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									Innovative search engines for non-
     textual biomedical data

                Chi-Ren Shyu

            Informatics Institute
        Computer Science Department

       University of Missouri - Columbia
These are talented minds behind the engines!
Engines to drive scientific discovery
Entropy-Balanced Statistical k-d tree




 Grant Scott, and Chi-Ren Shyu. Knowledge Driven Multidimensional Indexing Structure for Biomedical Media Database Retrieval,
 IEEE Transactions on Information Technology in Biomedicine, Vol. 11, No. 3 , May 2007; 320-331
Some experimental results
HRCT Lung Image Database                                                    Protein 3D structure global Match




P. H. Chi, B. Pang, D. Korkin, C. R. Shyu, Efficient SCOP fold classification and retrieval using index-based protein substructure alignments
(IPSA), Bioinformatics, 2009.
C. R. Shyu, B. Pang, P. H. Chi, N. Zhao, D. Korkin, and D. Xu, ProteinDBS v2.0: a web server for global and local protein structure search, in
Nucleic Acids Research, Vol 38 (S2) July 2010: W53-W58.
N. Zhao, B. Pang, C. R Shyu, and D. Korkin, Structural Similarity and Classification of Protein Interaction Interfaces, PLOS One, 6(5)
2011. doi:10.1371
Biological Images –
Multiple Visual Cues for Meaningful Interpretation




                PhenomicsWorld.org
Chi-Ren Shyu, Jason Green, D. P. K. Lun, Toni Kazic, M. Schaeffer, and Ed Coe. Image Analysis for Mapping Immeasurable
Phenotypes in Maize, in IEEE Signal Processing Magazine, Vol. 24, No. 3 , May 2007; 116-119

M. Klaric, G Scott, C. Davis, and C. R. Shyu, Multi-Index and Multi-Object Retrieval, IEEE Trans. on Geosciences and Remote
Sensing, 2012 (accepted)
Semantic-based search
Automatic phenotype annotations
       Analyzing Eye Activities




Mining patterns from fixations and saccades of the
eye tracking data.
X. Wang, S. Erdelez, C. Allen, B. Anderson, H. Cao, and C. R. Shyu, The Role of Domain Knowledge in Developing User-Centered Medical Image
Indexing, Journal of the American Society for Information Science and Technology (JASIST ), 2011 (accepted).
  Case-based reasoning system




Cool search methods and many potential applications.
Acknowledgement – Funding Sources

NSF DBI-0447794, IIS-0812515, DBI-1053024
NGA HM1582-04-1-2028
NLM 2T15LM007089-17

Shumaker Endowment for Biomedical Informatics
  Acknowledgement - Collaborators

Maize Phenotype Image Databases: Jerry Neuffer, Ph.D. (MU), Ed Coe, Ph.D. (USDA),
Mary Schaeffer, Ph.D. (USDA), Carolyn Lawrence, Ph.D. (Iowa), Guri Johal, Ph.D.
(Purdue), Peter Balint-Kurti (USDA), and Toni Kazic, Ph.D. (MU).

Mitochondrial image Database: Ge Yang, Ph.D. (CMU)

Current and former students: Grant Scott, Ph.D., Matthew Klaric, Ph.D., Adrian Barb,
Ph.D., Pin-Hao Chi, Ph.D., Jaturon Harnsomeburana, Ph.D., Jason Green, Jing Ginger
Han, Blake Anderson, Xin Wang, Hongfei Cao, Carla Allen, and Eric Armstrong.

								
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