papers and reports by year


2014

M. Staller, C. Fowlkes, M. Bragdon, Z. Wunderlich, A. DePace, "A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate", [preprint], doi: http://dx.doi.org/10.1101/004788

G. Ghiasi, C. Fowlkes, "Occlusion Coherence: Localizing Occluded Faces with a Hierarchcial Deformable Part Model",
CVPR, Columbus, OH, (June 2014). [pdf]

G. Ghiasi, Y. Yang, D. Ramanan, C. Fowlkes, "Parsing Occluded People", CVPR, Columbus, OH, (June 2014). [pdf]

2013

A. Chen, E. Lee, R. Tu, K. Santiago, A. Grosberg, C. Fowlkes, M. Khine, "Integrated Platform for Functional Monitoring of Biomimetic Heart Sheets Derived From Human Pluripotent Stem Cells", Biomaterials 35(2):675-683, [pdf]

L. Mander, M. Li, W. Mio, C. Fowlkes, S. Punyasena, "Classification of grass pollen through the quantitative analysis of surface ornamentation and texture", Proc. R. Soc. B. 2013 280 (1770) [pdf]

R. Díaz, S. Hallman, C. Fowlkes, "Detecting Dynamic Objects with Multi-View Background Subtraction", ICCV, Sydney, Australia (December 2013). [pdf]

B. Andres, J. Yarkony, B.S. Manjunath, S. Kirchhoff, E. Turetken, C. Fowlkes, H. Pfister, "Segmenting Planar Superpixel Adjacency Graphs w.r.t. non-planar Superpixel Affinity Graphs", EMMCVPR, Lund, Sweden, (Aug. 2013). [pdf][sup]

R. Díaz, S. Hallman, C. Fowlkes, "Multi-View Background Subtraction for Object Detection", Scene Understanding Workshop, Portland, OR, (June 2013).

H. Bae, C. Fowlkes, P. Chou, "Accurate Motion Deblurring using Camera Motion Tracking and Scene Depth", WACV, Clearwater Beach, Florida, (Jan. 2013). [pdf]

2012

H. Bae, C. Fowlkes, P. Chou, "Patch Mosaic for Fast Motion Deblurring", ACCV, Daejeon, Korea, (Nov. 2012). [pdf]

X. Zhu, C. Vondrick, D. Ramanan, C. Fowlkes, "Do we need more training data or better models for object detection?", BMVC, Surrey, UK (Sept. 2012). [pdf]

J. Yarkony, A. Ihler, C. Fowlkes, "Fast Planar Correlation Clustering for Image Segmentation'', ECCV, Firenze, Italy (Oct. 2012). arXiv:1208.0378v1 [extended pdf]

D. Keator, J. Fallon, A. Lakatos, C. Fowlkes, S. Potkin, A. Ihler, ``Feed-forward Hierarchical Model of the Ventral Visual Stream Applied to Functional Brain Image Classification'', Human Brain Mapping 35(1), p. 38–52, 2012. [pdf]

H. Kim, J. Park, J. Byun, W. Poon, C. Cotman, C. Fowlkes, N. Jeon, "Quantitative analysis of axonal transport by using compartmentalized and surface micropatterned culture of neurons", ACS Chemical Neuroscience, 2012. [pdf]

2011

J. Hengenius, M. Gribskov, A. Rundell, C. Fowlkes, D. Umulis, "Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosohpila melanogaster Embryo", PLoS ONE 6(11): e26797. doi:10.1371/journal.pone.0026797, 2011. [pdf][supplement]

Y. Yang, S. Hallman, D. Ramanan, C. Fowlkes, "Layered Object Models for Image Segmentation", TPAMI, 34(9):1731-1743, 2011. [pdf]

A. Chen, D. Lieu, L. Freschauf, V. Lew, H. Sharma, J. Wang, D. Nguyen, I. Karakikes, R. Hajjar, A. Gopinathan, E. Botvinick, C. Fowlkes, R. Li, M. Khine, "Shrink-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac Derivatives", 10.1002/adma.201103463, Advanced Materials, 2011. [pdf]

C. Fowlkes, K. Eckenrode, M. Bragdon, M. Meyer, Z. Wunderlich, L. Simirenko, C. Hendriks, S. Keranen, C. Henreiquez, M. Biggin, M. Eisen, A. DePace, "A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila," PLoS Genetics, 7(10): e1002346, 2011. [pdf]

Y. Chen, A. Gelfand, C. Fowlkes, M. Welling, "Integrating Local Classifiers through Nonlinear Dynamics on Label Graphs with an Application to Image Segmentation", ICCV, Barcelona, Spain, (Nov. 2011) [pdf]

J. Yarkony, R. Morshed, A. Ihler, C. Fowlkes. "Tightening MRF Relaxations with Planar Subproblems", UAI, Barcelona, Spain (July 2011). [pdf]    [NOTE: The original published version contained an erroroneous claim that was kindly pointed out by David Sontag. The one linked here is an updated version.]


J. Yarkony, A. Ihler, C. Fowlkes. "Planar Cycle Covering Graphs", UAI, Barcelona, Spain (July 2011). [pdf]

J. Yarkony, R. Morshed, A. Ihler, C. Fowlkes. "Planar Decompositions and Cycle Constraints", Workshop on Inference in Graphical Models with Structured Potentials, Colorado Springs, CO, (June 2011) [pdf]

J. Yarkony, A. Ihler, C. Fowlkes. "Planar Cycle Covering Graphs", Technical Report, arXiv:1104.1204v1, 2011 [pdf]

C. Desai, D. Ramanan, C. Fowlkes. "Discriminative models for multi-class object layout", 95(1), p. 1-12, International Journal of Computer Vision, 2011 [pdf]

Y. Bo, C. Fowlkes. "Shape-based Pedestrian Parsing", CVPR, Colorado Springs, CO, (June 2011) [pdf]

H. Pirsiavash, D. Ramanan, C. Fowlkes. "Globally-Optimal Greedy Algorithms for Tracking a Variable Number of Objects", CVPR, Colorado Springs, CO, (June 2011) [pdf]

J. Luna, J. Ciriza, M. Ojeda-Garcia, M. Kong, A. Herren, D. Lieu, R. Li, C. Fowlkes, M. Khine, K. McCloskey, "Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart Cells", Tissue Engineering: Part C , 17(5), p. 579-588 , 2011 [pdf]

P. Arbelaez, M. Maire, C. Fowlkes, J. Malik, "Contour Detection and Hierarchical Image Segmentation", TPAMI, 33(5), 2011 [pdf] [web page]

2010

S. Hallman, A. Skurikhin, C. Fowlkes. "Vehicle Detection on High-Resolution Commerical Satellite Imagery", Technical Report LA-UR-10-05877, Los Alamos National Laboratory, 2010

A. Aswani, S. Keranen, J. Brown, C. Fowlkes, D. Knowles, M. Biggin, P. Bickel, C. Tomlin "Nonparametric identification of regulatory interactions from spatial and temporal gene expression data" BMC Bioinformatics,11:413, 2010. [pdf] *highly accessed*

D. Park, D. Ramanan, C. Fowlkes "Multiresolution models for object detection" ECCV, Crete, Greece, (Sept. 2010) [pdf]

J. Yarkony, C. Fowlkes, A. Ihler, "Covering Trees and Lower-bounds on Quadratic Assignment", CVPR, San Francisco, (June 2010) [pdf]

Y. Yang, S. Hallman, D. Ramanan, C. Fowlkes, "Layered Object Detection for Multi-Class Segmentation" CVPR, San Francisco, (June 2010) [pdf]

C. Desai, D. Ramanan, C. Fowlkes, "Discriminative models for static human-object interactions", CVPR Workshop on Structured Models in Computer Vision, San Fransisco, CA, (June 2010) [pdf]

J. Burge, C. Fowlkes, M. Banks, ``Natural-scene statistics predict how the figure-ground cue of convexity affects human depth perception'', Journal of Neuroscience, 30(21):7269-7280 [pdf] [supplement]

2009

H. Pirsiavash, D. Ramanan, C. Fowlkes. "Bilinear classifiers for visual recognition", NIPS, Vancouver, Canada, (Dec. 2009). [pdf]

C. Desai, D. Ramanan, C. Fowlkes. "Discriminative models for multi-class object layout", ICCV Kyoto, Japan, (Sept. 2009). [pdf] [code]     *awarded the Marr Prize for best paper*

P. Arbelaez, M. Maire, C. Fowlkes and J. Malik. "From Contours to Regions: An Empirical Evaluation", CVPR Miami Beach, FL, (June 2009). [pdf] [code]. A fast GPU implementation here!

2008

M. Maire, P. Arbelaez, C. Fowlkes and J. Malik. "Using Contours to Detect and Localize Junctions in Natural Images", CVPR Anchorage, AK, (June 2008). [pdf]

O. Rübel, G. Weber, M-Y Huang, E. Bethel, M. Biggin, C. Fowlkes C. Leungo Hendriks, S. Keränen, M. Eisen, D. Knowles, J. Malik, H. Hagen, B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data" IEEE Transactions on Computational Biology and Bioinformatics, 7(1):64-79, 2010. [pdf]

C. Fowlkes, C. Luengo Hendriks, S. Keränen, G. Weber, O. Rübel, M-Y Huang, S. Chatoor, L. Simirenko, A. DePace C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. Knowles, M. Biggin, M. Eisen, J. Malik. "Constructing a quantitative spatio-temporal atlas of gene expression in the Drosophila blastoderm", Cell, 133(2), p. 364-374, 2008. [pdf] [supplement]
Reviews of this paper also appeared in Developmental Cell and Nature Methods.
The Drosophila blastoderm 3D gene expression atlas is online.

X. Ren, C. Fowlkes, J. Malik. "Learning Probabilistic Models for Contour Completion in Natural Images", IJCV, 77:47-63, 2008. [pdf]

2007

G. Weber, O. Rübel, M-Y Huang, A. DePace, C. Fowlkes, S. Keränen, C. Luengo Hendriks, H. Hagen, D. Knowles, J. Malik, M. Biggin, and B. Hamann "Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views", IEEE Transactions on Computational Biology and Bioinformatics, 6(2):296-309, 2009. [pdf]

C. Fowlkes, D. Martin, J. Malik. "Local Figure/Ground Cues are Valid for Natural Images" Journal of Vision, 7(8):2, 1-9. [pdf] [dataset]

2006

C. Luengo-Hendriks, S. Keränen, C. Fowlkes, L. Simirenko, G. Weber, C. Henriquez, D. Kaszuba, B. Hamann, M. Eisen, J. Malik, D. Sudar, M. Biggin D. Knowles, "3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline", Genome Biology 2006, 7:R123 , [pdf] *highly accessed*

S. Keränen, C. Fowlkes, C. Luengo Hendriks, D. Sudar, D. Knowles, J. Malik, M. Biggin, "3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution II: Dynamics", Genome Biology 2006, 7:R124, [pdf] *highly accessed*

C. Fowlkes, J. Malik. "Inferring nuclear movements from fixed material", Technical Report EECS-2006-142, EECS Department, University of California, Berkeley, (November 2006). [pdf]

X. Ren, C. Fowlkes, J. Malik. "Figure/Ground Assignment in Natural Images", ECCV, Graz, Austria, (May 2006). [pdf]

O. Rübel, G. Weber, S. Keränen, C. Fowlkes, C. Luengo Hendriks, N. Shah, M. Biggin, H. Hagen, D. Knowles, J. Malik, D. Sudar and B. Hamann. "PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates", EuroVIS, Lisbon, Portugal, (May 2006). [pdf]

2005

X. Ren, C. Fowlkes, J. Malik. "Cue Integration for Figure/Ground Labeling", NIPS, Vancouver, Canada, (Dec. 2005). [pdf]

X. Ren, C. Fowlkes, J. Malik. "Scale-Invariant Contour Completion using Conditional Random Fields", ICCV, Beijing, China, (Oct. 2005). [pdf]

C. Fowlkes, C. Luengo Hendriks, S. Keränen, M. Biggin, D. Knowles, D. Sudar, J. Malik. "Registering Drosophila Embryos at Cellular Resolution to Build a Quantitative 3D Atlas of Gene Expression Patterns and Morphology", CSB 2005 Workshop on BioImage Data Minning and Informatics, Palo Alto, CA, (Aug. 2005). [pdf]

X. Ren, C. Fowlkes, J. Malik. "Mid-level Cues Improve Boundary Detection", Technical Report CSD-05-1382, Division of Computer Science, University of California, Berkeley, (March 2005). [pdf]

2004

C. Fowlkes "A Note on Planar Factor Graphs", (Oct. 2004). [pdf]

C. Fowlkes, J. Malik. "How Much Does Globalization Help Segmentation?", Technical Report CSD-04-1340, Division of Computer Science, University of California, Berkeley, (July 2004). [pdf]

C. Fowlkes "Surveying Shape Spaces", survey article for Alan Weinstein's course on Reimannian Geometry [pdf]

D. Martin, C. Fowlkes, J. Malik. "Learning to Detect Natural Image Boundaries Using Local Brightness, Color and Texture Cues", TPAMI 26 (5) p.530-549 [pdf]

C. Fowlkes, S. Belongie, F. Chung, J. Malik. "Spectral Grouping Using The Nyström Method", TPAMI 26 (2) p.214-225 [pdf]

2003

C. Fowlkes, D. Martin, J. Malik. "Learning Affinity Functions for Image Segmentation: Combining Patch-based and Gradient-based Approaches", CVPR, Madison, WI, (June 2003). [pdf]

2002

D. Martin, C. Fowlkes, J. Malik. "Learning to Detect Natural Image Boundaries Using Brightness and Texture", NIPS , Vancouver, (Dec 2002). [pdf]

S. Belongie, C. Fowlkes, F. Chung, J. Malik. "Spectral Partitioning with Indefinite Kernels using the Nyström Extension", ECCV , Copenhagen, (May 2002). [pdf]

C. Fowlkes, Q. Shan, S. Belongie, J. Malik. "Extracting Global Structure from Gene Expression Profiles", in Methods of Microarray Data Analysis II, S. M. Lin and K. F. Johnson, editors. Kluwer Academic Publishers, 2002. [pdf]

2001 and before

C. Fowlkes, S. Belongie, J. Malik. "Efficient Spatiotemporal Grouping Using the Nyström Method", CVPR , Hawaii, (Dec. 2001). [pdf]

D. Martin, C. Fowlkes, D. Tal, J. Malik. "A Database of Human Segmented Natural Images and its Application to Evaluating Segmentation Algorithms and Measuring Ecological Statistics", ICCV, Vancouver, (July 2001). [pdf]

M.C. Burl, C. Fowlkes, J. Roden, "Mining for Image Content", SCI-ISAS '99 Session on Intelligent Data Mining and Knowledge Discovery, Orlando, FL, (Aug 1999) [pdf]

M.C. Burl, C. Fowlkes, J. Roden, A. Stechert, and S. Muukhtar, "Diamond Eye: A distributed Architecture for Image Data Mining", SPIE Conference on Data Minning and Knowledge Discovery, Orlando, FL (Apr 1999) [pdf]

C. W. Fowlkes and C. C. Fowlkes "Passive Solar Contributions to Residential Ventilation", Conservation in Buildings: Northwest Perspective, Butte, MT (May 1985) [pdf]



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