---
_id: '5429'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. \r\nThere have been two different views: (i) the
expectation semantics, where the goal is to optimize the expected mean-payoff
objective, and (ii) the satisfaction semantics, where the goal is to maximize
the probability of runs such that the mean-payoff value stays above a given vector.
\ \r\nWe consider the problem where the goal is to optimize the expectation under
the constraint that the satisfaction semantics is ensured, and thus consider a
generalization that unifies the existing semantics.\r\nOur problem captures the
notion of optimization with respect to strategies that are risk-averse (i.e.,
ensures certain probabilistic guarantee).\r\nOur main results are algorithms for
the decision problem which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions.\r\nFinally, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Komarkova, Zuzana
last_name: Komarkova
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v1-1
apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two
views on multiple mean-payoff objectives in Markov decision processes. IST
Austria. https://doi.org/10.15479/AT:IST-2015-318-v1-1
chicago: Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v1-1.
ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple
mean-payoff objectives in Markov decision processes. IST Austria, 2015.
ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes, IST Austria, 41p.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v1-1.
short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple
Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-01-12T00:00:00Z
date_updated: 2026-07-06T13:26:26Z
day: '12'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-318-v1-1
file:
- access_level: open_access
checksum: e4869a584567c506349abda9c8ec7db3
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:11Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5533'
file_name: IST-2015-318-v1+1_main.pdf
file_size: 689863
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
fulldoi: https://doi.org/10.15479/AT:IST-2015-318-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '41'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '318'
related_material:
record:
- id: '5435'
relation: later_version
status: public
- id: '1657'
relation: later_version
status: public
- id: '466'
relation: later_version
status: public
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5438'
abstract:
- lang: eng
text: "The edit distance between two words w1, w2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses.\r\nThe problem of computing edit
distance to a pushdown automaton is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown
Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance
for pushdown automata. IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata, IST Austria, 15p.
mla: Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata.
IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for
Pushdown Automata, IST Austria, 2015.
date_created: 2018-12-12T11:39:20Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2026-07-06T13:27:53Z
day: '05'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-334-v1-1
file:
- access_level: open_access
checksum: 8a5f2d77560e552af87eb1982437a43b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:56Z
date_updated: 2020-07-14T12:46:55Z
file_id: '5518'
file_name: IST-2015-334-v1+1_report.pdf
file_size: 422573
relation: main_file
file_date_updated: 2020-07-14T12:46:55Z
fulldoi: https://doi.org/10.15479/AT:IST-2015-334-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '15'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '334'
related_material:
record:
- id: '1610'
relation: later_version
status: public
- id: '465'
relation: later_version
status: public
status: public
title: Edit distance for pushdown automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1661'
abstract:
- lang: eng
text: The computation of the winning set for one-pair Streett objectives and for
k-pair Streett objectives in (standard) graphs as well as in game graphs are central
problems in computer-aided verification, with application to the verification
of closed systems with strong fairness conditions, the verification of open systems,
checking interface compatibility, well-formed ness of specifications, and the
synthesis of reactive systems. We give faster algorithms for the computation of
the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in
game graphs and (2) for k-pair Streett objectives in graphs. For both problems
this represents the first improvement in asymptotic running time in 15 years.
acknowledgement: 'K. C. is supported by the Austrian Science Fund (FWF): P23499-N23
and S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft
Faculty Fellows Award. M. H. is supported by the Austrian Science Fund (FWF): P23499-N23
and the Vienna Science and Technology Fund (WWTF) grant ICT10-002. V. L. is supported
by the Vienna Science and Technology Fund (WWTF) grant ICT10-002. The research leading
to these results has received funding from the European Research Council under the
European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement
no. 340506.'
article_number: '7174888'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Henzinger M, Loitzenbauer V. Improved algorithms for one-pair
and k-pair Streett objectives. In: Proceedings - Symposium on Logic in Computer
Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.34'
apa: 'Chatterjee, K., Henzinger, M., & Loitzenbauer, V. (2015). Improved algorithms
for one-pair and k-pair Streett objectives. In Proceedings - Symposium on Logic
in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.34'
chicago: Chatterjee, Krishnendu, Monika Henzinger, and Veronika Loitzenbauer. “Improved
Algorithms for One-Pair and k-Pair Streett Objectives.” In Proceedings - Symposium
on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.34.
ieee: K. Chatterjee, M. Henzinger, and V. Loitzenbauer, “Improved algorithms for
one-pair and k-pair Streett objectives,” in Proceedings - Symposium on Logic
in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.
ista: 'Chatterjee K, Henzinger M, Loitzenbauer V. 2015. Improved algorithms for
one-pair and k-pair Streett objectives. Proceedings - Symposium on Logic in Computer
Science. LICS: Logic in Computer Science vol. 2015–July, 7174888.'
mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for One-Pair and k-Pair
Streett Objectives.” Proceedings - Symposium on Logic in Computer Science,
vol. 2015–July, 7174888, IEEE, 2015, doi:10.1109/LICS.2015.34.
short: K. Chatterjee, M. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium
on Logic in Computer Science, IEEE, 2015.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:19Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2026-07-06T13:28:05Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/LICS.2015.34
ec_funded: 1
external_id:
isi:
- '000380427100026'
fulldoi: https://doi.org/10.1109/LICS.2015.34
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.cs.univie.ac.at/4368/
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings - Symposium on Logic in Computer Science
publication_status: published
publisher: IEEE
publist_id: '5489'
quality_controlled: '1'
related_material:
record:
- id: '464'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Improved algorithms for one-pair and k-pair Streett objectives
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2015-July
year: '2015'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2026-07-06T13:54:28Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
external_id:
isi:
- '000364399700067'
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1004541
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An exploration of the universe of polyglutamine structures
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2015'
...
---
_id: '9714'
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures - submission to PLOS journals. 2015.
doi:10.1371/journal.pcbi.1004541.s001
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures - submission to PLOS
journals. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541.s001
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission
to PLOS Journals.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures - submission to PLOS journals.” Public
Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures - submission to PLOS journals, Public
Library of Science, 10.1371/journal.pcbi.1004541.s001.
mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine
Structures - Submission to PLOS Journals. Public Library of Science, 2015,
doi:10.1371/journal.pcbi.1004541.s001.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).
date_created: 2021-07-23T12:05:28Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2026-07-06T13:54:29Z
day: '23'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541.s001
fulldoi: https://doi.org/10.1371/journal.pcbi.1004541.s001
month: '10'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1566'
relation: used_in_publication
status: public
status: public
title: An exploration of the universe of polyglutamine structures - submission to
PLOS journals
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1555'
abstract:
- lang: eng
text: We show that incorporating spatial dispersal of individuals into a simple
vaccination epidemic model may give rise to a model that exhibits rich dynamical
behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as
a basis, we describe the spread of an infectious disease in a population split
into two regions. In each subpopulation, both forward and backward bifurcations
can occur. This implies that for disconnected regions the two-patch system may
admit several steady states. We consider traveling between the regions and investigate
the impact of spatial dispersal of individuals on the model dynamics. We establish
conditions for the existence of multiple nontrivial steady states in the system,
and we study the structure of the equilibria. The mathematical analysis reveals
an unusually rich dynamical behavior, not normally found in the simple epidemic
models. In addition to the disease-free equilibrium, eight endemic equilibria
emerge from backward transcritical and saddle-node bifurcation points, forming
an interesting bifurcation diagram. Stability of steady states, their bifurcations,
and the global dynamics are investigated with analytical tools, numerical simulations,
and rigorous set-oriented numerical computations.
acknowledgement: Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg,
Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported
by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de
Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de
Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia
e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559
in the framework of the EPIDELAY project.
article_processing_charge: No
article_type: original
author:
- first_name: Diána
full_name: Knipl, Diána
last_name: Knipl
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Gergely
full_name: Röst, Gergely
last_name: Röst
citation:
ama: Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination
model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017.
doi:10.1137/140993934
apa: Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure
in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics. https://doi.org/10.1137/140993934
chicago: Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure
in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics, 2015. https://doi.org/10.1137/140993934.
ieee: D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two
patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol.
14, no. 2. Society for Industrial and Applied Mathematics, pp. 980–1017, 2015.
ista: Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch
vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.
mla: Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination
Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society
for Industrial and Applied Mathematics, 2015, pp. 980–1017, doi:10.1137/140993934.
short: D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems
14 (2015) 980–1017.
das_tickbox: '1'
date_created: 2018-12-11T11:52:42Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2026-07-06T13:59:25Z
day: '01'
ddc:
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doi: 10.1137/140993934
ec_funded: 1
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- '000357310400015'
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isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
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url: http://discovery.ucl.ac.uk/1473750/1/99393.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 980 - 1017
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: SIAM Journal on Applied Dynamical Systems
publication_identifier:
eissn:
- 1536-0040
publication_status: published
publisher: Society for Industrial and Applied Mathematics
publist_id: '5616'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rich bifurcation structure in a two patch vaccination model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2015'
...
---
OA_place: publisher
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abstract:
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text: 'Based on 16 recommendations, efforts should be made to achieve the following
goal: By 2025, all scholarly publication activity in Austria should be Open Access.
In other words, the final versions of all scholarly publications resulting from
the support of public resources must be freely accessible on the Internet without
delay (Gold Open Access). The resources required to meet this obligation shall
be provided to the authors, or the cost of the publication venues shall be borne
directly by the research organisations.'
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full_name: Bauer, Bruno
last_name: Bauer
- first_name: Guido
full_name: Blechl, Guido
last_name: Blechl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Anton
full_name: Graschopf, Anton
last_name: Graschopf
- first_name: Thomas
full_name: König, Thomas
last_name: König
- first_name: Katja
full_name: Mayer, Katja
last_name: Mayer
- first_name: Falk
full_name: Reckling, Falk
last_name: Reckling
- first_name: Katharina
full_name: Rieck, Katharina
last_name: Rieck
- first_name: Peter
full_name: Seitz, Peter
last_name: Seitz
- first_name: Herwig
full_name: Stöger, Herwig
last_name: Stöger
- first_name: Elvira
full_name: Welzig, Elvira
last_name: Welzig
citation:
ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open
Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178
apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., …
Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network
Austria OANA. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen
und Bibliothekare. https://doi.org/10.5281/zenodo.33178
chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus,
Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des
Open Access Network Austria OANA.” VÖB Mitteilungen. Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.
ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access
Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare, pp. 580–607, 2015.
ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer
K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale
Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.
mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network
Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.
short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König,
K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen
68 (2015) 580–607.
das_tickbox: '1'
date_created: 2018-12-11T11:52:31Z
date_published: 2015-11-12T00:00:00Z
date_updated: 2026-07-07T06:11:42Z
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ddc:
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department:
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doi: 10.5281/zenodo.33178
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language:
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month: '11'
oa: 1
oa_version: Published Version
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publication: VÖB Mitteilungen
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publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publist_id: '5648'
pubrep_id: '720'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA
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: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2015'
...
---
_id: '2034'
abstract:
- lang: eng
text: Opacity is a generic security property, that has been defined on (non-probabilistic)
transition systems and later on Markov chains with labels. For a secret predicate,
given as a subset of runs, and a function describing the view of an external observer,
the value of interest for opacity is a measure of the set of runs disclosing the
secret. We extend this definition to the richer framework of Markov decision processes,
where non-deterministicchoice is combined with probabilistic transitions, and
we study related decidability problems with partial or complete observation hypotheses
for the schedulers. We prove that all questions are decidable with complete observation
and ω-regular secrets. With partial observation, we prove that all quantitative
questions are undecidable but the question whether a system is almost surely non-opaquebecomes
decidable for a restricted class of ω-regular secrets, as well as for all ω-regular
secrets under finite-memory schedulers.
article_processing_charge: No
arxiv: 1
author:
- first_name: Béatrice
full_name: Bérard, Béatrice
last_name: Bérard
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathalie
full_name: Sznajder, Nathalie
last_name: Sznajder
citation:
ama: Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision
processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001
apa: Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity
for Markov decision processes. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2014.09.001
chicago: Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic
Opacity for Markov Decision Processes.” Information Processing Letters.
Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001.
ieee: B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov
decision processes,” Information Processing Letters, vol. 115, no. 1. Elsevier,
pp. 52–59, 2015.
ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov
decision processes. Information Processing Letters. 115(1), 52–59.
mla: Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.”
Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59,
doi:10.1016/j.ipl.2014.09.001.
short: B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115
(2015) 52–59.
das_tickbox: '1'
date_created: 2018-12-11T11:55:20Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2026-07-07T13:10:27Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ipl.2014.09.001
ec_funded: 1
external_id:
arxiv:
- '1407.4225'
isi:
- '000345478700010'
fulldoi: https://doi.org/10.1016/j.ipl.2014.09.001
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isi: 1
issue: '1'
language:
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main_file_link:
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url: http://arxiv.org/abs/1407.4225
month: '01'
oa: 1
oa_version: Preprint
page: 52 - 59
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal 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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information Processing Letters
publication_status: published
publisher: Elsevier
publist_id: '5025'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probabilistic opacity for Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2026-07-07T13:12:13Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
external_id:
isi:
- '000362056300005'
file:
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checksum: 33b60ecfea60764756a9ee9df5eb65ca
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date_created: 2018-12-12T10:16:53Z
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has_accepted_license: '1'
intvolume: ' 383'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unifying framework for evolutionary processes
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
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volume: 383
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...
---
OA_place: repository
OA_type: green
_id: '1656'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499-
N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games),
and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available
at: \r\nhttps://repository.ist.ac.at/331/\r\n"
article_number: '7174926'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: Proceedings
- Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.72'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata.
In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July).
Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.72'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” In Proceedings - Symposium on Logic in Computer Science, Vol.
2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.72.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in
Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015,
vol. 2015–July.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings
- Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol.
2015–July, 7174926.'
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” Proceedings -
Symposium on Logic in Computer Science, vol. 2015–July, 7174926, IEEE, 2015,
doi:10.1109/LICS.2015.72.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic
in Computer Science, IEEE, 2015.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
corr_author: '1'
date_created: 2018-12-11T11:53:17Z
date_published: 2015-07-31T00:00:00Z
date_updated: 2026-07-07T14:01:10Z
day: '31'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/LICS.2015.72
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
isi:
- '000380427100064'
fulldoi: https://doi.org/10.1109/LICS.2015.72
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1606.03598
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings - Symposium on Logic in Computer Science
publication_status: published
publisher: IEEE
publist_id: '5494'
quality_controlled: '1'
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title: Nested weighted automata
type: conference
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volume: 2015-July
year: '2015'
...
---
_id: '5436'
abstract:
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text: "Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time.\r\nIn nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria;
2015. doi:10.15479/AT:IST-2015-170-v2-2
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted
automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted
Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata.
IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria,
29p.
mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria,
2015, doi:10.15479/AT:IST-2015-170-v2-2.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria,
2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-04-24T00:00:00Z
date_updated: 2026-07-07T14:01:10Z
day: '24'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2015-170-v2-2
file:
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checksum: 3c402f47d3669c28d04d1af405a08e3f
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creator: system
date_created: 2018-12-12T11:54:19Z
date_updated: 2020-07-14T12:46:54Z
file_id: '5541'
file_name: IST-2015-170-v2+2_report.pdf
file_size: 569991
relation: main_file
file_date_updated: 2020-07-14T12:46:54Z
fulldoi: https://doi.org/10.15479/AT:IST-2015-170-v2-2
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language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '331'
related_material:
record:
- id: '5415'
relation: earlier_version
status: public
- id: '1656'
relation: later_version
status: public
- id: '467'
relation: later_version
status: public
status: public
title: Nested weighted automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
OA_place: repository
OA_type: green
_id: '22173'
abstract:
- lang: eng
text: 'The girth of a matrix is the least number of linearly dependent columns,
in contrast to the rank which is the largest number of linearly independent columns.
This paper considers the construction of high-girth matrices, whose probabilistic
girth is close to their rank. Random matrices can be used to show the existence
of high-girth matrices. This paper uses a recursive construction based on conditional
ranks (inspired by polar codes) to obtain a deterministic and efficient construction
of high-girth matrices for arbitrary relative ranks. Interestingly, the construction
is agnostic to the underlying field and applies to both finite and continuous
fields with the same binary matrix. The construction gives in particular the following:
(i) over the binary field, high-girth matrices are equivalent to capacity-achieving
codes, and our construction turns out to match exactly the BEC polar codes (even
at finite block length). It hence gives a different interpretation of BEC polar
codes, using the parity-check matrix instead of the generator matrix, and basic
linear algebra instead of the mutual information, and generalizes to larger fields;
(ii) for the BSC, our construction gives an operational meaning to the Bhattacharyya
upper-bound process used in polar codes; (iii) for the reals, it gives an explicit
candidate matrix for sparse recovery.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Emmanuel
full_name: Abbe, Emmanuel
last_name: Abbe
- first_name: Yuval
full_name: Wigderson, Yuval
id: 2d0023a0-1567-11f0-833d-d5c1e476d4b5
last_name: Wigderson
citation:
ama: 'Abbe E, Wigderson Y. High-girth matrices and polarization. In: 2015 IEEE
International Symposium on Information Theory. IEEE; 2015. doi:10.1109/isit.2015.7282898'
apa: 'Abbe, E., & Wigderson, Y. (2015). High-girth matrices and polarization.
In 2015 IEEE International Symposium on Information Theory. Hong Kong,
China: IEEE. https://doi.org/10.1109/isit.2015.7282898'
chicago: Abbe, Emmanuel, and Yuval Wigderson. “High-Girth Matrices and Polarization.”
In 2015 IEEE International Symposium on Information Theory. IEEE, 2015.
https://doi.org/10.1109/isit.2015.7282898.
ieee: E. Abbe and Y. Wigderson, “High-girth matrices and polarization,” in 2015
IEEE International Symposium on Information Theory, Hong Kong, China, 2015.
ista: 'Abbe E, Wigderson Y. 2015. High-girth matrices and polarization. 2015 IEEE
International Symposium on Information Theory. ISIT: International Symposium on
Information Theory.'
mla: Abbe, Emmanuel, and Yuval Wigderson. “High-Girth Matrices and Polarization.”
2015 IEEE International Symposium on Information Theory, IEEE, 2015, doi:10.1109/isit.2015.7282898.
short: E. Abbe, Y. Wigderson, in:, 2015 IEEE International Symposium on Information
Theory, IEEE, 2015.
conference:
end_date: 2015-06-19
location: Hong Kong, China
name: 'ISIT: International Symposium on Information Theory'
start_date: 2015-06-14
date_created: 2026-06-29T10:57:04Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2026-07-14T08:54:51Z
day: '01'
doi: 10.1109/isit.2015.7282898
extern: '1'
external_id:
arxiv:
- '1501.06528'
fulldoi: https://doi.org/10.1109/isit.2015.7282898
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1501.06528
month: '07'
oa: 1
oa_version: Preprint
publication: 2015 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781467377041'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-girth matrices and polarization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1792'
abstract:
- lang: eng
text: Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop
a new concept of variation of multivariate functions on a compact Hausdorff space
with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka
theorem that holds for this notion of variation and discrepancy with respect to
D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions,
such as extreme or isotropic discrepancy. For extreme discrepancy, our result
coincides with the usual Koksma-Hlawka theorem. We show that the space of functions
of bounded D-variation contains important discontinuous functions and is closed
under natural algebraic operations. Finally, we illustrate the results on concrete
integration problems from integral geometry and stereology.
acknowledgement: F.P. is supported by the Graduate School of IST Austria, A.M.S is
supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by
a grant from the Villum Foundation.
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Anne
full_name: Svane, Anne
last_name: Svane
citation:
ama: Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems.
Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002
apa: Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general
discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002
chicago: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General
Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002.
ieee: F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy
systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797,
2015.
ista: Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy
systems. Journal of Complexity. 31(6), 773–797.
mla: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General
Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press,
2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002.
short: F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.
corr_author: '1'
date_created: 2018-12-11T11:54:02Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2026-07-29T10:08:33Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jco.2015.06.002
external_id:
isi:
- '000362926900001'
fulldoi: https://doi.org/10.1016/j.jco.2015.06.002
intvolume: ' 31'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 773 - 797
publication: Journal of Complexity
publication_status: published
publisher: Academic Press
publist_id: '5320'
quality_controlled: '1'
related_material:
record:
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A Koksma-Hlawka inequality for general discrepancy systems
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2015'
...
---
OA_place: publisher
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
corr_author: '1'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2026-07-29T10:08:34Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi_confirm: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2015'
...
---
_id: '1709'
abstract:
- lang: eng
text: The competition for resources among cells, individuals or species is a fundamental
characteristic of evolution. Biological all-pay auctions have been used to model
situations where multiple individuals compete for a single resource. However,
in many situations multiple resources with various values exist and single reward
auctions are not applicable. We generalize the model to multiple rewards and study
the evolution of strategies. In biological all-pay auctions the bid of an individual
corresponds to its strategy and is equivalent to its payment in the auction. The
decreasingly ordered rewards are distributed according to the decreasingly ordered
bids of the participating individuals. The reproductive success of an individual
is proportional to its fitness given by the sum of the rewards won minus its payments.
Hence, successful bidding strategies spread in the population. We find that the
results for the multiple reward case are very different from the single reward
case. While the mixed strategy equilibrium in the single reward case with more
than two players consists of mostly low-bidding individuals, we show that the
equilibrium can convert to many high-bidding individuals and a few low-bidding
individuals in the multiple reward case. Some reward values lead to a specialization
among the individuals where one subpopulation competes for the rewards and the
other subpopulation largely avoids costly competitions. Whether the mixed strategy
equilibrium is an evolutionarily stable strategy (ESS) depends on the specific
values of the rewards.
acknowledgement: 'This work was supported by grants from the John Templeton Foundation,
ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE),
FWF Grant (No P23499N23) and a Microsoft faculty fellows award.'
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with
multiple rewards. Proceedings of the Royal Society of London Series B Biological
Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041
apa: Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015).
Biological auctions with multiple rewards. Proceedings of the Royal Society
of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041
chicago: Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu
Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the
Royal Society of London Series B Biological Sciences. Royal Society, 2015.
https://doi.org/10.1098/rspb.2015.1041.
ieee: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological
auctions with multiple rewards,” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.
ista: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions
with multiple rewards. Proceedings of the Royal Society of London Series B Biological
Sciences. 282(1812).
mla: Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.
short: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of
the Royal Society of London Series B Biological Sciences 282 (2015).
corr_author: '1'
date_created: 2018-12-11T11:53:35Z
date_published: 2015-07-15T00:00:00Z
date_updated: 2026-07-29T10:15:25Z
day: '15'
department:
- _id: KrCh
doi: 10.1098/rspb.2015.1041
external_id:
isi:
- '000362305500021'
pmid:
- '26180069'
fulldoi: https://doi.org/10.1098/rspb.2015.1041
intvolume: ' 282'
isi: 1
issue: '1812'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '5425'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Biological auctions with multiple rewards
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 282
year: '2015'
...
---
OA_place: publisher
_id: '1400'
abstract:
- lang: eng
text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially
accumulated genetic and epigenetic alterations decrease cell death and increase
cell replication. We used mathematical models to quantify the effect of driver
gene mutations. The recently developed targeted therapies can lead to dramatic
regressions. However, in solid cancers, clinical responses are often short-lived
because resistant cancer cells evolve. We estimated that approximately 50 different
mutations can confer resistance to a typical targeted therapeutic agent. We find
that resistant cells are likely to be present in expanded subclones before the
start of the treatment. The dominant strategy to prevent the evolution of resistance
is combination therapy. Our analytical results suggest that in most patients,
dual therapy, but not monotherapy, can result in long-term disease control. However,
long-term control can only occur if there are no possible mutations in the genome
that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous
therapy with two drugs is much more likely to result in long-term disease control
than sequential therapy with the same drugs. To improve our understanding of the
underlying subclonal evolution we reconstruct the evolutionary history of a patient's
cancer from next-generation sequencing data of spatially-distinct DNA samples.
Using a quantitative measure of genetic relatedness, we found that pancreatic
cancers and their metastases demonstrated a higher level of relatedness than that
expected for any two cells randomly taken from a normal tissue. This minimal amount
of genetic divergence among advanced lesions indicates that genetic heterogeneity,
when quantitatively defined, is not a fundamental feature of the natural history
of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics
finds evidence for seeding patterns of metastases and can directly be used to
discover rules governing the evolution of solid malignancies to transform cancer
into a more predictable disease.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
citation:
ama: Reiter J. The subclonal evolution of cancer. 2015.
apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science
and Technology Austria.
chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science
and Technology Austria, 2015.
ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology
Austria, 2015.
ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and
Technology Austria.
mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science
and Technology Austria, 2015.
short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
Austria, 2015.
corr_author: '1'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2026-07-29T10:15:25Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi_confirm: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: '183'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5807'
related_material:
record:
- id: '2000'
relation: part_of_dissertation
status: public
- id: '1709'
relation: part_of_dissertation
status: public
- id: '2858'
relation: part_of_dissertation
status: public
- id: '2816'
relation: part_of_dissertation
status: public
- id: '2247'
relation: part_of_dissertation
status: public
- id: '3260'
relation: part_of_dissertation
status: public
- id: '3157'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: The subclonal evolution of cancer
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2015'
...
---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2026-07-29T11:31:13Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
external_id:
isi:
- '000366179000022'
file:
- access_level: open_access
checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
fulldoi: https://doi.org/10.1371/journal.pgen.1005639
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamics of transcription factor binding site evolution
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2015'
...
---
_id: '1633'
abstract:
- lang: eng
text: "We present a method for simulating brittle fracture under the assumptions
of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element
method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture
surfaces. The computational cost of the BEM is alleviated by using a low-resolution
mesh and interpolating the resulting stress intensity factors when propagating
the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture
surfaces with high spatial and temporal resolution, taking spatial variation of
material toughness and/or strength into account. It also allows for crack initiation
to be handled separately from crack propagation, which is not only more reasonable
from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating
the resolution of the crack-front from the resolution of the computational mesh
increases the efficiency and therefore the amount of visual detail on the resulting
fracture surfaces. The BEM also allows us to re-use previously computed blocks
of the system matrix."
article_number: '151'
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary
elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896'
apa: 'Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation
with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States: ACM. https://doi.org/10.1145/2766896'
chicago: Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation
with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.
ieee: 'D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with
boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol.
34, no. 4.'
ista: 'Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with
boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 151.'
mla: Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation
with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896.
short: D. Hahn, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
corr_author: '1'
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2026-07-29T13:27:24Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766896
ec_funded: 1
external_id:
isi:
- '000358786600117'
file:
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checksum: 955aee971983f6b6152bcc1c9b4a7c20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:13Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5131'
file_name: IST-2016-609-v1+1_FractureBEM.pdf
file_size: 20154270
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
fulldoi: https://doi.org/10.1145/2766896
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
publication_status: published
publisher: ACM
publist_id: '5522'
pubrep_id: '609'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: High-resolution brittle fracture simulation with boundary elements
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2015'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: free access
_id: '22495'
abstract:
- lang: eng
text: An expression that separates biotic and abiotic controls on the temporal dynamics
of the soilmoisture spatial coefficient of variation C v(h) was explored via numerical
simulations using a mechanisticecohydrological model, Tethys-Chloris. Continuous
soil moisture spatiotemporal dynamics at an exemplaryhillslope domain were computed
for six case studies characterized by different climate and vegetationcover and
for three configurations of soil properties. It was shown that abiotic controls
largely exceed theirbiotic counterparts in wet climates. Biotic controls on C
v(h) were found to be more pronounced in Mediter-ranean climates. The relation
between Cv(h) and spatial mean soil moisture h was found to be unique in wetlocations,
regardless of the soil properties. For the case of homogeneous soil texture, hysteretic
cyclesbetween C v(h) and h were observed in all Mediterranean climate locations
considered here and to a lesserextent in a deciduous temperate forest. Heterogeneity
in soil properties increased C v(h) to values commen-surate with field observations
and weakened signatures of hysteresis at all of the studied locations. Thisfinding
highlights the role of site-specific heterogeneities in hiding or even eliminating
the signature ofclimatic and biotic controls on C v(h), thereby offering a new
perspective on causes of confounding resultsreported across field experiments.
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Gabriel G.
full_name: Katul, Gabriel G.
last_name: Katul
- first_name: Valeriy Y.
full_name: Ivanov, Valeriy Y.
last_name: Ivanov
- first_name: Christoforos
full_name: Pappas, Christoforos
last_name: Pappas
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
- first_name: Ada
full_name: Consolo, Ada
last_name: Consolo
- first_name: Jongho
full_name: Kim, Jongho
last_name: Kim
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
citation:
ama: Fatichi S, Katul GG, Ivanov VY, et al. Abiotic and biotic controls of soil
moisture spatiotemporal variability and the occurrence of hysteresis. Water
Resources Research. 2015;51(5):3505-3524. doi:10.1002/2014wr016102
apa: Fatichi, S., Katul, G. G., Ivanov, V. Y., Pappas, C., Paschalis, A., Consolo,
A., … Burlando, P. (2015). Abiotic and biotic controls of soil moisture spatiotemporal
variability and the occurrence of hysteresis. Water Resources Research.
American Geophysical Union. https://doi.org/10.1002/2014wr016102
chicago: Fatichi, Simone, Gabriel G. Katul, Valeriy Y. Ivanov, Christoforos Pappas,
Athanasios Paschalis, Ada Consolo, Jongho Kim, and Paolo Burlando. “Abiotic and
Biotic Controls of Soil Moisture Spatiotemporal Variability and the Occurrence
of Hysteresis.” Water Resources Research. American Geophysical Union, 2015.
https://doi.org/10.1002/2014wr016102.
ieee: S. Fatichi et al., “Abiotic and biotic controls of soil moisture spatiotemporal
variability and the occurrence of hysteresis,” Water Resources Research,
vol. 51, no. 5. American Geophysical Union, pp. 3505–3524, 2015.
ista: Fatichi S, Katul GG, Ivanov VY, Pappas C, Paschalis A, Consolo A, Kim J, Burlando
P. 2015. Abiotic and biotic controls of soil moisture spatiotemporal variability
and the occurrence of hysteresis. Water Resources Research. 51(5), 3505–3524.
mla: Fatichi, Simone, et al. “Abiotic and Biotic Controls of Soil Moisture Spatiotemporal
Variability and the Occurrence of Hysteresis.” Water Resources Research,
vol. 51, no. 5, American Geophysical Union, 2015, pp. 3505–24, doi:10.1002/2014wr016102.
short: S. Fatichi, G.G. Katul, V.Y. Ivanov, C. Pappas, A. Paschalis, A. Consolo,
J. Kim, P. Burlando, Water Resources Research 51 (2015) 3505–3524.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2026-08-03T13:39:10Z
day: '01'
ddc:
- '550'
doi: 10.1002/2014wr016102
extern: '1'
fulldoi: https://doi.org/10.1002/2014wr016102
intvolume: ' 51'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014WR016102
month: '05'
oa: 1
oa_version: Published Version
page: 3505-3524
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abiotic and biotic controls of soil moisture spatiotemporal variability and
the occurrence of hysteresis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2015'
...
---
OA_type: closed access
_id: '22509'
abstract:
- lang: eng
text: Hydrologic and geomorphic responses of watersheds to changes in climate are
difficult to assess due to projection uncertainties and nonlinearity of the processes
that are involved. Yet such assessments are increasingly needed and call for mechanistic
approaches within a probabilistic framework. This study employs an integrated
hydrology‐geomorphology model, the Triangulated Irregular Network‐based Real‐time
Integrated Basin Simulator (tRIBS)‐Erosion, to analyze runoff and erosion sensitivity
of seven semiarid headwater basins to projected climate conditions. The Advanced
Weather Generator is used to produce two climate ensembles representative of the
historic and future climate conditions for the Walnut Gulch Experimental Watershed
located in the southwest U.S. The former ensemble incorporates the stochastic
variability of the observed climate, while the latter includes the stochastic
variability and the uncertainty of multimodel climate change projections. The
ensembles are used as forcing for tRIBS‐Erosion that simulates runoff and sediment
basin responses leading to probabilistic inferences of future changes. The results
show that annual precipitation for the area is generally expected to decrease
in the future, with lower hourly intensities and similar daily rates. The smaller
hourly rainfall generally results in lower mean annual runoff. However, a non‐negligible
probability of runoff increase in the future is identified, resulting from stochastic
combinations of years with low and high runoff. On average, the magnitudes of
mean and extreme events of sediment yield are expected to decrease with a very
high probability. Importantly, the projected variability of annual sediment transport
for the future conditions is comparable to that for the historic conditions, despite
the fact that the former account for a much wider range of possible climate “alternatives.”
This result demonstrates that the historic natural climate variability of sediment
yield is already so high, that it is comparable to the variability for a projected
and highly uncertain future. Additionally, changes in the scaling relationship
between specific sediment yield/runoff and drainage basin area are detected.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Francipane, A.
last_name: Francipane
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: V. Y.
full_name: Ivanov, V. Y.
last_name: Ivanov
- first_name: L. V.
full_name: Noto, L. V.
last_name: Noto
citation:
ama: 'Francipane A, Fatichi S, Ivanov VY, Noto LV. Stochastic assessment of climate
impacts on hydrology and geomorphology of semiarid headwater basins using a physically
based model. Journal of Geophysical Research: Earth Surface. 2015;120(3):507-533.
doi:10.1002/2014jf003232'
apa: 'Francipane, A., Fatichi, S., Ivanov, V. Y., & Noto, L. V. (2015). Stochastic
assessment of climate impacts on hydrology and geomorphology of semiarid headwater
basins using a physically based model. Journal of Geophysical Research: Earth
Surface. American Geophysical Union. https://doi.org/10.1002/2014jf003232'
chicago: 'Francipane, A., Simone Fatichi, V. Y. Ivanov, and L. V. Noto. “Stochastic
Assessment of Climate Impacts on Hydrology and Geomorphology of Semiarid Headwater
Basins Using a Physically Based Model.” Journal of Geophysical Research: Earth
Surface. American Geophysical Union, 2015. https://doi.org/10.1002/2014jf003232.'
ieee: 'A. Francipane, S. Fatichi, V. Y. Ivanov, and L. V. Noto, “Stochastic assessment
of climate impacts on hydrology and geomorphology of semiarid headwater basins
using a physically based model,” Journal of Geophysical Research: Earth Surface,
vol. 120, no. 3. American Geophysical Union, pp. 507–533, 2015.'
ista: 'Francipane A, Fatichi S, Ivanov VY, Noto LV. 2015. Stochastic assessment
of climate impacts on hydrology and geomorphology of semiarid headwater basins
using a physically based model. Journal of Geophysical Research: Earth Surface.
120(3), 507–533.'
mla: 'Francipane, A., et al. “Stochastic Assessment of Climate Impacts on Hydrology
and Geomorphology of Semiarid Headwater Basins Using a Physically Based Model.”
Journal of Geophysical Research: Earth Surface, vol. 120, no. 3, American
Geophysical Union, 2015, pp. 507–33, doi:10.1002/2014jf003232.'
short: 'A. Francipane, S. Fatichi, V.Y. Ivanov, L.V. Noto, Journal of Geophysical
Research: Earth Surface 120 (2015) 507–533.'
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2026-08-03T14:15:02Z
day: '01'
doi: 10.1002/2014jf003232
extern: '1'
fulldoi: https://doi.org/10.1002/2014jf003232
intvolume: ' 120'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 507-533
publication: 'Journal of Geophysical Research: Earth Surface'
publication_identifier:
eissn:
- 2169-9011
issn:
- 2169-9003
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic assessment of climate impacts on hydrology and geomorphology of
semiarid headwater basins using a physically based model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2015'
...