---
_id: '3184'
abstract:
- lang: eng
text: 'Algorithms for discrete energy minimization play a fundamental role for low-level
vision. Known techniques include graph cuts, belief propagation (BP) and recently
introduced tree-reweighted message passing (TRW). So far, the standard benchmark
for their comparison has been a 4-connected grid-graph arising in pixel-labelling
stereo. This minimization problem, however, has been largely solved: recent work
shows that for many scenes TRW finds the global optimum. Furthermore, it is known
that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions
into account. We propose the problem of stereo with occlusions as a new test bed
for minimization algorithms. This is a more challenging graph since it has much
larger connectivity, and it also serves as a better stereo model. An attractive
feature of this problem is that increased connectivity does not result in increased
complexity of message passing algorithms. Indeed, one contribution of this paper
is to show that sophisticated implementations of BP and TRW have the same time
and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion
of our experimental study is that for our problem graph cut outperforms both TRW
and BP considerably. TRW achieves consistently a lower energy than BP. However,
as connectivity increases the speed of convergence of TRW becomes slower. Unlike
4-connected grids, the difference between the energy of the best optimization
method and the lower bound of TRW appears significant. This shows the hardness
of the problem and motivates future research.'
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly
connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1'
apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization
algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at
the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1'
chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization
Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1.
ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms
for highly connected graphs,” presented at the ECCV: European Conference on Computer
Vision, 2006, vol. 3952 LNCS, pp. 1–15.'
ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms
for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS,
vol. 3952 LNCS, 1–15.'
mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization
Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp.
1–15, doi:10.1007/11744047_1.
short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:52Z
date_published: 2006-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '03'
doi: 10.1007/11744047_1
extern: 1
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf
month: '05'
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3498'
quality_controlled: 0
status: public
title: Comparison of energy minimization algorithms for highly connected graphs
type: conference
volume: 3952 LNCS
year: '2006'
...
---
_id: '3185'
abstract:
- lang: eng
text: This paper describes models and algorithms for the real-time segmentation
of foreground from background layers in stereo video sequences. Automatic separation
of layers from color/contrast or from stereo alone is known to be error-prone.
Here, color, contrast, and stereo matching information are fused to infer layers
accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP),
solves stereo in an extended six-state space that represents both foreground/background
layers and occluded regions. The stereo-match likelihood is then fused with a
contrast-sensitive color model that is learned on-the-fly and stereo disparities
are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC),
does not directly solve stereo. Instead, the stereo match likelihood is marginalized
over disparities to evaluate foreground and background hypotheses and then fused
with a contrast-sensitive color model like the one used in LDP. Segmentation is
solved efficiently by ternary graph cut. Both algorithms are evaluated with respect
to ground truth data and found to have similar performance, substantially better
than either stereo or color/contrast alone. However, their characteristics with
respect to computational efficiency are rather different. The algorithms are demonstrated
in the application of background substitution and shown to give good quality composite
video output.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Antonio
full_name: Criminisi, Antonio
last_name: Criminisi
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
- first_name: Geoffrey
full_name: Cross, Geoffrey
last_name: Cross
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion
of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193
apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006).
Probabilistic fusion of stereo with color and contrast for bilayer segmentation.
IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193
chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross,
and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for
Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193.
ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic
fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492,
2006.
ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic
fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492.
mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and
Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and
Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193.
short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions
on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492.
date_created: 2018-12-11T12:01:53Z
date_published: 2006-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '01'
doi: 10.1109/TPAMI.2006.193
extern: 1
intvolume: ' 28'
issue: '9'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf
month: '09'
page: 1480 - 1492
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3496'
quality_controlled: 0
status: public
title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation
type: journal_article
volume: 28
year: '2006'
...
---
_id: '3186'
abstract:
- lang: eng
text: We introduce a new approach to modelling gradient flows of contours and surfaces.
While standard variational methods (e.g. level sets) compute local interface motion
in a differential fashion by estimating local contour velocity via energy derivatives,
we propose to solve surface evolution PDEs by explicitly estimating integral motion
of the whole surface. We formulate an optimization problem directly based on an
integral characterization of gradient flow as an infinitesimal move of the (whole)
surface giving the largest energy decrease among all moves of equal size. We show
that this problem can be efficiently solved using recent advances in algorithms
for global hypersurface optimization [4, 2, 11]. In particular, we employ the
geo-cuts method [4] that uses ideas from integral geometry to represent continuous
surfaces as cuts on discrete graphs. The resulting interface evolution algorithm
is validated on some 2D and 3D examples similar to typical demonstrations of level-set
methods. Our method can compute gradient flows of hypersurfaces with respect to
a fairly general class of continuous functional and it is flexible with respect
to distance metrics on the space of contours/surfaces. Preliminary tests for standard
L2 distance metric demonstrate numerical stability, topological changes and an
absence of any oscillatory motion.
alternative_title:
- LNCS
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Daniel
full_name: Cremers, Daniel
last_name: Cremers
- first_name: Andrew
full_name: Delong, Andrew
last_name: Delong
citation:
ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface
evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32'
apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral
solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented
at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32'
chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An
Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer,
2006. https://doi.org/10.1007/11744078_32.
ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution
to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference
on Computer Vision, 2006, vol. 3953, pp. 409–422.'
ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to
surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision,
LNCS, vol. 3953, 409–422.'
mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via
Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32.
short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp.
409–422.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:53Z
date_published: 2006-04-28T00:00:00Z
date_updated: 2021-01-12T07:41:39Z
day: '28'
doi: 10.1007/11744078_32
extern: 1
intvolume: ' 3953'
month: '04'
page: 409 - 422
publication_status: published
publisher: Springer
publist_id: '3497'
quality_controlled: 0
status: public
title: An integral solution to surface evolution PDEs via geo cuts
type: conference
volume: 3953
year: '2006'
...
---
_id: '3404'
alternative_title:
- Manuals in Biomedical Research
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ravi
full_name: Sawhney, Ravi K
last_name: Sawhney
- first_name: Martin
full_name: Stark, Martin
last_name: Stark
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques
in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing;
2006:213-284.'
apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force
microscopy. In Techniques in Microscopy for Biomedical Applications (Vol.
2, pp. 213–284). World Scientific Publishing.
chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic
Force Microscopy.” In Techniques in Microscopy for Biomedical Applications,
2:213–84. World Scientific Publishing, 2006.
ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,”
in Techniques in Microscopy for Biomedical Applications, vol. 2, World
Scientific Publishing, 2006, pp. 213–284.
ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy.
In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical
Research, vol. 2, 213–284.'
mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy
for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp.
213–84.
short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy
for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.
date_created: 2018-12-11T12:03:09Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '28'
extern: 1
intvolume: ' 2'
month: '09'
page: 213 - 284
publication: Techniques in Microscopy for Biomedical Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '2998'
quality_controlled: 0
status: public
title: Atomic force microscopy
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3413'
abstract:
- lang: eng
text: |-
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.
Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.
We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
author:
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Kay
full_name: Gottschalk, Kay E
last_name: Gottschalk
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
- first_name: Hermann
full_name: Gaub, Hermann
last_name: Gaub
citation:
ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065
apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006).
Bacteriorhodopsin folds into the membrane against an external force. Journal
of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065
chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann
Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal
of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.
ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin
folds into the membrane against an external force,” Journal of Molecular Biology,
vol. 357, no. 2. Elsevier, pp. 644–654, 2006.
ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin
folds into the membrane against an external force. Journal of Molecular Biology.
357(2), 644–654.
mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an
External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier,
2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065.
short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of
Molecular Biology 357 (2006) 644–654.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-03-24T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '24'
doi: 10.1016/j.jmb.2005.12.065
extern: 1
intvolume: ' 357'
issue: '2'
month: '03'
page: 644 - 654
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2988'
quality_controlled: 0
status: public
title: Bacteriorhodopsin folds into the membrane against an external force
type: journal_article
volume: 357
year: '2006'
...