Protein epitome: We are using
similar representations to build HIV vaccines. I have given presentations on
this at CROI 05, HVTN 04, and several talks at Hutch, and UW. Joint work with
Vladimir Jojic, David Heckerman and Brendan Frey on the ML side, and Jim
Mullins, Simon Mallal on the biology side. (Here's a short interview I
gave on MSNBC)
Probabilistic index maps (palette-invariant models):
CVPR 04, UAI 04.
CVPR Tutorial on graphical models (PAMI, September 2005):
paper, slides
An audio-visual graphical model, ICASSP 2002
A generative model for layered vision, CVPR
2001, detailed math
RESEARCH INTERESTS
I am interested in
machine learning approaches to automatic extraction of medium level
representations of natural signals. By structuring statistical
generative models to mimic the structure of the real world, the models should be
able to automatically adapt to audio, visual or multimodal signals during the
unsupervised model fitting (learning) stage, thus providing a medium-level
representation suitable for compression, transmission, search, editing, enhanced
viewing experience, etc. These models are object-based, where an object can
produce sounds, have a changing appearance, move and be exposed to attenuation
in audio domain, illumination in video domain, and, when other objects are
present, to occlusion or additive mixing in both domains. The main requirement
is complete adaptivity, and so I am trying to avoid application-specific
initialization parameters. For example, the same model should be
applicable to tracking a person in front of a cluttered background, and to
tracking a flock of birds. The tracking task, as well as many other tasks
performed jointly, such as de-noising, dynamic mosaic building or object
removal as well as separating audio sources and associating them to object
appearances, are all achievable as probabilistic queries, i.e., inference of the
hidden variables associated to the world structure. All this should be doable
using the data itself, without special application-specific initialization
procedure or the separate supervised training stage.
As of two years ago, I have also been working on biological data, such as
sequences, measurements of binding energies, etc. Biological sequences exhibit
similar structure to other natural signals and many of the algorithms I have
previously developed for other domains apply to a large extent to
biological sequences as well. A prime example is the epitome, which is now being
tested at the University of Washington and Harvard University (more precisely,
Mass General Hospital), as an immunogen for HIV vaccines. (Here's a short
interview I gave on MSNBC)
Matthew. Beal, Nebojsa
Jojic and Hagai Attias, "A graphical model for audiovisual object tracking," IEEE
Transactions on Pattern Analysis and Machine Intelligence (PAMI), 25:7,
July 2003, pp. 828-836.
Brendan Frey and Nebojsa Jojic, "Transformation-invariant clustering using
the EM algorithm," IEEE
Transactions on Pattern Analysis and Machine Intelligence (PAMI), 25:1,
January 2003, pp. 1-17.
Vladimir Jojic, Nebojsa Jojic, Dan Geiger, Chris Meek, Adam Siepel, David
Haussler and David Heckerman, "Efficient approximations for learning
phylogenetic HMM models from data," Bioinformatics, ISMB/ECCB 2004 Supplement
2004: 161-168
Nemanja Petrovic, Nebojsa Jojic, Thomas Huang, "Adaptive Video Fast
Forward", Multimedia Tools and Applications Journal, 2004
Brendan Frey and Nebojsa Jojic, "Advances in inference in complex
probability models," IEEE Transactions on Pattern Analysis and Machine
Intelligence (PAMI), 27:9, September 2005., pp. 1392-1416.
Manuel Reyes-Gomez, Nebojsa Jojic, and Dan Ellis,
"Deformable spectrograms for capturing sound dynamics," submitted, IEEE
Transactions on Signal Processing, 2005
Nebojsa Jojic, Manuel
Reyes-Gomez, David Heckerman, Carl Kadie, and Ora Schueler-Furman, "Learning
MHC I - peptide binding," Bioinformatics,vol
22(14), July 2006.
Vincent Cheung, Brendan Frey, and
Nebojsa Jojic, "Video
epitomes," International Journal of computer vision, ISSN:
0920-5691 (Print) 1573-1405 (Online).
Anitha Kannan, Nebojsa Jojic and Brendan
Frey, "Transformed component analysis," International Journal of Computer
Vision, under review.
David Nickle et al, Public Library of
Science (PLoS): Computational Biology, 2007, under review, minor revisions
stage.
Jojic et al, "HLA-driven optimization of HIV
immunogens using epitomes," in preparation.
Nemanja Petrovic, Aleksandar Ivanovic, Nebojsa Jojic, Sumit Basu, Thomas
Huang, "Recursive estimation of generative models of video", CVPR 2006.
Nebojsa Jojic, Sumit Basu, Nemanja Petrovic, "Home video browsing and
consumption through exploration of a learned generative model", Video
Proceedings for CVPR 2006.
Vincent Cheung, Brendan Frey, and Nebojsa Jojic, "Video epitomes," IEEE Conf. on Computer Vision and
Pattern Recognition (CVPR), 2005. (Best paper honorable mention)
Nebojsa Jojic, Vladimir Jojic, Brendan Frey, Christopher Meek, David
Heckerman, "Using ``epitomes to model genetic diversity: Rational design of
HIV vaccine cocktails," NIPS 05.
Mukund Narasimhan, Nebojsa Jojic,
and Jeff Bilmes, "Q-clustering," NIPS 05.
Nebojsa Jojic, Vladimir Jojic, Carl
Kadie, Chris Meek, David Heckerman, Corey Moore, Mina John, and Simon Mallal,
"HLA-driven optimization of HIV immunogens using epitomes," Conference on
Retroviruses and Opportunistic Infections (CROI) 2005.
Anitha Kannan,
Nebojsa Jojic and Brendan Frey, "A generative model of layers of appearance
and deformation," Artificial Intelligence and Statistics (AISTATS),
2005.
Manuel Reyes Gomez, Nebojsa Jojic, and Dan Ellis, "Deformable
spectrograms," Artificial Intelligence and Statistics (AISTATS), 2005.
Vladimir Jojic, Nebojsa Jojic, Dan Geiger, Chris Meek, Adam Siepel, David
Haussler and David Heckerman, "Efficient approximations for learning
phylogenetic HMM models from data," International Conference on Systems
Biology (ISMB), 2004. pp: 161-168
Nebojsa Jojic,
Vladimir Jojic, and David Heckerman, "Joint discovery of haplotype blocks and
complex trait associations from SNP sequences without family data,"
Uncertainty in Aritificial Intelligence (UAI), 2004
Nebojsa Jojic and Yaron Caspi, "Capturing
image structure with probabilistic index maps," IEEE Computer
Society Conference on Computer Vision and Pattern Recognition (CVPR),
2004. Volume 1, 27 June-2 July 2004 Page(s): 212-219
Chris Pal, Richard
Szeliski, Matthew Uyttendaele, and Nebojsa Jojic, "Probability
models for high dynamic range imaging," IEEE Computer Society
Conference on Computer Vision and Pattern Recognition (CVPR), 2004.
Volume 2, 27 June-2 July 2004 Page(s): 173-180.
Nemanja Petrovic, Nebojsa
Jojic and Thomas Huang, "Graphical models for video summarization", IEEE
Multimedia Signal Processing (MMSP), 2004
Darko Kirovski and Nebojsa
Jojic, "Cryptographically secure identity certificates," IEEE International
Conference on Acoustics, Speech, and Signal Processing, (ICASSP), Volume
5, 17-21 May 2004 Page(s):V-413 - V-416
Manuel Reyes-Gomez, Dan Ellis, and
Nebojsa Jojic, "Multiband audio modeling for
single-channel acoustic source separation," IEEE
International Conference on Acoustics, Speech, and Signal Processing, (ICASSP),
Volume 5, 17-21 May 2004 Page(s):V-641-644.
John Hershey, Hagai Attias,
Nebojsa Jojic and Trausti Kristjansson, "Audio-visual
graphical models for speech processing," IEEE International
Conference on Acoustics, Speech, and Signal Processing, (ICASSP), Volume
5, 17-21 May 2004 Page(s):V-649-652.
Nebojsa Jojic, Vladimir Jojic, Chris
Meek, and David Heckerman, "A graphical model for rational design of AIDS
cocktail vaccines," Machines that Learn (SNOWBIRD), 2004
Nebojsa Jojic,
Nemanja Petrovic, and Thomas Huang, "Scene generative models for
adaptive video fast forward," International Conference on Image Processing
(ICIP), 2003.
Nebojsa Jojic, Brendan Frey, and Anitha Kannan, "Epitomic
analysis of appearance and shape," International Conference on Computer
Vision (ICCV), 2003.
Darko Kirovski and Nebojsa Jojic, "FaceCerts,"
IEEE Data Compression Conference (DCC), 2003
Brendan Frey, Nebojsa Jojic, and Anitha Kannan, "Learning
appearance and transparency manifolds of occluded objects in layers,"
Computer Vision and Pattern Recognition (CVPR), 2003.
Nebojsa
Jojic, Sumit Basu, Nemanja Petrovic, Brendan Frey and Thomas Huang, "Joint
design of data analysis algorithms and user interface for video applications",
"Machine Learning meets the User Interface Workshop" (NIPS), 2003
Matt Beal, Nebojsa Jojic and Hagai Attias, "Audio-Assisted Visual Tracking: A
Probabilistic, Self-Calibrating Algorithm," European Conference on Computer Vision, 2002.
Chris
Pal, Brendan Frey and Nebojsa Jojic, "Learning and representing objects that
change in shape using montages of transformed latent images," submitted to
European Conference on Computer Vision (ECCV), 2002.
Matt Beal, Nebojsa Jojic
and Hagai Attias, "A self-calibrating algorithm for speaker tracking based on
audio-visual statistical models," accepted, IEEE International Conference
on Speech, Acoustics and Signal Processing, 2002
Brendan Frey, Anitha Kannan and Nebojsa Jojic, "Product Analysis,"
in Advances in Neural Information Processing Systems 14 (NIPS 2001).
Nebojsa Jojic, Patrice Simard, Brendan Frey and David Heckerman, "Separating
Appearance from Deformation," International Conference on Computer Vision
(ICCV),
July 2001, Vancouver, BC, Canada.
Nebojsa Jojic, Patrice Simard, Brendan
Frey and David Heckerman, "Learning mixtures of smooth nonuniform deformation
fields for probabilistic image matching," Eight International Workshop on AI
and Statistics (AISTATS), January 2001, Key West, Florida.
Nebojsa Jojic, Barry Brumitt, Brian Meyers and Steve Harris, "Detecting
and estimating pointing gestures in dense disparity maps," IEEE
International Conference on Face and Gesture Recognition 2000, Grenoble,
France, March 2000.
Brendan Frey and Nebojsa Jojic, “Learning Graphical
Models of Images, Videos and Their Spatial Transformations,” Uncertainty in
Artificial Intelligence, Palo Alto, 2000.
Brendan Frey and Nebojsa Jojic,
“Transformation-Invariant Filtering Using Expectation Maximization,” Symposium
2000 on Adaptive Systems for Signal Processing, Communications and Control,
Lake Lousie, Alberta, Oct 1-4.
Bridget Carragher, Nebojsa Jojic, et al., "Automated Acquisition of Cryo
Electron Micrographs Using Leginon," Microscopy and Microanalysis '99,
pp. 376-377. Portland, Oregon, August 1-5, 1999.
Brendan Frey and Nebojsa Jojic, "Transformation Invariant Mixture Models,"
(invited paper), Machines that Learn Workshop (Snowbird), March 1999.
Nebojsa Jojic, Matthew Turk, Thomas S. Huang, "Tracking Articulated
Structures in Stereo Sequences," IEEE Information Theory Workshop on
Detection, Estimation, Classification and Imaging, Santa Fe, February
1999. pp. 77
Nebojsa Jojic, Yong Rui, Yueting Zhuang, Thomas S. Huang, "Computer
Vision and Graphics Techniques for Garment Shopping over the Internet," International Computer Symposium, Taiwan, December 1998.
Nebojsa Jojic, Thomas Huang, "On analysis of
cloth drape range data", Asian Conference on Computer Vision (ACCV)
'98, Hong Kong, January 1998, pp. 463-470.
J. Gu, N. Jojic, I. Mak, H. Shen, S. Gopalsamy and T. Huang, "Camera-Based
Human Body Reconstruction," 1998 Symposium on Image, Speech, Signal
Processing, and Robotics (ISSPR), Workshop on Computer Vision, September
'98, Hong Kong, pp. I:79-84
J. Gu, N. Jojic, H. Shen, and T. Huang, "Design of a Camera-Based 3D
Data Acquisition System," 5th International Conference on Mechatronics and
Machine Vision in Practice (MVIP'98), September '98, Nanjing, China, pp.
93-98.
D. Nandy, J. Ben Arie, N. Jojic, Z. Wang, R. K. Rao, "On the use of
the Karhunen-Loeve transform and expansion matching for generalized feature
detection", 1996 IEEE International Conference on Acoustics, Speech, and
Signal Processing Conference Proceedings (ICASSP), pp. 2223-6 vol. 4, 5
refs. 1996.
Z. Wang, R. K. Rao, D. Nandy, J. Ben Arie, N. Jojic, "A generalized
expansion matching based feature extractor" in Proceedings of the 13th
International Conference on Pattern Recognition. pp. 29-33 vol.2, 5 refs.
1996.
Z. Wang, R. K. Rao, D. Nandy, Ben Arie, N. Jojic, "Generalized
feature detection using the Karhunen-Loeve transform and expansion
matching" in Proc. SPIE - Int. Soc. Opt. Eng. (USA). vol 2727,
pt 1, pp. 416-22, 5 refs. 1996
Mehdi N. Yu X. Wu D. Jojic N. Baker B. Gosavi P. Seyd A. Bodak S. Umetani
K. He B. EDITED BY: Bajpai P K. "Body surface Laplacian mapping from
potential recordings in man" in Proceedings of the 1996 Fifteenth Southern
Biomedical Engineering Conference, pp. 359-60, 4 refs. 1996.
HONORS
Best paper honorable mention, CVPR 2005.
Robert T. Chien Memorial Award for excellence in research, ECE Dept.
University of Illinois at Urbana Champaign, 2001.
Microsoft Graduate Fellowship for the school year 1999/2000.
Fellowship awarded by The Ministry of Science and Technology
(Yugoslavia) throughout undergraduate studies