--- _id: '5436' abstract: - lang: eng text: "Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time.\r\nIn nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-170-v2-2 apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2015. ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p. mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-170-v2-2. short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-24T00:00:00Z date_updated: 2023-02-23T12:25:21Z day: '24' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2015-170-v2-2 file: - access_level: open_access checksum: 3c402f47d3669c28d04d1af405a08e3f content_type: application/pdf creator: system date_created: 2018-12-12T11:54:19Z date_updated: 2020-07-14T12:46:54Z file_id: '5541' file_name: IST-2015-170-v2+2_report.pdf file_size: 569991 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '331' related_material: record: - id: '1656' relation: later_version status: public - id: '467' relation: later_version status: public - id: '5415' relation: earlier_version status: public status: public title: Nested weighted automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1659' abstract: - lang: eng text: 'The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata.' acknowledgement: 'A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439' article_processing_charge: No author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Boker U, Henzinger TA, Otop J. The target discounted-sum problem. In: LICS. Logic in Computer Science. IEEE; 2015:750-761. doi:10.1109/LICS.2015.74' apa: 'Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. In LICS (pp. 750–761). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.74' chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. “The Target Discounted-Sum Problem.” In LICS, 750–61. Logic in Computer Science. IEEE, 2015. https://doi.org/10.1109/LICS.2015.74. ieee: U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,” in LICS, Kyoto, Japan, 2015, pp. 750–761. ista: 'Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS. LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.' mla: Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE, 2015, pp. 750–61, doi:10.1109/LICS.2015.74. short: U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-007-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:27Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/LICS.2015.74 ec_funded: 1 file: - access_level: open_access checksum: 6abebca9c1a620e9e103a8f9222befac content_type: application/pdf creator: dernst date_created: 2020-05-15T08:53:29Z date_updated: 2020-07-14T12:45:10Z file_id: '7852' file_name: 2015_LICS_Boker.pdf file_size: 340215 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 750 - 761 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: LICS publication_identifier: eisbn: - '978-1-4799-8875-4 ' issn: - '1043-6871 ' publication_status: published publisher: IEEE publist_id: '5491' quality_controlled: '1' related_material: record: - id: '5439' relation: earlier_version status: public scopus_import: 1 series_title: Logic in Computer Science status: public title: The target discounted-sum problem type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 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 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: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:121-133. doi:10.1007/978-3-662-47666-6_10' apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. In 42nd International Colloquium (Vol. 9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium, 9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10. ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” in 42nd International Colloquium, 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.” 42nd International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp. 121–33, doi:10.1007/978-3-662-47666-6_10. 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: '5437' 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. \r\nThe 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.\r\nOur main theoretical results are as follows.\r\nFirst, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of $\\epsilon$ in time $O(n \\cdot \\log (n/\\epsilon))$ 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 $O(n \\cdot \\log (|a\\cdot b|))=O(n\\cdot\\log (n\\cdot W))$, when the output is $\\frac{a}{b}$, as compared to the previously best known algorithm with running time $O(n^2 \\cdot \\log (n\\cdot W))$. Third, for the minimum initial credit problem we show that (i)~for general graphs the problem can be solved in $O(n^2\\cdot m)$ time and the associated decision problem can be solved in $O(n\\cdot m)$ time, improving the previous known $O(n^3\\cdot m\\cdot \\log (n\\cdot W))$ and $O(n^2 \\cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs we present an algorithm that requires $O(n\\cdot \\log n)$ time, improving the previous known $O(n^4 \\cdot \\log (n \\cdot W))$ bound.\r\nWe have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: 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. IST Austria; 2015. doi:10.15479/AT:IST-2015-330-v2-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-330-v2-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-330-v2-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 27p. mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-330-v2-1. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-27T00:00:00Z date_updated: 2023-02-23T12:26:05Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-330-v2-1 file: - access_level: open_access checksum: f5917c20f84018b362d385c000a2e123 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:12Z date_updated: 2020-07-14T12:46:54Z file_id: '5473' file_name: IST-2015-330-v2+1_main.pdf file_size: 1072137 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '333' related_material: record: - id: '1607' relation: later_version status: public - id: '5430' relation: earlier_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5430' 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 mul- tiplicative factor of ∊ in time O ( n · log( n/∊ )) 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 · n | )) = O ( n · log( n · W )) , when the output is a b , as compared to the previously best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O ( n 2 · m ) time and the associated decision problem can be solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n · W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O ( n · log n ) time, improving the previous known O ( n 4 · log( n · W )) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: 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. IST Austria; 2015. doi:10.15479/AT:IST-2015-319-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-319-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-319-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 31p. mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-319-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:17Z date_published: 2015-02-10T00:00:00Z date_updated: 2023-02-23T12:26:22Z day: '10' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-319-v1-1 file: - access_level: open_access checksum: 62c6ea01e342553dcafb88a070fb1ad5 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:21Z date_updated: 2020-07-14T12:46:52Z file_id: '5482' file_name: IST-2015-319-v1+1_long.pdf file_size: 1089651 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '31' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '319' related_material: record: - id: '1607' relation: later_version status: public - id: '5437' relation: later_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5439' abstract: - lang: eng text: 'The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata. ' alternative_title: - IST Austria Technical Report author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1 apa: Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. IST Austria. https://doi.org/10.15479/AT:IST-2015-335-v1-1 chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. The Target Discounted-Sum Problem. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-335-v1-1. ieee: U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem. IST Austria, 2015. ista: Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST Austria, 20p. mla: Boker, Udi, et al. The Target Discounted-Sum Problem. IST Austria, 2015, doi:10.15479/AT:IST-2015-335-v1-1. short: U. Boker, T.A. Henzinger, J. Otop, The Target Discounted-Sum Problem, IST Austria, 2015. date_created: 2018-12-12T11:39:20Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:08:48Z day: '18' ddc: - '004' - '512' - '513' department: - _id: ToHe doi: 10.15479/AT:IST-2015-335-v1-1 file: - access_level: open_access checksum: 40405907aa012acece1bc26cf0be554d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:55Z date_updated: 2020-07-14T12:46:55Z file_id: '5517' file_name: IST-2015-335-v1+1_report.pdf file_size: 589619 relation: main_file file_date_updated: 2020-07-14T12:46:55Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '20' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '335' related_material: record: - id: '1659' relation: later_version status: public status: public title: The target discounted-sum problem type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5438' abstract: - lang: eng text: "The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1 apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1. ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance for pushdown automata. IST Austria, 2015. ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p. mla: Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1. short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015. date_created: 2018-12-12T11:39:20Z date_published: 2015-05-05T00:00:00Z date_updated: 2023-02-23T12:20:08Z day: '05' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-334-v1-1 file: - access_level: open_access checksum: 8a5f2d77560e552af87eb1982437a43b content_type: application/pdf creator: system date_created: 2018-12-12T11:53:56Z date_updated: 2020-07-14T12:46:55Z file_id: '5518' file_name: IST-2015-334-v1+1_report.pdf file_size: 422573 relation: main_file file_date_updated: 2020-07-14T12:46:55Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '15' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '334' related_material: record: - id: '1610' relation: later_version status: public - id: '465' relation: later_version status: public status: public title: Edit distance for pushdown automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5440' abstract: - lang: eng text: 'Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom for payoff in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. The fitness (or the reproductive rate) is a non-negative number, and depends on the payoff. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are as follows: First, we consider a special case of the general problem, where the residents do not reproduce. We show that the qualitative question is NP-complete, and the quantitative approximation question is #P-complete, and the hardness results hold even in the special case where the interaction and the replacement graphs coincide. Second, we show that in general both the qualitative and the quantitative approximation questions are PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds even when the fitness is always positive.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2 apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p. mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:21Z date_published: 2015-06-16T00:00:00Z date_updated: 2023-02-23T12:26:10Z day: '16' ddc: - '005' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-323-v2-2 file: - access_level: open_access checksum: 66aace7d367032af97c15e35c9be9636 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:23Z date_updated: 2020-07-14T12:46:56Z file_id: '5484' file_name: IST-2015-323-v2+2_main.pdf file_size: 466161 relation: main_file file_date_updated: 2020-07-14T12:46:56Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '18' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '338' related_material: record: - id: '5421' relation: earlier_version status: public - id: '5432' relation: earlier_version status: public status: public title: The complexity of evolutionary games on graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5432' abstract: - lang: eng text: "Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction. \r\nThe vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).\r\n(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.\r\n" alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p. mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:18Z date_published: 2015-02-19T00:00:00Z date_updated: 2023-02-23T12:26:33Z day: '19' ddc: - '005' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-323-v1-1 file: - access_level: open_access checksum: 546c1b291d545e7b24aaaf4199dac671 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:57Z date_updated: 2020-07-14T12:46:53Z file_id: '5519' file_name: IST-2015-323-v1+1_main.pdf file_size: 576347 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '323' related_material: record: - id: '5421' relation: earlier_version status: public - id: '5440' relation: later_version status: public status: public title: The complexity of evolutionary games on graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5444' abstract: - lang: eng text: A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal. alternative_title: - IST Austria Technical Report author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Alvin full_name: Makohon-Moore, Alvin last_name: Makohon-Moore - first_name: Jeffrey full_name: Gerold, Jeffrey last_name: Gerold - first_name: Ivana full_name: Bozic, Ivana last_name: Bozic - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christine full_name: Iacobuzio-Donahue, Christine last_name: Iacobuzio-Donahue - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1 apa: Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers. IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1 chicago: Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1. ieee: J. Reiter et al., Reconstructing robust phylogenies of metastatic cancers. IST Austria, 2015. ista: Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p. mla: Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1. short: J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015. date_created: 2018-12-12T11:39:22Z date_published: 2015-12-30T00:00:00Z date_updated: 2020-07-14T23:05:07Z day: '30' ddc: - '000' - '576' department: - _id: KrCh doi: 10.15479/AT:IST-2015-399-v1-1 file: - access_level: open_access checksum: c47d33bdda06181753c0af36f16e7b5d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:24Z date_updated: 2020-07-14T12:46:58Z file_id: '5485' file_name: IST-2015-399-v1+1_treeomics.pdf file_size: 3533200 relation: main_file file_date_updated: 2020-07-14T12:46:58Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '25' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '399' status: public title: Reconstructing robust phylogenies of metastatic cancers type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5443' abstract: - lang: eng text: POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIME-complete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Jessica full_name: Davies, Jessica id: 378E0060-F248-11E8-B48F-1D18A9856A87 last_name: Davies citation: ama: Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1 apa: Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1 chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1. ieee: K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria, 2015. ista: Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs, IST Austria, 23p. mla: Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1. short: K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015. date_created: 2018-12-12T11:39:22Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-02-21T16:24:05Z day: '06' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-325-v2-1 file: - access_level: open_access checksum: f0fa31ad8161ed655137e94012123ef9 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:05Z date_updated: 2020-07-14T12:46:57Z file_id: '5466' file_name: IST-2015-325-v2+1_main.pdf file_size: 412379 relation: main_file file_date_updated: 2020-07-14T12:46:57Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '23' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '362' related_material: record: - id: '1166' relation: later_version status: public status: public title: A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5804' abstract: - lang: eng text: We present here the first integer-based algorithm for constructing a well-defined lattice sphere specified by integer radius and integer center. The algorithm evolves from a unique correspondence between the lattice points comprising the sphere and the distribution of sum of three square numbers in integer intervals. We characterize these intervals to derive a useful set of recurrences, which, in turn, aids in efficient computation. Each point of the lattice sphere is determined by resorting to only a few primitive operations in the integer domain. The symmetry of its quadraginta octants provides an added advantage by confining the computation to its prima quadraginta octant. Detailed theoretical analysis and experimental results have been furnished to demonstrate its simplicity and elegance. author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72. doi:10.1016/j.tcs.2015.11.018 apa: Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018 chicago: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018. ieee: R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere through primitive integer operations,” Theoretical Computer Science, vol. 624, no. 4. Elsevier, pp. 56–72, 2015. ista: Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 624(4), 56–72. mla: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science, vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018. short: R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72. date_created: 2019-01-08T20:44:06Z date_published: 2015-04-18T00:00:00Z date_updated: 2021-01-12T08:03:36Z day: '18' doi: 10.1016/j.tcs.2015.11.018 extern: '1' intvolume: ' 624' issue: '4' language: - iso: eng month: '04' oa_version: None page: 56-72 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: From prima quadraginta octant to lattice sphere through primitive integer operations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 624 year: '2015' ... --- _id: '5807' author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: Biswas R, Bhowmick P. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163. doi:10.1016/j.tcs.2015.09.003 apa: Biswas, R., & Bhowmick, P. (2015). On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003 chicago: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003. ieee: R. Biswas and P. Bhowmick, “On different topological classes of spherical geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605, no. 11. Elsevier, pp. 146–163, 2015. ista: Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163. mla: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605, no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003. short: R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163. date_created: 2019-01-08T20:44:52Z date_published: 2015-11-09T00:00:00Z date_updated: 2021-01-12T08:03:37Z day: '09' doi: 10.1016/j.tcs.2015.09.003 extern: '1' intvolume: ' 605' issue: '11' language: - iso: eng month: '11' oa_version: None page: 146-163 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: On different topological classes of spherical geodesic paths and circles inZ3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 605 year: '2015' ... --- _id: '5808' author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797. doi:10.1007/s00371-015-1101-3 apa: Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-015-1101-3 chicago: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3. ieee: R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015. ista: Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 787–797. mla: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer, vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3. short: R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797. date_created: 2019-01-08T20:45:05Z date_published: 2015-05-08T00:00:00Z date_updated: 2021-01-12T08:03:37Z day: '08' doi: 10.1007/s00371-015-1101-3 extern: '1' intvolume: ' 31' issue: 6-8 language: - iso: eng month: '05' oa_version: None page: 787-797 publication: The Visual Computer publication_identifier: issn: - 0178-2789 - 1432-2315 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Layer the sphere type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '594' abstract: - lang: eng text: Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter. article_processing_charge: No author: - first_name: Sarah full_name: Sainsbury, Sarah last_name: Sainsbury - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143. doi:10.1038/nrm3952 apa: Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3952 chicago: Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3952. ieee: S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology, vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015. ista: Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143. mla: Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3, Nature Publishing Group, 2015, pp. 129–43, doi:10.1038/nrm3952. short: S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology 16 (2015) 129–143. date_created: 2018-12-11T11:47:23Z date_published: 2015-03-26T00:00:00Z date_updated: 2021-01-12T08:05:16Z day: '26' doi: 10.1038/nrm3952 extern: '1' intvolume: ' 16' issue: '3' language: - iso: eng month: '03' oa_version: None page: 129 - 143 publication: Nature Reviews Molecular Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '7206' status: public title: Structural basis of transcription initiation by RNA polymerase II type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2015' ... --- _id: '1511' abstract: - lang: eng text: 'The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel''s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.' acknowledgement: "The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948)." alternative_title: - LIPIcs author: - first_name: Xavier full_name: Goaoc, Xavier last_name: Goaoc - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:10.4230/LIPIcs.SOCG.2015.476' apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.476' chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.476.' ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.' ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.' mla: 'Goaoc, Xavier, et al. On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:10.4230/LIPIcs.SOCG.2015.476.' short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490. conference: end_date: 2015-06-25 location: Eindhoven, Netherlands name: 'SoCG: Symposium on Computational Geometry' start_date: 2015-06-22 date_created: 2018-12-11T11:52:27Z date_published: 2015-06-11T00:00:00Z date_updated: 2023-02-23T12:38:00Z day: '11' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SOCG.2015.476 ec_funded: 1 file: - access_level: open_access checksum: 0945811875351796324189312ca29e9e content_type: application/pdf creator: system date_created: 2018-12-12T10:11:18Z date_updated: 2020-07-14T12:44:59Z file_id: '4871' file_name: IST-2016-502-v1+1_42.pdf file_size: 636735 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 476 - 490 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5666' pubrep_id: '502' quality_controlled: '1' related_material: record: - id: '610' relation: later_version status: public scopus_import: 1 status: public title: 'On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '34 ' year: '2015' ... --- _id: '6118' abstract: - lang: eng text: 'Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry.' author: - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534. doi:10.1073/pnas.1423808112 apa: Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1423808112 chicago: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112. ieee: L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” Proceedings of the National Academy of Sciences, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015. ista: Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534. mla: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112. short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534. date_created: 2019-03-19T14:15:50Z date_published: 2015-07-07T00:00:00Z date_updated: 2021-01-12T08:06:12Z day: '07' ddc: - '570' doi: 10.1073/pnas.1423808112 extern: '1' external_id: pmid: - '26100886' file: - access_level: open_access checksum: 3d2da5af8d72467e382a565abc2e003d content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:21:07Z date_updated: 2020-07-14T12:47:20Z file_id: '6119' file_name: 2015_PNAS_Fenk.pdf file_size: 2822681 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 112' issue: '27' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: E3525-E3534 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '6120' abstract: - lang: eng text: Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed. article_number: e04241 author: - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: Zoltan full_name: Soltesz, Zoltan last_name: Soltesz - first_name: Geoffrey M full_name: Nelson, Geoffrey M last_name: Nelson - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Fausto full_name: Arellano-Carbajal, Fausto last_name: Arellano-Carbajal - first_name: Emmanuel full_name: Levy, Emmanuel last_name: Levy - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241 apa: Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy, E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241 chicago: Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/elife.04241. ieee: P. Laurent et al., “Decoding a neural circuit controlling global animal state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015. ista: Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. 2015. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 4, e04241. mla: Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications, 2015, doi:10.7554/elife.04241. short: P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy, M. de Bono, ELife 4 (2015). date_created: 2019-03-19T14:23:51Z date_published: 2015-03-11T00:00:00Z date_updated: 2021-01-12T08:06:13Z day: '11' ddc: - '570' doi: 10.7554/elife.04241 extern: '1' external_id: pmid: - '25760081' file: - access_level: open_access checksum: cf641b7a363aecd0a101755d23dee7e0 content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:29:43Z date_updated: 2020-07-14T12:47:20Z file_id: '6121' file_name: 2015_elife_Laurent.pdf file_size: 6723528 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' status: public title: Decoding a neural circuit controlling global animal state in C. elegans 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '1637' abstract: - lang: eng text: An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs. alternative_title: - 56th Annual Symposium on Foundations of Computer Science author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Andrei full_name: Krokhin, Andrei last_name: Krokhin - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: 'Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80' apa: 'Kolmogorov, V., Krokhin, A., & Rolinek, M. (2015). The complexity of general-valued CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States: IEEE. https://doi.org/10.1109/FOCS.2015.80' chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs,” 1246–58. IEEE, 2015. https://doi.org/10.1109/FOCS.2015.80. ieee: 'V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States, 2015, pp. 1246–1258.' ista: 'Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations of Computer Science, , 1246–1258.' mla: Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs. IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80. short: V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258. conference: end_date: 2015-10-20 location: Berkeley, CA, United States name: 'FOCS: Foundations of Computer Science' start_date: 2015-10-18 date_created: 2018-12-11T11:53:10Z date_published: 2015-12-01T00:00:00Z date_updated: 2023-02-23T12:44:26Z day: '01' department: - _id: VlKo doi: 10.1109/FOCS.2015.80 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07327 month: '12' oa: 1 oa_version: Preprint page: 1246 - 1258 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_status: published publisher: IEEE publist_id: '5518' quality_controlled: '1' related_material: record: - id: '644' relation: other status: public scopus_import: 1 status: public title: The complexity of general-valued CSPs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '6507' abstract: - lang: eng text: The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor with important roles in dendritic cell maturation and activation of inflammatory monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR ectodomain is presented, both free and in complex with a consensus triple-helical peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like domain (D1 and D2). The THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 is facilitated by the unusually wide D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due to an avidity effect. These data suggest a 2-stage model for the interaction of OSCAR with a collagen fibril, with transient, low-affinity interactions initiated by the membrane-distal D1, followed by firm adhesion to the primary binding site in D2. author: - first_name: Long full_name: Zhou, Long id: 3E751364-F248-11E8-B48F-1D18A9856A87 last_name: Zhou orcid: 0000-0002-1864-8951 - first_name: J. M. full_name: Hinerman, J. M. last_name: Hinerman - first_name: M. full_name: Blaszczyk, M. last_name: Blaszczyk - first_name: J. L. C. full_name: Miller, J. L. C. last_name: Miller - first_name: D. G. full_name: Conrady, D. G. last_name: Conrady - first_name: A. D. full_name: Barrow, A. D. last_name: Barrow - first_name: D. Y. full_name: Chirgadze, D. Y. last_name: Chirgadze - first_name: D. full_name: Bihan, D. last_name: Bihan - first_name: R. W. full_name: Farndale, R. W. last_name: Farndale - first_name: A. B. full_name: Herr, A. B. last_name: Herr citation: ama: Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 2015;127(5):529-537. doi:10.1182/blood-2015-08-667055 apa: Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G., Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition by the immune receptor OSCAR. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-08-667055 chicago: Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady, A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood. American Society of Hematology, 2015. https://doi.org/10.1182/blood-2015-08-667055. ieee: L. Zhou et al., “Structural basis for collagen recognition by the immune receptor OSCAR,” Blood, vol. 127, no. 5. American Society of Hematology, pp. 529–537, 2015. ista: Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 127(5), 529–537. mla: Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood, vol. 127, no. 5, American Society of Hematology, 2015, pp. 529–37, doi:10.1182/blood-2015-08-667055. short: L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow, D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537. date_created: 2019-05-31T09:38:50Z date_published: 2015-11-02T00:00:00Z date_updated: 2021-01-12T08:07:47Z day: '02' doi: 10.1182/blood-2015-08-667055 extern: '1' external_id: pmid: - '26552697' intvolume: ' 127' issue: '5' language: - iso: eng month: '11' oa_version: None page: 529-537 pmid: 1 publication: Blood publication_identifier: issn: - 0006-4971 - 1528-0020 publication_status: published publisher: American Society of Hematology quality_controlled: '1' status: public title: Structural basis for collagen recognition by the immune receptor OSCAR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2015' ...