Yan, Yuling

Professor and Founding Chair

Prof. Yuling Yan is the Phil and Bobbie Sanfilippo Professor and the Founding Chair of the Department of Bioengineering at SCU. She received a Ph.D. degree in mechanical engineering from Keio University, Yokohama, Japan, in 1991. She held post-doctoral fellow and research associate positions at McGill University (Montreal, Canada) and Max Planck Institute for Biochemistry, Munich, Germany from 1992-1996 where she dedicated her efforts to advancing the field by developing innovative methods for quantitative image and signal analysis in dynamic mechanical and biomolecular systems. Between 1997~1999, she served on the engineering faculty at the University of the Ryukyus, Japan, where she initiated research in an emerging area on robotic control of dexterous manipulators for biomedical applications.

Prof. Yan moved to the US in 1999 and while at the University of Wisconsin-Madison she collaborated with clinicians on high-speed digital imaging of human voice production. This period led to the development of novel methods and analytical platform for the processing of laryngeal images and the analysis of vocal fold vibrations that delivers useful clinical information. She was an assistant professor of engineering at the University of Hawaii-Manoa from 2002-2005 before moving to the Department of Otolaryngology at Stanford University where she is still affiliated as a consulting faculty. She was awarded an NSF grant (2004~2007) for her research on the technology development and application of the high-speed laryngeal imaging.

Professor Yan's research interests span a wide range of disciplines, including modeling, imaging, and analysis of biosignals and medical images for diverse biomedical applications. Presently, her research is primarily dedicated to leveraging machine learning and deep learning technologies for the early detection of various diseases. These include the identification of vocal pathologies, cardiac arrhythmia, and skin cancer, as well as the classification and localization of brain aneurysms, breast cancer, and multiple rib fractures using MRA, ultrasound, and CT imaging modalities. These projects are conducted in collaboration with a team of skilled radiologists based at the Santa Clara Valley Hospital.

Current Research Areas

• Biomedical imaging; Image/signal analysis and visualization
• AI-assisted disease classifications
• AI/Machine Learning for Human-Computer Interface
• Fluorescence imaging microscopy; contrast-enhanced imaging using molecular switch probes and optical lock-in detection

Courses Taught or Currently Teaching

Graduate-level courses:
BIOE 227A/177A Machine Learning for Biomedical Applications
BIOE 216/166 Biosignal and Medical Image Processing
BIOE 268/168 Biophotonics and Bioimaging
BIOE 281 Deep Learning and Applications in Medical Image Analysis

Undergraduate-level courses:
BIOE 10 Introduction to Bioengineering
BIOE 24 Mechanics and Modeling
BIOE 154 Biomechanics
BIOE 162 Biosignals and Systems

Research Funding

Active/Funded:

• Co-PI, NIH Multi-Investigator Award (2009-2013). "High-contrast imaging of single molecules in live cells". ($220,842)
• Co-PI, NIH R01 (Dec. 2006~2010); (2007 sub-contract $115,000) "New optical probes to study cell motility"
• PI, NSF BS# 0402439. July 1, 2004 - Dec.31, 2007 ($321,475). "Develop new analytical tools for high-speed laryngeal imaging for clinical applications"
• Co-PI, NIH R01 (Dec.1, 2002-Nov.30, 2007); "Protein structural dynamics in Ca2+-regulated thin filaments"
• PI; Hawaii State Biomedical Research Infrastructure Network award (2003)
• PI; Seed Money, College of Engineering, University of Hawaii-Manoa (2003)

Selected Research Publications:

Research articles (selected)

1. T.-R. Wei, S. Lu, Y. Yan. "Automated Atrial Fibrillation Detection with ECG." Bioengineering
   9(10), 523, 2022.
2. Khairy A.M. Khairuddin, K. Ahmad, H M Ibrahim and Y. Yan. “Description of the Features and
   Vibratory Behaviors of the Nyquist Plot Analyzed from Laryngeal High-speed Video-endoscopy
   Images.” Journal of Voice. 2022.
3. Khairy A.M. Khairuddin, K. Ahmad, H M Ibrahim and Y. Yan. “Analysis Method for Laryngeal
   High-Speed Videoendoscopy: Development of the Criteria for the Measurement Input.” Journal
   of Voice. 35(4), 636-645. 2021.
4. G. Patel, P. Ranawade, Y. Yan. “Detection of Melanoma Skin Cancer with Deep Neural
   Networks.” Med. Clin Res 2019; Vol 4, Issue 4. doi.org/10.33140/MCR.04.04.05
5. H. Liang, C. Zhu, Y. Iwata, S. Maedono, M. Mochita, C. Liu, P. Li, Y. Yan, F. Duan. “Feature
   Extraction of Shoulder Joint’s Voluntary Flexion-Extension Movement Based on
   Electroencephalography Signals for Power Assistance.” Bioengineering 6(1), 2, 2019.
6. M. Yoshioka, C. Zhu, K. Uemoto, H. Liang, F. Duang and Y. Yan. “Motion Classifier Generation
   by Mahalanobis Distance for BMI Robotic Arm Control System.”  Journal of Neuroscience and
   Neuroengineering, Vol 4, No. 1, June 2017, pp. 1-8(8).
7. A. Hoepker, Y. Yan and G. Marriott. “Genetically-encoded sensors of protein hydrodynamics.”
   Oncotarget. 2015 6(19): 16808-16809. 5-Year Impact Factor: 6.368.
8. A. Hoepker, A. Wang, A. Marois, K. Suhling, Y. Yan and G. Marriott. "New genetically-encoded
   sensors of protein hydrodynamics and molecular proximity." PNAS 2015, May19;112(20):E2569-74. (Impact Factor: 9.809)
9. T. Shi, J. Kim, T. Murry, P. Woo, and Y. Yan, "Tracing Vocal-fold Vibrations Using Level-set
   Segmentation Method." Int. Journal for Numerical Methods in Biomedical Engineering. Volume 31, Issue 6, June 2015.
10. G. Li, S. Luo, Y. Yan and G. Nin, "A method of extending the depth of focus of the high-
    resolution X-ray imaging system employing optical lens and scintillator: a phantom
    study," Biomed Eng Online. 2015;14 Suppl 1:S15. doi: 10.1186/1475-925X-14-S1-S15.
11. M. Yoshioka, C. Zhu, K. Imamura, F. Wang, H. Yu, F. Duan, and Y. Yan. "Experimental design
    and signal selection for construction of a robot control system based on EEG signals." Robotics
    and Biomimetics 2014, 1:22. doi:10.1186/s40638-014-0022-3.
12. Y. Yan, C. Petchprayoon, S. Mao and G. Marriott. "Reversible Optical Control of Cyanine
    Fluorescence in Fixed and Living Cells: Optical Lock-in Detection Immunofluorescence Imaging
    Microscopy." (2013) Philosophical Transactions of the Royal Society B – Biological
    Sciences. Philos Trans R Soc Lond B Biol Sci. 2012 Dec 24; 368(1611): 20120031. doi:
    10.1098/rstb.2012.0031. Print 2013 Feb 5. http://www.ncbi.nlm.nih.gov/pubmed/23267183.
    Impact Factor (2011): 6.401
13. M. Blanco, X. Chen and Y. Yan. "A Restricted, Adaptive Threshold Segmentation Approach for
    Processing High-speed Image Sequences of the Glottis." Engineering, 2013, Vol. 5, No.10B.
    p.357-362.
14. A, Bhandari, K. Izdebski1, C. Huang and Y. Yan, "Comparative Analysis of Normal Voice
    Characteristics Using Simultaneous Electroglottography and High-speed Digital
    Imaging." Biomedical Signal Processing & Control. Vol. 7, 1: 20-26. Jan. 2012. Yan, Y.,
    Marriott, M.E., Petchprayoon, C. and Marriott, G. "Optical Switch Probes and Optical Lock-in
    Detection (OLID) Imaging Microscopy: High-contrast Fluorescence Imaging with Living
    Systems." Biochemical Journal. 433, 411–422. 2011. (Impact Factor: 4.897) (Unofficial Impact
    factor for review articles: 17.902)
15. S. Luo and Y. Yan. "Implementation of a Virtual Laryngoscope System Using Efficient
    Reconstruction Algorithms." Med Sci Monit, 2009;15(8): MT 95-100.
16. Marriott, G., S. Mao, T. Gormez, E. Isacoff, and Y. Yan. "Optical Lock-in Detection Imaging Microscopy for Contrast-enhanced Imaging in Living Cells." PNAS (2008);105(46). pp 17789-17794. DOI: 10.1073/pnas.0808882105.  (Impact factor: 9.432)
17. Y. Yan, S. Luo, and A. Mcwhorter. "Virtual Laryngoscopy: A Noninvasive Tool for the Assessment of Laryngeal Tumor Extent." Laryngoscope 2007 (117) 6:1026-1030.
18. Y. Yan, X. Chen, D. Bless. "Automatic Tracing of the Vocal-fold Motion from High-speed Laryngeal Image Sequence." IEEE Trans. Biomedical Engineering 2006;53: 7: 1394-1400. (Impact factor: 2.154)
19. Y. Yan, K. Ahmad, M. Kunduk and D. Bless. (2005). "Analysis of Vocal-fold Vibrations from High-speed Laryngeal Images Using Hilbert Transform based Methodology." Journal of Voice. 2005;19:2;161-175.
20. Sakata, T., Yan, Y. & Marriott, G. (2005). "Optical Switching of Dipolar Interactions on Proteins." PNAS. 102, 4759-2764. DOI: 1073/pnas.0405265102. (Impact factor: 9.432)
21. Y. Yan and G. Marriott, “Analysis of Protein Interactions Using Biophotonics Technologies”. Current Opinion in Chemical Biology (2003). 7: 5; 635-640. (Impact factor: 9.850)
22. K. Matsumoto, Y. Yan, T. Kinjyo, T. Yamamoto, “Applications of Wavelets in Signal Recognition.” Trans. of Japan Society of Electrical Engineers, (2001) 21:1366-1378.
23. K. Nakazono, H. Kinjo, Y. Yan, T. Yamamoto (1999). “Load Swing Suppression of a Crane System by Neuro-Controller Utilizing Genetic Algorithm with Rough Evaluation.” Trans. Of the Japan Society of Mechanical Engineers 65, pp. 2779-2786.

Conference Papers/Abstracts (selected):

24. Vierra, Aren, Ting-Ruen Wei, R. Pan, M. Patel, Y. Yan, Y. Kang. “Benign or Malignant; The
    Breast Imaging Binary: Artificial Intelligence in Breast Sonography.” The American Roentgen
    Ray Society (ARRS) Annual Meeting, April 16-20, 2023
25. A. Chang, Ran, Chris, P. Patel, Y. Yan, M. Patel, Y. Kang. “Comparison of a deep learning model
    to radiologist diagnostic performance in sonographic breast mass assessment.” ARRS, 2022
    26. Aileen, P. Patel, Chris, Y. Yan, Ran, M. Patel, Y. Kang. “Utilization of a novel deep learning
    model in the differentiation of benign and malignant sonographic breast masses.” ARRS, April
    2022
26. R. Lee, P. Patel, M. Patel, Y. Yan, Y. Kang. “Utilization of a Novel Deep Learning Model for
    Diagnosing Intracranial Aneurysms Using MRA source and MIP Data.” ARRS, April 2022.
    28. H. Liang, C. Zhu, Y. Tian, Y. Iwata, S. Maedono, H. Yu, Y. Yan and F. Duan. “Construction of
    Power Assistive System for the Control of Upper Limb Wearable Exoskeleton Robot with
    Electro-encephalography Signals.” IEEE Int. Conf. on Cyborg and Bionic Systems. Oct. 17-19,
    2017.
27. H. Liang, C. Zhu, M. Yoshioka, N. Ueda, Y. Tian, Y. Iwata, H. Yu, Y. Yan. “Estimation of EMG
    signal for shoulder joint based on EEG signals for the control of upper-limb power assistance
    devices.”  IEEE Int. Conf. on Robotics and Automation, May 29-June 3, 2017. p. 6020-6025.
    30. H. Liang, C. Zhu, M. Yoshioka, N. Ueda, Y. Tian, Y. Iwata, Y. Yan. “Investigation of the EEG
    Scalp Distribution for Estimation of Shoulder Joint Torque in Upper-Limb Power Assistant
    System." Proc. of the 2016 IEEE Conference on Robotics and Biomimetics ROBIO 2016. Dec. 3-
    7, 2016. p. 1912-1917.
28. Chi Zhu, T. Nakayama, M. Shibayama, H. Liang, Y. Yan, H. Yu, H. Shibasaki. “A novel power
    add-on unit for attendant propelled wheelchairs with Sensorless Speed Control and Power
    Assistance”. IEEE Int. Conference on Rehabilitation Robotics (ICORR 2015). p.786-791.
    32. H. J. Kim, T. Shi and Y. Yan. “Delineating the Glottal Edge Using Region-Growing Method.”
    Proceedings of the 8th Int. Conf. on Bioinformatics and Biomedical Engineering (iCBBE 2014).
    Sept. 20-22, 2014. p. 115-121.
29. T. Suzuki, C. Zhu, Sakai, T., Okada, Y., Yoshikawa, Y., Y. Yan, H. Yu, F. Duan. “Power Assistance of an Omnidirectional Hybrid Walker with Admittance Model and Iterative Learning Control.” 2014 IEEE 13th International Workshop on Advanced Motion Control. p. 446-451. March 2014. DOI:10.1109/AMC.2014.6823323
30. T. Shi, G. Nin and Y. Yan. “Tracing Vocal-fold Vibrations Using Level-set Segmentation Method.” Proc. of the 3rd Inte. Conference on Computational and Mathematical Biomedical Engineering – CMBE2013. 16-18 Dec. 2013, Hong-Kong. P. Nithiarasu and R. Löhner (eds)
31. M. Yoshioka, C. Zhu, Yoshikawa, Y., Umemoto K., H. Yu, F. Duan and Y. Yan. “Motion Classifier Generation Using EEG for Robot Control.” Proc. 6th International IEEE/EMBS Conference on Neural Engineering (NER), Nov. 6-8, 2013. p. 711-714.
32. Y. Yoshikawa, C. Zhu, M. Yoshioka, K. Uemoto, Y. Yan, Y. Yu, F. Duan. "Muscular Activity Estimation from EEGs Using Principal Component Analysis for Brain Machine Interface,” Proc. International BCI (Brain-Computer Interface). June 3~7, 2013.
33. G. Li, T. Jiang, S. Luo and Y. Yan. “A New Method for Processing the High-speed Glottis Image Sequence.” Proc. of the IASTED /Signal and Image Processing 2012. Honolulu, August, 2012.
34. G. Hotson, J. Ang, C. Zhu, A. Bhandari and Y. Yan, "Nyquist Plot and Quantitative Characterizations of Acoustic Voice Signals for Speaker Recognition." Proc. 7th IEEE Conf. on Industrial Electronics and Applications (ICIEA 2012). Singapore, July 18-20, 2012.
35. Y. Yan, G. Du, C. Zhu and G. Marriott. “Snake Based Automatic Tracing of Vocal-fold Motion from High-speed Digital Imaging.” Proc. ICASSP (IEEE Int. Conf. on Acoustics, Speech and Signal Processing). April, 2012. pp. 593~596.

Edited Book and Book Chapters (selected):

36. Izdebski, Y. Yan, and B. Wong. "Normal and Abnormal Vocal Folds Kinematics: High Speed
    Digital Phonoscopy (HSDP), Optical Coherence Tomography (OCT) & Narrow Band Imaging
    (NBI®)" Volume I: Technology. April 7, 2015.
37. Y. Yan, T. Jiang and S. Luo. "Software for automatic analysis of image and sound data
    simultaneously acquired from high-speed videoendoscopy." In Normal and Abnormal Vocal
    Folds Kinematics: High Speed Digital Phonoscopy (HSDP), Optical Coherence Tomography
    (OCT) &Narrow Band Imaging (NBI®). Volume I: Technology. Izdebski, Yan et al. Ed. 2015.
    42. Y. Yan and G. Du. "Snake based automatic tracing of vocal fold motility from high-speed digital images." In Normal and Abnormal Vocal Folds Kinematics: High Speed Digital Phonoscopy
    (HSDP), Optical Coherence Tomography (OCT) & Narrow Band Imaging (NBI®). Volume I:
    Technology. Izdebski, Yan et al. Ed. 2015.
38. Y. Yan and K. Izdebski. “Integrated Spatio-temporal Analysis of High-Speed Laryngeal Imaging
    and Acoustic Signals -Their Role and Applications in the Study of Normal and Abnormal Vocal
    Functions, in Speech and Language Technology. G. Demenko, Ed. Poznan. 2012.
39. C. Zhu, M. Oda, H. Yu, H. Watanabe, and Y. Yan “Walking Support and Power Assistance of a
    Wheelchair Typed Omnidirectional Mobile Robot with Admittance Control," Mobile Robots -
    Current Trends, Published by InTech. October 2011.
40. Yan, Y. and Marriott, G. “Optical Manipulation of Protein Activity and Protein Interactions
    Using Caged Proteins and Optical Switch Protein Conjugates. In “Photosensitive Control of
    Biological Function”. Eds. James Chambers & Richard Kramer (2010 online), In print 2011. pp.
    213-232.