Quantitative BioImaging Lab.

"seeing more with deep learning"

Young Hwan Chang, Ph.D

Assistant Professor in the Department of Biomedical Engineering (BME); the Computational Biology Program in the School of Medicine; OHSU Center for Spatial Systems Biomedicine Oregon Health and Science University (OHSU)

Biography: Dr. Young Hwan Chang received his Ph.D in Mechanical Engineering from University of California, Berkeley under the supervision of Prof. Claire J. Tomlin (EECS). Then, he worked as a postdoctoral researcher at Hybrid Systems Laboratory in the Department of Electrical Engineering and Computer Sciences, UC Berkeley. Previously, he also worked at Cognitive Robotics Research Center, Korea Institute of Science and Technology (KIST) and Hyundai-Kia R&D Center.

Research Interests: Quantitative imaging analysis, Data-driven system identification, Control theory, Modeling of biological systems, Estimation, Brain-Machine-Interface, Machine Learning

".. Proving that something can be done that many people said was impossible. - Elon Musk"

Google Scholar ORCID

What's New

Jan, 2019: Our paper "Robust cell detection and segmentation for image cytometry reveal Th17 cell heterogeneity" is accepted in Cytometry: Part A. Congratulations!
Dec, 2018: Geoff got International Association for Breast Cancer Research (IABCR) conference 2019 travel award. Congratulations!
Dec, 2018: Our application to the Biomedical Innovation Program (BIP) was selected for funding! Congrats Erik and Geoff.
Dec, 2018: Collaborative paper with Dr. Beatty "VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy" is published in PNAS. Congrats Julia and Kimberly.
Nov, 2018: Geoff and Erik present their recent work @ CSBC/PS-ON Image Analysis Working Group
Oct, 2018: Attended the Oregon Translational Chemical Biology Symposium, Oct 30, 2018
- Poster: "A versatile peptide tag for labeling proteins for light and electron microscopy" (Julia Doh , J on White, Hannah Zane, Young Hwan Chang, Claudia Lopez, Caroline Enns, and Kimberly Beatty)
Oct, 2018: Collaborative paper with Dr. Lund "IFNγ-Activated Dermal Lymphatic Vessels Inhibit Cytotoxic T cells in Melanoma and Inflamed Skin" is accepted in Journal of Experimental Medicine.
Oct, 2018: Our paper "Variational Autoencoding Tissue Response to Microenvironment Perturbations" has been accepted at SPIE Medical Imaging 2018 (Oral Presentation).
Oct, 2018: attended PNW Tumor Microenvironment Symposium, Oct 8, 2018
Sept, 2018: attended several meetings
Sept, 2018: Elliot won best presentation in PMCB retreat. Congratulations!
Sept, 2018: Erik Burlingame rejoined my Lab for pursuing his Ph.D in BME.
Sept, 2018: Our collaborative paper with Samsung Medical Center has been accepted for publication in Scientific Reports. (link)
Aug, 2018: Our collaborative proposal “Deciphering the immune microenvironment in oesophageal adenocarcinoma and pre-cancerous lesions to a single cell resolution” has been selected for CRUK-OHSU Spark Award.
July, 2018: Our collaborative proposal on “Understanding Therapeutics Failures Through 4D Single-cell Analysis of Metabolic Heterogeneity” presented at the Innovations Lab has been selected for an award from the Jayne Koskinas Ted Giovanis Foundation for Health and Policy (Minjoung Kyoung, Michael Konopka, Tara Sigdel, Young Hwan Chang, and Jing Ma)
July, 2018: Our collaborative work just came out online (Cell): "Toward Minimal Residual Disease-Directed Therapy in Melanoma"
July, 2018: Congratulations Geoffrey for passing his PhD qualifying exam!
June, 2018: Attended 2018 Data Science Innovation Lab
June, 2018: Attended Systems Genetics of Cancer 2018
May, 2018: Our application to the Brenden-Colson Center for Pancreatic Care’s pilot award program was selected for funding! ($100K)
May, 2018: presented "Deep Understanding of Biomedical Images" M2CH workshop.
May, 2018: Our collaborative paper with Drs. Amanda Lund and Jean-Christophe Marine has been accepted for publication in Cell.
May, 2018: Our paper "Secure Estimation for Cyber-Physical Systems against Adversarial Attacks" has been accepted for publication in Automatica.
April, 2018: Erik presented "Predicting biomarker distribution in medical images with SHIFT" (Oral Presentation) @ OHSU Research Week 2018.
April, 2018: Will attend Systems Genetics of Cancer 2018 (Linking somatic mutations to molecular, cellular and patient phenotypes), June 11-13 2018 OHSU Collaborative Life Science Building, http://www.markowetzlab.org/SystemsGeneticsCancer2018/
April, 2018: Selected to attend the 2018 Data Science Innovation Lab: Mathematical Challenges of Single Cell Dynamics on June 25-29th, 2018 in Bend, Oregon https://bigdatau.ini.usc.edu/innovationlab2018
April, 2018: Elliot attended ISBI 2018 and presented our work "A method for quantification of calponin expression in myoepithelial cells in immunohistochemical images of ductal carcinoma in situ"
March, 2018: James Haddad (Univ. of Pittsburgh) will join CSBC/PS-ON Summer Undergraduate Research Program and work in our lab during the summer (research mentors: Drs. Gray and Chang).
March, 2018: Luke Ternes (BME, Georgia Institute of Technology, 2017) and Tina Ghodsi (BioE and BME, Iran University of Science and Technology) will join my group. Welcome!
March, 2018: Our collaborative paper with Dr. Kyoung-Mee Kim @ Samsung medical center, "Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability" is published in ESMO open. (link)
Feb, 2018: Delivered talk entitled "Deep Understanding of Biomedical Images" at DataJamboree: Machine Learning and GPU Computing, OHSU, February 2018.
Feb, 2018: Will serve as a CSBC/PS-ON Junior Investigator Meeting Planning Committee
Feb, 2018: Erik presented our work (SHIFT: Speedy Histopathological-to-ImmunoFluorescent Translation of whole slide images using conditional generative adversarial networks) at the SPIE Medical Imaging (link).
Feb, 2018: Congratulations Elliot for passing his PhD qualifying exam!
December, 2017: Our paper "A method for quantification of calponin expression in myoepithelial cells in immunohistochemical images of ductal carcinoma in situ" has been accepted at IEEE International Symposium on Biomedical Imaging (ISBI'18), Washington DC, April 4-7, 2018
December, 2017: Will serve as a PC Member for ICML 2018
December, 2017: Geoffrey Schau (PhD student) will join my group. Welcome!
October, 2017: Talk @ Knight Cancer Research Group Meeting (10/19) @ Knight Computational Lunchtime Seminars (10/23)
October, 2017: Our paper "SHIFT: Speedy Histopathological-to-ImmunoFluorescent Translation of whole slide images using conditional generative adversarial networks" has been accepted at SPIE Medical Imaging 2018 (Oral Presentation).
September, 2017: Attended Image-based Cell Atlas Workshop, 9/28-9/29, Allen Institute, Seattle
September, 2017: Attended the 2017 Early Detection of Cancer Conference, Cambridge, UK
July, 2017: Attended the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'17), presented two papers "Multiplexed Immunohistochemistry Image Analysis using Sparse Coding" and "Deep Leaning based Nucleus Classification in Pancreas Histological Images", and served as a co-chair for the session "Histologic Image Analysis".
June, 2017: Attended the 32nd Congress of the International Society for Advancement of Cytometry (CYTO 2017), Boston, June 11-14 and presented "Sparse coding-based image cytometry for multiplexed Immunohistochemistry"
June, 2017: The first pilot funds for cancer early detection have been awarded (link)
June, 2017: Elliot Gray (PhD student) will join my group. Welcome!
May, 2017: Selected as a recipient of a travel award to the 2017 CRUK/OHSU Knight Cancer Institute Early Detection Conference in Cambridge, UK, this coming September 20-22.
May, 2017: Our paper "Secure State Estimation and Control for Cyber Security of the Nonlinear Power Systems" has been accepted for publication in IEEE Transactions on Control of Network Systems.
April, 2017: Our application ("Risk Stratification of Early Melanomas by Deep Histopathological Analysis") to a Cancer Early Detection and Research (CEDAR) Center Seed Grant has been selected for milestone-driven funding. Congratulation Team!
April, 2017: Two papers, "Multiplexed Immunohistochemistry Image Analysis using Sparse Coding" and "Deep Leaning based Nucleus Classification in Pancreas Histological Images" have been accepted at the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.
March, 2017: Our paper, "Sparse coding-based image cytometry for multiplexed Immunohistochemistry" has been accepted at the 32nd Congress of the International Society for Advancement of Cytometry (CYTO2017), Hynes Convention Center Boston, Massachusetts, June 10-14, 2017 (Oral Presentation)
February, 2017: Our paper, Tsujikawa et al, "Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis" has been accepted for publication in Cell Reports. (link)
February, 2017: I am thrilled to join the team led by Joe W. Gray, that just becomes a new NCI Center for Cancer Systems Biology (U54).
February, 2017: Attended SPIE Medical Imaging (Digital Pathology) Conference and presented "Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity", Feb 11-16, 2017
January, 2017: Attended SMMART "Mechanisms of Resistance" Research Retreat (SMoRRR), Jan 30-31, 2017
January, 2017: Two papers "Secure state estimation for linear systems with sparse malicious packet drops" and "Secure State Estimation for Nonlinear Power Systems under Cyber Attacks" have been accepted at the American Control Conference (ACC'17), May 24-26, 2017
January, 2017: Our paper "Breast Cancer Histopathology Image Analysis Pipeline for Tumor Purity Estimation" has been accepted at the IEEE International Symposium on Biomedical Imaging (ISBI'17), April 18-21, 2017
October, 2016: Our paper "Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity" has been accepted at SPIE Medical Imaging (Digital Pathology), Feb. 11-16, 2017
September, 2016: Serving as a PC member for AISTATS 2017
August, 2016: Attended IEEE EMBC 2016, Aug 16-20, Orlando
June, 2016: Attended The SONDLAND-DURANT Early Detection of Cancer Conference, June 21-24, 2016, OHSU
May, 2016: Our paper "Quantitative Analysis of Histological Tissue Image based on Cytological Profiles and Spatial Statistics" has been accepted at the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’16, 4 pages paper)
April, 2016: Attended MEP LINCS Retreat, April 11-12, 2016, OHSU
March, 2016: Attended AMIGOS (Applied Mathematics in Germinating Oncology Solutions) Workshop March 22-23, 2016 NIH Campus, Bethesda, MD
February, 2016: Invited to participate in the Applied Mathematics in Germinating Oncology Solutions (AMIGOS) Workshop (hosted by the National Cancer Institute in collaboration with the Jayne Koskinas Ted Giovanis Foundation for Health and Policy (JKTGF) and the Breast Cancer Research Foundation (BCRF))
December, 2015: Attended CDC 2015, Osaka, Japan
November, 2015: Our paper "Secure estimation for unmanned aerial vehicles against adversarial attacks" has been accepted for oral presentation at ICAS 2016
October, 2015: Attended NCI-OHSU Cancer Heterogeneity Workshop (talk: "Quantitative Image Analysis of cell-to-cell Heterogeneity")
October, 2015: Our paper "Network Identifiability via Compressed Sensing" has been accepted for publication in Automatica.
August, 2015: Our paper "Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices" has been accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics 2015.
July, 2015: I have two papers accepted at CDC 2015 (Osaka, Japan)
July, 2015: I will join Oregon Health & Science University (OHSU) this fall as an assistant professor in the Department of Biomedical Engineering (BME) and the Computational Biology Program in the School of Medicine. I am looking forward to working with many great faculty members at OHSU.
June 4-5, 2015: Attended Swarm Lab Summer Retreat 2015, Berkeley (link)
May 28-29, 2015: Attended FORCES Research Exchange and Advisory Board Meeting, Berkeley (link)
May 5-7, 2015: Attended ICBP PI Meeting, NIH Campus, Washington DC
April 9, 2015: talk: "Bridging the gap: Data and Modeling", Stanford Center for Systems Biology Weekly Meeting
April 1-2, 2015: talk: "Bridging the gap: Data and Modeling", Oregon Health and Science University (Computational Biology)
Dec 15-17, 2014: Attended IEEE Conference on Decision and Control, LA, USA ("Design of Neural Decoder by Sensory Prediction and Error Correction")
Nov 15, 2014: Attended ICBP Retreat (Oregon Health & Science University), Portland, OR
Nov 9-14, 2014: Attended RECOMB/ISCB Conference on Regulatory & System Genomics 2014, San Diego CA (talk: "Reconstruction of Gene Regulatory Networks based on Repairing Sparse Low-rank Matrices")
Sept 4-5, 2014: Attended NCI's Early Stage Investigators Meeting, Broad Institute
June 24-27, 2014: talks: "A Design of Neural Decoder by Reducing Discrepancy between Manual Control (MC) and Brain Control (BC)", "Reconstruction of Gene Regulatory Networks with Hidden Node", European Control Conference, Strasbourg France
May 27, 2014: Attended Stanford Center for Systems Biology (1st Annual Center Meeting, Poster presentation)
May 5-7, 2014: Attended annual ICBP PI meeting (Poster presentation), Shady Grove NCI campus, Rockville, Maryland
April 7, 2014: talk: "Data-driven Graph Reconstruction using Compressive Sensing", Center for Systems and Synthetic Biology Meeting, UCSF
Dec 10-13, 2013: talk: "Low-rank Representation of Neural Activity and Detection of Submovements", IEEE Conference on Decision and Control, Florence, Italy
Dec 4, 2013: talk: "Towards a Systems Understanding in Biology: Data and Modeling", KI Field Robotics, KAIST
Dec 2, 2013: talk: "Towards a Systems Understanding in Biology: Data and Modeling", Dept. of Mechanical Engineering, UNIST
Oct 11-12, 2013: Visited Oregon Health and Science University (meetings, discussion), Portland, OR
June 12, 2013: Started as a Postdoctoral Researcher, Dept. of Electrical Engineering and Computer Sciences, UC Berkeley
May 19, 2013: Attended Graduation Ceremony, UC Berkeley
May 7, 2013: Dissertation talk: "Towards a Systems Understanding in Biology: Data and Modeling", Dept. of Mechanical Engineering, UC Berkeley
May 1, 2013: Attended ICBP Retreat, Oregon Health and Science University, Portland, OR
Dec 10-13, 2012: talk: “Data-driven Graph Reconstruction using Compressive Sensing", IEEE Conference on Decision and Control, Maui, HI
Oct 17-19, 2012: talk: "Modeling Response of Biological Signal Pathways using a Hybrid Boolean Framework", ASME DSCC2012, Fort Lauderdale, FL
May 7-9, 2012: Attended NCI's ICBP PI Meeting (Poster presentation), Embassy Suits, San Francisco Airport Waterfront in Burlingame, CA
Mar 7-9, 2012: Attended NSF EFRI Grantees Conference (Poster presentation), Key Bridge Marriott, Arlington, VA
Dec 12-15, 2011: talk: "Inference of Temporally Evolving Network Dynamics with Applications in Biological Systems", IEEE Conference on Decision and Control, Orlando, FL
Sept 14-16, 2011: Attended ICBP Steering Committee Meeting (Poster presentation), New York
Aug 22, 2011: Attended Bay Area Physical Science-Oncology Center (PSOC) 2nd Annual Site Visit (Poster presentation), Stanley Hall, UC Berkeley
June 29-July 1, 2011: talks: "Optimization-based Inference for Temporally Evolving Boolean Networks with Applications in Biology", "Biologically-inspired Coordination of Multiple UAVs using Sliding Mode Control", American Control Conference, San Francisco, CA
Nov 23, 2010: Passed Qualifying Exam.
Oct 20-22, 2010: Attended NCI ICBP Mathematical Modeling Meeting of Cancer Systems (Poster presentation), UC Berkeley
April 22, 2010: Presented "Can human exoskeleton suit help paralyzed people to grasp and walk?" , CITRIS Big Ideas Competition (Final top 10), UC Berkeley
May, 2009: Joined Hybrid Systems Lab, Dept. of Electrical Engineering and Computer Sciences, UC Berkeley
Aug, 2008: Started a PhD program, Dept. of Mechanical Engineering, UC Berkeley