Jinbo Bi

Ph.D., Rensselear Polytechnic Institute
M.Sc., Beijing Institute of Technology

Associate Professor
Department of Computer Science & Engineering
School of Engineering
University of Connecticut, Storrs, CT 06269

 

Department of Community Medicine and Health Care
School of Medicine
University of Connecticut Health Center, Farmington, CT 06030

 

Joint faculty of Department of Mathematics
Department of Statistics
College of Liberal Arts and Sciences
Department of Biomedical Engineering
School of Engineering

Contact Information: 371 Fairfield Way, Unit 4155
Storrs, CT 06269-4155
Office: ITEB 233
Tel: 860-486-1458
Fax: 860-486-4817 (CSE Dept)
Email: jinbo dot bi AT uconn dot edu
Research Interests: Artificial Intelligence, Machine learning, Data mining, Pattern recognition, Optimization, Computer vision, Bioinformatics, Medical informatics, Drug discovery

 


Laboratory


Openings


Research Projects

     National Science Foundation

    National Institutes of Health

    Department of Veterans Affairs


Teaching


Prior Working Experience

  • DoD Bioanalysis Institutes, (joint appointment with Partners Healthcare System), Boston, MA, November 2009 – June 2010
    Research Scientist II, develop and investigate informatics-based solutions to improve the medical protection and care of US military personel. Analyze and quantify physiology databases for computerized diagnosis of health conditions such as hemorrhage, traumatic brain injury, chest injury etc. Deploy the developed informatics tools also to the civilian health care settings, such as MedFlight. Establish partnerships with industry and academia, and participate in emerging technology development in medical informatics.
  • Siemens Medical Solutions, Inc. USA, Malvern, PA, September 2003 – October 2009
    Staff Scientist, develop algorithms that automatically identify and detect structures in human body that are possibly cancerous or that present abnormalities, based on medical images from CT, MRI, Ultrasound and other clinical imaging modalities. Applications include heart motion abnormality detection for coronary artery disease, lung nodule detection (Syngo Lung CAD – FDA approved product) and colon polyp detection for cancer prognosis, and detection of pulmonary embolism or diffuse parenchymal lung diseases. Investigate cutting-edge methods for medical applications where free text or natural language data are present in heterogeneous forms of clinical records. Supervise summer interns and associates to work on research projects and software implementations.
  • The Pennsylvania State University, Great Valley, PA, August 2008 – October 2009
    Adjunct Professor with The Engineering Division, teach courses, hold office hours, participate faculty meetings and seminars. Taught Soft Computing (SWENG 597C) in Fall 2008 (official course website is organized within Penn State ANGEL system).
  • NEC Laboratories America, Inc., Princeton, NJ, May 2002 – December 2002
    Research Associate with Dr. Vladimir N. Vapnik, conduct studies and research on rigorous support vector machines (developed a C++ RSVM package), and related feature selection algorithms using mathematical programming techniques.
  • Rensselaer Polytechnic Institute, Troy, NY, May 2000 – August 2003
    Research Assistant with Dr. Kristin P. Bennett at the Department of Mathematical Sciences, develop algorithms for machine learning, feature/variable selection, and support vector machines using mathematical programming, such as linear programming, quadratic programming, and integer programming. Apply the resulting algorithms to drug discovery, gene expression data analysis and portfolio selection analysis.
  • Rensselaer Polytechnic Institute, Troy, NY, August 1999 – April 2000
    Teaching Assistant at the Department of Mathematical Sciences, guide students’ computer labs using Matlab and C for assignments hold office hours for Numerical computing and Probability theory and statistics.

Selected Peer-Reviewed Publications


Professional Services


Patents


Abstracts and Clinical Publications

Conferences

  • An Adaptive, Knowledge-Driven Medical Image Search Engine for Interactive Diffuse Parenchymal Lung Disease Quantification ,
    Yimo Tao, Xiang Zhou, Jinbo Bi, Anna Jerebko, Matthias Wolf, Marcos Salganicoff and Arun Krishnan,
    Proceedings of SPIE medical imaging with an oral presentation, pages 7260-7263, 2009.
  • Assessment of Computer-aided Nodule Detection (CAD) Algorithm on Pathology Proved CT Data Sets,
    Sangmin Park, Tae-jung Kim, Vikas Raykar, Vikram Anald, Anna Jerebko, Maneesh Dewan, Jinbo Bi and Marcos Salganicoff,
    Abstract at Radiologist Society of North America (RSNA) with an oral presentation, Nov. 2008.
  • Computer-aided Detection of Pulmonary Nodules on CT: Evaluation of a New Prototype for Detection of Ground-glass and Part-Solid Nodules,
    Myrna Godoy, Tae Jung Kim, Jane Ko, Charles Florin, Anna Jerebko, David Naidich, Sangmin Park, Ioannis Vlahos, Jinbo Bi and Marcos Salganicoff,
    Abstract at Radiologist Society of North America (RSNA) with an oral presentation, Nov. 2008.
  • Reduction of Lymph Tissue False Positives in Pulmonary Embolism Detection,
    Bernard Ghanem, Jianming Liang, Jinbo Bi, Marcos Salganicoff and Arun Krishnan,
    Proceedings of SPIE Medical Imaging (SPIE’08), 2008.
  • Training a CAD Classifier with Correlated Data,
    Murat Dundar, Balaji Krishnapuram, Matthias Wolf, Sarang Lakare, Locu Bogoni, Jinbo Bi and Bharat Rao,
    Proceedings of SPIE Medical Imaging with an oral presentation, 2008.
  • Reducing a Biomarkers List via Mathematical Programming: Application to Gene Signatures to Detect Time-dependent Hypoxia in Cancer,
    Glenn Fung, Renaud Seigneuric, Sriram Krishnan, Bharat Rao, Brad Wouters, Philippe Lambin, Jinbo Bi presented at Special Session on Machine Learning Approaches to Medical Diagnosis and Health Care at INFORMS 2007 Annual Meeting, 2007.
  • Assessment of Computer-aided Lung Nodules Detection Algorithm on CT Data Sets Acquired Under Imaging Database Resources Initiative,
    Anna Jerebko, Jinbo Bi, Matthias Wolf, Senthil Periaswamy, Jianming Liang and Sanming Park,
    Abstract at Radiological Society of North America (RSNA) with an oral presentation, Nov. 2007.
  • Computer-aided Detection of Skeletal Metastases in MRI STIR Imaging of the Spine,
    A. Jerebko, G.P. Schmidt, X. Zhou, Jinbo Bi, V. Anand, J Liu, S. Schoenberg, I. Schmuecking, B. Kiefer and A. Krishnan,
    an oral presentation at International Society for Magnetic Resonance in Medicine, 2007.
  • Joint Optimization of Cascaded Classifiers for Computer Aided Detection,
    Oral presentation given by Jinbo Bi at IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR’07), June 2007.
  • CAD Performance Analysis for Pulmonary Nodule Detection on Thin-slice MDCT Scans,
    M. Wolf, A. Krishnan, M. Salganicoff, Jinbo Bi, M. Dundar, G. Fung, J. Stoeckel, S. Periaswamy, H. Shen, P. Herzog and D. Naidich,
    CARS 2005 Computer Assisted Radiology and Surgery , June 2005. (a related paper is published in its proceedings)
  • Clinical Evaluation of a Novel Automatic Real-time Myocardial Tracking and Wall Motion Scoring Algorithm for Echocardiography,
    A. Katz, S. Krishnan, X. Zhou, B. Georgescu, D. Comaniciu, Jinbo Bi, G. Fung, and J. Liang,
    American College of Cardiology, March 2005.
  • In Silico Screening for the hERG Potassium Channel Affinity,
    M. Song, Jinbo Bi, C. M. Breneman, K. P. Bennett,
    The 228th American Chemical Society meeting, Philadelphia, August 2004.
  • Developing in silico Carcinogenicity Classification model based on the kernel combination approach,
    M. Song, Jinbo Bi, K. P. Bennett, C. M. Breneman,
    ADMET-1 Conference, San Diego, Febuary 2004.
  • Prediction of Protein Retention Times in Anion-exchange Chromatography System using Support Vector Regression,
    M. Song, C. M. Breneman, N. Sukumar, K. P. Bennett, Jinbo Bi, S. Cramer and N. Tugcu,
    The 224th American Chemical Society meeting, Boston, August 2002.
  • QSPR Model Generation and Validation for Virtual High Throughput Screening,
    M. Song, C. M. Breneman, N. Sukumar, Jinbo Bi, K. P. Bennett, S. Cramer,
    Gordon Conference on Combinatorial & High Throughput Materials Science, Kimball Union Academy, 2002.
  • Caco-2 permeability modeling: Feature selection via sparse support vector machines,
    C. M. Breneman, K. P. Bennett, Jinbo Bi, Mark J. Embrechts, M. Song,
    The 223rd American Chemical Society meeting , Orlando, April, 2002
  • Displacer Efficacy prediction by Electronic Shape/Property-Encode descriptors,
    M. Song, Jinbo Bi, A. Ladiwala, W. Deng, N. Sukumar, M. Sundling, S. Cramer, C. M. Breneman,
    Albany Biotechnology Conference, September 2001.
  • Duality, Geometry, and Support Vector Regression,
    Jinbo Bi and K. P. Bennett,
    Advances in Neural Information Processing Systems (NIPS-2001). Vancouver. Dec. 2001
  • Dimensionality Reduction and Model Visualization via Sparse Support Vector Machines ,
    K. P. Bennett and Jinbo Bi,
    NIPS 2001 Workshop on Feature Selection. Vancouver. Dec. 2001
  • SVM, GAFEAT-NN, GA-PLS Modeling of Caco-2 Permeability using Electron Density-based Descriptors,
    M. Song, Jinbo Bi, M. Ozdemir, N. Sukumar, M. J. Embrechts, Kristin Bennett, Curt M. Breneman,
    The 222nd American Chemical Society meeting, Chicago, August 2001.
  • Support Vector Machines for Pharmaceutical Data Analysis,
    Jinbo Bi,
    A student poster at The 18th International Conference on Machine Learning (ICML-2001). Williams College. June 2001

Seminars and Invited Talks