Ruogu Fang,
ASO PROF
Department:
EG-BIOMEDICAL ENGINEERING
Business Phone:
(352) 392-0584
Business Email:
ruogu.fang@ufl.edu
About Ruogu Fang
Related Links:
Accomplishments
Best Paper Award
2024
·
The 17th International Conference on Health Informatics (HEALTHINF/BIOSTEC), Italy, Rome
Inaugural AI Course Award
2024
·
University of Florida
Pioneering Research HiPerGator Award
2024
·
University of Florida Research Computing
Senior Member Grade
2024
·
National Academy of Inventors (NAI)
Rising Star
2023
·
Academy of Science Engineering and Medicine of Florida
Faculty Award for Excellence in Innovation
2022
·
Herbert Wertheim College of Engineering, University of Florida
Faculty Research Excellence Award
2022
·
J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida
Pruitt Family Endowed Faculty Fellowship
2022
·
J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida
Artificial Intelligence Catalyst Award
2021
·
NVIDIA-University of Florida
IEEE Senior Member
2018
·
Institute of Electrical and Electronic Engineering
Top-ranked (#1) in “Fovea Detection” System, First International Diabetic Retinopathy Grading and Segmentation Challenge
2018
·
IEEE International Symposium of Biomedical Imaging
Top-ranked (#1) in “Optical Disc Segmentation” System, First International Diabetic Retinopathy Grading and Segmentation Challenge
2018
·
IEEE International Symposium of Biomedical Imaging
Inaugural Class of the ACM Future of Computing Academy
2017
·
Academy of Computing Machinery
Robin Sidhu Memorial Young Scientist Award
2017
·
Society of Brain Mapping and Therapeutics
Ralph Lowe Junior Faculty Enhancement Award
2016
·
Oak Ridge Associated Universities
CISE Research Initiation Initiative (CRII) Award
2015
·
National Science Foundation
Best Paper Award
2010
·
The 17th International Conference on Image Processing
Teaching Profile
Courses Taught
2017-2022
BME3053C Computer Applications for BME
2019
BME6905 Individual Work in Biomedical Engineering
2017-2019
BME7979 Advanced Research
2017-2019
EGN4912 Engineering Directed Independent Research
2019,2021-2023
BME6938 Special Topics in Biomedical Engineering
2017-2018
BME6940 Supervised Teaching
2018
GMS7979 Advanced Research
2018
EEL7979 Advanced Research
2023
CIS6930 Special Topics in CIS
2023
BME4931 Special Topics in Biomedical Engineering
Research Profile
Open Researcher and Contributor ID (ORCID)
0000-0003-3980-3532
Publications
Academic Articles
2025
A Comprehensive Survey of Foundation Models in Medicine
IEEE Reviews in Biomedical Engineering.
1-22
[DOI] 10.1109/rbme.2025.3531360.
2025
Automated Imaging Differentiation for Parkinsonism.
JAMA neurology.
82(5):495-505
[DOI] 10.1001/jamaneurol.2025.0112.
[PMID] 40094699.
2024
Analysis and Visualization of Single-Cell Sequencing Data with Scanpy and MetaCell: A Tutorial.
Methods in molecular biology (Clifton, N.J.).
2757:383-445
[DOI] 10.1007/978-1-0716-3642-8_17.
[PMID] 38668977.
2024
BrainSegFounder: Towards 3D foundation models for neuroimage segmentation
Medical Image Analysis.
97
[DOI] 10.1016/j.media.2024.103301.
[PMID] 39146701.
2024
BrainSegFounder: Towards 3D Foundation Models for Neuroimage Segmentation.
ArXiv.
[PMID] 39184544.
2024
Deep Learning Analysis of Retinal Structures and Risk Factors of Alzheimer’s Disease.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference.
2024:1-4
[DOI] 10.1109/EMBC53108.2024.10782580.
[PMID] 40040194.
2024
Deep learning predicts prevalent and incident Parkinson’s disease from UK Biobank fundus imaging.
Scientific reports.
14(1)
[DOI] 10.1038/s41598-024-54251-1.
[PMID] 38351326.
2024
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.
PLoS computational biology.
20(4)
[DOI] 10.1371/journal.pcbi.1011351.
[PMID] 38598563.
2024
Disagreement on foundational principles of biological aging
PNAS Nexus.
3(12)
[DOI] 10.1093/pnasnexus/pgae499.
[PMID] 39660064.
2024
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects
PLOS Computational Biology.
20(3)
[DOI] 10.1371/journal.pcbi.1011943.
[PMID] 38547053.
2024
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.04.16.537079.
[PMID] 37163104.
2024
Machine learning-optimized non-invasive brain stimulation and treatment response classification for major depression.
Bioelectronic medicine.
10(1)
[DOI] 10.1186/s42234-024-00157-2.
[PMID] 39473014.
2024
Morphological profiling for drug discovery in the era of deep learning
Briefings in Bioinformatics.
25(4)
[DOI] 10.1093/bib/bbae284.
[PMID] 38886164.
2024
Morphological Profiling for Drug Discovery in the Era of Deep Learning.
ArXiv.
[PMID] 38168460.
2024
Neuron-level explainable AI for Alzheimer’s Disease assessment from fundus images.
Scientific reports.
14(1)
[DOI] 10.1038/s41598-024-58121-8.
[PMID] 38565579.
2024
Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics.
Bioinformatics advances.
4(1)
[DOI] 10.1093/bioadv/vbae158.
[PMID] 39529841.
2024
Precise and Rapid Whole-Head Segmentation from Magnetic Resonance Images of Older Adults using Deep Learning.
Imaging neuroscience (Cambridge, Mass.).
2
[DOI] 10.1162/imag_a_00090.
[PMID] 38465203.
2023
Association of longitudinal cognitive decline with diffusion MRI in Gray Matter, Amyloid, and Tau deposition.
Neurobiology of aging.
121:166-178
[DOI] 10.1016/j.neurobiolaging.2022.10.013.
[PMID] 36455492.
2023
DOMINO: Domain-aware loss for deep learning calibration
Software Impacts.
15
[DOI] 10.1016/j.simpa.2023.100478.
[PMID] 37091721.
2023
Editorial: Frontiers of women in brain imaging and brain stimulation.
Frontiers in human neuroscience.
17
[DOI] 10.3389/fnhum.2023.1208253.
[PMID] 37266325.
2023
Ethnic disparity in diagnosing asymptomatic bacterial vaginosis using machine learning
npj Digital Medicine.
6(1)
[DOI] 10.1038/s41746-023-00953-1.
[PMID] 37978250.
2023
Machine-learning defined precision tDCS for improving cognitive function
Brain Stimulation.
16(3):969-974
[DOI] 10.1016/j.brs.2023.05.020.
[PMID] 37279860.
2023
Medical Imaging Denoising
Medical Image Synthesis.
99-119
[DOI] 10.1201/9781003243458-10.
2022
CADA: Multi-scale Collaborative Adversarial Domain Adaptation for unsupervised optic disc and cup segmentation
Neurocomputing.
469:209-220
[DOI] 10.1016/j.neucom.2021.10.076.
2022
Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods.
BMC medical informatics and decision making.
22(Suppl 3)
[DOI] 10.1186/s12911-022-01996-2.
[PMID] 36167551.
2022
PIMA-CT: Physical Model-Aware Cyclic Simulation and Denoising for Ultra-Low-Dose CT Restoration
Frontiers in Radiology.
2
[DOI] 10.3389/fradi.2022.904601.
[PMID] 37492656.
2021
Baseline Neuroimaging Predicts Decline to Dementia From Amnestic Mild Cognitive Impairment.
Frontiers in aging neuroscience.
13
[DOI] 10.3389/fnagi.2021.758298.
[PMID] 34950021.
2021
Identify Diabetic Retinopathy-related Clinical Concepts Using Transformer-based Natural Language Processing Methods
2021 IEEE 9th International Conference on Healthcare Informatics (ICHI).
[DOI] 10.1109/ichi52183.2021.00089.
2021
Machine learning for physics-informed generation of dispersed multiphase flow using generative adversarial networks
Theoretical and Computational Fluid Dynamics.
35(6):807-830
[DOI] 10.1007/s00162-021-00593-9.
2021
Modular machine learning for Alzheimer’s disease classification from retinal vasculature.
Scientific reports.
11(1)
[DOI] 10.1038/s41598-020-80312-2.
[PMID] 33420208.
2021
Rotational and reflectional equivariant convolutional neural network for data-limited applications: Multiphase flow demonstration
Physics of Fluids.
33(10)
[DOI] 10.1063/5.0066049.
2021
TL1 Team Approach to Predicting Response to Spinal Cord Stimulation for Chronic Low Back Pain
Journal of Clinical and Translational Science.
5(s1):111-112
[DOI] 10.1017/cts.2021.685.
2021
Unraveling somatotopic organization in the human brain using machine learning and adaptive supervoxel-based parcellations.
NeuroImage.
245
[DOI] 10.1016/j.neuroimage.2021.118710.
[PMID] 34780917.
2020
A survey on medical image analysis in diabetic retinopathy.
Medical image analysis.
64
[DOI] 10.1016/j.media.2020.101742.
[PMID] 32540699.
2020
Artificial Intelligence for Characterizing Heart Failure in Cardiac Magnetic Resonance Images
Circulation.
142(Suppl_3)
[DOI] 10.1161/circ.142.suppl_3.15036.
2020
Domain-invariant interpretable fundus image quality assessment.
Medical image analysis.
61
[DOI] 10.1016/j.media.2020.101654.
[PMID] 32066065.
2020
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting.
Journal of the American Medical Informatics Association : JAMIA.
27(1):65-72
[DOI] 10.1093/jamia/ocz144.
[PMID] 31504605.
2020
IDRiD: Diabetic Retinopathy – Segmentation and Grading Challenge.
Medical image analysis.
59
[DOI] 10.1016/j.media.2019.101561.
[PMID] 31671320.
2020
Low-rise gable roof buildings pressure prediction using deep neural networks
Journal of Wind Engineering and Industrial Aerodynamics.
196
[DOI] 10.1016/j.jweia.2019.104026.
2020
Machine learning and individual variability in electric field characteristics predict tDCS treatment response.
Brain stimulation.
13(6):1753-1764
[DOI] 10.1016/j.brs.2020.10.001.
[PMID] 33049412.
2020
Physiological wound assessment from coregistered and segmented tissue hemoglobin maps
Journal of the Optical Society of America A.
37(8)
[DOI] 10.1364/josaa.394985.
2020
REFUGE Challenge: A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs.
Medical image analysis.
59
[DOI] 10.1016/j.media.2019.101570.
[PMID] 31630011.
2020
TL1 Team Approach to Predicting Short-term and Long-term Effects of Spinal Cord Stimulation
Journal of Clinical and Translational Science.
4(s1):120-120
[DOI] 10.1017/cts.2020.362.
2020
Transfer generative adversarial network for multimodal CT image super-resolution (Conference Presentation)
Medical Imaging 2020: Image Processing.
[DOI] 10.1117/12.2549533.
2019
Automatic Choroid Layer Segmentation from Optical Coherence Tomography Images Using Deep Learning
Scientific Reports.
9(1)
[DOI] 10.1038/s41598-019-39795-x.
[PMID] 30816296.
2019
Deep Evolutionary Networks with Expedited Genetic Algorithms for Medical Image Denoising
Medical Image Analysis.
54:306-315
[DOI] 10.1016/j.media.2019.03.004.
[PMID] 30981133.
2019
Development and Validation of the Automated Imaging Differentiation in Parkinsonism (AID-P): A Multi-Site Machine Learning Study.
The Lancet. Digital health.
1(5):e222-e231
[DOI] 10.1016/s2589-7500(19)30105-0.
[PMID] 32259098.
2019
Retinal Vessel Segmentation Using Minimum Spanning Superpixel Tree Detector.
IEEE transactions on cybernetics.
49(7):2707-2719
[DOI] 10.1109/TCYB.2018.2833963.
[PMID] 29994327.
2019
STIR-Net: Deep Spatial-Temporal Image Restoration Net for Radiation Reduction in CT Perfusion.
Frontiers in neurology.
10
[DOI] 10.3389/fneur.2019.00647.
[PMID] 31297079.
2018
Clinical Report Guided Retinal Microaneurysm Detection With Multi-Sieving Deep Learning
IEEE Transactions on Medical Imaging.
37(5):1149-1161
[DOI] 10.1109/tmi.2018.2794988.
2018
Mining Big Neuron Morphological Data
Computational Intelligence and Neuroscience.
2018:1-13
[DOI] 10.1155/2018/8234734.
[PMID] 30034462.
2017
TENDER: Tensor non-local deconvolution enabled radiation reduction in CT perfusion.
Neurocomputing.
229:13-22
[DOI] 10.1016/j.neucom.2016.03.109.
[PMID] 32523255.
2015
Robust Low-Dose CT Perfusion Deconvolution via Tensor Total-Variation Regularization
IEEE Transactions on Medical Imaging.
34(7):1533-1548
[DOI] 10.1109/tmi.2015.2405015.
2015
Sparsity techniques in medical imaging.
Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society.
46 Pt 1(Pt 1)
[DOI] 10.1016/j.compmedimag.2015.07.002.
[PMID] 26216851.
2015
Tissue-specific sparse deconvolution for brain CT perfusion
Computerized Medical Imaging and Graphics.
46:64-72
[DOI] 10.1016/j.compmedimag.2015.04.008.
2014
Improving low-dose blood-brain barrier permeability quantification using sparse high-dose induced prior for Patlak model.
Medical image analysis.
18(6):866-80
[DOI] 10.1016/j.media.2013.09.008.
[PMID] 24200529.
2014
Tensor total-variation regularized deconvolution kegularlzea ueconvolution for efficient low-dose CT perfusion.
Medical image computing and computer-assisted intervention : MICCAI … International Conference on Medical Image Computing and Computer-Assisted Intervention.
17(Pt 1):154-61
[PMID] 25333113.
2013
Tissue-specific sparse deconvolution for low-dose CT perfusion.
Medical image computing and computer-assisted intervention : MICCAI … International Conference on Medical Image Computing and Computer-Assisted Intervention.
16(Pt 1):114-21
[PMID] 24505656.
2013
Towards robust deconvolution of low-dose perfusion CT: sparse perfusion deconvolution using online dictionary learning.
Medical image analysis.
17(4):417-28
[DOI] 10.1016/j.media.2013.02.005.
[PMID] 23542422.
2012
Sparsity-based deconvolution of low-dose perfusion CT using learned dictionaries.
Medical image computing and computer-assisted intervention : MICCAI … International Conference on Medical Image Computing and Computer-Assisted Intervention.
15(Pt 1):272-80
[PMID] 23285561.
Grants
Dec 2024
ACTIVE
A Mechanistic Study to Investigate tDCS and Working Memory in MCI Patients
Role: Other
Funding: NATL INST OF HLTH NIA
Sep 2024
ACTIVE
Artificial Intelligence Passport for Biomedical Research (AIPassportBMR ): Digital Experiential Learning Community for Upskilling in Artificial Intelligence for Biomedical, Behavioral and Clinical Research
Role: Co-Investigator
Funding: NATL INST OF HLTH NIGMS
Aug 2024
ACTIVE
Development and application of whole-body patient-specific computational mesh phantoms for organ dosimetry and second primary cancer risk quantification following external beam radiotherapy
Role: Other
Funding: NATL INST OF HLTH NCI
Aug 2024
ACTIVE
Mechanism, connectivity, and outcome prediction of anxiety intervention from MRI-derived models in tDCS augmented cognitive training
Role: Other
Funding: NATL INST OF HLTH NIA
Jun 2024
ACTIVE
Mechanisms, response heterogeneity and dosing from MRI-derived electric field models in tDCS augmented cognitive training: a secondary data analysis of the ACT study
Role: Principal Investigator
Funding: NATL INST OF HLTH NIA
Jan 2024
ACTIVE
Identification of Prospective Predictors of Alcohol Initiation During Early Adolescence
Role: Other
Funding: NATL INST OF HLTH NIAAA
Sep 2023
ACTIVE
NCS-FO: Brain-Inspired Goal-Oriented and Bidirectional Deep Emotion Inference
Role: Principal Investigator
Funding: NATL SCIENCE FOU
May 2023
ACTIVE
Using Artificial Intelligence to Predict Cognitive Training Response in Amnestic Mild Cognitive Impairment
Role: Other
Funding: NATL INST OF HLTH NIA
May 2023
ACTIVE
Cognitively engaging walking exercise and neuromodulation to enhance brain function in older adults
Role: Co-Investigator
Funding: NATL INST OF HLTH NIA
Mar 2022
ACTIVE
Multi-Scale Evaluation and Mitigation of Toxicities Following Internal Radionuclide Contamination
Role: Co-Investigator
Funding: NORTHWESTERN UNIV
via NATL INST OF HLTH NIAID
Oct 2021
ACTIVE
Collaborative Research: SCH: Trustworthy and Explainable AI for Neurodegenerative Diseases
Role: Co-Investigator
Funding: NATL SCIENCE FOU
Sep 2021
ACTIVE
Southern HIV and Alcohol Research Consortium Biomedical Data Repository
Role: Project Manager
Funding: NATL INST OF HLTH NIAAA
Sep 2021
ACTIVE
Interventions to improve alcohol-related comorbidities along the gut-brain axis in persons with HIV infection
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAAA
Sep 2021
ACTIVE
SHARE Program: Innovations in Translational Behavioral Science to Improve Self-management of HIV and Alcohol Reaching Emerging adults
Role: Other
Funding: FL STATE UNIV
via NATL INST OF HLTH NIAAA
Aug 2021
ACTIVE
Acquisition, extinction, and recall of attention biases to threat: Computational modeling and multimodal brain imaging
Role: Co-Investigator
Funding: NATL INST OF HLTH NIMH
Jun 2021
– May 2024
Mechanisms, response heterogeneity and dosing from MRI-derived electric field models in tDCS augmented cognitive training: a secondary data analysis of the ACT study
Role: Principal Investigator
Funding: NATL INST OF HLTH NIA
Apr 2021
ACTIVE
Web-based Automated Imaging Differentiation of Parkinsonism
Role: Co-Investigator
Funding: NATL INST OF HLTH NINDS
Jan 2021
– Dec 2022
Artificial Intelligence Research Catalyst Fund
Role: Project Manager
Funding: UF RESEARCH
May 2020
ACTIVE
Forecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning framework
Role: Project Manager
Funding: NATL INST OF HLTH NIAID
Oct 2019
– Dec 2024
III: Small: Modeling Multi-Level Connectivity of Brain Dynamics
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Jun 2017
– Apr 2019
CRII: SCH:Characterizing, Modeling and Evaluating Brain Dynamics
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Apr 2017
– Jun 2024
HSC COM Matching Commitment
Role: Project Manager
Funding: UNIV OF FLORIDA
Apr 2017
– Jun 2021
OoR CTSI Institutional Matching Support
Role: Project Manager
Funding: UF DIV OF SPONSORED RES MATCHING FUNDS
Contact Details
Phones:
- Business:
- (352) 392-0584
Emails:
- Business:
- ruogu.fang@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 118205
GAINESVILLE FL 32611 - Business Street:
-
BMS BLDG J287
1275 CENTER DR
Gainesville FL 32611