) (2016–2017)
- Mentor talented students from under-represented backgrounds who are focused on preparing for careers in STEM fields.; Collegiate Science and Technology Entry Program (CSTEP) Mentor (2016–present)
- Responsible for reviewing, discussing, and interviewing candidates for BME junior faculty positions.; Faculty Recruitment Committee Member (Biomedical Engineering) (2016–present)
- Responsible for reviewing, discussing, and interviewing candidates for the PAS junior faculty hires.; Faculty Recruitment Committee Member (Pathology & Anatomical Sciences) (2016–present)
- Responsible for running and moderating speaker sessions, reviewing papers, and contributing to the conference direction for SPIE Medical Imaging: Digital Pathology Sessions; SPIE Medical Imaging Program Committee and Session Chair (2016–present)
- Responsible for discussing and voting on matters concerning the governance of the graduate program. Also responsible for shaping the department vision for the future.; Graduate Program Steering & Executive Committee Member (Pathology & Anatomical Sciences) (2015–present)
- Responsible for reviewing papers and moderating the Bioimaging Session at Pattern Recognition in Bioinformatics; Pattern Recognition in Bioinformatics (PRIB) Session Chair and Committee Member (2010)
- Responsible for presenting research and fielding community questions during panel discussion and Q&A; Histology Image Analysis (HIMA) Conference Panel Member (2009–2015)
- Peer Reviewer for Journals Human Pathology, Medical Imagine Analysis, Medical Physics, Transactions on Biomedical Engineering, BioMedCentral (BMC) Cancer, BMC Bioinformatics, Society of Photonics and Imaging Engineers (SPIE), Medical Image Computing and Computer-Assisted Intervention, International Symposium on Biomedical Imaging (ISBI); Reviewer (2007–present)