---
_id: '3601'
abstract:
- lang: eng
text: In this paper, the multiobjective optimal design of space-based reconfigurable
sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective
evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II)
is employed to obtain multi-criteria Pareto-optimal solutions, which allows system
designers to easily make a reasonable trade-off choice from the set of non-dominated
solutions according to their preferences and system requirements. As a case study,
a cluster-based satellite sensing network is simulated under multiple objectives.
Most importantly, this paper also presents the application of our newly designed
adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal
design of space-based reconfigurable sensor networks.
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nakul
full_name: Haridas, Nakul
last_name: Haridas
- first_name: Ahmed
full_name: El-Rayis, Ahmed O
last_name: El Rayis
- first_name: Ahmet
full_name: Erdogan, Ahmet T
last_name: Erdogan
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. In: IEEE; 2007:27-34. doi:10.1109/AHS.2007.76'
apa: 'Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., & Barton,
N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable
sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA
Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2007.76'
chicago: Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan,
and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. https://doi.org/10.1109/AHS.2007.76.
ieee: 'E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton,
“Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications,” presented at the AHS: NASA/ESA Conference on
Adaptive Hardware and Systems, 2007, pp. 27–34.'
ista: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective
optimal design of MEMS-based reconfigurable and evolvable sensor networks for
space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems,
27–34.'
mla: Yang, Erfu, et al. Multiobjective Optimal Design of MEMS-Based Reconfigurable
and Evolvable Sensor Networks for Space Applications. IEEE, 2007, pp. 27–34,
doi:10.1109/AHS.2007.76.
short: E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:,
IEEE, 2007, pp. 27–34.
conference:
name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems'
date_created: 2018-12-11T12:04:11Z
date_published: 2007-08-20T00:00:00Z
date_updated: 2021-01-12T07:44:35Z
day: '20'
doi: 10.1109/AHS.2007.76
extern: 1
month: '08'
page: 27 - 34
publication_status: published
publisher: IEEE
publist_id: '2782'
quality_controlled: 0
status: public
title: Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor
networks for space applications
type: conference
year: '2007'
...
---
_id: '3674'
abstract:
- lang: eng
text: "Evolution permeates all of biology. But researchers in molecular and cellular
biology, genetics, developmental biology, microbiology, and neuroscience have
only recently begun to think seriously in terms of evolution. The chief reasons
for this shift are the growing list of organisms with sequenced genomes; the increasingly
sophisticated ways of interpreting those sequences; and the ever more powerful
experimental techniques (and wider range of model organisms) with which to ask
questions about evolution as well as mechanism.\r\n\r\nEvolution serves as a primary
text for undergraduate and graduate courses in evolution. It is also a text working
scientists can use to educate themselves on how evolution affects their fields.
It differs from currently available alternatives in containing more molecular
biology than is traditionally the case. But this is not at the expense of traditional
evolutionary theory. Indeed, a glance at the Table of Contents and the authors'
interests reveals the range of material covered in this book. The authors are
world-renowned in population genetics, bacterial genomics, paleontology, human
genetics, and developmental biology. The integration of molecular biology and
evolutionary biology reflects the current direction of much research among evolutionary
scientists."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Derek
full_name: Briggs, Derek
last_name: Briggs
- first_name: Jonathan
full_name: Eisen, Jonathan
last_name: Eisen
- first_name: David
full_name: Goldstein, David
last_name: Goldstein
- first_name: Nipam
full_name: Patel, Nipam
last_name: Patel
citation:
ama: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. Evolution. Cold
Spring Harbor Laboratory Press; 2007.
apa: Barton, N. H., Briggs, D., Eisen, J., Goldstein, D., & Patel, N. (2007).
Evolution. Cold Spring Harbor Laboratory Press.
chicago: Barton, Nicholas H, Derek Briggs, Jonathan Eisen, David Goldstein, and
Nipam Patel. Evolution. Cold Spring Harbor Laboratory Press, 2007.
ieee: N. H. Barton, D. Briggs, J. Eisen, D. Goldstein, and N. Patel, Evolution.
Cold Spring Harbor Laboratory Press, 2007.
ista: Barton NH, Briggs D, Eisen J, Goldstein D, Patel N. 2007. Evolution, Cold
Spring Harbor Laboratory Press, XIV, 833p.
mla: Barton, Nicholas H., et al. Evolution. Cold Spring Harbor Laboratory
Press, 2007.
short: N.H. Barton, D. Briggs, J. Eisen, D. Goldstein, N. Patel, Evolution, Cold
Spring Harbor Laboratory Press, 2007.
date_created: 2018-12-11T12:04:33Z
date_published: 2007-06-30T00:00:00Z
date_updated: 2021-12-21T15:55:28Z
day: '30'
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: XIV, 833
publication_identifier:
isbn:
- 978-087969684-9
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2709'
quality_controlled: '1'
related_material:
link:
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=3251&query_desc=au%2Cwrdl%3A%20nicholas%20barton
- relation: supplementary_material
url: http://www.evolution-textbook.org/
status: public
title: Evolution
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2007'
...
---
_id: '3681'
abstract:
- lang: eng
text: |-
The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.
alternative_title:
- LCNS
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Daniel
full_name: Keysers,Daniel
last_name: Keysers
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation
using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213.
doi:10.1007/978-3-540-74936-3_21'
apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant
motion estimation using adaptive search of transformation space (Vol. 4713, pp.
204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer.
https://doi.org/10.1007/978-3-540-74936-3_21'
chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal
Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13.
Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21.
ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion
estimation using adaptive search of transformation space,” presented at the DAGM:
German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.'
ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation
using adaptive search of transformation space. DAGM: German Association For Pattern
Recognition, LCNS, vol. 4713, 204–213.'
mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive
Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21.
short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:35Z
date_published: 2007-11-09T00:00:00Z
date_updated: 2021-01-12T07:45:06Z
day: '09'
doi: 10.1007/978-3-540-74936-3_21
extern: 1
intvolume: ' 4713'
month: '11'
page: 204 - 213
publication_status: published
publisher: Springer
publist_id: '2695'
quality_controlled: 0
status: public
title: Optimal dominant motion estimation using adaptive search of transformation
space
type: conference
volume: 4713
year: '2007'
...
---
_id: '3687'
abstract:
- lang: eng
text: |-
Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.
We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.
We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Blaschko M, Hofmann T, Lampert C. Efficient Subwindow Search for Object
Localization. Max-Planck-Institute for Biological Cybernetics; 2007.
apa: Blaschko, M., Hofmann, T., & Lampert, C. (2007). Efficient subwindow
search for object localization. Unknown. Max-Planck-Institute for Biological
Cybernetics.
chicago: Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. Efficient
Subwindow Search for Object Localization. Unknown. Max-Planck-Institute
for Biological Cybernetics, 2007.
ieee: M. Blaschko, T. Hofmann, and C. Lampert, Efficient subwindow search for
object localization, no. 164. Max-Planck-Institute for Biological Cybernetics,
2007.
ista: Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object
localization, Max-Planck-Institute for Biological Cybernetics,p.
mla: Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.”
Unknown, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007.
short: M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object
Localization, Max-Planck-Institute for Biological Cybernetics, 2007.
date_created: 2018-12-11T12:04:37Z
date_published: 2007-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:33Z
day: '01'
extern: 1
issue: '164'
main_file_link:
- open_access: '0'
url: http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf
month: '08'
publication: Unknown
publication_status: published
publisher: Max-Planck-Institute for Biological Cybernetics
publist_id: '2681'
quality_controlled: 0
status: public
title: Efficient subwindow search for object localization
type: report
year: '2007'
...
---
_id: '3723'
abstract:
- lang: eng
text: 'The folding and function of proteins is guided by their multidimensional
energy landscapes. Local corrugations on rugged energy surfaces determine the
dynamics of functionally related conformational changes and molecular flexibilities.
By varying the temperature during the force-induced unfolding of the membrane
protein bacteriorhodopsin, we directly determined the energy roughness of individual
transmembrane α-helices. All helices have rugged energy surfaces with an overall
roughness scale of 4−6 kBT, in line with the vital roles of transmembrane helices
as functional and structural building blocks. Interestingly, the mechanical unfolding
of misfolded membrane proteins in vivo is likely to occur on similarly energy
rugged surfaces, which may also provide an energetic framework for small vertical
motions of functionally relevant helices. Finally, our results also indicate that
transmembrane protein structures can have rough energy surfaces despite their
highly restricted conformational spaces in confining lipid bilayer environments. '
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: Helene
full_name: Knaus, Helene
last_name: Knaus
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Knaus H, Mueller D. Transmembrane helices have rough energy surfaces.
Journal of the American Chemical Society. 2007;129(2):246-247. doi:10.1021/ja065684a
apa: Janovjak, H. L., Knaus, H., & Mueller, D. (2007). Transmembrane helices
have rough energy surfaces. Journal of the American Chemical Society. ACS.
https://doi.org/10.1021/ja065684a
chicago: Janovjak, Harald L, Helene Knaus, and Daniel Mueller. “Transmembrane Helices
Have Rough Energy Surfaces.” Journal of the American Chemical Society.
ACS, 2007. https://doi.org/10.1021/ja065684a.
ieee: H. L. Janovjak, H. Knaus, and D. Mueller, “Transmembrane helices have rough
energy surfaces,” Journal of the American Chemical Society, vol. 129, no.
2. ACS, pp. 246–247, 2007.
ista: Janovjak HL, Knaus H, Mueller D. 2007. Transmembrane helices have rough energy
surfaces. Journal of the American Chemical Society. 129(2), 246–247.
mla: Janovjak, Harald L., et al. “Transmembrane Helices Have Rough Energy Surfaces.”
Journal of the American Chemical Society, vol. 129, no. 2, ACS, 2007, pp.
246–47, doi:10.1021/ja065684a.
short: H.L. Janovjak, H. Knaus, D. Mueller, Journal of the American Chemical Society
129 (2007) 246–247.
date_created: 2018-12-11T12:04:49Z
date_published: 2007-01-17T00:00:00Z
date_updated: 2021-01-12T07:51:44Z
day: '17'
doi: 10.1021/ja065684a
extern: 1
intvolume: ' 129'
issue: '2'
month: '01'
page: 246 - 247
publication: Journal of the American Chemical Society
publication_status: published
publisher: ACS
publist_id: '2507'
quality_controlled: 0
status: public
title: Transmembrane helices have rough energy surfaces
type: journal_article
volume: 129
year: '2007'
...
---
_id: '3727'
abstract:
- lang: eng
text: Since its invention in the 1990s single-molecule force spectroscopy has been
increasingly applied to study protein (un-)folding, cell adhesion, and ligand–receptor
interactions. In most force spectroscopy studies, the cantilever of an atomic
force microscope (AFM) is separated from a surface at a constant velocity, thus
applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently,
Fernandez and co-workers introduced the so-called force-clamp technique. Single
proteins were subjected to a defined constant force allowing their life times
and life time distributions to be directly measured. Up to now, the force-clamping
was performed by analogue PID controllers, which require complex additional hardware
and might make it difficult to combine the force-feedback with other modes such
as constant velocity. These points may be limiting the applicability and versatility
of this technique. Here we present a simple, fast, and all-digital (software-based)
PID controller that yields response times of a few milliseconds in combination
with a commercial AFM. We demonstrate the performance of our feedback loop by
force-clamp unfolding of single Ig27 domains of titin and the membrane proteins
bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.
author:
- first_name: Christian
full_name: Bippes, Christian A
last_name: Bippes
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Bippes C, Janovjak HL, Kedrov A, Mueller D. Digital force-feedback for protein
unfolding experiments using atomic force microscopy. Nanotechnology. 2007;18(4).
doi:10.1088/0957-4484/18/4/044022
apa: Bippes, C., Janovjak, H. L., Kedrov, A., & Mueller, D. (2007). Digital
force-feedback for protein unfolding experiments using atomic force microscopy.
Nanotechnology. IOP Publishing Ltd. https://doi.org/10.1088/0957-4484/18/4/044022
chicago: Bippes, Christian, Harald L Janovjak, Alexej Kedrov, and Daniel Mueller.
“Digital Force-Feedback for Protein Unfolding Experiments Using Atomic Force Microscopy.”
Nanotechnology. IOP Publishing Ltd., 2007. https://doi.org/10.1088/0957-4484/18/4/044022.
ieee: C. Bippes, H. L. Janovjak, A. Kedrov, and D. Mueller, “Digital force-feedback
for protein unfolding experiments using atomic force microscopy,” Nanotechnology,
vol. 18, no. 4. IOP Publishing Ltd., 2007.
ista: Bippes C, Janovjak HL, Kedrov A, Mueller D. 2007. Digital force-feedback for
protein unfolding experiments using atomic force microscopy. Nanotechnology. 18(4).
mla: Bippes, Christian, et al. “Digital Force-Feedback for Protein Unfolding Experiments
Using Atomic Force Microscopy.” Nanotechnology, vol. 18, no. 4, IOP Publishing
Ltd., 2007, doi:10.1088/0957-4484/18/4/044022.
short: C. Bippes, H.L. Janovjak, A. Kedrov, D. Mueller, Nanotechnology 18 (2007).
date_created: 2018-12-11T12:04:50Z
date_published: 2007-01-31T00:00:00Z
date_updated: 2021-01-12T07:51:46Z
day: '31'
doi: 10.1088/0957-4484/18/4/044022
extern: 1
intvolume: ' 18'
issue: '4'
month: '01'
publication: Nanotechnology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '2501'
quality_controlled: 0
status: public
title: Digital force-feedback for protein unfolding experiments using atomic force
microscopy
type: journal_article
volume: 18
year: '2007'
...
---
_id: '3731'
abstract:
- lang: eng
text: A cell's ability to regulate gene transcription depends in large part on the
energy with which transcription factors (TFs) bind their DNA regulatory sites.
Obtaining accurate models of this binding energy is therefore an important goal
for quantitative biology. In this article, we present a principled likelihood-based
approach for inferring physical models of TF-DNA binding energy from the data
produced by modern high-throughput binding assays. Central to our analysis is
the ability to assess the relative likelihood of different model parameters given
experimental observations. We take a unique approach to this problem and show
how to compute likelihood without any explicit assumptions about the noise that
inevitably corrupts such measurements. Sampling possible choices for model parameters
according to this likelihood function, we can then make probabilistic predictions
for the identities of binding sites and their physical binding energies. Applying
this procedure to previously published data on the Saccharomyces cerevisiae TF
Abf1p, we find models of TF binding whose parameters are determined with remarkable
precision. Evidence for the accuracy of these models is provided by an astonishing
level of phylogenetic conservation in the predicted energies of putative binding
sites. Results from in vivo and in vitro experiments also provide highly consistent
characterizations of Abf1p, a result that contrasts with a previous analysis of
the same data.
author:
- first_name: Justin
full_name: Kinney,Justin B
last_name: Kinney
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
citation:
ama: Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction
from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104
apa: Kinney, J., Tkačik, G., & Callan, C. (2007). Precise physical models of
protein-DNA interaction from high-throughput data. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.0609908104
chicago: Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models
of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy
of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104.
ieee: J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA
interaction from high-throughput data,” PNAS, vol. 104, no. 2. National
Academy of Sciences, pp. 501–506, 2007.
ista: Kinney J, Tkačik G, Callan C. 2007. Precise physical models of protein-DNA
interaction from high-throughput data. PNAS. 104(2), 501–506.
mla: Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction
from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of
Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
short: J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.
date_created: 2018-12-11T12:04:51Z
date_published: 2007-01-09T00:00:00Z
date_updated: 2021-01-12T07:51:48Z
day: '09'
doi: 10.1073/pnas.0609908104
extern: 1
intvolume: ' 104'
issue: '2'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766414
month: '01'
page: 501 - 506
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2495'
quality_controlled: 0
status: public
title: Precise physical models of protein-DNA interaction from high-throughput data
type: journal_article
volume: 104
year: '2007'
...
---
_id: '3742'
abstract:
- lang: eng
text: 'Recent work has shown that probabilistic models based on pairwise interactions-in
the simplest case, the Ising model-provide surprisingly accurate descriptions
of experiments on real biological networks ranging from neurons to genes. Finding
these models requires us to solve an inverse problem: given experimentally measured
expectation values, what are the parameters of the underlying Hamiltonian? This
problem sits at the intersection of statistical physics and machine learning,
and we suggest that more efficient solutions are possible by merging ideas from
the two fields. We use a combination of recent coordinate descent algorithms with
an adaptation of the histogram Monte Carlo method, and implement these techniques
to take advantage of the sparseness found in data on real neurons. The resulting
algorithm learns the parameters of an Ising model describing a network of forty
neurons within a few minutes. This opens the possibility of analyzing much larger
data sets now emerging, and thus testing hypotheses about the collective behaviors
of these networks.'
author:
- first_name: Tamara
full_name: Broderick,Tamara
last_name: Broderick
- first_name: Miroslav
full_name: Dudik,Miroslav
last_name: Dudik
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Robert
full_name: Schapire,Robert E
last_name: Schapire
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. Faster solutions of the
inverse pairwise Ising problem. ArXiv. 2007;q-QM.
apa: Broderick, T., Dudik, M., Tkačik, G., Schapire, R., & Bialek, W. (2007).
Faster solutions of the inverse pairwise Ising problem. ArXiv. ArXiv.
chicago: Broderick, Tamara, Miroslav Dudik, Gašper Tkačik, Robert Schapire, and
William Bialek. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv.
ArXiv, 2007.
ieee: T. Broderick, M. Dudik, G. Tkačik, R. Schapire, and W. Bialek, “Faster solutions
of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
ista: Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. 2007. Faster solutions
of the inverse pairwise Ising problem. ArXiv, q-QM, .
mla: Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.”
ArXiv, vol. q-QM, ArXiv, 2007.
short: T. Broderick, M. Dudik, G. Tkačik, R. Schapire, W. Bialek, ArXiv q-QM (2007).
date_created: 2018-12-11T12:04:55Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0712.2437v2
month: '01'
oa: 1
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2486'
quality_controlled: 0
status: public
title: Faster solutions of the inverse pairwise Ising problem
type: preprint
volume: q-bio.QM
year: '2007'
...
---
_id: '3762'
abstract:
- lang: eng
text: In this paper, we present a simple method for animating natural phenomena
such as erosion, sedimentation, and acidic corrosion. We discretize the appropriate
physical or chemical equations using finite differences, and we use the results
to modify the shape of a solid body. We remove mass from an object by treating
its surface as a level set and advecting it inward, and we deposit the chemical
and physical byproducts into simulated fluid. Similarly, our technique deposits
sediment onto a surface by advecting the level set outward. Our idea can be used
for off-line high quality animations as well as interactive applications such
as games, and we demonstrate both in this paper.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Mark
full_name: Carlson, Mark
last_name: Carlson
- first_name: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: 'Wojtan C, Carlson M, Mucha P, Turk G. Animating corrosion and erosion. In:
Eurographics Association; 2007:15-22. doi:10.2312/NPH/NPH07/015-022'
apa: 'Wojtan, C., Carlson, M., Mucha, P., & Turk, G. (2007). Animating corrosion
and erosion (pp. 15–22). Presented at the EGWNP: Eurographics Workshop on Natural
Phenomena, Eurographics Association. https://doi.org/10.2312/NPH/NPH07/015-022'
chicago: Wojtan, Chris, Mark Carlson, Peter Mucha, and Greg Turk. “Animating Corrosion
and Erosion,” 15–22. Eurographics Association, 2007. https://doi.org/10.2312/NPH/NPH07/015-022.
ieee: 'C. Wojtan, M. Carlson, P. Mucha, and G. Turk, “Animating corrosion and erosion,”
presented at the EGWNP: Eurographics Workshop on Natural Phenomena, 2007, pp.
15–22.'
ista: 'Wojtan C, Carlson M, Mucha P, Turk G. 2007. Animating corrosion and erosion.
EGWNP: Eurographics Workshop on Natural Phenomena, 15–22.'
mla: Wojtan, Chris, et al. Animating Corrosion and Erosion. Eurographics
Association, 2007, pp. 15–22, doi:10.2312/NPH/NPH07/015-022.
short: C. Wojtan, M. Carlson, P. Mucha, G. Turk, in:, Eurographics Association,
2007, pp. 15–22.
conference:
name: 'EGWNP: Eurographics Workshop on Natural Phenomena'
date_created: 2018-12-11T12:05:02Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2023-02-23T11:41:34Z
day: '01'
doi: 10.2312/NPH/NPH07/015-022
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.amath.unc.edu/Faculty/mucha/Reprints/EGNPerosion.pdf
month: '09'
oa_version: None
page: 15 - 22
publication_status: published
publisher: Eurographics Association
publist_id: '2464'
status: public
title: Animating corrosion and erosion
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '3765'
abstract:
- lang: eng
text: We present an extension to Lagrangian finite element methods to allow for
large plastic deformations of solid materials. These behaviors are seen in such
everyday materials as shampoo, dough, and clay as well as in fantastic gooey and
blobby creatures in special effects scenes. To account for plastic deformation,
we explicitly update the linear basis functions defined over the finite elements
during each simulation step. When these updates cause the basis functions to become
ill-conditioned, we remesh the simulation domain to produce a new high-quality
finite-element mesh, taking care to preserve the original boundary. We also introduce
an enhanced plasticity model that preserves volume and includes creep and work
hardening/softening. We demonstrate our approach with simulations of synthetic
objects that squish, dent, and flow. To validate our methods, we compare simulation
results to videos of real materials.
article_processing_charge: No
author:
- first_name: Adam
full_name: Bargteil, Adam
last_name: Bargteil
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Jessica
full_name: Hodgins, Jessica
last_name: Hodgins
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Bargteil A, Wojtan C, Hodgins J, Turk G. A finite element method for animating
large viscoplastic flow. ACM Transactions on Graphics. 2007;26(3). doi:10.1145/1276377.1276397
apa: Bargteil, A., Wojtan, C., Hodgins, J., & Turk, G. (2007). A finite element
method for animating large viscoplastic flow. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/1276377.1276397
chicago: Bargteil, Adam, Chris Wojtan, Jessica Hodgins, and Greg Turk. “A Finite
Element Method for Animating Large Viscoplastic Flow.” ACM Transactions on
Graphics. ACM, 2007. https://doi.org/10.1145/1276377.1276397.
ieee: A. Bargteil, C. Wojtan, J. Hodgins, and G. Turk, “A finite element method
for animating large viscoplastic flow,” ACM Transactions on Graphics, vol.
26, no. 3. ACM, 2007.
ista: Bargteil A, Wojtan C, Hodgins J, Turk G. 2007. A finite element method for
animating large viscoplastic flow. ACM Transactions on Graphics. 26(3).
mla: Bargteil, Adam, et al. “A Finite Element Method for Animating Large Viscoplastic
Flow.” ACM Transactions on Graphics, vol. 26, no. 3, ACM, 2007, doi:10.1145/1276377.1276397.
short: A. Bargteil, C. Wojtan, J. Hodgins, G. Turk, ACM Transactions on Graphics
26 (2007).
date_created: 2018-12-11T12:05:03Z
date_published: 2007-07-29T00:00:00Z
date_updated: 2023-02-23T11:41:41Z
day: '29'
doi: 10.1145/1276377.1276397
extern: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2462'
status: public
title: A finite element method for animating large viscoplastic flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2007'
...
---
_id: '3816'
abstract:
- lang: eng
text: Gamma frequency oscillations are thought to provide a temporal structure for
information processing in the brain. They contribute to cognitive functions, such
as memory formation and sensory processing, and are disturbed in some psychiatric
disorders. Fast-spiking, parvalbumin-expressing, soma-inhibiting interneurons
have a key role in the generation of these oscillations. Experimental analysis
in the hippocampus and the neocortex reveals that synapses among these interneurons
are highly specialized. Computational analysis further suggests that synaptic
specialization turns interneuron networks into robust gamma frequency oscillators.
author:
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bartos M, Vida I, Jonas PM. Synaptic mechanisms of synchronized gamma oscillations
in inhibitory interneuron networks (Review). Nature Reviews Neuroscience.
2007;8(1):45-56. doi:10.1038/nrn2044
apa: Bartos, M., Vida, I., & Jonas, P. M. (2007). Synaptic mechanisms of synchronized
gamma oscillations in inhibitory interneuron networks (Review). Nature Reviews
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn2044
chicago: Bartos, Marlene, Imre Vida, and Peter M Jonas. “Synaptic Mechanisms of
Synchronized Gamma Oscillations in Inhibitory Interneuron Networks (Review).”
Nature Reviews Neuroscience. Nature Publishing Group, 2007. https://doi.org/10.1038/nrn2044 .
ieee: M. Bartos, I. Vida, and P. M. Jonas, “Synaptic mechanisms of synchronized
gamma oscillations in inhibitory interneuron networks (Review),” Nature Reviews
Neuroscience, vol. 8, no. 1. Nature Publishing Group, pp. 45–56, 2007.
ista: Bartos M, Vida I, Jonas PM. 2007. Synaptic mechanisms of synchronized gamma
oscillations in inhibitory interneuron networks (Review). Nature Reviews Neuroscience.
8(1), 45–56.
mla: Bartos, Marlene, et al. “Synaptic Mechanisms of Synchronized Gamma Oscillations
in Inhibitory Interneuron Networks (Review).” Nature Reviews Neuroscience,
vol. 8, no. 1, Nature Publishing Group, 2007, pp. 45–56, doi:10.1038/nrn2044 .
short: M. Bartos, I. Vida, P.M. Jonas, Nature Reviews Neuroscience 8 (2007) 45–56.
date_created: 2018-12-11T12:05:20Z
date_published: 2007-01-21T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '21'
doi: '10.1038/nrn2044 '
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
page: 45 - 56
publication: Nature Reviews Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2393'
quality_controlled: 0
status: public
title: Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron
networks (Review)
type: journal_article
volume: 8
year: '2007'
...
---
_id: '3819'
abstract:
- lang: eng
text: Voltage-gated Ca2+ channels in presynaptic terminals initiate the Ca2+ inflow
necessary for transmitter release. At a variety of synapses, multiple Ca2+ channel
subtypes are involved in synaptic transmission and plasticity. However, it is
unknown whether presynaptic Ca2+ channels differ in gating properties and whether
they are differentially activated by action potentials or subthreshold voltage
signals. We examined Ca2+ channels in hippocampal mossy fiber boutons (MFBs) by
presynaptic recording, using the selective blockers omega-agatoxin IVa, omega-conotoxin
GVIa, and SNX-482 to separate P/Q-, N-, and R-type components. Nonstationary fluctuation
analysis combined with blocker application revealed a single MFB contained on
average approximately 2000 channels, with 66% P/Q-, 26% N-, and 8% R-type channels.
Whereas both P/Q-type and N-type Ca2+ channels showed high activation threshold
and rapid activation and deactivation, R-type Ca2+ channels had a lower activation
threshold and slower gating kinetics. To determine the efficacy of activation
of different Ca2+ channel subtypes by physiologically relevant voltage waveforms,
a six-state gating model reproducing the experimental observations was developed.
Action potentials activated P/Q-type Ca2+ channels with high efficacy, whereas
N- and R-type channels were activated less efficiently. Action potential broadening
selectively recruited N- and R-type channels, leading to an equalization of the
efficacy of channel activation. In contrast, subthreshold presynaptic events activated
R-type channels more efficiently than P/Q- or N-type channels. In conclusion,
single MFBs coexpress multiple types of Ca2+ channels, which are activated differentially
by subthreshold and suprathreshold presynaptic voltage signals.
author:
- first_name: Liyi
full_name: Li, Liyi
last_name: Li
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Li L, Bischofberger J, Jonas PM. Differential gating and recruitment of P/Q-,
N-, and R-type Ca(2+) channels in hippocampal mossy fiber boutons. Journal
of Neuroscience. 2007;27(49):13420-13429. doi:10.1523/JNEUROSCI.1709-07.2007
apa: Li, L., Bischofberger, J., & Jonas, P. M. (2007). Differential gating and
recruitment of P/Q-, N-, and R-type Ca(2+) channels in hippocampal mossy fiber
boutons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1709-07.2007
chicago: Li, Liyi, Josef Bischofberger, and Peter M Jonas. “Differential Gating
and Recruitment of P/Q-, N-, and R-Type Ca(2+) Channels in Hippocampal Mossy Fiber
Boutons.” Journal of Neuroscience. Society for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.1709-07.2007.
ieee: L. Li, J. Bischofberger, and P. M. Jonas, “Differential gating and recruitment
of P/Q-, N-, and R-type Ca(2+) channels in hippocampal mossy fiber boutons,” Journal
of Neuroscience, vol. 27, no. 49. Society for Neuroscience, pp. 13420–9, 2007.
ista: Li L, Bischofberger J, Jonas PM. 2007. Differential gating and recruitment
of P/Q-, N-, and R-type Ca(2+) channels in hippocampal mossy fiber boutons. Journal
of Neuroscience. 27(49), 13420–9.
mla: Li, Liyi, et al. “Differential Gating and Recruitment of P/Q-, N-, and R-Type
Ca(2+) Channels in Hippocampal Mossy Fiber Boutons.” Journal of Neuroscience,
vol. 27, no. 49, Society for Neuroscience, 2007, pp. 13420–29, doi:10.1523/JNEUROSCI.1709-07.2007.
short: L. Li, J. Bischofberger, P.M. Jonas, Journal of Neuroscience 27 (2007) 13420–9.
date_created: 2018-12-11T12:05:20Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:25Z
day: '01'
doi: 10.1523/JNEUROSCI.1709-07.2007
extern: 1
intvolume: ' 27'
issue: '49'
month: '01'
page: 13420 - 9
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2389'
quality_controlled: 0
status: public
title: Differential gating and recruitment of P/Q-, N-, and R-type Ca(2+) channels
in hippocampal mossy fiber boutons
type: journal_article
volume: 27
year: '2007'
...
---
_id: '3820'
abstract:
- lang: eng
text: 'Synapses are the key elements for signal processing and plasticity in the
brain. To determine the structural factors underlying the unique functional properties
of the hippocampal mossy fiber synapse, the complete quantitative geometry was
investigated, using electron microscopy of serial ultrathin sections followed
by computer-assisted three-dimensional reconstruction. In particular, parameters
relevant for transmitter release and synaptic plasticity were examined. Two membrane
specializations were found: active zones (AZs), transmitter release sites, and
puncta adherentia, putative adhesion complexes. Individual boutons had, on average,
25 AZs (range, 7-45) that varied in shape and size (mean, 0.1 microm2; range,
0.07-0.17 microm2). The mean distance between individual AZs was 0.45 microm.
Mossy fiber boutons and their target structures were mostly ensheathed by astrocytes,
but fine glial processes never reached the active zones. Two structural factors
are likely to promote synaptic cross talk: the short distance between AZs and
the absence of fine glial processes at AZs. Thus, synaptic cross talk may contribute
to the efficacy of hippocampal mossy fiber synapses. On average, a bouton contained
20,400 synaptic vesicles; approximately 900 vesicles were located within 60 nm
from the active zone, approximately 4400 between 60 and 200 nm, and the remaining
beyond 200 nm, suggesting large readily releasable, recycling, and reserve pools.
The organization of the different pools may be a key structural correlate of presynaptic
plasticity at this synapse. Thus, the mossy fiber bouton differs fundamentally
in structure and function from the calyx of Held and other central synapses.'
author:
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
- first_name: Kurt
full_name: Satzler, Kurt
last_name: Satzler
- first_name: E Patricia
full_name: Rodriguez, E Patricia
last_name: Rodriguez
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Joachim
full_name: Lubke, Joachim H
last_name: Lubke
citation:
ama: Rollenhagen A, Satzler K, Rodriguez EP, Jonas PM, Frotscher M, Lubke J. Structural
determinants of transmission at large hippocampal mossy fiber synapses. Journal
of Neuroscience. 2007;27(39):10434-10444. doi:10.1523/JNEUROSCI.1946-07.2007
apa: Rollenhagen, A., Satzler, K., Rodriguez, E. P., Jonas, P. M., Frotscher, M.,
& Lubke, J. (2007). Structural determinants of transmission at large hippocampal
mossy fiber synapses. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.1946-07.2007
chicago: Rollenhagen, Astrid, Kurt Satzler, E Patricia Rodriguez, Peter M Jonas,
Michael Frotscher, and Joachim Lubke. “Structural Determinants of Transmission
at Large Hippocampal Mossy Fiber Synapses.” Journal of Neuroscience. Society
for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.1946-07.2007.
ieee: A. Rollenhagen, K. Satzler, E. P. Rodriguez, P. M. Jonas, M. Frotscher, and
J. Lubke, “Structural determinants of transmission at large hippocampal mossy
fiber synapses,” Journal of Neuroscience, vol. 27, no. 39. Society for
Neuroscience, pp. 10434–44, 2007.
ista: Rollenhagen A, Satzler K, Rodriguez EP, Jonas PM, Frotscher M, Lubke J. 2007.
Structural determinants of transmission at large hippocampal mossy fiber synapses.
Journal of Neuroscience. 27(39), 10434–44.
mla: Rollenhagen, Astrid, et al. “Structural Determinants of Transmission at Large
Hippocampal Mossy Fiber Synapses.” Journal of Neuroscience, vol. 27, no.
39, Society for Neuroscience, 2007, pp. 10434–44, doi:10.1523/JNEUROSCI.1946-07.2007.
short: A. Rollenhagen, K. Satzler, E.P. Rodriguez, P.M. Jonas, M. Frotscher, J.
Lubke, Journal of Neuroscience 27 (2007) 10434–44.
date_created: 2018-12-11T12:05:21Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:26Z
day: '01'
doi: 10.1523/JNEUROSCI.1946-07.2007
extern: 1
intvolume: ' 27'
issue: '39'
month: '01'
page: 10434 - 44
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2390'
quality_controlled: 0
status: public
title: Structural determinants of transmission at large hippocampal mossy fiber synapses
type: journal_article
volume: 27
year: '2007'
...
---
_id: '3821'
abstract:
- lang: eng
text: Although dendritic signal processing has been extensively investigated in
hippocampal pyramidal cells, only little is known about dendritic integration
of synaptic potentials in dentate gyrus granule cells, the first stage in the
hippocampal trisynaptic circuit. Here we combined dual whole-cell patch-clamp
recordings with high-resolution two-photon microscopy to obtain detailed passive
cable models of hippocampal granule cells from adult mice. Passive cable properties
were determined by direct fitting of the compartmental model to the experimentally
measured voltage responses to short and long current pulses. The data are best
fit by a cable model with homogenously distributed parameters, including an average
specific membrane resistance (R(m)) of 38.0 kohms cm2, a membrane capacitance
(C(m)) of 1.0 microF cm(-2), and an intracellular resistivity (R(i)) of 194 ohms
cm. Computational analysis shows that signal propagation from somata into dendrites
is more efficient in granule cells compared with CA1 pyramidal cells for both
steady-state and sinusoidal voltage waveforms up to the gamma frequency range
(f50% of 74 Hz). Similarly, distal synaptic inputs from entorhinal fibers can
efficiently depolarize the somatic membrane of granule cells. Furthermore, the
time course of distal dendritic synaptic potentials is remarkably fast, and temporal
summation is restricted to a narrow time window in the range of approximately
10 ms attributable to the rapid dendritic charge redistribution during transient
voltage signals. Therefore, the structure of the granule cell dendritic tree may
be critically important for precise dendritic signal processing and coincidence
detection during hippocampus-dependent memory formation and retrieval.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Subthreshold dendritic signal
processing and coincidence detection in dentate gyrus granule cells. Journal
of Neuroscience. 2007;27(31):8430-8441. doi:10.1523/JNEUROSCI.1787-07.2007
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2007). Subthreshold
dendritic signal processing and coincidence detection in dentate gyrus granule
cells. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1787-07.2007
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Subthreshold
Dendritic Signal Processing and Coincidence Detection in Dentate Gyrus Granule
Cells.” Journal of Neuroscience. Society for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.1787-07.2007.
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Subthreshold dendritic
signal processing and coincidence detection in dentate gyrus granule cells,” Journal
of Neuroscience, vol. 27, no. 31. Society for Neuroscience, pp. 8430–8441,
2007.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2007. Subthreshold dendritic
signal processing and coincidence detection in dentate gyrus granule cells. Journal
of Neuroscience. 27(31), 8430–8441.
mla: Schmidt Hieber, Christoph, et al. “Subthreshold Dendritic Signal Processing
and Coincidence Detection in Dentate Gyrus Granule Cells.” Journal of Neuroscience,
vol. 27, no. 31, Society for Neuroscience, 2007, pp. 8430–41, doi:10.1523/JNEUROSCI.1787-07.2007.
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Neuroscience
27 (2007) 8430–8441.
date_created: 2018-12-11T12:05:21Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:26Z
day: '01'
doi: 10.1523/JNEUROSCI.1787-07.2007
extern: 1
intvolume: ' 27'
issue: '31'
month: '01'
page: 8430 - 8441
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2391'
quality_controlled: 0
status: public
title: Subthreshold dendritic signal processing and coincidence detection in dentate
gyrus granule cells
type: journal_article
volume: 27
year: '2007'
...
---
_id: '3881'
abstract:
- lang: eng
text: We present Qualitative Randomized CTL (QRCTL), a qualitative version of pCTL,
for specifying properties of Markov Decision Processes (MDPs). QRCTL formulas
can express the fact that certain temporal properties hold with probability 0
or 1, but they do not distinguish other probabilities values. We present a symbolic,
polynomial time model-checking algorithm for QRCTL on MDPs. Then, we study the
equivalence relation induced by QRCTL, called qualitative equivalence. We show
that for finite alternating MDPs, where nondeterministic and probabilistic choice
occur in different states, qualitative equivalence coincides with alternating
bisimulation, and can thus be computed via efficient partition-refinement algorithms.
Surprisingly, the result does not hold for non-alternating MDPs. Indeed, we show
that no local partition refinement algorithm can compute qualitative equivalence
on non-alternating MDPs. Finally, we consider QRCTL*, that is the “star extension”
of QRCTL. We show that QRCTL and QRCTL* induce the same qualitative equivalence
on alternating MDPs, while on non-alternating MDPs, the equivalence, arising from
QRCTL* can be strictly finer We also provide a full characterization of the relation
between qualitative equivalence, bisimulation, and alternating bisimulation, according
to whether the MDPs are finite, and to whether their transition relations are
finite-branching.
author:
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
citation:
ama: 'De Alfaro L, Chatterjee K, Faella M, Legay A. Qualitative logics and equivalences
for probabilistic systems. In: IEEE; 2007:237-248. doi:10.1109/QEST.2007.15'
apa: 'De Alfaro, L., Chatterjee, K., Faella, M., & Legay, A. (2007). Qualitative
logics and equivalences for probabilistic systems (pp. 237–248). Presented at
the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2007.15'
chicago: De Alfaro, Luca, Krishnendu Chatterjee, Marco Faella, and Axel Legay. “Qualitative
Logics and Equivalences for Probabilistic Systems,” 237–48. IEEE, 2007. https://doi.org/10.1109/QEST.2007.15.
ieee: 'L. De Alfaro, K. Chatterjee, M. Faella, and A. Legay, “Qualitative logics
and equivalences for probabilistic systems,” presented at the QEST: Quantitative
Evaluation of Systems, 2007, pp. 237–248.'
ista: 'De Alfaro L, Chatterjee K, Faella M, Legay A. 2007. Qualitative logics and
equivalences for probabilistic systems. QEST: Quantitative Evaluation of Systems,
237–248.'
mla: De Alfaro, Luca, et al. Qualitative Logics and Equivalences for Probabilistic
Systems. IEEE, 2007, pp. 237–48, doi:10.1109/QEST.2007.15.
short: L. De Alfaro, K. Chatterjee, M. Faella, A. Legay, in:, IEEE, 2007, pp. 237–248.
conference:
name: 'QEST: Quantitative Evaluation of Systems'
date_created: 2018-12-11T12:05:40Z
date_published: 2007-10-08T00:00:00Z
date_updated: 2021-01-12T07:52:55Z
day: '08'
doi: 10.1109/QEST.2007.15
extern: 1
month: '10'
page: 237 - 248
publication_status: published
publisher: IEEE
publist_id: '2289'
quality_controlled: 0
status: public
title: Qualitative logics and equivalences for probabilistic systems
type: conference
year: '2007'
...
---
_id: '3882'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by two players over a finite state
space, with objectives specified by sets of infinite traces. The games are concurrent
(players make moves simultaneously and independently), stochastic (the next state
is determined by a probability distribution that depends on the current state
and chosen moves of the players) and infinite (proceed for an infinite number
of rounds). The analysis of concurrent stochastic games can be classified into:
quantitative analysis, analyzing the optimum value of the game and epsilon-optimal
strategies that ensure values within epsilon of the optimum value; and qualitative
analysis, analyzing the set of states with optimum value 1 and epsilon-optimal
strategies for the states with optimum value 1. We consider concurrent games with
tail objectives, i.e., objectives that are independent of the finite-prefix of
traces, and show that the class of tail objectives is strictly richer than that
of the omega-regular objectives. We develop new proof techniques to extend several
properties of concurrent games with omega-regular objectives to concurrent games
with tail objectives. We prove the positive limit-one property for tail objectives.
The positive limit-one property states that for all concurrent games if the optimum
value for a player is positive for a tail objective Phi at some state, then there
is a state where the optimum value is 1 for the player for the objective Phi.
We also show that the optimum values of zero-sum (strictly conflicting objectives)
games with tail objectives can be related to equilibrium values of nonzerosum
(not strictly conflicting objectives) games with simpler reachability objectives.
A consequence of our analysis presents a polynomial time reduction of the quantitative
analysis of tail objectives to the qualitative analysis for the subclass of one-player
stochastic games (Markov decision processes). '
acknowledgement: A preliminary version of the paper appeared in Computer Science Logic
(CSL) 2006.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Chatterjee K. Concurrent games with tail objectives. Theoretical Computer
Science. 2007;388(1-3):181-198. doi:10.1016/j.tcs.2007.07.047
apa: Chatterjee, K. (2007). Concurrent games with tail objectives. Theoretical
Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2007.07.047
chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives.” Theoretical
Computer Science. Elsevier, 2007. https://doi.org/10.1016/j.tcs.2007.07.047.
ieee: K. Chatterjee, “Concurrent games with tail objectives,” Theoretical Computer
Science, vol. 388, no. 1–3. Elsevier, pp. 181–198, 2007.
ista: Chatterjee K. 2007. Concurrent games with tail objectives. Theoretical Computer
Science. 388(1–3), 181–198.
mla: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives.” Theoretical
Computer Science, vol. 388, no. 1–3, Elsevier, 2007, pp. 181–98, doi:10.1016/j.tcs.2007.07.047.
short: K. Chatterjee, Theoretical Computer Science 388 (2007) 181–198.
date_created: 2018-12-11T12:05:41Z
date_published: 2007-12-05T00:00:00Z
date_updated: 2021-01-12T07:52:56Z
day: '05'
doi: 10.1016/j.tcs.2007.07.047
extern: 1
intvolume: ' 388'
issue: 1-3
month: '12'
page: 181 - 198
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '2290'
quality_controlled: 0
status: public
title: Concurrent games with tail objectives
type: journal_article
volume: 388
year: '2007'
...
---
_id: '3883'
abstract:
- lang: eng
text: We consider games where the winning conditions are disjunctions (or dually,
conjunctions) of parity conditions; we call them generalized parity games. These
winning conditions, while omega-regular, arise naturally when considering fair
simulation between parity automata, secure equilibria for parity conditions, and
determinization of Rabin automata. We show that these games retain the computational
complexity of Rabin and Streett conditions; i.e., they are NP-complete and co-NP-complete,
respectively. The (co-) NP-hardness is proved for the special case of a conjunction/disjunction
of two parity conditions, which is the case that arises in fair simulation and
secure equilibria. However, considering these games as Rabin or Streett games
is not optimal. We give an exposition of Zielonka's algorithm when specialized
to this kind of games. The complexity of solving these games for k parity objectives
with d priorities, n states, and m edges is O(n(2kd) (.) m) (.) (k(.)d)!/ d!(k),
as compared to O(n(2kd .) m) - (k (.) d)! when these games are solved as Rabin/Streett
games. We also extend the subexponential algorithm for solving parity games recently
introduced by Jurdzinski, Paterson, and Zwick to generalized parity games. The
resulting complexity of solving generalized parity games is n(O(root n)) (.) (k(.)d)!/d!(k).
As a corollary we obtain an improved ald!k gorithm for Rabin and Streett games
with d pairs, with time complexity n(O(root n)) (.) d!.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation, and by the NSF grants CCR-0225610 and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Chatterjee K, Henzinger TA, Piterman N. Generalized parity games. In: Vol
4423. Springer; 2007:153-167. doi:10.1007/978-3-540-71389-0_12'
apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2007). Generalized parity
games (Vol. 4423, pp. 153–167). Presented at the FoSSaCS: Foundations of Software
Science and Computation Structures, Springer. https://doi.org/10.1007/978-3-540-71389-0_12'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Generalized
Parity Games,” 4423:153–67. Springer, 2007. https://doi.org/10.1007/978-3-540-71389-0_12.
ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Generalized parity games,”
presented at the FoSSaCS: Foundations of Software Science and Computation Structures,
2007, vol. 4423, pp. 153–167.'
ista: 'Chatterjee K, Henzinger TA, Piterman N. 2007. Generalized parity games. FoSSaCS:
Foundations of Software Science and Computation Structures, LNCS, vol. 4423, 153–167.'
mla: Chatterjee, Krishnendu, et al. Generalized Parity Games. Vol. 4423,
Springer, 2007, pp. 153–67, doi:10.1007/978-3-540-71389-0_12.
short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, Springer, 2007, pp. 153–167.
conference:
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
date_created: 2018-12-11T12:05:41Z
date_published: 2007-03-09T00:00:00Z
date_updated: 2021-01-12T07:52:56Z
day: '09'
doi: 10.1007/978-3-540-71389-0_12
extern: 1
intvolume: ' 4423'
month: '03'
page: 153 - 167
publication_status: published
publisher: Springer
publist_id: '2287'
quality_controlled: 0
status: public
title: Generalized parity games
type: conference
volume: 4423
year: '2007'
...
---
_id: '3884'
abstract:
- lang: eng
text: We introduce strategy logic, a logic that treats strategies in two-player
games as explicit first-order objects. The explicit treatment of strategies allows
us to specify properties of nonzero-sum games in a simple and natural way. We
show that the one-alternation fragment of strategy logic is strong enough to express
the existence of Nash equilibria and secure equilibria, and subsumes other logics
that were introduced to reason about games, such as ATL, ATL*, and game logic.
We show that strategy logic is decidable, by constructing tree automata that recognize
sets of strategies. While for the general logic, our decision procedure is nonelementary,
for the simple fragment that is used above we show that the complexity is polynomial
in the size of the game graph and optimal in the size of the formula (ranging
from polynomial to 2EXPTIME depending on the form of the formula).
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Chatterjee K, Henzinger TA, Piterman N. Strategy logic. In: Vol 4703. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2007:59-73. doi:10.1007/978-3-540-74407-8_5'
apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2007). Strategy logic
(Vol. 4703, pp. 59–73). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-74407-8_5'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Strategy
Logic,” 4703:59–73. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2007. https://doi.org/10.1007/978-3-540-74407-8_5.
ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Strategy logic,” presented
at the CONCUR: Concurrency Theory, 2007, vol. 4703, pp. 59–73.'
ista: 'Chatterjee K, Henzinger TA, Piterman N. 2007. Strategy logic. CONCUR: Concurrency
Theory, LNCS, vol. 4703, 59–73.'
mla: Chatterjee, Krishnendu, et al. Strategy Logic. Vol. 4703, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2007, pp. 59–73, doi:10.1007/978-3-540-74407-8_5.
short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2007, pp. 59–73.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:41Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2025-09-30T09:32:17Z
day: '01'
doi: 10.1007/978-3-540-74407-8_5
extern: 1
intvolume: ' 4703'
month: '09'
page: 59 - 73
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2286'
quality_controlled: 0
related_material:
record:
- id: '3861'
relation: later_version
status: public
status: public
title: Strategy logic
type: conference
volume: 4703
year: '2007'
...
---
_id: '3885'
abstract:
- lang: eng
text: 'The theory of graph games with ω-regular winning conditions is the foundation
for modeling and synthesizing reactive processes. In the case of stochastic reactive
processes, the corresponding stochastic graph games have three players, two of
them (System and Environment) behaving adversarially, and the third (Uncertainty)
behaving probabilistically. We consider two problems for stochastic graph games:
the qualitative problem asks for the set of states from which a player can win
with probability 1 (almost-sure winning); and the quantitative problem asks for
the maximal probability of winning (optimal winning) from each state. We consider
ω-regular winning conditions formalized as Müller winning conditions. We present
optimal memory bounds for pure almost-sure winning and optimal winning strategies
in stochastic graph games with Müller winning conditions. We also present improved
memory bounds for randomized almost-sure winning and optimal strategies.'
acknowledgement: This research was supported in part by the the AFOSR MURI grant F49620-00-1-
0327, and the NSF grant CCR-0225610.
alternative_title:
- 'LNCS '
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Optimal strategy synthesis in stochastic Müller games. In: Vol
4423. Springer; 2007:138-152. doi:10.1007/978-3-540-71389-0_11'
apa: 'Chatterjee, K. (2007). Optimal strategy synthesis in stochastic Müller games
(Vol. 4423, pp. 138–152). Presented at the FoSSaCS: Foundations of Software Science
and Computation Structures, Springer. https://doi.org/10.1007/978-3-540-71389-0_11'
chicago: Chatterjee, Krishnendu. “Optimal Strategy Synthesis in Stochastic Müller
Games,” 4423:138–52. Springer, 2007. https://doi.org/10.1007/978-3-540-71389-0_11.
ieee: 'K. Chatterjee, “Optimal strategy synthesis in stochastic Müller games,” presented
at the FoSSaCS: Foundations of Software Science and Computation Structures, 2007,
vol. 4423, pp. 138–152.'
ista: 'Chatterjee K. 2007. Optimal strategy synthesis in stochastic Müller games.
FoSSaCS: Foundations of Software Science and Computation Structures, LNCS , vol.
4423, 138–152.'
mla: Chatterjee, Krishnendu. Optimal Strategy Synthesis in Stochastic Müller
Games. Vol. 4423, Springer, 2007, pp. 138–52, doi:10.1007/978-3-540-71389-0_11.
short: K. Chatterjee, in:, Springer, 2007, pp. 138–152.
conference:
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
date_created: 2018-12-11T12:05:42Z
date_published: 2007-07-02T00:00:00Z
date_updated: 2021-01-12T07:52:57Z
day: '02'
doi: 10.1007/978-3-540-71389-0_11
extern: 1
intvolume: ' 4423'
month: '07'
page: 138 - 152
publication_status: published
publisher: Springer
publist_id: '2284'
quality_controlled: 0
status: public
title: Optimal strategy synthesis in stochastic Müller games
type: conference
volume: 4423
year: '2007'
...
---
_id: '3886'
abstract:
- lang: eng
text: 'The theory of graph games with ω-regular winning conditions is the foundation
for modeling and synthesizing reactive processes. In the case of stochastic reactive
processes, the corresponding stochastic graph games have three players, two of
them (System and Environment) behaving adversarially, and the third (Uncertainty)
behaving probabilistically. We consider two problems for stochastic graph games:
the qualitative problem asks for the set of states from which a player can win
with probability 1 (almost-sure winning); and the quantitative problem asks for
the maximal probability of winning (optimal winning) from each state. We consider
ω-regular winning conditions formalized as Müller winning conditions. We show
that both the qualitative and quantitative problem for stochastic Müller games
are PSPACE-complete. We also consider two well-known sub-classes of Müller objectives,
namely, upward-closed and union-closed objectives, and show that both the qualitative
and quantitative problem for these sub-classes are coNP-complete.'
acknowledgement: This research was supported in part by the the AFOSR MURI grant F49620-00-1-
0327, and the NSF grant CCR-0225610.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Stochastic Müller games are PSPACE-complete. In: Vol 4855. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2007:436-448. doi:10.1007/978-3-540-77050-3_36'
apa: 'Chatterjee, K. (2007). Stochastic Müller games are PSPACE-complete (Vol. 4855,
pp. 436–448). Presented at the FSTTCS: Foundations of Software Technology and
Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.1007/978-3-540-77050-3_36'
chicago: Chatterjee, Krishnendu. “Stochastic Müller Games Are PSPACE-Complete,”
4855:436–48. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2007. https://doi.org/10.1007/978-3-540-77050-3_36.
ieee: 'K. Chatterjee, “Stochastic Müller games are PSPACE-complete,” presented at
the FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
2007, vol. 4855, pp. 436–448.'
ista: 'Chatterjee K. 2007. Stochastic Müller games are PSPACE-complete. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LNCS, vol.
4855, 436–448.'
mla: Chatterjee, Krishnendu. Stochastic Müller Games Are PSPACE-Complete.
Vol. 4855, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2007, pp. 436–48,
doi:10.1007/978-3-540-77050-3_36.
short: K. Chatterjee, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2007,
pp. 436–448.
conference:
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
date_created: 2018-12-11T12:05:42Z
date_published: 2007-12-15T00:00:00Z
date_updated: 2021-01-12T07:52:57Z
day: '15'
doi: 10.1007/978-3-540-77050-3_36
extern: 1
intvolume: ' 4855'
month: '12'
page: 436 - 448
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2282'
quality_controlled: 0
status: public
title: Stochastic Müller games are PSPACE-complete
type: conference
volume: 4855
year: '2007'
...