---
_id: '958'
abstract:
- lang: eng
text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used
to visualize biological and physiological processes and are capable of providing
detailed information in both spatial and temporal dimensions. In a FRET-based
biosensor, substrate binding is associated with a change in the relative positions
of two fluorophores, leading to a change in FRET efficiency that may be observed
in the fluorescence spectrum. As a result, their design requires a ligand-binding
protein that exhibits a conformational change upon binding. However, not all ligand-binding
proteins produce responsive sensors upon conjugation to fluorescent proteins or
dyes, and identifying the optimum locations for the fluorophores often involves
labor-intensive iterative design or high-throughput screening. Combining the genetic
fusion of a fluorescent protein to the ligand-binding protein with site-specific
covalent attachment of a fluorescent dye can allow fine control over the positions
of the two fluorophores, allowing the construction of very sensitive sensors.
This relies upon the accurate prediction of the locations of the two fluorophores
in bound and unbound states. In this chapter, we describe a method for computational
identification of dye-attachment sites that allows the use of cysteine modification
to attach synthetic dyes that can be paired with a fluorescent protein for the
purposes of creating FRET sensors.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors
using a synthetic dye fluorescent protein FRET pair and computational modeling
and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596.
Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6'
apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara,
M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic
dye fluorescent protein FRET pair and computational modeling and assessment. In
V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_6
chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald
L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors
Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling
and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein,
1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.
ieee: J. Mitchell et al., “Method for developing optical sensors using a
synthetic dye fluorescent protein FRET pair and computational modeling and assessment,”
in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017,
pp. 89–99.
ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2017.Method for developing optical sensors using a synthetic dye fluorescent
protein FRET pair and computational modeling and assessment. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 89–99.'
mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic
Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.”
Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer,
2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.
short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp.
89–99.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2025-07-10T12:01:54Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_6
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '05'
oa_version: None
page: 89 - 99
publication: Synthetic Protein Switches
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6450'
quality_controlled: '1'
scopus_import: '1'
series_title: Synthetic Protein Switches
status: public
title: Method for developing optical sensors using a synthetic dye fluorescent protein
FRET pair and computational modeling and assessment
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9588'
abstract:
- lang: eng
text: 'Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero
reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that
is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for
the best possible upper bound on the concentration probabilities Pr[X=x] . In
this paper we study a resilience version of the Littlewood-Offord problem: how
many of the ξi is an adversary typically allowed to change without being able
to force concentration on a particular value? We solve this problem asymptotically,
and present a few interesting open problems.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Afonso S.
full_name: Bandeira, Afonso S.
last_name: Bandeira
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem.
Advances in Mathematics. 2017;319:292-312. doi:10.1016/j.aim.2017.08.031
apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood–Offord
problem. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2017.08.031
chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for
the Littlewood–Offord Problem.” Advances in Mathematics. Elsevier, 2017.
https://doi.org/10.1016/j.aim.2017.08.031.
ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord
problem,” Advances in Mathematics, vol. 319. Elsevier, pp. 292–312, 2017.
ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord
problem. Advances in Mathematics. 319, 292–312.
mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.”
Advances in Mathematics, vol. 319, Elsevier, 2017, pp. 292–312, doi:10.1016/j.aim.2017.08.031.
short: A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312.
date_created: 2021-06-22T11:51:27Z
date_published: 2017-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:57Z
day: '15'
doi: 10.1016/j.aim.2017.08.031
extern: '1'
external_id:
arxiv:
- '1609.08136'
intvolume: ' 319'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08136
month: '10'
oa: 1
oa_version: Preprint
page: 292-312
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resilience for the Littlewood–Offord problem
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 319
year: '2017'
...
---
_id: '9589'
abstract:
- lang: eng
text: We give an asymptotic expression for the expected number of spanning trees
in a random graph with a given degree sequence , provided that the number of edges
is at least , where is the maximum degree. A key part of our argument involves
establishing a concentration result for a certain family of functions over random
trees with given degrees, using Prüfer codes.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Mikhail
full_name: Isaev, Mikhail
last_name: Isaev
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Brendan D.
full_name: McKay, Brendan D.
last_name: McKay
citation:
ama: Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees
in sparse graphs with given degrees. European Journal of Combinatorics.
2017;63:6-25. doi:10.1016/j.ejc.2017.02.003
apa: Greenhill, C., Isaev, M., Kwan, M. A., & McKay, B. D. (2017). The average
number of spanning trees in sparse graphs with given degrees. European Journal
of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2017.02.003
chicago: Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D.
McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.”
European Journal of Combinatorics. Elsevier, 2017. https://doi.org/10.1016/j.ejc.2017.02.003.
ieee: C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of
spanning trees in sparse graphs with given degrees,” European Journal of Combinatorics,
vol. 63. Elsevier, pp. 6–25, 2017.
ista: Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning
trees in sparse graphs with given degrees. European Journal of Combinatorics.
63, 6–25.
mla: Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse
Graphs with given Degrees.” European Journal of Combinatorics, vol. 63,
Elsevier, 2017, pp. 6–25, doi:10.1016/j.ejc.2017.02.003.
short: C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics
63 (2017) 6–25.
date_created: 2021-06-22T12:18:59Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:02:00Z
day: '01'
doi: 10.1016/j.ejc.2017.02.003
extern: '1'
external_id:
arxiv:
- '1606.01586'
intvolume: ' 63'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ejc.2017.02.003
month: '06'
oa: 1
oa_version: Published Version
page: 6-25
publication: European Journal of Combinatorics
publication_identifier:
issn:
- 0195-6698
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The average number of spanning trees in sparse graphs with given degrees
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 63
year: '2017'
...
---
_id: '9590'
abstract:
- lang: eng
text: We show that for any fixed dense graph G and bounded-degree tree T on the
same number of vertices, a modest random perturbation of G will typically contain
a copy of T . This combines the viewpoints of the well-studied problems of embedding
trees into fixed dense graphs and into random graphs, and extends a sizeable body
of existing research on randomly perturbed graphs. Specifically, we show that
there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least
αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn
uniformly random edges to G, the resulting graph will contain T asymptotically
almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of
a dense graph into super-regular pairs of comparable sizes, which may be of independent
interest.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly
perturbed graphs. SIAM Journal on Discrete Mathematics. 2017;31(1):155-171.
doi:10.1137/15m1032910
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2017). Bounded-degree spanning
trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1032910
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree
Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics, 2017. https://doi.org/10.1137/15m1032910.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees
in randomly perturbed graphs,” SIAM Journal on Discrete Mathematics, vol.
31, no. 1. Society for Industrial & Applied Mathematics, pp. 155–171, 2017.
ista: Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in
randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171.
mla: Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed
Graphs.” SIAM Journal on Discrete Mathematics, vol. 31, no. 1, Society
for Industrial & Applied Mathematics, 2017, pp. 155–71, doi:10.1137/15m1032910.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics
31 (2017) 155–171.
date_created: 2021-06-22T12:26:25Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-02-23T14:02:05Z
day: '12'
doi: 10.1137/15m1032910
extern: '1'
external_id:
arxiv:
- '1507.07960'
intvolume: ' 31'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.07960
month: '01'
oa: 1
oa_version: Preprint
page: 155-171
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
eissn:
- 1095-7146
issn:
- 0895-4801
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bounded-degree spanning trees in randomly perturbed graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 31
year: '2017'
...
---
OA_place: publisher
_id: '961'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes the first step in the emergence of multicellularity in
evolution, thereby allowing the differentiation of specialized cell types. In metazoan
development, cell-cell contact formation is thought to influence cell fate specification,
and cell fate specification has been implicated in cell-cell contact
formation. However, remarkably little is yet known about whether and how the
interaction and feedback between cell-cell contact formation and cell fate specification
affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and
mesendoderm cell fate specification during zebrafish gastrulation. We show that long
lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor
cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further
show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an
effective positive feedback loop between ppl cell-cell contact duration and cell fate
specification. Finally, by using a combination of theoretical modeling and experimentation,
we show that this feedback loop determines whether anterior axial mesendoderm cells
become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal
that the gene regulatory networks leading to cell fate diversification within the developing
embryo are controlled by the interdependent activities of cell-cell signaling and contact
formation.
acknowledgement: "Many people accompanied me during this trip: I would not have reached
my destination nor \r\nenjoyed the travelling without them. First of all, thanks
to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting
and incredibly competent people and thanks for \r\nall the good science I witnessed
\ and participated in. It has been a \r\nblast, an incredibly \r\nexciting
\ one! Thanks to JLo, for teaching me how to master my pipettes and
\ showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching
me basically everything \r\nabout zebrafish and being always there to advice,
\ sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the
critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing
kicker matches, and Keisuke, for showing me the light, and to the three of them
\r\ntogether for all the good laughs we\r\nhad. My start in Vienna would
\ have been a lot more \r\ndifficult without you guys. Also it would not
\ have been possible without Elena and Inês: \r\nthanks for helping setting
\ up this lab and for the dinners in Gugging. Thanks to Martin, for
\r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp,
\ for the interest and \r\nadvice, and to Michael, for the Viennise take on things.
Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend
in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel
for the enthusiasm and the neverending energy and for all your \r\nhelp over the
years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.
\ To Shayan, for being such a motivated student. To Matt, for helping
\ out\r\nwith coding \r\nand for finding punk solutions to data analysis problems.
Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla,
Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful
\ atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments
would have been much more difficult without your help. Special thanks to Katjia
\r\nfor setting up an amazing imaging facility and for building the best
\ team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith
all the late sortings and for helping with all \r\nthe technical problems. Thanks
to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald
Janovjak for being a present and helpful committee member over the years \r\nand
\ to Patrick Lemaire f\r\nor the helpful insight and extremely interesting
\ discussion we had \r\nabout the project. Also, this journey would not
\ have been the same without all the friends \r\nthat I met in Dresden and
then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne,
Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph,
\r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled
my days with \r\nfun and support. A special thank to my family, always close even
if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William,
\ e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri
di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe
crazy life of a scientist, the living apart for\r\nso long, never knowing when things
are going \r\nto happen. Thanks for being a great partner and my number one fan!"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
citation:
ama: 'Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish
gastrulation. 2017. doi:10.15479/AT:ISTA:th_825'
apa: 'Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop
during zebrafish gastrulation. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th_825'
chicago: 'Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017.
https://doi.org/10.15479/AT:ISTA:th_825.'
ieee: 'V. Barone, “Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.'
ista: 'Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation. Institute of Science and Technology Austria.'
mla: 'Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation. Institute of Science and Technology Austria,
2017, doi:10.15479/AT:ISTA:th_825.'
short: 'V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during
Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.'
corr_author: '1'
date_created: 2018-12-11T11:49:25Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2026-06-18T18:12:40Z
day: '01'
ddc:
- '570'
- '590'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:th_825
file:
- access_level: closed
checksum: 242f88c87f2cf267bf05049fa26a687b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6205'
file_name: 2017_Barone_thesis_final.docx
file_size: 14497822
relation: source_file
- access_level: open_access
checksum: ba5b0613ed8bade73a409acdd880fb8a
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6206'
file_name: 2017_Barone_thesis_.pdf
file_size: 14995941
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6444'
pubrep_id: '825'
related_material:
record:
- id: '735'
relation: part_of_dissertation
status: public
- id: '1100'
relation: part_of_dissertation
status: public
- id: '1537'
relation: part_of_dissertation
status: public
- id: '3246'
relation: part_of_dissertation
status: public
- id: '2926'
relation: part_of_dissertation
status: public
- id: '676'
relation: part_of_dissertation
status: public
- id: '1912'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-16T09:58:05Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10427
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science,
Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark, 2017,
vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-07-10T12:01:59Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
- access_level: open_access
checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
record:
- id: '6005'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Timed network games with clocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '9660'
abstract:
- lang: eng
text: In this paper we discuss how the information contained in atomistic simulations
of homogeneous nucleation should be used when fitting the parameters in macroscopic
nucleation models. We show how the number of solid and liquid atoms in such simulations
can be determined unambiguously by using a Gibbs dividing surface and how the
free energy as a function of the number of solid atoms in the nucleus can thus
be extracted. We then show that the parameters (the chemical potential, the interfacial
free energy, and a Tolman correction) of a model based on classical nucleation
theory can be fitted using the information contained in these free-energy profiles
but that the parameters in such models are highly correlated. This correlation
is unfortunate as it ensures that small errors in the computed free energy surface
can give rise to large errors in the extrapolated properties of the fitted model.
To resolve this problem we thus propose a method for fitting macroscopic nucleation
models that uses simulations of planar interfaces and simulations of three-dimensional
nuclei in tandem. We show that when the chemical potentials and the interface
energy are pinned to their planar-interface values, more precise estimates for
the Tolman length are obtained. Extrapolating the free energy profile obtained
from small simulation boxes to larger nuclei is thus more reliable.
article_number: '104707'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation:
From atomistic nuclei to the planar limit. The Journal of Chemical Physics.
2017;147(10). doi:10.1063/1.4997180'
apa: 'Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy
of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180'
chicago: 'Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs
Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.”
The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.'
ieee: 'B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical
Physics, vol. 147, no. 10. AIP Publishing, 2017.'
ista: 'Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical
Physics. 147(10), 104707.'
mla: 'Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation:
From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics,
vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.'
short: B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147
(2017).
date_created: 2021-07-15T08:13:29Z
date_published: 2017-09-14T00:00:00Z
date_updated: 2023-02-23T14:04:02Z
day: '14'
doi: 10.1063/1.4997180
extern: '1'
external_id:
arxiv:
- '1703.06062'
pmid:
- '28915742'
intvolume: ' 147'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html
month: '09'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to
the planar limit'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 147
year: '2017'
...
---
_id: '9661'
abstract:
- lang: eng
text: Macroscopic theories of nucleation such as classical nucleation theory envision
that clusters of the bulk stable phase form inside the bulk metastable phase.
Molecular dynamics simulations are often used to elucidate nucleation mechanisms,
by capturing the microscopic configurations of all the atoms. In this paper, we
introduce a thermodynamic model that links macroscopic theories and atomic-scale
simulations and thus provide a simple and elegant framework for testing the limits
of classical nucleation theory.
article_number: '034106'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models
of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3).
doi:10.1063/1.4973883
apa: Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and
macroscopic models of homogeneous nucleation. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/1.4973883
chicago: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883.
ieee: B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation,” The Journal of Chemical Physics, vol.
146, no. 3. AIP Publishing, 2017.
ista: Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.
mla: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).
date_created: 2021-07-15T08:27:31Z
date_published: 2017-01-21T00:00:00Z
date_updated: 2021-08-09T12:31:57Z
day: '21'
doi: 10.1063/1.4973883
extern: '1'
external_id:
arxiv:
- '1610.01322'
pmid:
- '28109231'
intvolume: ' 146'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01322
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bridging the gap between atomistic and macroscopic models of homogeneous nucleation
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 146
year: '2017'
...
---
_id: '9707'
abstract:
- lang: eng
text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting
duct system and is critical for normal nephron number, while low nephron number
is implicated in hypertension and renal disease. Ureteric bud growth and branching
requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric
bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling
up-regulates transcription factors Etv4 and Etv5, which are also critical for
branching. Despite extensive knowledge of the genetic control of these events,
it is not understood, at the cellular level, how renal branching morphogenesis
is achieved or how Ret signaling influences epithelial cell behaviors to promote
this process. Analysis of chimeric embryos previously suggested a role for Ret
signaling in promoting cell rearrangements in the nephric duct, but this method
was unsuited to study individual cell behaviors during ureteric bud branching.
Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture
and time-lapse imaging, to trace the movements and divisions of individual ureteric
bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
clones in which the mutant and wild-type sister cells are differentially and heritably
marked by green and red fluorescent proteins. We find that, in normal kidneys,
most individual tip cells behave as self-renewing progenitors, some of whose progeny
remain at the tips while others populate the growing UB trunks. In Ret or Etv4
MADM clones, the wild-type cells generated at a UB tip are much more likely to
remain at, or move to, the new tips during branching and elongation, while their
Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
By tracking successive mitoses in a cell lineage, we find that Ret signaling has
little effect on proliferation, in contrast to its effects on cell movement. Our
results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric
bud tips, and suggest a model in which these cell movements mediate branching
morphogenesis.
article_processing_charge: No
author:
- first_name: Paul
full_name: Riccio, Paul
last_name: Riccio
- first_name: Christina
full_name: Cebrián, Christina
last_name: Cebrián
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Frank
full_name: Costantini, Frank
last_name: Costantini
citation:
ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and
Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.
2017. doi:10.5061/dryad.pk16b'
apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017).
Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b'
chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank
Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor
Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.'
ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data
from: Ret and Etv4 promote directed movements of progenitor cells during renal
branching morphogenesis.” Dryad, 2017.'
ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from:
Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis, Dryad, 10.5061/dryad.pk16b.'
mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements
of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.'
short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).
date_created: 2021-07-23T09:39:34Z
date_published: 2017-01-14T00:00:00Z
date_updated: 2022-08-25T13:34:55Z
day: '14'
department:
- _id: SiHi
doi: 10.5061/dryad.pk16b
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.pk16b
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9702'
relation: used_in_publication
status: deleted
status: public
title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2025-09-22T09:43:12Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2025-04-15T07:11:04Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '642'
abstract:
- lang: eng
text: Cauchy problems with SPDEs on the whole space are localized to Cauchy problems
on a ball of radius R. This localization reduces various kinds of spatial approximation
schemes to finite dimensional problems. The error is shown to be exponentially
small. As an application, a numerical scheme is presented which combines the localization
and the space and time discretization, and thus is fully implementable.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: István
full_name: Gyöngy, István
last_name: Gyöngy
citation:
ama: Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential
equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397.
doi:10.1090/mcom/3201
apa: Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic
partial differential equations in the whole space. Mathematics of Computation.
American Mathematical Society. https://doi.org/10.1090/mcom/3201
chicago: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation.
American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201.
ieee: M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial
differential equations in the whole space,” Mathematics of Computation,
vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.
ista: Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial
differential equations in the whole space. Mathematics of Computation. 86(307),
2373–2397.
mla: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation,
vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.
short: M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.
corr_author: '1'
date_created: 2018-12-11T11:47:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-09-11T07:20:20Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/mcom/3201
external_id:
arxiv:
- '1508.05535'
isi:
- '000400929100013'
intvolume: ' 86'
isi: 1
issue: '307'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.05535
month: '01'
oa: 1
oa_version: Submitted Version
page: 2373 - 2397
publication: Mathematics of Computation
publication_identifier:
issn:
- 0025-5718
publication_status: published
publisher: American Mathematical Society
publist_id: '7144'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Localization errors in solving stochastic partial differential equations in
the whole space
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 86
year: '2017'
...
---
_id: '6426'
abstract:
- lang: eng
text: Synchronous programs are easy to specify because the side effects of an operation
are finished by the time the invocation of the operation returns to the caller.
Asynchronous programs, on the other hand, are difficult to specify because there
are side effects due to pending computation scheduled as a result of the invocation
of an operation. They are also difficult to verify because of the large number
of possible interleavings of concurrent asynchronous computation threads. We show
that specifications and correctness proofs for asynchronous programs can be structured
by introducing the fiction, for proof purposes, that intermediate, non-quiescent
states of asynchronous operations can be ignored. Then, the task of specification
becomes relatively simple and the task of verification can be naturally decomposed
into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure
of an asynchronous program, the atomic effect of non-atomic operations and the
synchronous effect of asynchronous operations. This structuring of specifications
and proofs corresponds to the introduction of multiple layers of stepwise refinement
for asynchronous programs. We present the first proof rule, called synchronization,
to reduce asynchronous invocations on a lower layer to synchronous invocations
on a higher layer. We implemented our proof method in CIVL and evaluated it on
a collection of benchmark programs.
alternative_title:
- IST Austria Technical Report
author:
- 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: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST
Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2
apa: Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the
asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2
chicago: Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing
the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2.
ieee: T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous.
IST Austria, 2017.
ista: Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST
Austria, 28p.
mla: Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria,
2017, doi:10.15479/AT:IST-2018-853-v2-2.
short: T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST
Austria, 2017.
date_created: 2019-05-13T08:15:55Z
date_published: 2017-08-04T00:00:00Z
date_updated: 2025-04-15T08:11:53Z
day: '04'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2018-853-v2-2
file:
- access_level: open_access
checksum: b48d42725182d7ca10107a118815f4cf
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T08:14:44Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6431'
file_name: main(1).pdf
file_size: 971347
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '28'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '133'
relation: later_version
status: public
status: public
title: Synchronizing the asynchronous
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
OA_type: closed access
_id: '643'
abstract:
- lang: eng
text: It has been reported that nicotinamide-overload induces oxidative stress associated
with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This
study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance
tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without
cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT)
were also carried out in adult Sprague-Dawley rats treated with or without cumulative
doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration
significantly increased the plasma H2O2 levels associated with high insulin levels.
Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration
of nicotinic acid, another form of Vitamin B3, also significantly increased plasma
insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic
acid or nicotinamide impaired glucose metabolism. This study suggested that excess
Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.
article_processing_charge: No
article_type: original
author:
- first_name: Wuping
full_name: Sun, Wuping
last_name: Sun
- first_name: Ming-Zhu
full_name: Zhai, Ming-Zhu
id: 34009CFA-F248-11E8-B48F-1D18A9856A87
last_name: Zhai
- first_name: Qian
full_name: Zhou, Qian
last_name: Zhou
- first_name: Chengrui
full_name: Qian, Chengrui
last_name: Qian
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
citation:
ama: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on
plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469
apa: Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of
B vitamins overload on plasma insulin level and hydrogen peroxide generation in
rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469
chicago: Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang.
“Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide
Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological
Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.
ieee: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins
overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese
Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp.
207–214, 2017.
ista: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload
on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 60(4), 207–214.
mla: Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level
and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology,
vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.
short: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology
60 (2017) 207–214.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-08-31T00:00:00Z
date_updated: 2025-09-11T07:19:13Z
day: '31'
ddc:
- '570'
department:
- _id: RySh
doi: 10.4077/CJP.2017.BAF469
external_id:
isi:
- '000409566300002'
pmid:
- '28847140'
intvolume: ' 60'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 207 - 214
pmid: 1
publication: Chinese Journal of Physiology
publication_identifier:
issn:
- 0304-4920
publication_status: published
publisher: Chinese Physiological Society
publist_id: '7142'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of B vitamins overload on plasma insulin level and hydrogen peroxide
generation in rats
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 60
year: '2017'
...
---
_id: '644'
abstract:
- lang: eng
text: An instance of the valued constraint satisfaction problem (VCSP) is given
by a finite set of variables, a finite domain of labels, and a sum of functions,
each function depending on a subset of the variables. Each function can take finite
values specifying costs of assignments of labels to its variables or the infinite
value, which indicates an infeasible assignment. The goal is to find an assignment
of labels to the variables that minimizes the sum. We study, assuming that P 6=
NP, how the complexity of this very general problem depends on the set of functions
allowed in the instances, the so-called constraint language. The case when all
allowed functions take values in f0;1g corresponds to ordinary CSPs, where one
deals only with the feasibility issue, and there is no optimization. This case
is the subject of the algebraic CSP dichotomy conjecture predicting for which
constraint languages CSPs are tractable (i.e., solvable in polynomial time) and
for which they are NP-hard. The case when all allowed functions take only finite
values corresponds to a finitevalued CSP, where the feasibility aspect is trivial
and one deals only with the optimization issue. The complexity of finite-valued
CSPs was fully classified by Thapper and Živný. An algebraic necessary condition
for tractability of a general-valued CSP with a fixed constraint language was
recently given by Kozik and Ochremiak. As our main result, we prove that if a
constraint language satisfies this algebraic necessary condition, and the feasibility
CSP (i.e., the problem of deciding whether a given instance has a feasible solution)
corresponding to the VCSP with this language is tractable, then the VCSP is tractable.
The algorithm is a simple combination of the assumed algorithm for the feasibility
CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy
for ordinary CSPs would imply a dichotomy for general-valued CSPs.
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrei
full_name: Krokhin, Andrei
last_name: Krokhin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs.
SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836
apa: Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued
CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836
chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity
of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.
ieee: V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued
CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110,
2017.
ista: Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued
CSPs. SIAM Journal on Computing. 46(3), 1087–1110.
mla: Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM
Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.
short: V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017)
1087–1110.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-06-29T00:00:00Z
date_updated: 2025-09-23T13:45:56Z
day: '29'
department:
- _id: VlKo
doi: 10.1137/16M1091836
ec_funded: 1
external_id:
arxiv:
- '1502.07327'
isi:
- '000404774300010'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.07327
month: '06'
oa: 1
oa_version: Preprint
page: 1087 - 1110
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: SIAM Journal on Computing
publication_status: published
publisher: SIAM
publist_id: '7138'
quality_controlled: '1'
related_material:
record:
- id: '1637'
relation: other
status: public
scopus_import: '1'
status: public
title: The complexity of general-valued CSPs
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2017'
...
---
_id: '645'
abstract:
- lang: eng
text: Markov decision processes (MDPs) are standard models for probabilistic systems
with non-deterministic behaviours. Long-run average rewards provide a mathematically
elegant formalism for expressing long term performance. Value iteration (VI) is
one of the simplest and most efficient algorithmic approaches to MDPs with other
properties, such as reachability objectives. Unfortunately, a naive extension
of VI does not work for MDPs with long-run average rewards, as there is no known
stopping criterion. In this work our contributions are threefold. (1) We refute
a conjecture related to stopping criteria for MDPs with long-run average rewards.
(2) We present two practical algorithms for MDPs with long-run average rewards
based on VI. First, we show that a combination of applying VI locally for each
maximal end-component (MEC) and VI for reachability objectives can provide approximation
guarantees. Second, extending the above approach with a simulation-guided on-demand
variant of VI, we present an anytime algorithm that is able to deal with very
large models. (3) Finally, we present experimental results showing that our methods
significantly outperform the standard approaches on several benchmarks.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
last_name: Meggendorfer
citation:
ama: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration
for long run average reward in markov decision processes. In: Majumdar R, Kunčak
V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10'
apa: 'Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T.
(2017). Value iteration for long run average reward in markov decision processes.
In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at
the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10'
chicago: Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and
Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision
Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer,
2017. https://doi.org/10.1007/978-3-319-63387-9_10.
ieee: 'P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value
iteration for long run average reward in markov decision processes,” presented
at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426,
pp. 201–221.'
ista: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration
for long run average reward in markov decision processes. CAV: Computer Aided
Verification, LNCS, vol. 10426, 201–221.'
mla: Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov
Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426,
Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.
short: P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R.
Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:47:41Z
date_published: 2017-07-13T00:00:00Z
date_updated: 2025-09-11T07:18:04Z
day: '13'
department:
- _id: KrCh
doi: 10.1007/978-3-319-63387-9_10
ec_funded: 1
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
arxiv:
- '1705.02326'
isi:
- '000432196400010'
intvolume: ' 10426'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02326
month: '07'
oa: 1
oa_version: Submitted Version
page: 201 - 221
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
isbn:
- 978-331963386-2
publication_status: published
publisher: Springer
publist_id: '7135'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Value iteration for long run average reward in markov decision processes
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10426
year: '2017'
...
---
_id: '646'
abstract:
- lang: eng
text: We present a novel convex relaxation and a corresponding inference algorithm
for the non-binary discrete tomography problem, that is, reconstructing discrete-valued
images from few linear measurements. In contrast to state of the art approaches
that split the problem into a continuous reconstruction problem for the linear
measurement constraints and a discrete labeling problem to enforce discrete-valued
reconstructions, we propose a joint formulation that addresses both problems simultaneously,
resulting in a tighter convex relaxation. For this purpose a constrained graphical
model is set up and evaluated using a novel relaxation optimized by dual decomposition.
We evaluate our approach experimentally and show superior solutions both mathematically
(tighter relaxation) and experimentally in comparison to previously proposed relaxations.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Jan
full_name: Kuske, Jan
last_name: Kuske
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Stefanie
full_name: Petra, Stefanie
last_name: Petra
citation:
ama: 'Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete
tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246.
doi:10.1007/978-3-319-58771-4_19'
apa: 'Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation
for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl
(Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational
Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19'
chicago: Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation
for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and
Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.
ieee: 'J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary
discrete tomography,” presented at the SSVM: Scale Space and Variational Methods
in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.'
ista: 'Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary
discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision,
LNCS, vol. 10302, 235–246.'
mla: Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography.
Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19.
short: J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl
(Eds.), Springer, 2017, pp. 235–246.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:47:41Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-09-11T07:16:00Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-319-58771-4_19
ec_funded: 1
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
external_id:
arxiv:
- '1703.03769'
isi:
- '000432210900019'
intvolume: ' 10302'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.03769
month: '06'
oa: 1
oa_version: Submitted Version
page: 235 - 246
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-331958770-7
publication_status: published
publisher: Springer
publist_id: '7132'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel convex relaxation for non binary discrete tomography
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10302
year: '2017'
...
---
_id: '647'
abstract:
- lang: eng
text: Despite researchers’ efforts in the last couple of decades, reachability analysis
is still a challenging problem even for linear hybrid systems. Among the existing
approaches, the most practical ones are mainly based on bounded-time reachable
set over-approximations. For the purpose of unbounded-time analysis, one important
strategy is to abstract the original system and find an invariant for the abstraction.
In this paper, we propose an approach to constructing a new kind of abstraction
called conic abstraction for affine hybrid systems, and to computing reachable
sets based on this abstraction. The essential feature of a conic abstraction is
that it partitions the state space of a system into a set of convex polyhedral
cones which is derived from a uniform conic partition of the derivative space.
Such a set of polyhedral cones is able to cut all trajectories of the system into
almost straight segments so that every segment of a reach pipe in a polyhedral
cone tends to be straight as well, and hence can be over-approximated tightly
by polyhedra using similar techniques as HyTech or PHAVer. In particular, for
diagonalizable affine systems, our approach can guarantee to find an invariant
for unbounded reachable sets, which is beyond the capability of bounded-time reachability
analysis tools. We implemented the approach in a tool and experiments on benchmarks
show that our approach is more powerful than SpaceEx and PHAVer in dealing with
diagonalizable systems.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- 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: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
citation:
ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid
systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7'
apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic
abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS:
Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7'
chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic
Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7.
ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions
for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of
Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.'
ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for
hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS,
vol. 10419, 116–132.'
mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol.
10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7.
short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017,
pp. 116–132.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'FORMATS: Formal Modelling and Analysis of Timed Systems'
start_date: 2017-09-05
corr_author: '1'
date_created: 2018-12-11T11:47:41Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2026-04-08T07:47:13Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-65765-3_7
external_id:
isi:
- '000611678300007'
file:
- access_level: open_access
checksum: faf546914ba29bcf9974ee36b6b16750
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:38Z
date_updated: 2020-07-14T12:47:31Z
file_id: '4956'
file_name: IST-2017-831-v1+1_main.pdf
file_size: 3806864
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 116 - 132
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
isbn:
- 978-331965764-6
publication_status: published
publisher: Springer
publist_id: '7129'
pubrep_id: '831'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Conic abstractions for hybrid systems
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: '10419 '
year: '2017'
...
---
_id: '648'
abstract:
- lang: eng
text: 'Pseudoentropy has found a lot of important applications to cryptography and
complexity theory. In this paper we focus on the foundational problem that has
not been investigated so far, namely by how much pseudoentropy (the amount seen
by computationally bounded attackers) differs from its information-theoretic counterpart
(seen by unbounded observers), given certain limits on attacker’s computational
power? We provide the following answer for HILL pseudoentropy, which exhibits
a threshold behavior around the size exponential in the entropy amount:– If the
attacker size (s) and advantage () satisfy s (formula presented) where k is the
claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic
smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily
bigger than the information-theoretic smooth entropy. Besides answering the posted
question, we show an elegant application of our result to the complexity theory,
namely that it implies the clas-sical result on the existence of functions hard
to approximate (due to Pippenger). In our approach we utilize non-constructive
techniques: the duality of linear programming and the probabilistic method.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila
S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43'
apa: 'Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger
& S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory
and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43'
chicago: Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited
by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.
ieee: 'M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the
TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017,
vol. 10185, pp. 600–613.'
ista: 'Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory
and Applications of Models of Computation, LNCS, vol. 10185, 600–613.'
mla: Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited
by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.
short: M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.
conference:
end_date: 2017-04-22
location: Bern, Switzerland
name: 'TAMC: Theory and Applications of Models of Computation'
start_date: 2017-04-20
corr_author: '1'
date_created: 2018-12-11T11:47:42Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2025-09-11T07:14:42Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-55911-7_43
editor:
- first_name: Gerhard
full_name: Jäger, Gerhard
last_name: Jäger
- first_name: Silvia
full_name: Steila, Silvia
last_name: Steila
external_id:
isi:
- '000425175500043'
intvolume: ' 10185'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/1186.pdf
month: '04'
oa: 1
oa_version: Submitted Version
page: 600 - 613
publication_identifier:
isbn:
- 978-331955910-0
publication_status: published
publisher: Springer
publist_id: '7125'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the complexity of breaking pseudoentropy
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10185
year: '2017'
...