---
_id: '1883'
abstract:
- lang: eng
text: "We introduce a one-parametric family of tree growth models, in which branching
probabilities decrease with branch age τ as τ-α. Depending on the exponent α,
the scaling of tree depth with tree size n displays a transition between the logarithmic
scaling of random trees and an algebraic growth. At the transition (α=1) tree
depth grows as (logn)2. This anomalous scaling is in good agreement with the trend
observed in evolution of biological species, thus providing a theoretical support
for age-dependent speciation and associating it to the occurrence of a critical
point.\r\n"
article_number: '022803'
article_processing_charge: No
article_type: original
author:
- first_name: Stephanie
full_name: Keller-Schmidt, Stephanie
last_name: Keller-Schmidt
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Víctor
full_name: Eguíluz, Víctor
last_name: Eguíluz
- first_name: Emilio
full_name: Hernandez Garcia, Emilio
last_name: Hernandez Garcia
- first_name: Konstantin
full_name: Klemm, Konstantin
last_name: Klemm
citation:
ama: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous
scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803
apa: Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm,
K. (2015). Anomalous scaling in an age-dependent branching model. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.91.022803
chicago: Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez
Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.
ieee: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm,
“Anomalous scaling in an age-dependent branching model,” Physical Review E
Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute
of Physics, 2015.
ista: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015.
Anomalous scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 91(2), 022803.
mla: Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.
short: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm,
Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:31Z
date_published: 2015-02-02T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '02'
department:
- _id: NiBa
doi: 10.1103/PhysRevE.91.022803
external_id:
arxiv:
- '1012.3298'
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1012.3298
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anomalous scaling in an age-dependent branching model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1878'
abstract:
- lang: eng
text: Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian
Peninsula, with some localized populations in the French Pyrenees. Within the
genus, a dozen species have been recognized based on morphological diversity,
most of them with limited distribution area, in small populations and frequently
with potential threats to their survival. To date, however, a molecular evaluation
of the current systematic treatments has not been carried out. The aim of the
present study is to infer phylogenetic relationships among its subordinate taxa
by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS)
DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis
within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by
both ITS and rps16 intron sequence analyses. Furthermore, time estimates using
BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26
Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD,
for rps16 intron).
author:
- first_name: Eduardo
full_name: Cires Rodriguez, Eduardo
id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87
last_name: Cires Rodriguez
- first_name: José
full_name: Prieto, José
last_name: Prieto
citation:
ama: Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun
ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal
of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6
apa: Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of
Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian
Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6
chicago: Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships
of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the
Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6.
ieee: E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis
A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,”
Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.
ista: Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis
A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula.
Journal of Plant Research. 128(2), 223–238.
mla: Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis
A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.”
Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38,
doi:10.1007/s10265-014-0691-6.
short: E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.
date_created: 2018-12-11T11:54:30Z
date_published: 2015-01-24T00:00:00Z
date_updated: 2021-01-12T06:53:47Z
day: '24'
department:
- _id: JiFr
doi: 10.1007/s10265-014-0691-6
intvolume: ' 128'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 223 - 238
publication: Journal of Plant Research
publication_status: published
publisher: Springer
publist_id: '5217'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae),
a discussed genus from the Iberian Peninsula
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1885'
abstract:
- lang: eng
text: 'The concept of positional information is central to our understanding of
how cells determine their location in a multicellular structure and thereby their
developmental fates. Nevertheless, positional information has neither been defined
mathematically nor quantified in a principled way. Here we provide an information-theoretic
definition in the context of developmental gene expression patterns and examine
the features of expression patterns that affect positional information quantitatively.
We connect positional information with the concept of positional error and develop
tools to directly measure information and error from experimental data. We illustrate
our framework for the case of gap gene expression patterns in the early Drosophila
embryo and show how information that is distributed among only four genes is sufficient
to determine developmental fates with nearly single-cell resolution. Our approach
can be generalized to a variety of different model systems; procedures and examples
are discussed in detail. '
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Mariela
full_name: Petkova, Mariela
last_name: Petkova
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: 'Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
2015;199(1):39-59. doi:10.1534/genetics.114.171850'
apa: 'Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850'
chicago: 'Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional
Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical
Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.'
ieee: 'G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework,”
Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.'
ista: 'Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
199(1), 39–59.'
mla: 'Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout
Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199,
no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.'
short: G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
date_created: 2018-12-11T11:54:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1534/genetics.114.171850
intvolume: ' 199'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.5599
month: '01'
oa: 1
oa_version: Preprint
page: 39 - 59
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5210'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Positional information, positional error, and readout precision in morphogenesis:
A mathematical framework'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2015'
...
---
_id: '1940'
abstract:
- lang: eng
text: We typically think of cells as responding to external signals independently
by regulating their gene expression levels, yet they often locally exchange information
and coordinate. Can such spatial coupling be of benefit for conveying signals
subject to gene regulatory noise? Here we extend our information-theoretic framework
for gene regulation to spatially extended systems. As an example, we consider
a lattice of nuclei responding to a concentration field of a transcriptional regulator
(the "input") by expressing a single diffusible target gene. When input
concentrations are low, diffusive coupling markedly improves information transmission;
optimal gene activation functions also systematically change. A qualitatively
new regulatory strategy emerges where individual cells respond to the input in
a nearly step-like fashion that is subsequently averaged out by strong diffusion.
While motivated by early patterning events in the Drosophila embryo, our framework
is generically applicable to spatially coupled stochastic gene expression models.
article_number: '062710'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks.
IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
apa: Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in
small genetic networks. IV. Spatial coupling. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710
chicago: Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in
Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
ieee: T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic
networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and
Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
ista: Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic
networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft
Matter Physics. 91(6), 062710.
mla: Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small
Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics,
2015, doi:10.1103/PhysRevE.91.062710.
short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft
Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:49Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T06:54:13Z
day: '15'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.91.062710
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04015
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5145'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing information flow in small genetic networks. IV. Spatial coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1938'
abstract:
- lang: eng
text: 'We numerically investigate the distribution of extrema of ''chaotic'' Laplacian
eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a)
we count extrema on grid graphs with a small number of randomly added edges and
show the behavior to coincide with the 1957 prediction of Longuet-Higgins for
the continuous case and (b) we compute the regularity of their spatial distribution
using discrepancy, which is a classical measure from the theory of Monte Carlo
integration. The first part suggests that grid graphs with randomly added edges
should behave like two-dimensional surfaces with ergodic geodesic flow; in the
second part we show that the extrema are more regularly distributed in space than
the grid Z2.'
acknowledgement: "F.P. was supported by the Graduate School of IST Austria. S.S. was
partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and
Michael Kerber for sharing their implementation of the persistence algorithm. "
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Stefan
full_name: Steinerberger, Stefan
last_name: Steinerberger
citation:
ama: Pausinger F, Steinerberger S. On the distribution of local extrema in quantum
chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010
apa: Pausinger, F., & Steinerberger, S. (2015). On the distribution of local
extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010
chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015.
https://doi.org/10.1016/j.physleta.2014.12.010.
ieee: F. Pausinger and S. Steinerberger, “On the distribution of local extrema in
quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier,
pp. 535–541, 2015.
ista: Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in
quantum chaos. Physics Letters, Section A. 379(6), 535–541.
mla: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6,
Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.
short: F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.
date_created: 2018-12-11T11:54:49Z
date_published: 2015-03-06T00:00:00Z
date_updated: 2021-01-12T06:54:12Z
day: '06'
department:
- _id: HeEd
doi: 10.1016/j.physleta.2014.12.010
intvolume: ' 379'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 535 - 541
publication: Physics Letters, Section A
publication_status: published
publisher: Elsevier
publist_id: '5152'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the distribution of local extrema in quantum chaos
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 379
year: '2015'
...
---
_id: '1944'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology
(IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions)
of the European Union
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002
apa: Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking
and PIN-mediated cell polarity during tropic responses in plants. Current Opinion
in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002
chicago: Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking
and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current
Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.
ieee: H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants,” Current Opinion in Plant
Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.
ista: Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
23(2), 116–123.
mla: Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity
during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol.
23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.
short: H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015)
116–123.
date_created: 2018-12-11T11:54:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2014.12.002
ec_funded: 1
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 116 - 123
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '5140'
quality_controlled: '1'
scopus_import: 1
status: public
title: Intracellular trafficking and PIN-mediated cell polarity during tropic responses
in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: 1
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1997'
abstract:
- lang: eng
text: We prove that the three-state toric homogeneous Markov chain model has Markov
degree two. In algebraic terminology this means, that a certain class of toric
ideals is generated by quadratic binomials. This was conjectured by Haws, Martin
del Campo, Takemura and Yoshida, who proved that they are generated by degree
six binomials.
author:
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Noren P. The three-state toric homogeneous Markov chain model has Markov degree
two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296.
doi:10.1016/j.jsc.2014.09.014
apa: Noren, P. (2015). The three-state toric homogeneous Markov chain model has
Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014
chicago: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has
Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.
ieee: P. Noren, “The three-state toric homogeneous Markov chain model has Markov
degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June.
Elsevier, pp. 285–296, 2015.
ista: Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov
degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.
mla: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov
Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June,
Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.
short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.
date_created: 2018-12-11T11:55:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:35Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jsc.2014.09.014
issue: May-June
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0077
month: '05'
oa: 1
oa_version: Preprint
page: 285 - 296
publication: Journal of Symbolic Computation
publication_status: published
publisher: Elsevier
publist_id: '5082'
quality_controlled: '1'
scopus_import: 1
status: public
title: The three-state toric homogeneous Markov chain model has Markov degree two
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68/Part 2
year: '2015'
...
---
_id: '2008'
abstract:
- lang: eng
text: The paper describes a generalized iterative proportional fitting procedure
that can be used for maximum likelihood estimation in a special class of the general
log-linear model. The models in this class, called relational, apply to multivariate
discrete sample spaces that do not necessarily have a Cartesian product structure
and may not contain an overall effect. When applied to the cell probabilities,
the models without the overall effect are curved exponential families and the
values of the sufficient statistics are reproduced by the MLE only up to a constant
of proportionality. The paper shows that Iterative Proportional Fitting, Generalized
Iterative Scaling, and Improved Iterative Scaling fail to work for such models.
The algorithm proposed here is based on iterated Bregman projections. As a by-product,
estimates of the multiplicative parameters are also obtained. An implementation
of the algorithm is available as an R-package.
acknowledgement: Part of the material presented here was contained in the PhD thesis
of the first author to which the second author and Thomas Richardson were advisers.
The authors wish to thank him for several comments and suggestions. We also thank
the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1
uses the idea of Olga Klimova, to whom the authors are also indebted. The second
author was supported in part by Grant K-106154 from the Hungarian National Scientific
Research Fund (OTKA).
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian
Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139
apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential
families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139
chicago: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential
Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.
ieee: A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,”
Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847,
2015.
ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families.
Scandinavian Journal of Statistics. 42(3), 832–847.
mla: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.”
Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47,
doi:10.1111/sjos.12139.
short: A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.
date_created: 2018-12-11T11:55:11Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:54:41Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/sjos.12139
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3282
month: '09'
oa: 1
oa_version: Preprint
page: 832 - 847
publication: Scandinavian Journal of Statistics
publication_status: published
publisher: Wiley
publist_id: '5068'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative scaling in curved exponential families
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '2006'
abstract:
- lang: eng
text: 'The monotone secant conjecture posits a rich class of polynomial systems,
all of whose solutions are real. These systems come from the Schubert calculus
on flag manifolds, and the monotone secant conjecture is a compelling generalization
of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko).
We present some theoretical evidence for this conjecture, as well as computational
evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of
the phenomena we observed in our data. '
article_processing_charge: No
author:
- first_name: Nicolas
full_name: Hein, Nicolas
last_name: Hein
- first_name: Christopher
full_name: Hillar, Christopher
last_name: Hillar
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
- first_name: Zach
full_name: Teitler, Zach
last_name: Teitler
citation:
ama: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone
secant conjecture in the real Schubert calculus. Experimental Mathematics.
2015;24(3):261-269. doi:10.1080/10586458.2014.980044
apa: Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler,
Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental
Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044
chicago: Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank
Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.
ieee: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler,
“The monotone secant conjecture in the real Schubert calculus,” Experimental
Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.
ista: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015.
The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics.
24(3), 261–269.
mla: Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis,
2015, pp. 261–69, doi:10.1080/10586458.2014.980044.
short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler,
Experimental Mathematics 24 (2015) 261–269.
date_created: 2018-12-11T11:55:10Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:54:40Z
day: '23'
department:
- _id: CaUh
doi: 10.1080/10586458.2014.980044
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.3436
month: '06'
oa: 1
oa_version: Preprint
page: 261 - 269
publication: Experimental Mathematics
publication_status: published
publisher: Taylor & Francis
publist_id: '5070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The monotone secant conjecture in the real Schubert calculus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...