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.
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
retrieval, and topic modeling.
For more information on my research
please visit my
Google Scholar research
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.
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.
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.
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.
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.
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.
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
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%)
James C. Costello et al.,
"A community effort to assess and improve drug sensitivity prediction algorithms," Nature Biotechnology, 2014.
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.
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.
doctoral/master programs in computer sciences awards Purdue University
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.
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.