---
_id: '1593'
abstract:
- lang: eng
  text: 'Plants are sessile organisms that are permanently restricted to their site
    of germination. To compensate for their lack of mobility, plants evolved unique
    mechanisms enabling them to rapidly react to ever changing environmental conditions
    and flexibly adapt their postembryonic developmental program. A prominent demonstration
    of this developmental plasticity is their ability to bend organs in order to reach
    the position most optimal for growth and utilization of light, nutrients, and
    other resources. Shortly after germination, dicotyledonous seedlings form a bended
    structure, the so-called apical hook, to protect the delicate shoot meristem and
    cotyledons from damage when penetrating through the soil. Upon perception of a
    light stimulus, the apical hook rapidly opens and the photomorphogenic developmental
    program is activated. After germination, plant organs are able to align their
    growth with the light source and adopt the most favorable orientation through
    bending, in a process named phototropism. On the other hand, when roots and shoots
    are diverted from their upright orientation, they immediately detect a change
    in the gravity vector and bend to maintain a vertical growth direction. Noteworthy,
    despite the diversity of external stimuli perceived by different plant organs,
    all plant tropic movements share a common mechanistic basis: differential cell
    growth. In our review, we will discuss the molecular principles underlying various
    tropic responses with the focus on mechanisms mediating the perception of external
    signals, transduction cascades and downstream responses that regulate differential
    cell growth and consequently, organ bending. In particular, we highlight common
    and specific features of regulatory pathways in control of the bending of organs
    and a role for the plant hormone auxin as a key regulatory component.'
author:
- first_name: Petra
  full_name: Žádníková, Petra
  last_name: Žádníková
- first_name: Dajo
  full_name: Smet, Dajo
  last_name: Smet
- first_name: Qiang
  full_name: Zhu, Qiang
  id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
  last_name: Zhu
- first_name: Dominique
  full_name: Van Der Straeten, Dominique
  last_name: Van Der Straeten
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
citation:
  ama: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings
    to overcome their sessile nature: Auxin in mobility control. <i>Frontiers in Plant
    Science</i>. 2015;6(4). doi:<a href="https://doi.org/10.3389/fpls.2015.00218">10.3389/fpls.2015.00218</a>'
  apa: 'Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., &#38; Benková, E.
    (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility
    control. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a
    href="https://doi.org/10.3389/fpls.2015.00218">https://doi.org/10.3389/fpls.2015.00218</a>'
  chicago: 'Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and
    Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin
    in Mobility Control.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation,
    2015. <a href="https://doi.org/10.3389/fpls.2015.00218">https://doi.org/10.3389/fpls.2015.00218</a>.'
  ieee: 'P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies
    of seedlings to overcome their sessile nature: Auxin in mobility control,” <i>Frontiers
    in Plant Science</i>, vol. 6, no. 4. Frontiers Research Foundation, 2015.'
  ista: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies
    of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers
    in Plant Science. 6(4).'
  mla: 'Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile
    Nature: Auxin in Mobility Control.” <i>Frontiers in Plant Science</i>, vol. 6,
    no. 4, Frontiers Research Foundation, 2015, doi:<a href="https://doi.org/10.3389/fpls.2015.00218">10.3389/fpls.2015.00218</a>.'
  short: P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers
    in Plant Science 6 (2015).
date_created: 2018-12-11T11:52:55Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2021-01-12T06:51:50Z
day: '14'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3389/fpls.2015.00218
ec_funded: 1
file:
- access_level: open_access
  checksum: c454d642e18dfa86820b97a86cd6d3cc
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:15:23Z
  date_updated: 2020-07-14T12:45:03Z
  file_id: '5142'
  file_name: IST-2016-471-v1+1_fpls-06-00218.pdf
  file_size: 965690
  relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: '         6'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '207362'
  name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5578'
pubrep_id: '471'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Strategies of seedlings to overcome their sessile nature: Auxin in mobility
  control'
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: 6
year: '2015'
...
---
_id: '1594'
abstract:
- lang: eng
  text: Quantitative extensions of temporal logics have recently attracted significant
    attention. In this work, we study frequency LTL (fLTL), an extension of LTL which
    allows to speak about frequencies of events along an execution. Such an extension
    is particularly useful for probabilistic systems that often cannot fulfil strict
    qualitative guarantees on the behaviour. It has been recently shown that controller
    synthesis for Markov decision processes and fLTL is decidable when all the bounds
    on frequencies are 1. As a step towards a complete quantitative solution, we show
    that the problem is decidable for the fragment fLTL\GU, where U does not occur
    in the scope of G (but still F can). Our solution is based on a novel translation
    of such quantitative formulae into equivalent deterministic automata.
acknowledgement: "This work is partly supported by the German Research Council (DFG)
  as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by
  the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework
  Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the
  CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative
  Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie
  Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013)
  REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE),
  and by the ERC Start Grant (279307: Graph Games).\r\n"
alternative_title:
- LNCS
author:
- first_name: Vojtěch
  full_name: Forejt, Vojtěch
  last_name: Forejt
- first_name: Jan
  full_name: Krčál, Jan
  last_name: Krčál
- first_name: Jan
  full_name: Kretinsky, Jan
  id: 44CEF464-F248-11E8-B48F-1D18A9856A87
  last_name: Kretinsky
  orcid: 0000-0002-8122-2881
citation:
  ama: 'Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency
    LTL\GU. In: Vol 9450. Springer; 2015:162-177. doi:<a href="https://doi.org/10.1007/978-3-662-48899-7_12">10.1007/978-3-662-48899-7_12</a>'
  apa: 'Forejt, V., Krčál, J., &#38; Kretinsky, J. (2015). Controller synthesis for
    MDPs and frequency LTL\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic
    for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer.
    <a href="https://doi.org/10.1007/978-3-662-48899-7_12">https://doi.org/10.1007/978-3-662-48899-7_12</a>'
  chicago: Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for
    MDPs and Frequency LTL\GU,” 9450:162–77. Springer, 2015. <a href="https://doi.org/10.1007/978-3-662-48899-7_12">https://doi.org/10.1007/978-3-662-48899-7_12</a>.
  ieee: 'V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and
    frequency LTL\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
    and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.'
  ista: 'Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency
    LTL\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS,
    vol. 9450, 162–177.'
  mla: Forejt, Vojtěch, et al. <i>Controller Synthesis for MDPs and Frequency LTL\GU</i>.
    Vol. 9450, Springer, 2015, pp. 162–77, doi:<a href="https://doi.org/10.1007/978-3-662-48899-7_12">10.1007/978-3-662-48899-7_12</a>.
  short: V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.
conference:
  end_date: 2015-11-28
  location: Suva, Fiji
  name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
  start_date: 2015-11-24
date_created: 2018-12-11T11:52:55Z
date_published: 2015-11-22T00:00:00Z
date_updated: 2021-01-12T06:51:50Z
day: '22'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-662-48899-7_12
ec_funded: 1
intvolume: '      9450'
language:
- iso: eng
month: '11'
oa_version: None
page: 162 - 177
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _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_status: published
publisher: Springer
publist_id: '5577'
quality_controlled: '1'
scopus_import: 1
status: public
title: Controller synthesis for MDPs and frequency LTL\GU
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9450
year: '2015'
...
---
_id: '1595'
abstract:
- lang: eng
  text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
    circles C1, . . . , Ck with common center c, and edges are drawn radially: every
    edge intersects every circle centered at c at most once. G is radial planar if
    it has a radial embedding, that is, a crossing- free radial drawing. If the vertices
    of G are ordered or partitioned into ordered levels (as they are for leveled graphs),
    we require that the assignment of vertices to circles corresponds to the given
    ordering or leveling. We show that a graph G is radial planar if G has a radial
    drawing in which every two edges cross an even number of times; the radial embedding
    has the same leveling as the radial drawing. In other words, we establish the
    weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes
    a result by Pach and Tóth.'
acknowledgement: The research leading to these results has received funding from the
  People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
  Programme (FP7/2007-2013) under REA grant agreement no [291734].
alternative_title:
- LNCS
author:
- first_name: Radoslav
  full_name: Fulek, Radoslav
  id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
  last_name: Fulek
  orcid: 0000-0001-8485-1774
- first_name: Michael
  full_name: Pelsmajer, Michael
  last_name: Pelsmajer
- first_name: Marcus
  full_name: Schaefer, Marcus
  last_name: Schaefer
citation:
  ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol
    9411. Springer; 2015:99-110. doi:<a href="https://doi.org/10.1007/978-3-319-27261-0_9">10.1007/978-3-319-27261-0_9</a>'
  apa: 'Fulek, R., Pelsmajer, M., &#38; Schaefer, M. (2015). Hanani-Tutte for radial
    planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network
    Visualization, Los Angeles, CA, USA: Springer. <a href="https://doi.org/10.1007/978-3-319-27261-0_9">https://doi.org/10.1007/978-3-319-27261-0_9</a>'
  chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
    for Radial Planarity,” 9411:99–110. Springer, 2015. <a href="https://doi.org/10.1007/978-3-319-27261-0_9">https://doi.org/10.1007/978-3-319-27261-0_9</a>.
  ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,”
    presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA,
    USA, 2015, vol. 9411, pp. 99–110.'
  ista: 'Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity.
    GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.'
  mla: Fulek, Radoslav, et al. <i>Hanani-Tutte for Radial Planarity</i>. Vol. 9411,
    Springer, 2015, pp. 99–110, doi:<a href="https://doi.org/10.1007/978-3-319-27261-0_9">10.1007/978-3-319-27261-0_9</a>.
  short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.
conference:
  end_date: 2015-09-26
  location: Los Angeles, CA, USA
  name: 'GD: Graph Drawing and Network Visualization'
  start_date: 2015-09-24
date_created: 2018-12-11T11:52:55Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2023-02-21T16:23:36Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_9
ec_funded: 1
file:
- access_level: open_access
  checksum: 685f91bd077a951ba067d42cce75409e
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:36Z
  date_updated: 2020-07-14T12:45:03Z
  file_id: '4697'
  file_name: IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf
  file_size: 330135
  relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: '      9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 99 - 110
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5576'
pubrep_id: '594'
quality_controlled: '1'
related_material:
  record:
  - id: '1113'
    relation: later_version
    status: public
  - id: '1164'
    relation: later_version
    status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9411
year: '2015'
...
---
_id: '1596'
abstract:
- lang: eng
  text: Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon
    in the plane with the stacking order. The collection C forms a visibility clique
    if for everyi &lt; j the intersection Ci and (Ci ∩ Cj)\⋃i&lt;l&lt;jCl =∅.elements
    that are stacked between them, i.e., We show that if C forms a visibility clique
    its size is bounded from above by O(k4) thereby improving the upper bound of 22k
    from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the
    size of a visibility clique for homothetes of a convex (not necessarily regular)
    k-gon.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
  full_name: Fulek, Radoslav
  id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
  last_name: Fulek
  orcid: 0000-0001-8485-1774
- first_name: Radoš
  full_name: Radoičić, Radoš
  last_name: Radoičić
citation:
  ama: 'Fulek R, Radoičić R. Vertical visibility among parallel polygons in three
    dimensions. In: <i>Graph Drawing and Network Visualization</i>. Vol 9411. Springer
    Nature; 2015:373-379. doi:<a href="https://doi.org/10.1007/978-3-319-27261-0_31">10.1007/978-3-319-27261-0_31</a>'
  apa: 'Fulek, R., &#38; Radoičić, R. (2015). Vertical visibility among parallel polygons
    in three dimensions. In <i>Graph Drawing and Network Visualization</i> (Vol. 9411,
    pp. 373–379). Los Angeles, CA, United States: Springer Nature. <a href="https://doi.org/10.1007/978-3-319-27261-0_31">https://doi.org/10.1007/978-3-319-27261-0_31</a>'
  chicago: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel
    Polygons in Three Dimensions.” In <i>Graph Drawing and Network Visualization</i>,
    9411:373–79. Springer Nature, 2015. <a href="https://doi.org/10.1007/978-3-319-27261-0_31">https://doi.org/10.1007/978-3-319-27261-0_31</a>.
  ieee: R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in
    three dimensions,” in <i>Graph Drawing and Network Visualization</i>, vol. 9411,
    Springer Nature, 2015, pp. 373–379.
  ista: 'Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in
    three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411,
    373–379.'
  mla: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons
    in Three Dimensions.” <i>Graph Drawing and Network Visualization</i>, vol. 9411,
    Springer Nature, 2015, pp. 373–79, doi:<a href="https://doi.org/10.1007/978-3-319-27261-0_31">10.1007/978-3-319-27261-0_31</a>.
  short: R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer
    Nature, 2015, pp. 373–379.
conference:
  end_date: 2015-09-26
  location: Los Angeles, CA, United States
  name: 'GD: Graph Drawing and Network Visualization'
  start_date: 2015-09-24
date_created: 2018-12-11T11:52:56Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2022-01-28T09:20:50Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_31
ec_funded: 1
file:
- access_level: open_access
  checksum: eec04f86c5921d04f025d5791db9b965
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:17:06Z
  date_updated: 2020-07-14T12:45:04Z
  file_id: '5258'
  file_name: IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf
  file_size: 312992
  relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: '      9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 373 - 379
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication: Graph Drawing and Network Visualization
publication_identifier:
  isbn:
  - 978-3-319-27260-3
publication_status: published
publisher: Springer Nature
publist_id: '5575'
pubrep_id: '595'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vertical visibility among parallel polygons in three dimensions
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1598'
abstract:
- lang: eng
  text: 'We consider Markov decision processes (MDPs) with specifications given as
    Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure
    winning vertices such that the objective can be ensured with probability 1 from
    these vertices. We study for the first time the average-case complexity of the
    classical algorithm for computing the set of almost-sure winning vertices for
    MDPs with Büchi objectives. Our contributions are as follows: First, we show that
    for MDPs with constant out-degree the expected number of iterations is at most
    logarithmic and the average-case running time is linear (as compared to the worst-case
    linear number of iterations and quadratic time complexity). Second, for the average-case
    analysis over all MDPs we show that the expected number of iterations is constant
    and the average-case running time is linear (again as compared to the worst-case
    linear number of iterations and quadratic time complexity). Finally we also show
    that when all MDPs are equally likely, the probability that the classical algorithm
    requires more than a constant number of iterations is exponentially small.'
acknowledgement: "The research was supported by FWF Grant No. P 23499-N23, FWF NFN
  Grant No. S11407-N23 (RiSE), ERC Start Grant (279307: Graph Games), and the Microsoft
  Faculty Fellows Award. Nisarg Shah is also supported by NSF Grant CCF-1215883.\r\n"
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: Manas
  full_name: Joglekar, Manas
  last_name: Joglekar
- first_name: Nisarg
  full_name: Shah, Nisarg
  last_name: Shah
citation:
  ama: Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm
    for Markov decision processes with Büchi objectives. <i>Theoretical Computer Science</i>.
    2015;573(3):71-89. doi:<a href="https://doi.org/10.1016/j.tcs.2015.01.050">10.1016/j.tcs.2015.01.050</a>
  apa: Chatterjee, K., Joglekar, M., &#38; Shah, N. (2015). Average case analysis
    of the classical algorithm for Markov decision processes with Büchi objectives.
    <i>Theoretical Computer Science</i>. Elsevier. <a href="https://doi.org/10.1016/j.tcs.2015.01.050">https://doi.org/10.1016/j.tcs.2015.01.050</a>
  chicago: Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case
    Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.”
    <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href="https://doi.org/10.1016/j.tcs.2015.01.050">https://doi.org/10.1016/j.tcs.2015.01.050</a>.
  ieee: K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical
    algorithm for Markov decision processes with Büchi objectives,” <i>Theoretical
    Computer Science</i>, vol. 573, no. 3. Elsevier, pp. 71–89, 2015.
  ista: Chatterjee K, Joglekar M, Shah N. 2015. Average case analysis of the classical
    algorithm for Markov decision processes with Büchi objectives. Theoretical Computer
    Science. 573(3), 71–89.
  mla: Chatterjee, Krishnendu, et al. “Average Case Analysis of the Classical Algorithm
    for Markov Decision Processes with Büchi Objectives.” <i>Theoretical Computer
    Science</i>, vol. 573, no. 3, Elsevier, 2015, pp. 71–89, doi:<a href="https://doi.org/10.1016/j.tcs.2015.01.050">10.1016/j.tcs.2015.01.050</a>.
  short: K. Chatterjee, M. Joglekar, N. Shah, Theoretical Computer Science 573 (2015)
    71–89.
date_created: 2018-12-11T11:52:56Z
date_published: 2015-03-30T00:00:00Z
date_updated: 2023-02-23T10:55:03Z
day: '30'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2015.01.050
ec_funded: 1
external_id:
  arxiv:
  - '1202.4175'
intvolume: '       573'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1202.4175
month: '03'
oa: 1
oa_version: Preprint
page: 71 - 89
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: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '5571'
quality_controlled: '1'
related_material:
  record:
  - id: '2715'
    relation: earlier_version
    status: public
scopus_import: 1
status: public
title: Average case analysis of the classical algorithm for Markov decision processes
  with Büchi objectives
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 573
year: '2015'
...
---
_id: '1601'
abstract:
- lang: eng
  text: We propose a flexible exchange format for ω-automata, as typically used in
    formal verification, and implement support for it in a range of established tools.
    Our aim is to simplify the interaction of tools, helping the research community
    to build upon other people’s work. A key feature of the format is the use of very
    generic acceptance conditions, specified by Boolean combinations of acceptance
    primitives, rather than being limited to common cases such as Büchi, Streett,
    or Rabin. Such flexibility in the choice of acceptance conditions can be exploited
    in applications, for example in probabilistic model checking, and furthermore
    encourages the development of acceptance-agnostic tools for automata manipulations.
    The format allows acceptance conditions that are either state-based or transition-based,
    and also supports alternating automata.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomáš
  full_name: Babiak, Tomáš
  last_name: Babiak
- first_name: František
  full_name: Blahoudek, František
  last_name: Blahoudek
- first_name: Alexandre
  full_name: Duret Lutz, Alexandre
  last_name: Duret Lutz
- first_name: Joachim
  full_name: Klein, Joachim
  last_name: Klein
- first_name: Jan
  full_name: Kretinsky, Jan
  id: 44CEF464-F248-11E8-B48F-1D18A9856A87
  last_name: Kretinsky
  orcid: 0000-0002-8122-2881
- first_name: Daniel
  full_name: Mueller, Daniel
  last_name: Mueller
- first_name: David
  full_name: Parker, David
  last_name: Parker
- first_name: Jan
  full_name: Strejček, Jan
  last_name: Strejček
citation:
  ama: 'Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format.
    In: Vol 9206. Springer; 2015:479-486. doi:<a href="https://doi.org/10.1007/978-3-319-21690-4_31">10.1007/978-3-319-21690-4_31</a>'
  apa: 'Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller,
    D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486).
    Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States:
    Springer. <a href="https://doi.org/10.1007/978-3-319-21690-4_31">https://doi.org/10.1007/978-3-319-21690-4_31</a>'
  chicago: Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein,
    Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata
    Format,” 9206:479–86. Springer, 2015. <a href="https://doi.org/10.1007/978-3-319-21690-4_31">https://doi.org/10.1007/978-3-319-21690-4_31</a>.
  ieee: 'T. Babiak <i>et al.</i>, “The Hanoi omega-automata format,” presented at
    the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
    vol. 9206, pp. 479–486.'
  ista: 'Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker
    D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification,
    LNCS, vol. 9206, 479–486.'
  mla: Babiak, Tomáš, et al. <i>The Hanoi Omega-Automata Format</i>. Vol. 9206, Springer,
    2015, pp. 479–86, doi:<a href="https://doi.org/10.1007/978-3-319-21690-4_31">10.1007/978-3-319-21690-4_31</a>.
  short: T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller,
    D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.
conference:
  end_date: 2015-07-24
  location: San Francisco, CA, United States
  name: 'CAV: Computer Aided Verification'
  start_date: 2015-07-18
date_created: 2018-12-11T11:52:57Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2021-01-12T06:51:54Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_31
ec_funded: 1
file:
- access_level: open_access
  checksum: 5885236fa88a439baba9ac6f3e801e93
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-15T08:38:12Z
  date_updated: 2020-07-14T12:45:04Z
  file_id: '7850'
  file_name: 2015_CAV_Babiak.pdf
  file_size: 1651779
  relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: '      9206'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 479 - 486
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5566'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Hanoi omega-automata format
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1602'
abstract:
- lang: eng
  text: Interprocedural analysis is at the heart of numerous applications in programming
    languages, such as alias analysis, constant propagation, etc. Recursive state
    machines (RSMs) are standard models for interprocedural analysis. We consider
    a general framework with RSMs where the transitions are labeled from a semiring,
    and path properties are algebraic with semiring operations. RSMs with algebraic
    path properties can model interprocedural dataflow analysis problems, the shortest
    path problem, the most probable path problem, etc. The traditional algorithms
    for interprocedural analysis focus on path properties where the starting point
    is fixed as the entry point of a specific method. In this work, we consider possible
    multiple queries as required in many applications such as in alias analysis. The
    study of multiple queries allows us to bring in a very important algorithmic distinction
    between the resource usage of the one-time preprocessing vs for each individual
    query. The second aspect that we consider is that the control flow graphs for
    most programs have constant treewidth. Our main contributions are simple and implementable
    algorithms that supportmultiple queries for algebraic path properties for RSMs
    that have constant treewidth. Our theoretical results show that our algorithms
    have small additional one-time preprocessing, but can answer subsequent queries
    significantly faster as compared to the current best-known solutions for several
    important problems, such as interprocedural reachability and shortest path. We
    provide a prototype implementation for interprocedural reachability and intraprocedural
    shortest path that gives a significant speed-up on several benchmarks.
acknowledgement: We thank anonymous reviewers for helpful comments to improve the
  presentation of the paper.
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: Rasmus
  full_name: Ibsen-Jensen, Rasmus
  id: 3B699956-F248-11E8-B48F-1D18A9856A87
  last_name: Ibsen-Jensen
  orcid: 0000-0003-4783-0389
- first_name: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
- first_name: Prateesh
  full_name: Goyal, Prateesh
  last_name: Goyal
citation:
  ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for
    algebraic path properties in recursive state machines with constant treewidth.
    <i>ACM SIGPLAN Notices</i>. 2015;50(1):97-109. doi:<a href="https://doi.org/10.1145/2676726.2676979">10.1145/2676726.2676979</a>
  apa: 'Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., &#38; Goyal, P. (2015).
    Faster algorithms for algebraic path properties in recursive state machines with
    constant treewidth. <i>ACM SIGPLAN Notices</i>. Mumbai, India: ACM. <a href="https://doi.org/10.1145/2676726.2676979">https://doi.org/10.1145/2676726.2676979</a>'
  chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and
    Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive
    State Machines with Constant Treewidth.” <i>ACM SIGPLAN Notices</i>. ACM, 2015.
    <a href="https://doi.org/10.1145/2676726.2676979">https://doi.org/10.1145/2676726.2676979</a>.
  ieee: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms
    for algebraic path properties in recursive state machines with constant treewidth,”
    <i>ACM SIGPLAN Notices</i>, vol. 50, no. 1. ACM, pp. 97–109, 2015.
  ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms
    for algebraic path properties in recursive state machines with constant treewidth.
    ACM SIGPLAN Notices. 50(1), 97–109.
  mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties
    in Recursive State Machines with Constant Treewidth.” <i>ACM SIGPLAN Notices</i>,
    vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:<a href="https://doi.org/10.1145/2676726.2676979">10.1145/2676726.2676979</a>.
  short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices
    50 (2015) 97–109.
conference:
  end_date: 2015-01-17
  location: Mumbai, India
  name: 'SIGPLAN: Symposium on Principles of Programming Languages'
  start_date: 2015-01-15
date_created: 2018-12-11T11:52:58Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676979
ec_funded: 1
external_id:
  arxiv:
  - '1410.7724'
intvolume: '        50'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1410.7724
month: '01'
oa: 1
oa_version: Preprint
page: 97 - 109
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: 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: ACM SIGPLAN Notices
publication_status: published
publisher: ACM
publist_id: '5565'
quality_controlled: '1'
related_material:
  record:
  - id: '821'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Faster algorithms for algebraic path properties in recursive state machines
  with constant treewidth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1603'
abstract:
- lang: eng
  text: "For deterministic systems, a counterexample to a property can simply be an
    error trace, whereas counterexamples in probabilistic systems are necessarily
    more complex. For instance, a set of erroneous traces with a sufficient cumulative
    probability mass can be used. Since these are too large objects to understand
    and manipulate, compact representations such as subchains have been considered.
    In the case of probabilistic systems with non-determinism, the situation is even
    more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism)
    is a straightforward choice, we take a different approach. Instead, we focus on
    the strategy itself, and extract the most important decisions it makes, and present
    its succinct representation.\r\nThe key tools we employ to achieve this are (1)
    introducing a concept of importance of a state w.r.t. the strategy, and (2) learning
    using decision trees. There are three main consequent advantages of our approach.
    Firstly, it exploits the quantitative information on states, stressing the more
    important decisions. Secondly, it leads to a greater variability and degree of
    freedom in representing the strategies. Thirdly, the representation uses a self-explanatory
    data structure. In summary, our approach produces more succinct and more explainable
    strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental
    results show that we can extract several rules describing the strategy even for
    very large systems that do not fit in memory, and based on the rules explain the
    erroneous behaviour."
acknowledgement: This research was funded in part by Austrian Science Fund (FWF) Grant
  No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
  European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989
  (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme
  (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013)
  REA Grant No 291734.
alternative_title:
- LNCS
author:
- first_name: Tomáš
  full_name: Brázdil, Tomáš
  last_name: Brázdil
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Martin
  full_name: Chmelik, Martin
  id: 3624234E-F248-11E8-B48F-1D18A9856A87
  last_name: Chmelik
- first_name: Andreas
  full_name: Fellner, Andreas
  id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
  last_name: Fellner
- first_name: Jan
  full_name: Kretinsky, Jan
  id: 44CEF464-F248-11E8-B48F-1D18A9856A87
  last_name: Kretinsky
  orcid: 0000-0002-8122-2881
citation:
  ama: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample
    explanation by learning small strategies in Markov decision processes. In: Vol
    9206. Springer; 2015:158-177. doi:<a href="https://doi.org/10.1007/978-3-319-21690-4_10">10.1007/978-3-319-21690-4_10</a>'
  apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., &#38; Kretinsky, J.
    (2015). Counterexample explanation by learning small strategies in Markov decision
    processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification,
    San Francisco, CA, United States: Springer. <a href="https://doi.org/10.1007/978-3-319-21690-4_10">https://doi.org/10.1007/978-3-319-21690-4_10</a>'
  chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner,
    and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in
    Markov Decision Processes,” 9206:158–77. Springer, 2015. <a href="https://doi.org/10.1007/978-3-319-21690-4_10">https://doi.org/10.1007/978-3-319-21690-4_10</a>.
  ieee: 'T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample
    explanation by learning small strategies in Markov decision processes,” presented
    at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
    vol. 9206, pp. 158–177.'
  ista: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample
    explanation by learning small strategies in Markov decision processes. CAV: Computer
    Aided Verification, LNCS, vol. 9206, 158–177.'
  mla: Brázdil, Tomáš, et al. <i>Counterexample Explanation by Learning Small Strategies
    in Markov Decision Processes</i>. Vol. 9206, Springer, 2015, pp. 158–77, doi:<a
    href="https://doi.org/10.1007/978-3-319-21690-4_10">10.1007/978-3-319-21690-4_10</a>.
  short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer,
    2015, pp. 158–177.
conference:
  end_date: 2015-07-24
  location: San Francisco, CA, United States
  name: 'CAV: Computer Aided Verification'
  start_date: 2015-07-18
date_created: 2018-12-11T11:52:58Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2024-02-21T13:52:07Z
day: '16'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-21690-4_10
ec_funded: 1
intvolume: '      9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1502.02834
month: '07'
oa: 1
oa_version: Preprint
page: 158 - 177
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: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _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
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication_identifier:
  eisbn:
  - 978-3-319-21690-4
publication_status: published
publisher: Springer
publist_id: '5564'
quality_controlled: '1'
related_material:
  record:
  - id: '5549'
    relation: research_paper
    status: public
scopus_import: 1
status: public
title: Counterexample explanation by learning small strategies in Markov decision
  processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1604'
abstract:
- lang: eng
  text: We consider the quantitative analysis problem for interprocedural control-flow
    graphs (ICFGs). The input consists of an ICFG, a positive weight function that
    assigns every transition a positive integer-valued number, and a labelling of
    the transitions (events) as good, bad, and neutral events. The weight function
    assigns to each transition a numerical value that represents ameasure of how good
    or bad an event is. The quantitative analysis problem asks whether there is a
    run of the ICFG where the ratio of the sum of the numerical weights of good events
    versus the sum of weights of bad events in the long-run is at least a given threshold
    (or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
    The quantitative analysis problem for ICFGs can be solved in polynomial time,
    and we present an efficient and practical algorithm for the problem. We show that
    several problems relevant for static program analysis, such as estimating the
    worst-case execution time of a program or the average energy consumption of a
    mobile application, can be modeled in our framework. We have implemented our algorithm
    as a tool in the Java Soot framework. We demonstrate the effectiveness of our
    approach with two case studies. First, we show that our framework provides a sound
    approach (no false positives) for the analysis of inefficiently-used containers.
    Second, we show that our approach can also be used for static profiling of programs
    which reasons about methods that are frequently invoked. Our experimental results
    show that our tool scales to relatively large benchmarks, and discovers relevant
    and useful information that can be used to optimize performance of the programs.
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
- first_name: Yaron
  full_name: Velner, Yaron
  last_name: Velner
citation:
  ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis.
    <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>. 2015;50(1):539-551.
    doi:<a href="https://doi.org/10.1145/2676726.2676968">10.1145/2676726.2676968</a>
  apa: 'Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2015). Quantitative interprocedural
    analysis. <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>. Mumbai, India:
    ACM. <a href="https://doi.org/10.1145/2676726.2676968">https://doi.org/10.1145/2676726.2676968</a>'
  chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative
    Interprocedural Analysis.” <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT
    </i>. ACM, 2015. <a href="https://doi.org/10.1145/2676726.2676968">https://doi.org/10.1145/2676726.2676968</a>.
  ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural
    analysis,” <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>, vol. 50,
    no. 1. ACM, pp. 539–551, 2015.
  ista: Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural
    analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.
  mla: Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” <i>Proceedings
    of the 42nd Annual ACM SIGPLAN-SIGACT </i>, vol. 50, no. 1, ACM, 2015, pp. 539–51,
    doi:<a href="https://doi.org/10.1145/2676726.2676968">10.1145/2676726.2676968</a>.
  short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual
    ACM SIGPLAN-SIGACT  50 (2015) 539–551.
conference:
  end_date: 2015-01-17
  location: Mumbai, India
  name: 'SIGPLAN: Symposium on Principles of Programming Languages'
  start_date: 2015-01-15
date_created: 2018-12-11T11:52:59Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676968
ec_funded: 1
intvolume: '        50'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 539 - 551
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: 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 of the 42nd Annual ACM SIGPLAN-SIGACT '
publication_identifier:
  isbn:
  - 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5563'
pubrep_id: '523'
quality_controlled: '1'
related_material:
  record:
  - id: '5445'
    relation: earlier_version
    status: public
  - id: '821'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Quantitative interprocedural analysis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1605'
abstract:
- lang: eng
  text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model
    complex dynamical systems. This formalism is particularly suited for the representation
    of biological systems which often exhibit highly non-linear behavior. In this
    paper, we consider the problem of parameter identification for MHA. We present
    an abstraction of MHA based on linear hybrid automata, which can be analyzed by
    the SpaceEx model checker. This abstraction enables a precise handling of time-dependent
    properties. We demonstrate the potential of our approach on a model of a genetic
    regulatory network and a myocyte model.
acknowledgement: This work was partly supported by the European Research Council (ERC)
  under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23,
  S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by
  the German Research Foundation (DFG) as part of the Transregional Collaborative
  Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR
  14 AVACS, http://www.avacs.org/).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergiy
  full_name: Bogomolov, Sergiy
  id: 369D9A44-F248-11E8-B48F-1D18A9856A87
  last_name: Bogomolov
  orcid: 0000-0002-0686-0365
- first_name: Christian
  full_name: Schilling, Christian
  id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
  last_name: Schilling
  orcid: 0000-0003-3658-1065
- first_name: Ezio
  full_name: Bartocci, Ezio
  last_name: Bartocci
- first_name: Grégory
  full_name: Batt, Grégory
  last_name: Batt
- first_name: Hui
  full_name: Kong, Hui
  id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
  last_name: Kong
  orcid: 0000-0002-3066-6941
- first_name: Radu
  full_name: Grosu, Radu
  last_name: Grosu
citation:
  ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based
    parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35.
    doi:<a href="https://doi.org/10.1007/978-3-319-26287-1_2">10.1007/978-3-319-26287-1_2</a>'
  apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., &#38; Grosu,
    R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol.
    9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa,
    Israel: Springer. <a href="https://doi.org/10.1007/978-3-319-26287-1_2">https://doi.org/10.1007/978-3-319-26287-1_2</a>'
  chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui
    Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,”
    9434:19–35. Springer, 2015. <a href="https://doi.org/10.1007/978-3-319-26287-1_2">https://doi.org/10.1007/978-3-319-26287-1_2</a>.
  ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu,
    “Abstraction-based parameter synthesis for multiaffine systems,” presented at
    the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.'
  ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based
    parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference,
    LNCS, vol. 9434, 19–35.'
  mla: Bogomolov, Sergiy, et al. <i>Abstraction-Based Parameter Synthesis for Multiaffine
    Systems</i>. Vol. 9434, Springer, 2015, pp. 19–35, doi:<a href="https://doi.org/10.1007/978-3-319-26287-1_2">10.1007/978-3-319-26287-1_2</a>.
  short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:,
    Springer, 2015, pp. 19–35.
conference:
  end_date: 2015-11-19
  location: Haifa, Israel
  name: 'HVC: Haifa Verification Conference'
  start_date: 2015-11-17
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2021-01-12T06:51:56Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_2
ec_funded: 1
file:
- access_level: open_access
  checksum: 3aab260f3f34641d622030ba22645b3e
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-15T08:43:19Z
  date_updated: 2020-07-14T12:45:05Z
  file_id: '7851'
  file_name: 2015_LNCS_Bogomolov.pdf
  file_size: 1053207
  relation: main_file
file_date_updated: 2020-07-14T12:45:05Z
has_accepted_license: '1'
intvolume: '      9434'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 19 - 35
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Abstraction-based parameter synthesis for multiaffine systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1606'
abstract:
- lang: eng
  text: 'In this paper, we present the first steps toward a runtime verification framework
    for monitoring hybrid and cyber-physical systems (CPS) development tools based
    on randomized differential testing. The development tools include hybrid systems
    reachability analysis tools, model-based development environments like Simulink/Stateflow
    (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these
    hybrid automaton models are translated to a number of different tools (currently,
    SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using
    the HyST source transformation and translation tool. Then, the hybrid automaton
    models are executed in the different tools and their outputs are parsed. The final
    step is the differential comparison: the outputs of the different tools are compared.
    If the results do not agree (in the sense that an analysis or verification result
    from one tool does not match that of another tool, ignoring timeouts, etc.), a
    candidate bug is flagged and the model is saved for future analysis by the user.
    The process then repeats and the monitoring continues until the user terminates
    the process. We present preliminary results that have been useful in identifying
    a few bugs in the analysis methods of different development tools, and in an earlier
    version of HyST.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luan
  full_name: Nguyen, Luan
  last_name: Nguyen
- first_name: Christian
  full_name: Schilling, Christian
  last_name: Schilling
- first_name: Sergiy
  full_name: Bogomolov, Sergiy
  id: 369D9A44-F248-11E8-B48F-1D18A9856A87
  last_name: Bogomolov
  orcid: 0000-0002-0686-0365
- first_name: Taylor
  full_name: Johnson, Taylor
  last_name: Johnson
citation:
  ama: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid
    analysis tools. In: <i>6th International Conference</i>. Vol 9333. Springer Nature;
    2015:281-286. doi:<a href="https://doi.org/10.1007/978-3-319-23820-3_19">10.1007/978-3-319-23820-3_19</a>'
  apa: 'Nguyen, L., Schilling, C., Bogomolov, S., &#38; Johnson, T. (2015). Runtime
    verification for hybrid analysis tools. In <i>6th International Conference</i>
    (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. <a href="https://doi.org/10.1007/978-3-319-23820-3_19">https://doi.org/10.1007/978-3-319-23820-3_19</a>'
  chicago: Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson.
    “Runtime Verification for Hybrid Analysis Tools.” In <i>6th International Conference</i>,
    9333:281–86. Springer Nature, 2015. <a href="https://doi.org/10.1007/978-3-319-23820-3_19">https://doi.org/10.1007/978-3-319-23820-3_19</a>.
  ieee: L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification
    for hybrid analysis tools,” in <i>6th International Conference</i>, Vienna, Austria,
    2015, vol. 9333, pp. 281–286.
  ista: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification
    for hybrid analysis tools. 6th International Conference. RV: Runtime Verification,
    LNCS, vol. 9333, 281–286.'
  mla: Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” <i>6th
    International Conference</i>, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:<a
    href="https://doi.org/10.1007/978-3-319-23820-3_19">10.1007/978-3-319-23820-3_19</a>.
  short: L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International
    Conference, Springer Nature, 2015, pp. 281–286.
conference:
  end_date: 2015-09-25
  location: Vienna, Austria
  name: 'RV: Runtime Verification'
  start_date: 2015-09-22
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2022-02-01T14:52:59Z
day: '15'
department:
- _id: ToHe
doi: 10.1007/978-3-319-23820-3_19
ec_funded: 1
intvolume: '      9333'
language:
- iso: eng
month: '11'
oa_version: None
page: 281 - 286
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication: 6th International Conference
publication_identifier:
  isbn:
  - 978-3-319-23819-7
publication_status: published
publisher: Springer Nature
publist_id: '5562'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Runtime verification for hybrid analysis tools
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9333
year: '2015'
...
---
_id: '1607'
abstract:
- lang: eng
  text: We consider the core algorithmic problems related to verification of systems
    with respect to three classical quantitative properties, namely, the mean-payoff
    property, the ratio property, and the minimum initial credit for energy property.
    The algorithmic problem given a graph and a quantitative property asks to compute
    the optimal value (the infimum value over all traces) from every node of the graph.
    We consider graphs with constant treewidth, and it is well-known that the control-flow
    graphs of most programs have constant treewidth. Let n denote the number of nodes
    of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W
    the largest absolute value of the weights. Our main theoretical results are as
    follows. First, for constant treewidth graphs we present an algorithm that approximates
    the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ))
    and linear space, as compared to the classical algorithms that require quadratic
    time. Second, for the ratio property we present an algorithm that for constant
    treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output
    is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)).
    Third, for the minimum initial credit problem we show that (i) for general graphs
    the problem can be solved in O(n2⋅m) time and the associated decision problem
    can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and
    O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present
    an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W))
    bound. We have implemented some of our algorithms and show that they present a
    significant speedup on standard benchmarks.
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
  Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
  (279307: Graph Games), and Microsoft faculty fellows award.'
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: Rasmus
  full_name: Ibsen-Jensen, Rasmus
  id: 3B699956-F248-11E8-B48F-1D18A9856A87
  last_name: Ibsen-Jensen
  orcid: 0000-0003-4783-0389
- first_name: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
citation:
  ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative
    verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157.
    doi:<a href="https://doi.org/10.1007/978-3-319-21690-4_9">10.1007/978-3-319-21690-4_9</a>'
  apa: 'Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2015). Faster algorithms
    for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157).
    Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer.
    <a href="https://doi.org/10.1007/978-3-319-21690-4_9">https://doi.org/10.1007/978-3-319-21690-4_9</a>'
  chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
    “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,”
    9206:140–57. Springer, 2015. <a href="https://doi.org/10.1007/978-3-319-21690-4_9">https://doi.org/10.1007/978-3-319-21690-4_9</a>.
  ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for
    quantitative verification in constant treewidth graphs,” presented at the CAV:
    Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.'
  ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
    quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification,
    LNCS, vol. 9206, 140–157.'
  mla: Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Quantitative Verification
    in Constant Treewidth Graphs</i>. Vol. 9206, Springer, 2015, pp. 140–57, doi:<a
    href="https://doi.org/10.1007/978-3-319-21690-4_9">10.1007/978-3-319-21690-4_9</a>.
  short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp.
    140–157.
conference:
  end_date: 2015-07-24
  location: San Francisco, CA, USA
  name: 'CAV: Computer Aided Verification'
  start_date: 2015-07-18
date_created: 2018-12-11T11:52:59Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_9
ec_funded: 1
intvolume: '      9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1504.07384
month: '07'
oa: 1
oa_version: Preprint
page: 140 - 157
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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
  name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5560'
quality_controlled: '1'
related_material:
  record:
  - id: '5430'
    relation: earlier_version
    status: public
  - id: '5437'
    relation: earlier_version
    status: public
  - id: '821'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1609'
abstract:
- lang: eng
  text: The synthesis problem asks for the automatic construction of a system from
    its specification. In the traditional setting, the system is “constructed from
    scratch” rather than composed from reusable components. However, this is rare
    in practice, and almost every non-trivial software system relies heavily on the
    use of libraries of reusable components. Recently, Lustig and Vardi introduced
    dataflow and controlflow synthesis from libraries of reusable components. They
    proved that dataflow synthesis is undecidable, while controlflow synthesis is
    decidable. The problem of controlflow synthesis from libraries of probabilistic
    components was considered by Nain, Lustig and Vardi, and was shown to be decidable
    for qualitative analysis (that asks that the specification be satisfied with probability
    1). Our main contribution for controlflow synthesis from probabilistic components
    is to establish better complexity bounds for the qualitative analysis problem,
    and to show that the more general quantitative problem is undecidable. For the
    qualitative analysis, we show that the problem (i) is EXPTIME-complete when the
    specification is given as a deterministic parity word automaton, improving the
    previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games
    hard, when the specification is given directly as a parity condition on the components,
    improving the previously known EXPTIME upper bound.
acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant
  No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph
  Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF
  Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program
  Engineering”, by BSF grant 9800096, and by gift from Intel.'
alternative_title:
- LNCS
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: Laurent
  full_name: Doyen, Laurent
  last_name: Doyen
- first_name: Moshe
  full_name: Vardi, Moshe
  last_name: Vardi
citation:
  ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic
    components. In: <i>42nd International Colloquium</i>. Vol 9135. Springer Nature;
    2015:108-120. doi:<a href="https://doi.org/10.1007/978-3-662-47666-6_9">10.1007/978-3-662-47666-6_9</a>'
  apa: 'Chatterjee, K., Doyen, L., &#38; Vardi, M. (2015). The complexity of synthesis
    from probabilistic components. In <i>42nd International Colloquium</i> (Vol. 9135,
    pp. 108–120). Kyoto, Japan: Springer Nature. <a href="https://doi.org/10.1007/978-3-662-47666-6_9">https://doi.org/10.1007/978-3-662-47666-6_9</a>'
  chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity
    of Synthesis from Probabilistic Components.” In <i>42nd International Colloquium</i>,
    9135:108–20. Springer Nature, 2015. <a href="https://doi.org/10.1007/978-3-662-47666-6_9">https://doi.org/10.1007/978-3-662-47666-6_9</a>.
  ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic
    components,” in <i>42nd International Colloquium</i>, Kyoto, Japan, 2015, vol.
    9135, pp. 108–120.
  ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic
    components. 42nd International Colloquium. ICALP: Automata, Languages and Programming,
    LNCS, vol. 9135, 108–120.'
  mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic
    Components.” <i>42nd International Colloquium</i>, vol. 9135, Springer Nature,
    2015, pp. 108–20, doi:<a href="https://doi.org/10.1007/978-3-662-47666-6_9">10.1007/978-3-662-47666-6_9</a>.
  short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer
    Nature, 2015, pp. 108–120.
conference:
  end_date: 2015-07-10
  location: Kyoto, Japan
  name: 'ICALP: Automata, Languages and Programming'
  start_date: 2015-07-06
date_created: 2018-12-11T11:53:00Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2022-02-01T15:04:44Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-662-47666-6_9
ec_funded: 1
intvolume: '      9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1502.04844
month: '06'
oa: 1
oa_version: Preprint
page: 108 - 120
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'
publication: 42nd International Colloquium
publication_identifier:
  isbn:
  - 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The complexity of synthesis from probabilistic components
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1610'
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. The problem of computing edit
    distance to pushdown automata 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:
- LNCS
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: 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. In: <i>42nd International Colloquium</i>. Vol 9135. Springer Nature;
    2015:121-133. doi:<a href="https://doi.org/10.1007/978-3-662-47666-6_10">10.1007/978-3-662-47666-6_10</a>'
  apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., &#38; Otop, J. (2015).
    Edit distance for pushdown automata. In <i>42nd International Colloquium</i> (Vol.
    9135, pp. 121–133). Kyoto, Japan: Springer Nature. <a href="https://doi.org/10.1007/978-3-662-47666-6_10">https://doi.org/10.1007/978-3-662-47666-6_10</a>'
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
    Otop. “Edit Distance for Pushdown Automata.” In <i>42nd International Colloquium</i>,
    9135:121–33. Springer Nature, 2015. <a href="https://doi.org/10.1007/978-3-662-47666-6_10">https://doi.org/10.1007/978-3-662-47666-6_10</a>.
  ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
    for pushdown automata,” in <i>42nd International Colloquium</i>, Kyoto, Japan,
    2015, vol. 9135, no. Part II, pp. 121–133.
  ista: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
    pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and
    Programming, LNCS, vol. 9135, 121–133.'
  mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” <i>42nd
    International Colloquium</i>, vol. 9135, no. Part II, Springer Nature, 2015, pp.
    121–33, doi:<a href="https://doi.org/10.1007/978-3-662-47666-6_10">10.1007/978-3-662-47666-6_10</a>.
  short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International
    Colloquium, Springer Nature, 2015, pp. 121–133.
conference:
  end_date: 2015-07-10
  location: Kyoto, Japan
  name: 'ICALP: Automata, Languages and Programming'
  start_date: 2015-07-06
date_created: 2018-12-11T11:53:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-47666-6_10
ec_funded: 1
external_id:
  arxiv:
  - '1504.08259'
intvolume: '      9135'
issue: Part II
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1504.08259
month: '07'
oa: 1
oa_version: None
page: 121 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _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
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication: 42nd International Colloquium
publication_identifier:
  isbn:
  - 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5556'
pubrep_id: '321'
quality_controlled: '1'
related_material:
  record:
  - id: '465'
    relation: later_version
    status: public
  - id: '5438'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Edit distance for pushdown automata
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1611'
abstract:
- lang: eng
  text: Biosensors for signaling molecules allow the study of physiological processes
    by bringing together the fields of protein engineering, fluorescence imaging,
    and cell biology. Construction of genetically encoded biosensors generally relies
    on the availability of a binding &quot;core&quot; that is both specific and stable,
    which can then be combined with fluorescent molecules to create a sensor. However,
    binding proteins with the desired properties are often not available in nature
    and substantial improvement to sensors can be required, particularly with regard
    to their durability. Ancestral protein reconstruction is a powerful protein-engineering
    tool able to generate highly stable and functional proteins. In this work, we
    sought to establish the utility of ancestral protein reconstruction to biosensor
    development, beginning with the construction of an l-arginine biosensor. l-arginine,
    as the immediate precursor to nitric oxide, is an important molecule in many physiological
    contexts including brain function. Using a combination of ancestral reconstruction
    and circular permutation, we constructed a Förster resonance energy transfer (FRET)
    biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity,
    with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was
    highly robust, enabling accurate l-arginine measurement at physiological temperatures.
    We established that cpFLIPR is compatible with two-photon excitation fluorescence
    microscopy and report l-arginine concentrations in brain tissue.
author:
- first_name: Jason
  full_name: Whitfield, Jason
  last_name: Whitfield
- first_name: William
  full_name: Zhang, William
  last_name: Zhang
- first_name: Michel
  full_name: Herde, Michel
  last_name: Herde
- first_name: Ben
  full_name: Clifton, Ben
  last_name: Clifton
- first_name: Johanna
  full_name: Radziejewski, Johanna
  last_name: Radziejewski
- first_name: Harald L
  full_name: Janovjak, Harald L
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Christian
  full_name: Henneberger, Christian
  last_name: Henneberger
- first_name: Colin
  full_name: Jackson, Colin
  last_name: Jackson
citation:
  ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive
    arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>.
    2015;24(9):1412-1422. doi:<a href="https://doi.org/10.1002/pro.2721">10.1002/pro.2721</a>
  apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak,
    H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor
    through ancestral protein reconstruction. <i>Protein Science</i>. Wiley. <a href="https://doi.org/10.1002/pro.2721">https://doi.org/10.1002/pro.2721</a>
  chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski,
    Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of
    a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.”
    <i>Protein Science</i>. Wiley, 2015. <a href="https://doi.org/10.1002/pro.2721">https://doi.org/10.1002/pro.2721</a>.
  ieee: J. Whitfield <i>et al.</i>, “Construction of a robust and sensitive arginine
    biosensor through ancestral protein reconstruction,” <i>Protein Science</i>, vol.
    24, no. 9. Wiley, pp. 1412–1422, 2015.
  ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger
    C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor
    through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.
  mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor
    through Ancestral Protein Reconstruction.” <i>Protein Science</i>, vol. 24, no.
    9, Wiley, 2015, pp. 1412–22, doi:<a href="https://doi.org/10.1002/pro.2721">10.1002/pro.2721</a>.
  short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak,
    C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.
date_created: 2018-12-11T11:53:01Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: HaJa
doi: 10.1002/pro.2721
external_id:
  pmid:
  - '26061224'
intvolume: '        24'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1412 - 1422
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
  grant_number: RGY0084/2012
  name: In situ real-time imaging of neurotransmitter signaling using designer optical
    sensors (HFSP Young Investigator)
publication: Protein Science
publication_status: published
publisher: Wiley
publist_id: '5555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Construction of a robust and sensitive arginine biosensor through ancestral
  protein reconstruction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '1614'
abstract:
- lang: eng
  text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively
    control the activity of large neuron populations by their wide axonal arborizations.
    It is generally assumed that the output of one PII to its target cells is strong
    and rapid. Here, we show that, unexpectedly, both strength and time course of
    PII-mediated perisomatic inhibition change with distance between synaptically
    connected partners in the rodent hippocampus. Synaptic signals become weaker due
    to lower contact numbers and decay more slowly with distance, very likely resulting
    from changes in GABAA receptor subunit composition. When distance-dependent synaptic
    inhibition is introduced to a rhythmically active neuronal network model, randomly
    driven principal cell assemblies are strongly synchronized by the PIIs, leading
    to higher precision in principal cell spike times than in a network with uniform
    synaptic inhibition. '
author:
- first_name: Michael
  full_name: Strüber, Michael
  last_name: Strüber
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: Marlene
  full_name: Bartos, Marlene
  last_name: Bartos
citation:
  ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic
    inhibition depend on distance between synaptically connected cells. <i>PNAS</i>.
    2015;112(4):1220-1225. doi:<a href="https://doi.org/10.1073/pnas.1412996112">10.1073/pnas.1412996112</a>
  apa: Strüber, M., Jonas, P. M., &#38; Bartos, M. (2015). Strength and duration of
    perisomatic GABAergic inhibition depend on distance between synaptically connected
    cells. <i>PNAS</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.1412996112">https://doi.org/10.1073/pnas.1412996112</a>
  chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration
    of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected
    Cells.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href="https://doi.org/10.1073/pnas.1412996112">https://doi.org/10.1073/pnas.1412996112</a>.
  ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic
    GABAergic inhibition depend on distance between synaptically connected cells,”
    <i>PNAS</i>, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.
  ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic
    GABAergic inhibition depend on distance between synaptically connected cells.
    PNAS. 112(4), 1220–1225.
  mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition
    Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>, vol. 112,
    no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:<a href="https://doi.org/10.1073/pnas.1412996112">10.1073/pnas.1412996112</a>.
  short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '27'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1073/pnas.1412996112
ec_funded: 1
external_id:
  pmid:
  - '25583495'
file:
- access_level: open_access
  checksum: 6703309a1f58493cf5a704211fb6ebed
  content_type: application/pdf
  creator: dernst
  date_created: 2019-01-17T07:52:40Z
  date_updated: 2020-07-14T12:45:07Z
  file_id: '5838'
  file_name: 2015_PNAS_Strueber.pdf
  file_size: 1280860
  relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: '       112'
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1220 - 1225
pmid: 1
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P24909-B24
  name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '268548'
  name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5552'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strength and duration of perisomatic GABAergic inhibition depend on distance
  between synaptically connected cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
  text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
    network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
    impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
    exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
    (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
    impairing secretion and recycling of the brassinosteroid receptor and the cellulose
    synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
    V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
    defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
    Thus, our results provide strong evidence that acidification of the TGN/EE, but
    not of the vacuole, is indispensable for functional secretion and recycling in
    plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
  full_name: Yu, Luo
  last_name: Yu
- first_name: Stefan
  full_name: Scholl, Stefan
  last_name: Scholl
- first_name: Anett
  full_name: Doering, Anett
  last_name: Doering
- first_name: Zhang
  full_name: Yi, Zhang
  last_name: Yi
- first_name: Niloufer
  full_name: Irani, Niloufer
  last_name: Irani
- first_name: Simone
  full_name: Di Rubbo, Simone
  last_name: Di Rubbo
- first_name: Lutz
  full_name: Neumetzler, Lutz
  last_name: Neumetzler
- first_name: Praveen
  full_name: Krishnamoorthy, Praveen
  last_name: Krishnamoorthy
- first_name: Isabelle
  full_name: Van Houtte, Isabelle
  last_name: Van Houtte
- first_name: Evelien
  full_name: Mylle, Evelien
  last_name: Mylle
- first_name: Volker
  full_name: Bischoff, Volker
  last_name: Bischoff
- first_name: Samantha
  full_name: Vernhettes, Samantha
  last_name: Vernhettes
- first_name: Johan
  full_name: Winne, Johan
  last_name: Winne
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: York
  full_name: Stierhof, York
  last_name: Stierhof
- first_name: Karin
  full_name: Schumacher, Karin
  last_name: Schumacher
- first_name: Staffan
  full_name: Persson, Staffan
  last_name: Persson
- first_name: Eugenia
  full_name: Russinova, Eugenia
  last_name: Russinova
citation:
  ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
    for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. 2015;1(7).
    doi:<a href="https://doi.org/10.1038/nplants.2015.94">10.1038/nplants.2015.94</a>
  apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
    E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
    in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/nplants.2015.94">https://doi.org/10.1038/nplants.2015.94</a>
  chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
    Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
    for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing
    Group, 2015. <a href="https://doi.org/10.1038/nplants.2015.94">https://doi.org/10.1038/nplants.2015.94</a>.
  ieee: L. Yu <i>et al.</i>, “V-ATPase activity in the TGN/EE is required for exocytosis
    and recycling in Arabidopsis,” <i>Nature Plants</i>, vol. 1, no. 7. Nature Publishing
    Group, 2015.
  ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
    P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
    Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
    is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
    15094.
  mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
    and Recycling in Arabidopsis.” <i>Nature Plants</i>, vol. 1, no. 7, 15094, Nature
    Publishing Group, 2015, doi:<a href="https://doi.org/10.1038/nplants.2015.94">10.1038/nplants.2015.94</a>.
  short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
    P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
    J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
    1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
  pmid:
  - '27250258'
intvolume: '         1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
  Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_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). <i>On the approximation of intrinsic volumes</i>. 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. <i>On the Approximation of Intrinsic Volumes</i>. Institute
    of Science and Technology Austria, 2015.
  short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
    and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_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). <i>The subclonal evolution of cancer</i>. 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. <i>The Subclonal Evolution of Cancer</i>. Institute of Science
    and Technology Austria, 2015.
  short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
    Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:44Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
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: '1709'
    relation: part_of_dissertation
    status: public
  - id: '2000'
    relation: part_of_dissertation
    status: public
  - id: '2247'
    relation: part_of_dissertation
    status: public
  - id: '2816'
    relation: part_of_dissertation
    status: public
  - id: '2858'
    relation: part_of_dissertation
    status: public
  - id: '3157'
    relation: part_of_dissertation
    status: public
  - id: '3260'
    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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1401'
abstract:
- lang: eng
  text: 'The human ability to recognize objects in complex scenes has driven research
    in the computer vision field over couple of decades. This thesis focuses on the
    object recognition task in images. That is, given the image, we want the computer
    system to be able to predict the class of the object that appears in the image.
    A recent successful attempt to bridge semantic understanding of the image perceived
    by humans and by computers uses attribute-based models. Attributes are semantic
    properties of the objects shared across different categories, which humans and
    computers can decide on. To explore the attribute-based models we take a statistical
    machine learning approach, and address two key learning challenges in view of
    object recognition task: learning augmented attributes as mid-level discriminative
    feature representation, and learning with attributes as privileged information.
    Our main contributions are parametric and non-parametric models and algorithms
    to solve these frameworks. In the parametric approach, we explore an autoencoder
    model combined with the large margin nearest neighbor principle for mid-level
    feature learning, and linear support vector machines for learning with privileged
    information. In the non-parametric approach, we propose a supervised Indian Buffet
    Process for automatic augmentation of semantic attributes, and explore the Gaussian
    Processes classification framework for learning with privileged information. A
    thorough experimental analysis shows the effectiveness of the proposed models
    in both parametric and non-parametric views.'
acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance
  throughout my studies and for patience in transforming me into a scientist, and
  my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice.
  \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative
  needs and was always nice and friendly to me, and the campus team for making the
  IST Austria campus my second home. \r\nI was honored to collaborate with brilliant
  researchers and to learn from their experience. Undoubtedly, I learned most of all
  from Novi Quadrianto: brainstorming our projects and getting exciting results was
  the most enjoyable part of my work – thank you! I am also grateful to David Knowles,
  Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina
  for the fantastic projects we worked on together, and to Kristen Grauman and Adriana
  Kovashka for the exceptional experience working with user studies. I would like
  to thank my colleagues at IST Austria and my office mates who shared their happy
  moods, scientific breakthroughs and thought-provoking conversations with me: Chao,
  Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina,
  Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael,
  Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games
  of table soccer we played together and the tournaments we teamed up for: we will
  definitely win next time:) A very warm hug to Asya for always being so inspiring
  and supportive to me, and for helping me to increase the proportion of female computer
  scientists in our group. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktoriia
  full_name: Sharmanska, Viktoriia
  id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
  last_name: Sharmanska
  orcid: 0000-0003-0192-9308
citation:
  ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric
    and non-parametrics views. 2015. doi:<a href="https://doi.org/10.15479/at:ista:1401">10.15479/at:ista:1401</a>'
  apa: 'Sharmanska, V. (2015). <i>Learning with attributes for object recognition:
    Parametric and non-parametrics views</i>. Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/at:ista:1401">https://doi.org/10.15479/at:ista:1401</a>'
  chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition:
    Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria,
    2015. <a href="https://doi.org/10.15479/at:ista:1401">https://doi.org/10.15479/at:ista:1401</a>.'
  ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric
    and non-parametrics views,” Institute of Science and Technology Austria, 2015.'
  ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric
    and non-parametrics views. Institute of Science and Technology Austria.'
  mla: 'Sharmanska, Viktoriia. <i>Learning with Attributes for Object Recognition:
    Parametric and Non-Parametrics Views</i>. Institute of Science and Technology
    Austria, 2015, doi:<a href="https://doi.org/10.15479/at:ista:1401">10.15479/at:ista:1401</a>.'
  short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric
    and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:11Z
day: '01'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
- _id: GradSch
doi: 10.15479/at:ista:1401
file:
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  date_updated: 2021-02-22T11:33:17Z
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has_accepted_license: '1'
language:
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main_file_link:
- url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '144'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5806'
status: public
supervisor:
- first_name: Christoph
  full_name: Lampert, Christoph
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
title: 'Learning with attributes for object recognition: Parametric and non-parametrics
  views'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
