---
_id: '1364'
abstract:
- lang: eng
text: We present a computational method for designing wire sculptures consisting
of interlocking wires. Our method allows the computation of aesthetically pleasing
structures that are structurally stable, efficiently fabricatable with a 2D wire
bending machine, and assemblable without the need of additional connectors. Starting
from a set of planar contours provided by the user, our method automatically tests
for the feasibility of a design, determines a discrete ordering of wires at intersection
points, and optimizes for the rest shape of the individual wires to maximize structural
stability under frictional contact. In addition to their application to art, wire
sculptures present an extremely efficient and fast alternative for low-fidelity
rapid prototyping because manufacturing time and required material linearly scales
with the physical size of objects. We demonstrate the effectiveness of our approach
on a varied set of examples, all of which we fabricated.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under grant agreement No 645599.
alternative_title:
- ACM Transactions on Graphics
article_number: '86'
author:
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
- first_name: Mathias
full_name: Lepoutre, Mathias
last_name: Lepoutre
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod
structures. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925978'
apa: 'Miguel Villalba, E., Lepoutre, M., & Bickel, B. (2016). Computational
design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH,
Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925978'
chicago: Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational
Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925978.
ieee: E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable
planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016,
vol. 35, no. 4.
ista: Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable
planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86.
mla: Miguel Villalba, Eder, et al. Computational Design of Stable Planar-Rod
Structures. Vol. 35, no. 4, 86, ACM, 2016, doi:10.1145/2897824.2925978.
short: E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:36Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:10Z
day: '01'
ddc:
- '006'
department:
- _id: BeBi
doi: 10.1145/2897824.2925978
ec_funded: 1
file:
- access_level: open_access
checksum: d00c2664a43d945df8876ea0193734e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:01Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4853'
file_name: IST-2017-763-v1+1_wirebending.pdf
file_size: 44766392
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
publication_status: published
publisher: ACM
publist_id: '5878'
pubrep_id: '763'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational design of stable planar-rod structures
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1365'
abstract:
- lang: eng
text: A memory-hard function (MHF) f is equipped with a space cost σ and time cost
τ parameter such that repeatedly computing fσ,τ on an application specific integrated
circuit (ASIC) is not economically advantageous relative to a general purpose
computer. Technically we would like that any (generalized) circuit for evaluating
an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent
MHF (iMHF) has the added property that it can be computed with almost optimal
memory and time complexity by an algorithm which accesses memory in a pattern
independent of the input value. Such functions can be specified by fixing a directed
acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph.
In this work we develop new tools for analyzing iMHFs. First we define and motivate
a new complexity measure capturing the amount of energy (i.e. electricity) required
to compute a function. We argue that, in practice, this measure is at least as
important as the more traditional AT-complexity. Next we describe an algorithm
A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound
both its energy and AT complexities per instance evaluated in terms of a certain
combinatorial property of G. Next we instantiate our attack for several general
classes of DAGs which include those underlying many of the most important iMHF
candidates in the literature. In particular, we obtain the following results which
hold for all choices of parameters σ and τ (and thread-count) such that n = σ
∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities
O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67).
-The Double-Buffer and the Linear functions of [CGBS16] both have complexities
in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing
Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function
of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm
with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1
this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ )
is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness
of any DAG which may prove to be of independent interest.
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
citation:
ama: 'Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions.
In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9'
apa: 'Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent
memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International
Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9'
chicago: Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent
Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9.
ieee: 'J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard
functions,” presented at the CRYPTO: International Cryptology Conference, Santa
Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.'
ista: 'Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard
functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.'
mla: Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent
Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9.
short: J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.
conference:
end_date: 2016-08-18
location: Santa Barbara, CA, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2016-08-14
date_created: 2018-12-11T11:51:36Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:50:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53008-5_9
intvolume: ' 9815'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2016/115
month: '08'
oa: 1
oa_version: Preprint
page: 241 - 271
publication_status: published
publisher: Springer
publist_id: '5876'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficiently computing data-independent memory-hard functions
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9815
year: '2016'
...
---
_id: '1366'
abstract:
- lang: eng
text: 'We study the problem of devising provably secure PRNGs with input based on
the sponge paradigm. Such constructions are very appealing, as efficient software/hardware
implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box
way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES
2010), fails to achieve the security notion of robustness recently considered
by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic,
and thus there are high-entropy input distributions on which the construction
fails to extract random bits, and (2) The construction is not forward secure,
and presented solutions aiming at restoring forward security have not been rigorously
analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which
we prove secure in the sense of robustness, delivering in particular concrete
security bounds. On the way, we make what we believe to be an important conceptual
contribution, developing a variant of the security framework of Dodis et al. tailored
at the ideal permutation model that captures PRNG security in settings where the
weakly random inputs are provided from a large class of possible adversarial samplers
which are also allowed to query the random permutation. As a further application
of our techniques, we also present an efficient sponge-based key-derivation function
(which can be instantiated from SHA-3 in a black-box fashion), which we also prove
secure when fed with samples from permutation-dependent distributions.'
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665.
Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4'
apa: 'Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and
KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4'
chicago: Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and
KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4.
ieee: 'P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna,
Austria, 2016, vol. 9665, pp. 87–116.'
ista: 'Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT:
Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.'
mla: Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and
KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4.
short: P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.
conference:
end_date: 2016-05-12
location: Vienna, Austria
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2016-05-08
date_created: 2018-12-11T11:51:36Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-49890-3_4
ec_funded: 1
intvolume: ' 9665'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/169/20160219:201940
month: '05'
oa: 1
oa_version: Preprint
page: 87 - 116
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5872'
quality_controlled: '1'
scopus_import: 1
status: public
title: Provably robust sponge-based PRNGs and KDFs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9665
year: '2016'
...
---
_id: '1368'
abstract:
- lang: eng
text: Superconductivity in heavy-fermion systems has an unconventional nature and
is considered to originate from the universal features of the electronic structure.
Here, the Anderson lattice model is studied by means of the full variational Gutzwiller
wave function incorporating nonlocal effects of the on-site interaction. We show
that the d-wave superconducting ground state can be driven solely by interelectronic
correlations. The proposed microscopic mechanism leads to a multigap superconductivity
with the dominant contribution due to f electrons and in the dx2−y2-wave channel.
Our results rationalize several important observations for CeCoIn5.
acknowledgement: "The work has been supported by the National Science Center
\ (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. "
article_number: '024517'
author:
- first_name: Marcin
full_name: Wysokiński, Marcin
last_name: Wysokiński
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Jozef
full_name: Spałek, Jozef
last_name: Spałek
citation:
ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity
in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and
Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517'
apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven
d wave superconductivity in Anderson lattice model: Two gaps. Physical Review
B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517'
chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven
d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2016.
https://doi.org/10.1103/PhysRevB.94.024517.'
ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave
superconductivity in Anderson lattice model: Two gaps,” Physical Review B -
Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical
Society, 2016.'
ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity
in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and
Materials Physics. 94(2), 024517.'
mla: 'Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in
Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and
Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016,
doi:10.1103/PhysRevB.94.024517.'
short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter
and Materials Physics 94 (2016).
date_created: 2018-12-11T11:51:37Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:12Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.94.024517
ec_funded: 1
intvolume: ' 94'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.00224
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5844'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Correlation driven d wave superconductivity in Anderson lattice model: Two
gaps'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2016'
...
---
_id: '1369'
abstract:
- lang: eng
text: 'We introduce a new loss function for the weakly-supervised training of semantic
image segmentation models based on three guiding principles: to seed with weak
localization cues, to expand objects based on the information about which classes
can occur in an image, and to constrain the segmentations to coincide with object
boundaries. We show experimentally that training a deep convolutional neural network
using the proposed loss function leads to substantially better segmentations than
previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset.
We furthermore give insight into the working mechanism of our method by a detailed
experimental study that illustrates how the segmentation quality is affected by
each term of the proposed loss function as well as their combinations.'
alternative_title:
- LNCS
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for
weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42'
apa: 'Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three
principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711).
Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The
Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42'
chicago: 'Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain:
Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer,
2016. https://doi.org/10.1007/978-3-319-46493-0_42.'
ieee: 'A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles
for weakly-supervised image segmentation,” presented at the ECCV: European Conference
on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.'
ista: 'Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles
for weakly-supervised image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 9908, 695–711.'
mla: 'Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain:
Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer,
2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42.'
short: A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.
conference:
end_date: 2016-10-14
location: Amsterdam, The Netherlands
name: 'ECCV: European Conference on Computer Vision'
start_date: 2016-10-11
date_created: 2018-12-11T11:51:37Z
date_published: 2016-09-15T00:00:00Z
date_updated: 2021-01-12T06:50:12Z
day: '15'
department:
- _id: ChLa
doi: 10.1007/978-3-319-46493-0_42
ec_funded: 1
intvolume: ' 9908'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.06098
month: '09'
oa: 1
oa_version: Preprint
page: 695 - 711
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Springer
publist_id: '5842'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Seed, expand and constrain: Three principles for weakly-supervised image segmentation'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9908
year: '2016'
...
---
_id: '1370'
abstract:
- lang: eng
text: 'We study coherent phonon oscillations and tunneling between two coupled nonlinear
nanomechanical resonators. We show that the coupling between two nanomechanical
resonators creates an effective phonon Josephson junction, which exhibits two
different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation)
and macroscopic self-trapping (phonon blockade). Self-trapping originates from
mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical
value, the energy exchange between the two resonators is suppressed, and phonon
Josephson oscillations between them are completely blocked. An effective classical
Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics
is studied in phase space. Finally, we study the phonon-phonon coherence quantified
by the mean fringe visibility, and show that the interaction between the two resonators
may lead to the loss of coherence in the phononic junction.'
acknowledgement: 'The work of S.B. has been supported by the European Commission (Belgium)
via the SCALEQIT program and by the Alexander von Humboldt Foundation. '
article_number: '033846'
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: David
full_name: Vitali, David
last_name: Vitali
citation:
ama: Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators.
Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3).
doi:10.1103/PhysRevA.93.033846
apa: Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical
resonators. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846
chicago: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical
Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846.
ieee: S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical
resonators,” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 93, no. 3. American Physical Society, 2016.
ista: Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical
resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3),
033846.
mla: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical
Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846.
short: S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical
Physics 93 (2016).
date_created: 2018-12-11T11:51:38Z
date_published: 2016-03-28T00:00:00Z
date_updated: 2023-02-21T10:36:32Z
day: '28'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.93.033846
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1601.01818
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5841'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phonon Josephson junction with nanomechanical resonators
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1371'
abstract:
- lang: eng
text: Living cells can maintain their internal states, react to changing environments,
grow, differentiate, divide, etc. All these processes are tightly controlled by
what can be called a regulatory program. The logic of the underlying control can
sometimes be guessed at by examining the network of influences amongst genetic
components. Some associated gene regulatory networks have been studied in prokaryotes
and eukaryotes, unveiling various structural features ranging from broad distributions
of out-degrees to recurrent "motifs", that is small subgraphs having
a specific pattern of interactions. To understand what factors may be driving
such structuring, a number of groups have introduced frameworks to model the dynamics
of gene regulatory networks. In that context, we review here such in silico approaches
and show how selection for phenotypes, i.e., network function, can shape network
structure.
acknowledgement: 'MZ has been supported by Polish National Science Centre Grant No.
DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. '
author:
- first_name: Olivier
full_name: Martin, Olivier
last_name: Martin
- first_name: André
full_name: Krzywicki, André
last_name: Krzywicki
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
citation:
ama: 'Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene
regulatory networks: From biophysical constraints to biological function. Physics
of Life Reviews. 2016;17:124-158. doi:10.1016/j.plrev.2016.06.002'
apa: 'Martin, O., Krzywicki, A., & Zagórski, M. P. (2016). Drivers of structural
features in gene regulatory networks: From biophysical constraints to biological
function. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.002'
chicago: 'Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural
Features in Gene Regulatory Networks: From Biophysical Constraints to Biological
Function.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.002.'
ieee: 'O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function,”
Physics of Life Reviews, vol. 17. Elsevier, pp. 124–158, 2016.'
ista: 'Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function.
Physics of Life Reviews. 17, 124–158.'
mla: 'Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory
Networks: From Biophysical Constraints to Biological Function.” Physics of
Life Reviews, vol. 17, Elsevier, 2016, pp. 124–58, doi:10.1016/j.plrev.2016.06.002.'
short: O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016)
124–158.
date_created: 2018-12-11T11:51:38Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:13Z
day: '01'
department:
- _id: AnKi
doi: 10.1016/j.plrev.2016.06.002
ec_funded: 1
intvolume: ' 17'
language:
- iso: eng
month: '07'
oa_version: None
page: 124 - 158
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '5840'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Drivers of structural features in gene regulatory networks: From biophysical
constraints to biological function'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1372'
abstract:
- lang: eng
text: Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED
3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for
the root gravitropic response. Cytokinins have also been proposed to play a role
in controlling root gravitropism, but conclusive evidence is lacking. We present
a detailed study of the dynamics of root bending early after gravistimulation,
which revealed a delayed gravitropic response in transgenic lines with depleted
endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX
lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the
auxin response distribution in columella cells consistent with defects in the
auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP
in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization
of PIN proteins in the columella early after gravistimulation, with gravity-induced
relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution
of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was
affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity
in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather
than columella-located PIN proteins as a target of endogenous cytokinins in the
control of root gravitropism.
acknowledgement: 'Funded by Ministry of Education, Youth and Sports Czech Republic.
Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council.
Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant
Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P'
author:
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Danka
full_name: Haruštiaková, Danka
last_name: Haruštiaková
- first_name: Martina
full_name: Matonohova, Martina
last_name: Matonohova
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
citation:
ama: Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism
via differential regulation of auxin transporter expression and localization in
Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049
apa: Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal,
L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis. New
Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049
chicago: Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina
Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins
Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression
and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016.
https://doi.org/10.1111/nph.14049.
ieee: M. Pernisová et al., “Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis,” New
Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.
ista: Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński
T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis. New
Phytologist. 212(2), 497–509.
mla: Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential
Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New
Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049.
short: M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal,
T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.
date_created: 2018-12-11T11:51:38Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:50:13Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1111/nph.14049
file:
- access_level: open_access
checksum: 27fd841ceaf0403559d7048ef51500f9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:53Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5108'
file_name: IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf
file_size: 972763
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 212'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 497 - 509
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5839'
pubrep_id: '1006'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinins influence root gravitropism via differential regulation of auxin
transporter expression and localization in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2016'
...
---
_id: '1373'
article_processing_charge: No
author:
- first_name: Olivier
full_name: Martin, Olivier
last_name: Martin
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
citation:
ama: 'Martin O, Zagórski MP. Network architectures and operating principles. Reply
to comments on "Drivers of structural features in gene regulatory networks:
From biophysical constraints to biological function" Physics of Life
Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006'
apa: 'Martin, O., & Zagórski, M. P. (2016). Network architectures and operating
principles. Reply to comments on "Drivers of structural features in gene
regulatory networks: From biophysical constraints to biological function"
Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006'
chicago: 'Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating
Principles. Reply to Comments on "Drivers of Structural Features in Gene
Regulatory Networks: From Biophysical Constraints to Biological Function"”
Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.'
ieee: 'O. Martin and M. P. Zagórski, “Network architectures and operating principles.
Reply to comments on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function",” Physics
of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.'
ista: 'Martin O, Zagórski MP. 2016. Network architectures and operating principles.
Reply to comments on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" Physics
of Life Reviews. 17, 168–171.'
mla: 'Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating
Principles. Reply to Comments on "Drivers of Structural Features in Gene
Regulatory Networks: From Biophysical Constraints to Biological Function"”
Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.'
short: O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.
date_created: 2018-12-11T11:51:39Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2022-08-26T09:39:27Z
day: '01'
department:
- _id: AnKi
doi: 10.1016/j.plrev.2016.06.006
intvolume: ' 17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01531698
month: '07'
oa: 1
oa_version: Preprint
page: 168 - 171
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '5838'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Network architectures and operating principles. Reply to comments on "Drivers
of structural features in gene regulatory networks: From biophysical constraints
to biological function"'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1377'
abstract:
- lang: eng
text: We consider the problem of minimizing the continuous valued total variation
subject to different unary terms on trees and propose fast direct algorithms based
on dynamic programming to solve these problems. We treat both the convex and the
nonconvex case and derive worst-case complexities that are equal to or better
than existing methods. We show applications to total variation based two dimensional
image processing and computer vision problems based on a Lagrangian decomposition
approach. The resulting algorithms are very effcient, offer a high degree of parallelism,
and come along with memory requirements which are only in the order of the number
of image pixels.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thomas
full_name: Pock, Thomas
last_name: Pock
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal
on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257
apa: Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree.
SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics
. https://doi.org/10.1137/15M1010257
chicago: Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation
on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and
Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257.
ieee: V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM
Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied
Mathematics , pp. 605–636, 2016.
ista: Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal
on Imaging Sciences. 9(2), 605–636.
mla: Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on
Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics
, 2016, pp. 605–36, doi:10.1137/15M1010257.
short: V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016)
605–636.
date_created: 2018-12-11T11:51:40Z
date_published: 2016-05-03T00:00:00Z
date_updated: 2021-01-12T06:50:15Z
day: '03'
department:
- _id: VlKo
doi: 10.1137/15M1010257
ec_funded: 1
intvolume: ' 9'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.07770
month: '05'
oa: 1
oa_version: Preprint
page: 605 - 636
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 Imaging Sciences
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5834'
quality_controlled: '1'
scopus_import: 1
status: public
title: Total variation on a tree
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1378'
abstract:
- lang: eng
text: 'We give a detailed and easily accessible proof of Gromov''s Topological Overlap
Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral
cell complex of dimension d. Informally, the theorem states that if X has sufficiently
strong higher-dimensional expansion properties (which generalize edge expansion
of graphs and are defined in terms of cellular cochains of X) then X has the following
topological overlap property: for every continuous map X → ℝd there exists a point
p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of
X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional
piecewise-linear (PL) manifold M, with a constant μ that depends only on d and
on the expansion properties of X, but not on M.'
alternative_title:
- LIPIcs
author:
- first_name: Dominic
full_name: Dotterrer, Dominic
last_name: Dotterrer
- first_name: Tali
full_name: Kaufman, Tali
last_name: Kaufman
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In:
Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:35.1-35.10. doi:10.4230/LIPIcs.SoCG.2016.35'
apa: 'Dotterrer, D., Kaufman, T., & Wagner, U. (2016). On expansion and topological
overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational
Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.35'
chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.35.
ieee: 'D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA,
2016, vol. 51, p. 35.1-35.10.'
ista: 'Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.'
mla: Dotterrer, Dominic, et al. On Expansion and Topological Overlap. Vol.
51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 35.1-35.10, doi:10.4230/LIPIcs.SoCG.2016.35.
short: D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-09-27T12:29:56Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.35
file:
- access_level: open_access
checksum: cee65b0e722d50f9d1cc70c90ec1d59b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:38Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4699'
file_name: IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf
file_size: 536923
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 35.1 - 35.10
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5833'
pubrep_id: '623'
quality_controlled: '1'
related_material:
record:
- id: '742'
relation: later_version
status: public
scopus_import: 1
status: public
title: On expansion and topological overlap
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1379'
abstract:
- lang: eng
text: We investigate the complexity of finding an embedded non-orientable surface
of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural
question in low-dimensional topology, and as a first non-trivial instance of embeddability
of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding
to the relatively few hardness results that are currently known in 3-manifold
topology. In addition, we show that the problem lies in NP when the Euler genus
g is odd, and we give an explicit algorithm in this case.
alternative_title:
- LIPIcs
author:
- first_name: Benjamin
full_name: Burton, Benjamin
last_name: Burton
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds.
In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24'
apa: 'Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable
surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium
on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24'
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur
Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24.
ieee: 'B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford,
MA, USA, 2016, vol. 51, p. 24.1-24.15.'
ista: 'Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in
3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.'
mla: Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds.
Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24.
short: B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-23T12:23:20Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.24
file:
- access_level: open_access
checksum: f04248a61c24297cfabd30c5f8e0deb9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:12Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4930'
file_name: IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf
file_size: 574770
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 24.1 - 24.15
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5832'
pubrep_id: '622'
quality_controlled: '1'
related_material:
record:
- id: '534'
relation: later_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-manifolds
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1380'
abstract:
- lang: eng
text: We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem
- determining whether a target vector space V may be reached from a starting point
x under repeated applications of a linear transformation A. Answering two questions
posed by Kannan and Lipton in the 1980s, we show that when V has dimension one,
this problem is solvable in polynomial time, and when V has dimension two or three,
the problem is in NPRP.
article_number: '23'
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal
of the ACM. 2016;63(3). doi:10.1145/2857050
apa: Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of
the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity
of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050.
ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit
problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016.
ista: Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem.
Journal of the ACM. 63(3), 23.
mla: Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal
of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050.
short: V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:17Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2857050
intvolume: ' 63'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.2981
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '5831'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the complexity of the orbit problem
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2016'
...
---
_id: '1381'
abstract:
- lang: eng
text: 'Motivated by Tverberg-type problems in topological combinatorics and by classical
results about embeddings (maps without double points), we study the question whether
a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity
intersections. We focus on conditions for the existence of almost r-embeddings,
i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1,
..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber
embeddability criterion, we show that a well-known necessary deleted product condition
for the existence of almost r-embeddings is sufficient in a suitable r-metastable
range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding
K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr
Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1
is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly
extends one of the main results of our previous paper (which treated the special
case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question
raised there.'
alternative_title:
- LIPIcs
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II.
The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51'
apa: 'Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12).
Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51'
chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections,
II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51.
ieee: 'I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range,” presented at the
SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p.
51.1-51.12.'
ista: 'Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range. SoCG: Symposium on
Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.'
mla: Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections,
II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51.
short: I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
GmbH, 2016, p. 51.1-51.12.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:17Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.51
file:
- access_level: open_access
checksum: 92c0c3735fe908f8ded6e484005cb3b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:06Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4791'
file_name: IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf
file_size: 622969
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 51.1 - 51.12
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH
publist_id: '5830'
pubrep_id: '621'
quality_controlled: '1'
scopus_import: 1
status: public
title: Eliminating higher-multiplicity intersections, II. The deleted product criterion
in the r-metastable range
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1382'
abstract:
- lang: eng
text: Background and aims Angiosperms display remarkable diversity in flower colour,
implying that transitions between pigmentation phenotypes must have been common.
Despite progress in understanding transitions between anthocyanin (blue, purple,
pink or red) and unpigmented (white) flowers, little is known about the evolutionary
patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented
flowers. This study investigates the relative rates of evolutionary transitions
between different combinations of yellow- and anthocyanin-pigmentation phenotypes
in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on
anthocyanin and yellow floral pigmentation for 369 species across the tribe. We
then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative
methods to estimate transition rates among pigmentation phenotypes across the
phylogeny. Key Results In contrast to previous studies we found a bias towards
transitions involving a gain in pigmentation, although transitions to phenotypes
with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite
the dominance of yellow and anthocyanin-pigmented taxa, transitions between these
phenotypes are constrained to move through a white intermediate stage, whereas
transitions to double-pigmentation are very rare. The most abundant transitions
are between anthocyanin-pigmented and unpigmented flowers, and similarly the most
abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented
flowers. Conclusions Our findings show that pigment evolution is limited by the
presence of other floral pigments. This interaction between anthocyanin and yellow
pigments constrains the breadth of potential floral diversity observed in nature.
In particular, they suggest that selection has repeatedly acted to promote the
spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore,
the correlation between transition rates and polymorphism suggests that the forces
causing and maintaining variance in the short term reflect evolutionary processes
on longer time scales.
acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous
reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for
her efforts in tracking down the more obscure references.
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in
flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140.
doi:10.1093/aob/mcw043
apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin
pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany.
Oxford University Press. https://doi.org/10.1093/aob/mcw043
chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin
Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany.
Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.
ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae,” Annals of Botany, vol.
117, no. 7. Oxford University Press, pp. 1133–1140, 2016.
ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.
mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation
in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol.
117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.
short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.
date_created: 2018-12-11T11:51:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-02-21T13:49:53Z
day: '1'
department:
- _id: NiBa
doi: 10.1093/aob/mcw043
intvolume: ' 117'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 1133 - 1140
publication: Annals of Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5828'
quality_controlled: '1'
related_material:
record:
- id: '5550'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions
in the Antirrhineae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...
---
_id: '1386'
abstract:
- lang: eng
text: We consider nondeterministic probabilistic programs with the most basic liveness
property of termination. We present efficient methods for termination analysis
of nondeterministic probabilistic programs with polynomial guards and assignments.
Our approach is through synthesis of polynomial ranking supermartingales, that
on one hand significantly generalizes linear ranking supermartingales and on the
other hand is a counterpart of polynomial ranking-functions for proving termination
of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales
through Positivstellensatz's, yielding an efficient method which is not only sound,
but also semi-complete over a large subclass of programs. We show experimental
results to demonstrate that our approach can handle several classical programs
with complex polynomial guards and assignments, and can synthesize efficient quadratic
ranking-supermartingales when a linear one does not exist even for simple affine
programs.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs
through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1'
apa: 'Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis
of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22).
Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer.
https://doi.org/10.1007/978-3-319-41528-4_1'
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination
Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer,
2016. https://doi.org/10.1007/978-3-319-41528-4_1.
ieee: 'K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic
programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification,
Toronto, Canada, 2016, vol. 9779, pp. 3–22.'
ista: 'Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic
programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS,
vol. 9779, 3–22.'
mla: Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs
through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1.
short: K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:43Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-03-25T23:30:18Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-41528-4_1
ec_funded: 1
intvolume: ' 9779'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1604.07169
month: '07'
oa: 1
oa_version: Preprint
page: 3 - 22
project:
- _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'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '5824'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Termination analysis of probabilistic programs through Positivstellensatz's
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9779
year: '2016'
...
---
_id: '1389'
abstract:
- lang: eng
text: "The continuous evolution of a wide variety of systems, including continous-time
Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear
differential equations. In this paper we study the decision problem of whether
the solution x(t) of a system of linear differential equations dx/dt = Ax reaches
a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently
be formulated as the following Infinite Zeros Problem: does a real-valued function
f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely
many zeros? Our main decidability result is that if the differential equation
has order at most 7, then the Infinite Zeros Problem is decidable. On the other
hand, we show that a decision procedure for the Infinite Zeros Problem at order
9 (and above) would entail a major breakthrough in Diophantine Approximation,
specifically an algorithm for computing the Lagrange constants of arbitrary real
algebraic numbers to arbitrary precision."
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: 'Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous
linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548'
apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability
for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New
York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548'
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability
for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016.
https://doi.org/10.1145/2933575.2934548.
ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for
continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016,
pp. 515–524.
ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous
linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.'
mla: Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear
Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548.
short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.
conference:
end_date: 2018-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-05
date_created: 2018-12-11T11:51:44Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:50:20Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2934548
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.03632
month: '07'
oa: 1
oa_version: Preprint
page: 515 - 524
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: LICS '16
publication_status: published
publisher: IEEE
publist_id: '5820'
quality_controlled: '1'
scopus_import: 1
status: public
title: On recurrent reachability for continuous linear dynamical systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1390'
abstract:
- lang: eng
text: "The goal of automatic program repair is to identify a set of syntactic changes
that can turn a program that is incorrect with respect\r\nto a given specification
into a correct one. Existing program repair techniques typically aim to find any
program that meets the given specification. Such “best-effort” strategies can
end up generating a program that is quite different from the original one. Novel
techniques have been proposed to compute syntactically minimal program fixes,
but the smallest syntactic fix to a program can still significantly alter the
original program’s behaviour. We propose a new approach to program repair based
on program distances, which can quantify changes not only to the program syntax
but also to the program semantics. We call this the quantitative program repair
problem where the “optimal” repair is derived using multiple distances. We implement
a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively
close), using the program synthesizer Sketch. We evaluate the effectiveness of
different distances in obtaining desirable repairs by evaluating\r\nQlose on programs
taken from educational tools such as CodeHunt and edX."
alternative_title:
- LNCS
author:
- first_name: Loris
full_name: D'Antoni, Loris
last_name: D'Antoni
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Rishabh
full_name: Singh, Rishabh
last_name: Singh
citation:
ama: 'D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives.
In: Vol 9780. Springer; 2016:383-401. doi:10.1007/978-3-319-41540-6_21'
apa: 'D’Antoni, L., Samanta, R., & Singh, R. (2016). QLOSE: Program repair with
quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer
Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_21'
chicago: 'D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair
with Quantitative Objectives,” 9780:383–401. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_21.'
ieee: 'L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative
objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada,
2016, vol. 9780, pp. 383–401.'
ista: 'D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative
objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401.'
mla: 'D’Antoni, Loris, et al. QLOSE: Program Repair with Quantitative Objectives.
Vol. 9780, Springer, 2016, pp. 383–401, doi:10.1007/978-3-319-41540-6_21.'
short: L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:45Z
date_published: 2016-07-13T00:00:00Z
date_updated: 2021-01-12T06:50:21Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-319-41540-6_21
ec_funded: 1
intvolume: ' 9780'
language:
- iso: eng
month: '07'
oa_version: None
page: 383 - 401
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: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5819'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'QLOSE: Program repair with quantitative objectives'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9780
year: '2016'
...
---
_id: '1391'
abstract:
- lang: eng
text: "We present an extension to the quantifier-free theory of integer arrays which
allows us to express counting. The properties expressible in Array Folds Logic
(AFL) include statements such as "the first array cell contains the array
length," and "the array contains equally many minimal and maximal elements."
These properties cannot be expressed in quantified fragments of the theory of
arrays, nor in the theory of concatenation. Using reduction to counter machines,
we show that the satisfiability problem of AFL is PSPACE-complete, and with a
natural restriction the complexity decreases to NP. We also show that adding either
universal quantifiers or concatenation leads to undecidability.\r\nAFL contains
terms that fold a function over an array. We demonstrate that folding, a well-known
concept from functional languages, allows us to concisely summarize loops that
count over arrays, which occurs frequently in real-life programs. We provide a
tool that can discharge proof obligations in AFL, and we demonstrate on practical
examples that our decision procedure can solve a broad range of problems in symbolic
testing and program verification."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Andrey
full_name: Kupriyanov, Andrey
id: 2C311BF8-F248-11E8-B48F-1D18A9856A87
last_name: Kupriyanov
citation:
ama: 'Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer;
2016:230-248. doi:10.1007/978-3-319-41540-6_13'
apa: 'Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic
(Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto,
Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13'
chicago: Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds
Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13.
ieee: 'P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented
at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp.
230–248.'
ista: 'Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer
Aided Verification, LNCS, vol. 9780, 230–248.'
mla: Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016,
pp. 230–48, doi:10.1007/978-3-319-41540-6_13.
short: P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:45Z
date_published: 2016-07-13T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-319-41540-6_13
ec_funded: 1
intvolume: ' 9780'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1603.06850
month: '07'
oa: 1
oa_version: Preprint
page: 230 - 248
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: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5818'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Array folds logic
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9780
year: '2016'
...
---
_id: '1394'
abstract:
- lang: eng
text: "The solution space of genome-scale models of cellular metabolism provides
a map between physically\r\nviable flux configurations and cellular metabolic
phenotypes described, at the most basic level, by the\r\ncorresponding growth
rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat
empirical growth rate distributions recently obtained in experiments at single-cell
resolution can\r\nbe explained in terms of a trade-off between the higher fitness
of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based
on this, we propose a minimal model for the evolution of\r\na large bacterial
population that captures this trade-off. The scaling relationships observed in\r\nexperiments
encode, in such frameworks, for the same distance from the maximum achievable
growth\r\nrate, the same degree of growth rate maximization, and/or the same rate
of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions,
these results allow for multiple\r\nimplications and extensions in spite of the
underlying conceptual simplicity."
acknowledgement: "The research leading to these results has received funding from
the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038."
article_number: '036005'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: 'De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial
metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005'
apa: 'De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy
in bacterial metabolism: the phenotypic trade-off behind empirical growth rate
distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005'
chicago: 'De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth
against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical
Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing
Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.'
ieee: 'D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in
bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.'
ista: 'De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial
metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli. Physical Biology. 13(3), 036005.'
mla: 'De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism:
The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.”
Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.'
short: D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).
date_created: 2018-12-11T11:51:46Z
date_published: 2016-05-27T00:00:00Z
date_updated: 2021-01-12T06:50:23Z
day: '27'
department:
- _id: GaTk
doi: 10.1088/1478-3975/13/3/036005
ec_funded: 1
intvolume: ' 13'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.03243
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Biology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5815'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Growth against entropy in bacterial metabolism: the phenotypic trade-off behind
empirical growth rate distributions in E. coli'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2016'
...