Dr. Murat Dundar
Associate Professor
Computer & Information Science Dept.

   

Contact Information

Mailing Address:
Computer & Information Science Dept.
723 W. Michigan St., SL 280C, IUPUI
Indianapolis, IN 46202

Office Address:
550 University Blvd., University Hospital Building, Room AOC 5027
Indianapolis, IN 46202

Tel: 317-278-6488
Fax: 317-274-9742

E-mail:
mdundar 'at' iupui.edu

 

 

SHORT BIO:

I received my BS degree from Bogazici University, Istanbul, Turkey, in 1997 and MS and PhD degrees from Purdue University, West Lafayette, IN, USA, in 1999 and 2003 respectively, all in Electrical Engineering. I have joined IUPUI as a tenure-track assistant professor in 2008. Between 2003 and 2008 I was with the CAD and Knowledge Solutions group of Siemens Health. At Siemens Health, I was involved in the development of a broad spectrum of computer aided diagnosis/detection applications including FDA-approved Lung and Colon CAD products. I am a co-author on over 40 peer-reviewed publications and a co-inventor in 5 patents. I have served as a PC member for ACM SIGKDD, IEEE ICDM, SIAM SDM conferences and as a panelist for NIH and NSF review panels. I and my colleagues at Siemens Health received the Data Mining Practice Prize Award for our work on medical image mining by ACM SIGKDD in 2009. I am the main author of the paper that received the best scientific paper award in the Bioinformatics and Biomedical Applications track at the 20th International Conference on Pattern Recognition (ICPR'10) in 2010. I have received the NSF Early Faculty Career Development (CAREER) Award in 2013.

RESEARCH INTERESTS:

My area of expertise is in machine learning and data mining with a more recent focus on non-parametric Bayesian models and inference, learning with partially-observed data, online and offline class discovery and modeling. My research is mainly driven by real-world problems in computer aided diagnosis/detection, hyper-spectral data analysis and remote sensing, bio-detection, flow cytometry data analysis,  information retrieval, and topic modeling. For more information on my research please visit my Google Scholar research profile.

RECENT PAPERS:

Halid. Z. Yerebakan, Bartek Rajwa, Bethany Ehlmann, and Murat Dundar, "The Infinite Mixture of Infinite Gaussian Mixtures for Clustering Data Sets with Multi-mode and Rare Clusters," under review. PDF Supplementary

Bartek Rajwa, Paul K. Wallace, Elizabeth Griffiths, and Murat Dundar, "Automated Assessment of Disease Progression in Acute Myeloid Leukemia by Probabilistic Analysis of Flow Cytometry Data," to appear in IEEE Transactions on Biomedical Engineering. PDF

Murat Dundar, Qiang Kou, Baichuan Zhang, Yicheng He, and Bartek Rajwa, “Simplicity of Kmeans versus Deepness of Deep Learning: A Case of Unsupervised Feature Learning with Limited Data,” to appear in IEEE International Conference on Machine Learning Applications, 2015. PDF

Bethany Ehlmann and Murat Dundar, “Are Noachian/Hesperian Acidic Waters Key to Generating Mars' Regional-scale Aluminum Phyllosilicates? The Importance of Jarosite Co-occurrences with Al-Phyllosilicate Units,” 46th Lunar and Planetary Science Conference, 2015. PDF

Renata Duchnowska et al., "Predicting early brain metastases based on clinicopathological factors and gene expression analysis in advanced HER2-positive breast cancer patients," Journal of Neuro-Oncology 2015. Online

Halid Z. Yerebakan, Bartek Rajwa, Murat Dundar, "The Infinite Mixture of Infinite Gaussian Mixtures," in Proceedings of the Advances on Neural Information Processing Systems (NIPS'14), Montreal, CA, Dec 2014. PDF

Xiaofan Zhang, Wei Liu, Murat Dundar, Sunil Badve, Shaoting Zhang "Large-Scale Histopathological Image Analysis: Hashing-Based Image Retrieval," IEEE Transactions on Medical Imaging, Vol.34, No.2, pp.496-506, Feb. 2015. Online

Murat Dundar, Ferit Akova, Halid Z. Yerebakan, Bartek Rajwa, "A Non-parametric Bayesian Model for Joint Cell Clustering and Cluster Matching: Identification of Anomalous Sample Phenotypes with Random Effects," BMC Bioinformatics 15 (1), 314, 2014. Online

Mukesh Bansal et al., "Predicting activity of drug combinations through crowdsourcing," to appear in Nature Biotechnology, 2014.

Murat Dundar, Halid Z. Yerebakan, Bartek Rajwa, "Batch Discovery of Recurring Rare Classes toward Identifying Anomalous Samples," In Proceedings of the 20th Annual SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD'14), New York, USA, Aug 24-27 2014. (acceptance rate: 15%) PDF Video Lecture

James C. Costello et al., "A community effort to assess and improve drug sensitivity prediction algorithms," Nature Biotechnology, 2014. Online

Atul K Singh, Amanda M Bettasso, Euiwon Bae, Bartek Rajwa, Murat Dundar, Mark D Forster, Lixia Liu, Brent Barrett, Judith Lovchik, J Paul Robinson, E Daniel Hirleman, Arun K Bhunia, "Laser Optical Sensor, a Label-Free On-Plate Salmonella enterica Colony Detection Tool," mBio 5(1), 2014. Online

FUTURE STUDENTS:

I am actively recruiting graduate students who have keen interest in machine learning and data mining and their applications to problems in life sciences. An ideal candidate should have a BS in CS/ECE/Math/Stats and have a strong background in linear algebra, calculus, probability and random variables. Extensive experience with Matlab/C programming is also required. The IUPUI doctoral/master programs in computer sciences awards Purdue University degrees.

NEWS:

Undergraduate Research Award (3/15)
Congratulations to Nhan Do for receiving IUPUI Undergraduate Research Program (RISE) Award.

New Software (5/14)
Group clustering with random effects implemented in C++ for clustering and cluster matching across a batch of samples. Download Here.

PhD Thesis Defense (6/13)
Congratulations to Ferit Akova for successfully defending his PhD Thesis entitled "A Non-parametric Bayesian Perspective for Machine Learning in Partially-observed Settings".

CAREER Grant Awarded (3/13)
CAREER Grant “CAREER: Self-adjusting Models as a New Direction in Machine Learning” was awarded by NSF.

NIH Grant Awarded (7/12)
Grant with Bartek Rajwa “Automated spectral data transformations and analysis pipeline for high-throughput flow cytometry” was awarded by NIH/NIBIB.