[{"date_published":"2011-04-10T00:00:00Z","scopus_import":"1","title":"Scheduling large jobs by abstraction refinement","_id":"3358","corr_author":"1","oa":1,"department":[{"_id":"ToHe"}],"page":"329 - 342","publisher":"ACM","main_file_link":[{"open_access":"1","url":"http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf"}],"abstract":[{"text":"The static scheduling problem often arises as a fundamental problem in real-time systems and grid computing. We consider the problem of statically scheduling a large job expressed as a task graph on a large number of computing nodes, such as a data center. This paper solves the large-scale static scheduling problem using abstraction refinement, a technique commonly used in formal verification to efficiently solve computationally hard problems. A scheduler based on abstraction refinement first attempts to solve the scheduling problem with abstract representations of the job and the computing resources. As abstract representations are generally small, the scheduling can be done reasonably fast. If the obtained schedule does not meet specified quality conditions (like data center utilization or schedule makespan) then the scheduler refines the job and data center abstractions and, again solves the scheduling problem. We develop different schedulers based on abstraction refinement. We implemented these schedulers and used them to schedule task graphs from various computing domains on simulated data centers with realistic topologies. We compared the speed of scheduling and the quality of the produced schedules with our abstraction refinement schedulers against a baseline scheduler that does not use any abstraction. We conclude that abstraction refinement techniques give a significant speed-up compared to traditional static scheduling heuristics, at a reasonable cost in the quality of the produced schedules. We further used our static schedulers in an actual system that we deployed on Amazon EC2 and compared it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments indicate that there is great potential for static scheduling techniques.","lang":"eng"}],"fulldoi":"https://doi.org/10.1145/1966445.1966476","day":"10","year":"2011","doi":"10.1145/1966445.1966476","quality_controlled":"1","publication_status":"published","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Singh, Vasu","first_name":"Vasu","last_name":"Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wies, Thomas","first_name":"Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736"}],"type":"conference","citation":{"chicago":"Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. <a href=\"https://doi.org/10.1145/1966445.1966476\">https://doi.org/10.1145/1966445.1966476</a>.","ieee":"T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011, pp. 329–342.","apa":"Henzinger, T. A., Singh, V., Wies, T., &#38; Zufferey, D. (2011). Scheduling large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys, Salzburg, Austria: ACM. <a href=\"https://doi.org/10.1145/1966445.1966476\">https://doi.org/10.1145/1966445.1966476</a>","ama":"Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction refinement. In: ACM; 2011:329-342. doi:<a href=\"https://doi.org/10.1145/1966445.1966476\">10.1145/1966445.1966476</a>","short":"T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.","ista":"Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by abstraction refinement. EuroSys, 329–342.","mla":"Henzinger, Thomas A., et al. <i>Scheduling Large Jobs by Abstraction Refinement</i>. ACM, 2011, pp. 329–42, doi:<a href=\"https://doi.org/10.1145/1966445.1966476\">10.1145/1966445.1966476</a>."},"oa_version":"Published Version","month":"04","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2011-04-13","start_date":"2011-04-10","name":"EuroSys","location":"Salzburg, Austria"},"date_updated":"2026-06-18T18:44:21Z","date_created":"2018-12-11T12:02:53Z","language":[{"iso":"eng"}],"ddc":["000"],"status":"public","publist_id":"3257"},{"quality_controlled":"1","date_published":"2011-10-09T00:00:00Z","type":"conference","scopus_import":"1","author":[{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"title":"From boolean to quantitative synthesis","publication_status":"published","_id":"3359","month":"10","citation":{"ista":"Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT: Embedded Software , 149–154.","short":"P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.","mla":"Cerny, Pavol, and Thomas A. Henzinger. <i>From Boolean to Quantitative Synthesis</i>. ACM, 2011, pp. 149–54, doi:<a href=\"https://doi.org/10.1145/2038642.2038666\">10.1145/2038642.2038666</a>.","chicago":"Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,” 149–54. ACM, 2011. <a href=\"https://doi.org/10.1145/2038642.2038666\">https://doi.org/10.1145/2038642.2038666</a>.","ama":"Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154. doi:<a href=\"https://doi.org/10.1145/2038642.2038666\">10.1145/2038642.2038666</a>","ieee":"P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.","apa":"Cerny, P., &#38; Henzinger, T. A. (2011). From boolean to quantitative synthesis (pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM. <a href=\"https://doi.org/10.1145/2038642.2038666\">https://doi.org/10.1145/2038642.2038666</a>"},"oa_version":"None","department":[{"_id":"ToHe"}],"conference":{"location":"Taipei; Taiwan","end_date":"2011-10-14","start_date":"2011-10-09","name":"EMSOFT: Embedded Software "},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","corr_author":"1","publisher":"ACM","date_updated":"2024-10-21T06:03:04Z","date_created":"2018-12-11T12:02:53Z","page":"149 - 154","ec_funded":1,"abstract":[{"text":"Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification.\r\n\r\nIn this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow.","lang":"eng"}],"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publist_id":"3256","status":"public","doi":"10.1145/2038642.2038666","year":"2011","day":"09","acknowledgement":"This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign.","fulldoi":"https://doi.org/10.1145/2038642.2038666"},{"type":"journal_article","author":[{"first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"first_name":"Pablo","full_name":"Guardia, Pablo","last_name":"Guardia"},{"last_name":"Shavel","full_name":"Shavel, Alexey","first_name":"Alexey"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Joan","full_name":"Morante, Joan","last_name":"Morante"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"publication_status":"published","quality_controlled":"1","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"04","citation":{"short":"M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot, Journal of Physical Chemistry C 115 (2011) 7947–7955.","ista":"Ibáñez M, Guardia P, Shavel A, Cadavid D, Arbiol J, Morante J, Cabot A. 2011. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. 115(16), 7947–7955.","mla":"Ibáñez, Maria, et al. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” <i>Journal of Physical Chemistry C</i>, vol. 115, no. 16, American Chemical Society, 2011, pp. 7947–55, doi:<a href=\"https://doi.org/10.1021/jp2002904\">10.1021/jp2002904</a>.","chicago":"Ibáñez, Maria, Pablo Guardia, Alexey Shavel, Doris Cadavid, Jordi Arbiol, Joan Morante, and Andreu Cabot. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” <i>Journal of Physical Chemistry C</i>. American Chemical Society, 2011. <a href=\"https://doi.org/10.1021/jp2002904\">https://doi.org/10.1021/jp2002904</a>.","ama":"Ibáñez M, Guardia P, Shavel A, et al. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. <i>Journal of Physical Chemistry C</i>. 2011;115(16):7947-7955. doi:<a href=\"https://doi.org/10.1021/jp2002904\">10.1021/jp2002904</a>","ieee":"M. Ibáñez <i>et al.</i>, “Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods,” <i>Journal of Physical Chemistry C</i>, vol. 115, no. 16. American Chemical Society, pp. 7947–7955, 2011.","apa":"Ibáñez, M., Guardia, P., Shavel, A., Cadavid, D., Arbiol, J., Morante, J., &#38; Cabot, A. (2011). Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. <i>Journal of Physical Chemistry C</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp2002904\">https://doi.org/10.1021/jp2002904</a>"},"oa_version":"None","date_created":"2018-12-11T11:45:53Z","date_updated":"2021-01-12T07:42:56Z","status":"public","publist_id":"7493","issue":"16","language":[{"iso":"eng"}],"intvolume":"       115","title":"Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods","article_type":"original","date_published":"2011-04-28T00:00:00Z","_id":"336","publisher":"American Chemical Society","publication":"Journal of Physical Chemistry C","page":"7947 - 7955","year":"2011","doi":"10.1021/jp2002904","acknowledgement":"This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, and ENE2008-03277-E/CON. Maria Ibáñez thanks the Ph.D. grant from the Spanish MICINN.","day":"28","fulldoi":"https://doi.org/10.1021/jp2002904","abstract":[{"text":"The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation, the length distribution of the growing Bi 2S3 nanorods narrows with the reaction time until a bimodal length distribution appears. From this critical reaction time on, the smallest nanorods of the ensemble dissolve, feeding with monomer the growth of the largest ones. A comprehensive characterization of the size-distribution evolution of Bi2S3 nanorods is used here to illustrate the dependences of the anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions and the monomer concentration in solution. With this goal in mind, a diffusion-reaction model is presented to explain the origin of the experimentally obtained length distribution focusing mechanism. The model is able to reproduce the decrease of the growth rate in the nanorod axial direction with both its thickness and length. On the other hand, low lateral reaction rates prevent the nanorod thickness distribution to be focused. In both crystallographic growth directions, a concentration-dependent critical thickness exists, which discriminates between nanorods with positive growth rates and those dissolving in the reaction solution. ","lang":"eng"}],"volume":115},{"ddc":["004"],"language":[{"iso":"eng"}],"status":"public","publist_id":"3255","has_accepted_license":"1","date_updated":"2021-01-12T07:42:56Z","pubrep_id":"82","date_created":"2018-12-11T12:02:53Z","file":[{"file_id":"4803","file_size":504270,"access_level":"open_access","file_name":"IST-2012-82-v1+1_Determinizing_discounted-sum_automata.pdf","creator":"system","date_updated":"2020-07-14T12:46:10Z","relation":"main_file","date_created":"2018-12-12T10:10:17Z","content_type":"application/pdf","checksum":"250603c6be8ccad4fbd4d7b24221f0ee"}],"month":"08","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"chicago":"Boker, Udi, and Thomas A Henzinger. “Determinizing Discounted-Sum Automata,” 12:82–96. Springer, 2011. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">https://doi.org/10.4230/LIPIcs.CSL.2011.82</a>.","apa":"Boker, U., &#38; Henzinger, T. A. (2011). Determinizing discounted-sum automata (Vol. 12, pp. 82–96). Presented at the CSL: Computer Science Logic, Bergen, Norway: Springer. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">https://doi.org/10.4230/LIPIcs.CSL.2011.82</a>","ieee":"U. Boker and T. A. Henzinger, “Determinizing discounted-sum automata,” presented at the CSL: Computer Science Logic, Bergen, Norway, 2011, vol. 12, pp. 82–96.","ama":"Boker U, Henzinger TA. Determinizing discounted-sum automata. In: Vol 12. Springer; 2011:82-96. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">10.4230/LIPIcs.CSL.2011.82</a>","ista":"Boker U, Henzinger TA. 2011. Determinizing discounted-sum automata. CSL: Computer Science Logic, LIPIcs, vol. 12, 82–96.","short":"U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.","mla":"Boker, Udi, and Thomas A. Henzinger. <i>Determinizing Discounted-Sum Automata</i>. Vol. 12, Springer, 2011, pp. 82–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">10.4230/LIPIcs.CSL.2011.82</a>."},"oa_version":"Published Version","conference":{"location":"Bergen, Norway","end_date":"2011-09-15","start_date":"2011-09-12","name":"CSL: Computer Science Logic"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","type":"conference","author":[{"full_name":"Boker, Udi","first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"publication_status":"published","alternative_title":["LIPIcs"],"ec_funded":1,"abstract":[{"lang":"eng","text":"A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, which values a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by lambda^i, where the discount factor lambda is a fixed rational number greater than 1. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, which reflects the assumption that earlier weights are more important than later weights. Determinizing automata is often essential, for example, in formal verification, where there are polynomial algorithms for comparing two deterministic NDAs, while the equivalence problem for NDAs is not known to be decidable. Unfortunately, however, discounted-sum automata are, in general, not determinizable: it is currently known that for every rational discount factor 1 &lt; lambda &lt; 2, there is an NDA with lambda (denoted lambda-NDA) that cannot be determinized. We provide positive news, showing that every NDA with an integral factor is determinizable. We also complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: we show that for every non-integral rational factor lambda, there is a nondeterminizable lambda-NDA. Finally, we prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. This shows that for integral discount factors, the class of NDAs forms an attractive specification formalism in quantitative formal verification. All our results hold equally for automata over finite words and for automata over infinite words. "}],"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"grant_number":"214373","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"volume":12,"doi":"10.4230/LIPIcs.CSL.2011.82","year":"2011","day":"31","fulldoi":"https://doi.org/10.4230/LIPIcs.CSL.2011.82","publisher":"Springer","page":"82 - 96","_id":"3360","oa":1,"department":[{"_id":"ToHe"}],"date_published":"2011-08-31T00:00:00Z","intvolume":"        12","scopus_import":1,"title":"Determinizing discounted-sum automata","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"date_created":"2018-12-11T12:02:54Z","date_updated":"2025-09-30T09:04:15Z","pubrep_id":"81","file":[{"file_id":"4792","access_level":"open_access","file_size":299069,"creator":"system","file_name":"IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf","date_created":"2018-12-12T10:10:07Z","date_updated":"2020-07-14T12:46:10Z","relation":"main_file","content_type":"application/pdf","checksum":"1a25be0c62459fc7640db88af08ff63a"}],"isi":1,"ddc":["000","005"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publist_id":"3254","status":"public","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"type":"conference","publication_status":"published","month":"06","citation":{"ista":"Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative information flow problems. CSF: Computer Security Foundations, 205–217.","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.","mla":"Cerny, Pavol, et al. <i>The Complexity of Quantitative Information Flow Problems</i>. IEEE, 2011, pp. 205–17, doi:<a href=\"https://doi.org/10.1109/CSF.2011.21\">10.1109/CSF.2011.21</a>.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. <a href=\"https://doi.org/10.1109/CSF.2011.21\">https://doi.org/10.1109/CSF.2011.21</a>.","ama":"Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information flow problems. In: IEEE; 2011:205-217. doi:<a href=\"https://doi.org/10.1109/CSF.2011.21\">10.1109/CSF.2011.21</a>","ieee":"P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative information flow problems,” presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France, 2011, pp. 205–217.","apa":"Cerny, P., Chatterjee, K., &#38; Henzinger, T. A. (2011). The complexity of quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France: IEEE. <a href=\"https://doi.org/10.1109/CSF.2011.21\">https://doi.org/10.1109/CSF.2011.21</a>"},"oa_version":"Submitted Version","conference":{"end_date":"2011-06-29","start_date":"2011-06-27","name":"CSF: Computer Security Foundations","location":"Cernay-la-Ville, France"},"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000300766400014"]},"page":"205 - 217","publisher":"IEEE","ec_funded":1,"abstract":[{"text":"In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard.","lang":"eng"}],"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1109/CSF.2011.21","year":"2011","fulldoi":"https://doi.org/10.1109/CSF.2011.21","day":"27","date_published":"2011-06-27T00:00:00Z","title":"The complexity of quantitative information flow problems","scopus_import":"1","_id":"3361","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa":1,"corr_author":"1"},{"year":"2011","doi":"10.1007/978-3-642-23217-6_27","fulldoi":"https://doi.org/10.1007/978-3-642-23217-6_27","day":"01","ec_funded":1,"abstract":[{"text":"State-transition systems communicating by shared variables have been the underlying model of choice for applications of model checking. Such formalisms, however, have difficulty with modeling process creation or death and communication reconfigurability. Here, we introduce “dynamic reactive modules” (DRM), a state-transition modeling formalism that supports dynamic reconfiguration and creation/death of processes. The resulting formalism supports two types of variables, data variables and reference variables. Reference variables enable changing the connectivity between processes and referring to instances of processes. We show how this new formalism supports parallel composition and refinement through trace containment. DRM provide a natural language for modeling (and ultimately reasoning about) biological systems and multiple threads communicating through shared variables.","lang":"eng"}],"volume":6901,"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"}],"page":"404 - 418","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"department":[{"_id":"ToHe"}],"_id":"3362","scopus_import":1,"title":"Dynamic reactive modules","intvolume":"      6901","date_published":"2011-01-01T00:00:00Z","has_accepted_license":"1","publist_id":"3253","status":"public","ddc":["000"],"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:10Z","date_created":"2020-05-19T16:17:48Z","relation":"main_file","file_name":"2011_CONCUR_Fisher.pdf","creator":"dernst","checksum":"6bf2453d8e52e979ddb58d17325bad26","content_type":"application/pdf","file_id":"7870","access_level":"open_access","file_size":337125}],"date_updated":"2021-01-12T07:42:57Z","date_created":"2018-12-11T12:02:54Z","conference":{"location":"Aachen, Germany","start_date":"2011-09-06","name":"CONCUR: Concurrency Theory","end_date":"2011-09-09"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Submitted Version","citation":{"ista":"Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. 2011. Dynamic reactive modules. CONCUR: Concurrency Theory, LNCS, vol. 6901, 404–418.","short":"J. Fisher, T.A. Henzinger, D. Nickovic, N. Piterman, A. Singh, M. Vardi, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–418.","mla":"Fisher, Jasmin, et al. <i>Dynamic Reactive Modules</i>. Vol. 6901, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">10.1007/978-3-642-23217-6_27</a>.","chicago":"Fisher, Jasmin, Thomas A Henzinger, Dejan Nickovic, Nir Piterman, Anmol Singh, and Moshe Vardi. “Dynamic Reactive Modules,” 6901:404–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">https://doi.org/10.1007/978-3-642-23217-6_27</a>.","ama":"Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. Dynamic reactive modules. In: Vol 6901. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2011:404-418. doi:<a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">10.1007/978-3-642-23217-6_27</a>","apa":"Fisher, J., Henzinger, T. A., Nickovic, D., Piterman, N., Singh, A., &#38; Vardi, M. (2011). Dynamic reactive modules (Vol. 6901, pp. 404–418). Presented at the CONCUR: Concurrency Theory, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">https://doi.org/10.1007/978-3-642-23217-6_27</a>","ieee":"J. Fisher, T. A. Henzinger, D. Nickovic, N. Piterman, A. Singh, and M. Vardi, “Dynamic reactive modules,” presented at the CONCUR: Concurrency Theory, Aachen, Germany, 2011, vol. 6901, pp. 404–418."},"author":[{"full_name":"Fisher, Jasmin","first_name":"Jasmin","last_name":"Fisher"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic"},{"full_name":"Piterman, Nir","first_name":"Nir","last_name":"Piterman"},{"full_name":"Singh, Anmol","first_name":"Anmol","last_name":"Singh"},{"last_name":"Vardi","full_name":"Vardi, Moshe","first_name":"Moshe"}],"type":"conference","alternative_title":["LNCS"],"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z"},{"date_created":"2018-12-11T12:02:54Z","date_updated":"2025-06-26T09:19:59Z","language":[{"iso":"eng"}],"publist_id":"3251","status":"public","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol","first_name":"Mathieu","full_name":"Tracol, Mathieu"}],"type":"preprint","publication_status":"submitted","month":"04","oa_version":"Preprint","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>The Decidability Frontier for Probabilistic Automata on Infinite Words</i>. 1104.0127, ArXiv, doi:<a href=\"https://doi.org/10.48550/arXiv.1104.0127\">10.48550/arXiv.1104.0127</a>.","ista":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. 1104.0127.","short":"K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.).","ama":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. doi:<a href=\"https://doi.org/10.48550/arXiv.1104.0127\">10.48550/arXiv.1104.0127</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Tracol, M. (n.d.). The decidability frontier for probabilistic automata on infinite words. ArXiv. <a href=\"https://doi.org/10.48550/arXiv.1104.0127\">https://doi.org/10.48550/arXiv.1104.0127</a>","ieee":"K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier for probabilistic automata on infinite words.” ArXiv.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d. <a href=\"https://doi.org/10.48550/arXiv.1104.0127\">https://doi.org/10.48550/arXiv.1104.0127</a>."},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"19","external_id":{"arxiv":["1104.0127"]},"publisher":"ArXiv","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1104.0127"}],"ec_funded":1,"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present a complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words.","lang":"eng"}],"project":[{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"214373"}],"doi":"10.48550/arXiv.1104.0127","year":"2011","fulldoi":"https://doi.org/10.48550/arXiv.1104.0127","day":"01","date_published":"2011-04-01T00:00:00Z","title":"The decidability frontier for probabilistic automata on infinite words","article_number":"1104.0127","_id":"3363","oa":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"corr_author":"1"},{"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"05","citation":{"mla":"Didier, Frédéric, et al. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>, vol. 412, no. 21, Elsevier, 2011, pp. 2128–41, doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2011. Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. 412(21), 2128–2141.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. 2011;412(21):2128-2141. doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Approximation of event probabilities in noisy cellular processes,” <i>Theoretical Computer Science</i>, vol. 412, no. 21. Elsevier, pp. 2128–2141, 2011.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2011). Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>."},"oa_version":"Submitted Version","author":[{"last_name":"Didier","full_name":"Didier, Frédéric","first_name":"Frédéric"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"},{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","has_accepted_license":"1","publist_id":"3249","status":"public","issue":"21","isi":1,"language":[{"iso":"eng"}],"ddc":["000","004"],"related_material":{"record":[{"id":"4535","relation":"earlier_version","status":"public"}]},"file":[{"file_id":"4862","access_level":"open_access","file_size":230503,"file_name":"IST-2012-79-v1+1_Approximation_of_event_probabilities_in_noisy_cellular_processes.pdf","creator":"system","date_updated":"2020-07-14T12:46:10Z","relation":"main_file","date_created":"2018-12-12T10:11:09Z","content_type":"application/pdf","checksum":"e5503e25ce020d753e06b3431e16841e"}],"pubrep_id":"79","date_created":"2018-12-11T12:02:55Z","date_updated":"2025-09-30T09:03:30Z","department":[{"_id":"ToHe"}],"oa":1,"_id":"3364","title":"Approximation of event probabilities in noisy cellular processes","scopus_import":"1","intvolume":"       412","date_published":"2011-05-06T00:00:00Z","year":"2011","doi":"10.1016/j.tcs.2010.10.022","fulldoi":"https://doi.org/10.1016/j.tcs.2010.10.022","day":"06","abstract":[{"lang":"eng","text":"Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required."}],"volume":412,"page":"2128 - 2141","publication":"Theoretical Computer Science","external_id":{"isi":["000290078000005"]},"publisher":"Elsevier"},{"page":"267 - 271","publisher":"Springer","abstract":[{"text":"We present the tool Quasy, a quantitative synthesis tool. Quasy takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. The user can choose between a system that satisfies and optimizes the specifications (a) under all possible environment behaviors or (b) under the most-likely environment behaviors given as a probability distribution on the possible input sequences. Quasy solves these two quantitative synthesis problems by reduction to instances of 2-player games and Markov Decision Processes (MDPs) with quantitative winning objectives. Quasy can also be seen as a game solver for quantitative games. Most notable, it can solve lexicographic mean-payoff games with 2 players, MDPs with mean-payoff objectives, and ergodic MDPs with mean-payoff parity objectives.","lang":"eng"}],"volume":6605,"year":"2011","doi":"10.1007/978-3-642-19835-9_24","fulldoi":"https://doi.org/10.1007/978-3-642-19835-9_24","day":"29","date_published":"2011-09-29T00:00:00Z","title":"QUASY: quantitative synthesis tool","scopus_import":1,"intvolume":"      6605","_id":"3365","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"oa":1,"date_updated":"2021-01-12T07:42:58Z","date_created":"2018-12-11T12:02:55Z","pubrep_id":"77","file":[{"date_updated":"2020-07-14T12:46:10Z","relation":"main_file","date_created":"2018-12-12T10:13:37Z","creator":"system","file_name":"IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf","checksum":"762e52eb296f6dbfbf2a75d98b8ebaee","content_type":"application/pdf","file_id":"5022","access_level":"open_access","file_size":475661}],"language":[{"iso":"eng"}],"ddc":["000","005"],"has_accepted_license":"1","publist_id":"3248","status":"public","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"},{"full_name":"Singh, Rohit","first_name":"Rohit","last_name":"Singh"}],"type":"conference","alternative_title":["LNCS"],"publication_status":"published","month":"09","citation":{"ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. QUASY: quantitative synthesis tool. In: Vol 6605. Springer; 2011:267-271. doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Singh, R. (2011). QUASY: quantitative synthesis tool (Vol. 6605, pp. 267–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “QUASY: quantitative synthesis tool,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany, 2011, vol. 6605, pp. 267–271.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “QUASY: Quantitative Synthesis Tool,” 6605:267–71. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>.","mla":"Chatterjee, Krishnendu, et al. <i>QUASY: Quantitative Synthesis Tool</i>. Vol. 6605, Springer, 2011, pp. 267–71, doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>.","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2011. QUASY: quantitative synthesis tool. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 6605, 267–271.","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011, pp. 267–271."},"oa_version":"Submitted Version","conference":{"start_date":"2011-03-26","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2011-04-03","location":"Saarbrucken, Germany"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2020-07-14T12:46:10Z","quality_controlled":"1","alternative_title":["LNCS"],"publication_status":"published","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"type":"conference","oa_version":"Submitted Version","citation":{"ista":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. 2011. Quantitative synthesis for concurrent programs. CAV: Computer Aided Verification, LNCS, vol. 6806, 243–259.","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.","mla":"Cerny, Pavol, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 243–59, doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. “Quantitative Synthesis for Concurrent Programs.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:243–59. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>.","ieee":"P. Cerny, K. Chatterjee, T. A. Henzinger, A. Radhakrishna, and R. Singh, “Quantitative synthesis for concurrent programs,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 243–259.","apa":"Cerny, P., Chatterjee, K., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2011). Quantitative synthesis for concurrent programs. In G. Gopalakrishnan &#38; S. Qadeer (Eds.) (Vol. 6806, pp. 243–259). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>","ama":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. Quantitative synthesis for concurrent programs. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:243-259. doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>"},"month":"04","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2011-07-14","name":"CAV: Computer Aided Verification","end_date":"2011-07-20","location":"Snowbird, USA"},"pubrep_id":"76","date_updated":"2024-10-21T06:03:04Z","date_created":"2018-12-11T12:02:55Z","file":[{"checksum":"c033689355f45742dc7c99b5af13ce7a","content_type":"application/pdf","date_created":"2018-12-12T10:15:51Z","relation":"main_file","date_updated":"2020-07-14T12:46:10Z","file_name":"IST-2012-76-v1+1_Quantitative_synthesis_for_concurrent_programs.pdf","creator":"system","access_level":"open_access","file_size":508946,"file_id":"5174"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5388"}]},"ddc":["000","004"],"has_accepted_license":"1","publist_id":"3247","status":"public","date_published":"2011-04-21T00:00:00Z","scopus_import":"1","title":"Quantitative synthesis for concurrent programs","intvolume":"      6806","_id":"3366","corr_author":"1","editor":[{"full_name":"Gopalakrishnan, Ganesh","first_name":"Ganesh","last_name":"Gopalakrishnan"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"}],"oa":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"page":"243 - 259","publisher":"Springer","volume":6806,"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373","call_identifier":"FP7"}],"abstract":[{"lang":"eng","text":"We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized &quot;specification free&quot;, in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. "}],"ec_funded":1,"fulldoi":"https://doi.org/10.1007/978-3-642-22110-1_20","day":"21","year":"2011","doi":"10.1007/978-3-642-22110-1_20"},{"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"2939","status":"public"}]},"abstract":[{"text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ&gt;0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity of computing the rank of an n x n matrix with O(n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376) algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo algorithm for an arbitrary ε&gt;0.","lang":"eng"}],"fulldoi":"https://doi.org/10.1145/1998196.1998228","day":"13","year":"2011","doi":"10.1145/1998196.1998228","publist_id":"3245","status":"public","page":"207 - 216","date_updated":"2025-09-29T13:26:20Z","date_created":"2018-12-11T12:02:56Z","publisher":"ACM","citation":{"chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology,” 207–16. ACM, 2011. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>.","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” presented at the SoCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 207–216.","apa":"Chen, C., &#38; Kerber, M. (2011). An output sensitive algorithm for persistent homology (pp. 207–216). Presented at the SoCG: Symposium on Computational Geometry, Paris, France: ACM. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. In: ACM; 2011:207-216. doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>","ista":"Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology. SoCG: Symposium on Computational Geometry, 207–216.","short":"C. Chen, M. Kerber, in:, ACM, 2011, pp. 207–216.","mla":"Chen, Chao, and Michael Kerber. <i>An Output Sensitive Algorithm for Persistent Homology</i>. ACM, 2011, pp. 207–16, doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>."},"oa_version":"None","_id":"3367","month":"06","article_processing_charge":"No","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"conference":{"end_date":"2011-06-15","start_date":"2011-06-13","name":"SoCG: Symposium on Computational Geometry","location":"Paris, France"},"date_published":"2011-06-13T00:00:00Z","quality_controlled":"1","publication_status":"published","scopus_import":1,"author":[{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","first_name":"Chao"},{"orcid":"0000-0002-8030-9299","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","first_name":"Michael"}],"title":"An output sensitive algorithm for persistent homology","type":"conference"},{"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","citation":{"chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>.","ieee":"A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” <i>Neuron</i>, vol. 69, no. 2. Elsevier, pp. 185–187, 2011.","apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2011). The multiple faces of RIM. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>","ama":"Pernia-Andrade A, Jonas PM. The multiple faces of RIM. <i>Neuron</i>. 2011;69(2):185-187. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.","ista":"Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2), 185–187.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>, vol. 69, no. 2, Elsevier, 2011, pp. 185–87, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>."},"month":"01","publication_status":"published","author":[{"id":"36963E98-F248-11E8-B48F-1D18A9856A87","last_name":"Pernia-Andrade","first_name":"Alejandro","full_name":"Pernia-Andrade, Alejandro"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"type":"journal_article","quality_controlled":"1","publist_id":"3243","status":"public","language":[{"iso":"eng"}],"issue":"2","isi":1,"date_updated":"2025-09-30T09:01:26Z","date_created":"2018-12-11T12:02:56Z","corr_author":"1","department":[{"_id":"PeJo"}],"_id":"3369","title":"The multiple faces of RIM","scopus_import":"1","intvolume":"        69","date_published":"2011-01-27T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.neuron.2011.01.010","day":"27","year":"2011","doi":"10.1016/j.neuron.2011.01.010","volume":69,"abstract":[{"lang":"eng","text":"Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13."}],"external_id":{"isi":["000286792900002"]},"page":"185 - 187","publication":"Neuron","publisher":"Elsevier"},{"language":[{"iso":"eng"}],"issue":"2","isi":1,"publist_id":"3241","status":"public","date_updated":"2025-09-30T08:59:18Z","date_created":"2018-12-11T12:02:57Z","oa_version":"Submitted Version","citation":{"chicago":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>.","apa":"Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>","ieee":"A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” <i>Systematic Biology</i>, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011.","ama":"Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. 2011;60(2):218-225. doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225.","mla":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>."},"month":"03","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publication_status":"published","author":[{"first_name":"Anne","full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok"}],"type":"journal_article","volume":60,"abstract":[{"text":"Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data.","lang":"eng"}],"fulldoi":"https://doi.org/10.1093/sysbio/syq086","day":"01","doi":"10.1093/sysbio/syq086","year":"2011","publication":"Systematic Biology","external_id":{"isi":["000287255100009"]},"page":"218 - 225","publisher":"Oxford University Press","main_file_link":[{"url":"http://eprints.cs.univie.ac.at/3226/","open_access":"1"}],"_id":"3370","corr_author":"1","oa":1,"department":[{"_id":"JoBo"}],"date_published":"2011-03-01T00:00:00Z","title":"Consequences of different null models on the tree shape bias of supertree methods","intvolume":"        60"},{"external_id":{"isi":["000288368200010"]},"page":"724","publication":"Molecular Biology and Evolution","publisher":"Oxford University Press","doi":"10.1091/mbc.E10-12-0958","year":"2011","fulldoi":"https://doi.org/10.1091/mbc.E10-12-0958","day":"15","abstract":[{"lang":"eng","text":"The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance."}],"volume":22,"title":"Cells on the move in Philadelphia","scopus_import":"1","intvolume":"        22","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2011-03-15T00:00:00Z","article_type":"original","oa":1,"department":[{"_id":"MiSi"}],"_id":"3371","file":[{"file_id":"5283","file_size":105421,"access_level":"open_access","file_name":"IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf","creator":"system","date_created":"2018-12-12T10:17:29Z","date_updated":"2020-07-14T12:46:11Z","relation":"main_file","content_type":"application/pdf","checksum":"3467986ab7a64e7694ffd1013b5d9da9"}],"date_updated":"2025-09-30T08:58:51Z","pubrep_id":"373","date_created":"2018-12-11T12:02:57Z","has_accepted_license":"1","status":"public","publist_id":"3238","isi":1,"issue":"6","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"},{"full_name":"Parent, Carole","first_name":"Carole","last_name":"Parent"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:11Z","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"chicago":"Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>.","ieee":"M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6. Oxford University Press, p. 724, 2011.","apa":"Sixt, M. K., &#38; Parent, C. (2011). Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>","ama":"Sixt MK, Parent C. Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. 2011;22(6):724. doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>","ista":"Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724.","short":"M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724.","mla":"Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>."}},{"abstract":[{"text":"Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.","lang":"eng"}],"volume":471,"year":"2011","doi":"10.1038/nature09831","day":"23","fulldoi":"https://doi.org/10.1038/nature09831","pmid":1,"publisher":"Nature Publishing Group","publication":"Nature","external_id":{"pmid":["21430721"],"isi":["000288702200001"]},"page":"E1 - E4","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/","open_access":"1"}],"_id":"3372","department":[{"_id":"NiBa"}],"oa":1,"date_published":"2011-03-23T00:00:00Z","intvolume":"       471","scopus_import":"1","title":"Inclusive fitness theory and eusociality","isi":1,"issue":"7339","language":[{"iso":"eng"}],"status":"public","publist_id":"3237","date_created":"2018-12-11T12:02:57Z","date_updated":"2025-09-30T08:58:00Z","month":"03","citation":{"ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. <i>Nature</i>. 2011;471(7339):E1-E4. doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>","ieee":"P. Abbot <i>et al.</i>, “Inclusive fitness theory and eusociality,” <i>Nature</i>, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.","apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>","chicago":"Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>.","mla":"Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>.","short":"P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4.","ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4."},"oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","author":[{"first_name":"Patrick","full_name":"Abbot, Patrick","last_name":"Abbot"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Alcock","full_name":"Alcock, John","first_name":"John"},{"full_name":"Alizon, Samuel","first_name":"Samuel","last_name":"Alizon"},{"full_name":"Alpedrinha, Joao","first_name":"Joao","last_name":"Alpedrinha"},{"full_name":"Andersson, Malte","first_name":"Malte","last_name":"Andersson"},{"last_name":"Andre","first_name":"Jean","full_name":"Andre, Jean"},{"last_name":"Van Baalen","first_name":"Minus","full_name":"Van Baalen, Minus"},{"last_name":"Balloux","full_name":"Balloux, Francois","first_name":"Francois"},{"last_name":"Balshine","full_name":"Balshine, Sigal","first_name":"Sigal"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Beukeboom, Leo","first_name":"Leo","last_name":"Beukeboom"},{"last_name":"Biernaskie","first_name":"Jay","full_name":"Biernaskie, Jay"},{"first_name":"Trine","full_name":"Bilde, Trine","last_name":"Bilde"},{"last_name":"Borgia","first_name":"Gerald","full_name":"Borgia, Gerald"},{"last_name":"Breed","first_name":"Michael","full_name":"Breed, Michael"},{"last_name":"Brown","first_name":"Sam","full_name":"Brown, Sam"},{"last_name":"Bshary","full_name":"Bshary, Redouan","first_name":"Redouan"},{"first_name":"Angus","full_name":"Buckling, Angus","last_name":"Buckling"},{"last_name":"Burley","full_name":"Burley, Nancy","first_name":"Nancy"},{"last_name":"Burton Chellew","full_name":"Burton Chellew, Max","first_name":"Max"},{"full_name":"Cant, Michael","first_name":"Michael","last_name":"Cant"},{"full_name":"Chapuisat, Michel","first_name":"Michel","last_name":"Chapuisat"},{"first_name":"Eric","full_name":"Charnov, Eric","last_name":"Charnov"},{"first_name":"Tim","full_name":"Clutton Brock, Tim","last_name":"Clutton Brock"},{"full_name":"Cockburn, Andrew","first_name":"Andrew","last_name":"Cockburn"},{"full_name":"Cole, Blaine","first_name":"Blaine","last_name":"Cole"},{"first_name":"Nick","full_name":"Colegrave, Nick","last_name":"Colegrave"},{"last_name":"Cosmides","first_name":"Leda","full_name":"Cosmides, Leda"},{"first_name":"Iain","full_name":"Couzin, Iain","last_name":"Couzin"},{"first_name":"Jerry","full_name":"Coyne, Jerry","last_name":"Coyne"},{"full_name":"Creel, Scott","first_name":"Scott","last_name":"Creel"},{"last_name":"Crespi","full_name":"Crespi, Bernard","first_name":"Bernard"},{"full_name":"Curry, Robert","first_name":"Robert","last_name":"Curry"},{"first_name":"Sasha","full_name":"Dall, Sasha","last_name":"Dall"},{"last_name":"Day","first_name":"Troy","full_name":"Day, Troy"},{"full_name":"Dickinson, Janis","first_name":"Janis","last_name":"Dickinson"},{"full_name":"Dugatkin, Lee","first_name":"Lee","last_name":"Dugatkin"},{"first_name":"Claire","full_name":"El Mouden, Claire","last_name":"El Mouden"},{"last_name":"Emlen","first_name":"Stephen","full_name":"Emlen, Stephen"},{"last_name":"Evans","full_name":"Evans, Jay","first_name":"Jay"},{"first_name":"Regis","full_name":"Ferriere, Regis","last_name":"Ferriere"},{"last_name":"Field","first_name":"Jeremy","full_name":"Field, Jeremy"},{"full_name":"Foitzik, Susanne","first_name":"Susanne","last_name":"Foitzik"},{"last_name":"Foster","first_name":"Kevin","full_name":"Foster, Kevin"},{"last_name":"Foster","first_name":"William","full_name":"Foster, William"},{"full_name":"Fox, Charles","first_name":"Charles","last_name":"Fox"},{"last_name":"Gadau","first_name":"Juergen","full_name":"Gadau, Juergen"},{"last_name":"Gandon","full_name":"Gandon, Sylvain","first_name":"Sylvain"},{"last_name":"Gardner","full_name":"Gardner, Andy","first_name":"Andy"},{"last_name":"Gardner","full_name":"Gardner, Michael","first_name":"Michael"},{"full_name":"Getty, Thomas","first_name":"Thomas","last_name":"Getty"},{"last_name":"Goodisman","full_name":"Goodisman, Michael","first_name":"Michael"},{"last_name":"Grafen","first_name":"Alan","full_name":"Grafen, Alan"},{"last_name":"Grosberg","full_name":"Grosberg, Rick","first_name":"Rick"},{"first_name":"Christina","full_name":"Grozinger, Christina","last_name":"Grozinger"},{"last_name":"Gouyon","first_name":"Pierre","full_name":"Gouyon, Pierre"},{"last_name":"Gwynne","full_name":"Gwynne, Darryl","first_name":"Darryl"},{"last_name":"Harvey","first_name":"Paul","full_name":"Harvey, Paul"},{"full_name":"Hatchwell, Ben","first_name":"Ben","last_name":"Hatchwell"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"last_name":"Helantera","full_name":"Helantera, Heikki","first_name":"Heikki"},{"last_name":"Helms","full_name":"Helms, Ken","first_name":"Ken"},{"first_name":"Kim","full_name":"Hill, Kim","last_name":"Hill"},{"last_name":"Jiricny","full_name":"Jiricny, Natalie","first_name":"Natalie"},{"full_name":"Johnstone, Rufus","first_name":"Rufus","last_name":"Johnstone"},{"first_name":"Alex","full_name":"Kacelnik, Alex","last_name":"Kacelnik"},{"last_name":"Kiers","full_name":"Kiers, E Toby","first_name":"E Toby"},{"last_name":"Kokko","first_name":"Hanna","full_name":"Kokko, Hanna"},{"first_name":"Jan","full_name":"Komdeur, Jan","last_name":"Komdeur"},{"first_name":"Judith","full_name":"Korb, Judith","last_name":"Korb"},{"full_name":"Kronauer, Daniel","first_name":"Daniel","last_name":"Kronauer"},{"first_name":"Rolf","full_name":"Kümmerli, Rolf","last_name":"Kümmerli"},{"first_name":"Laurent","full_name":"Lehmann, Laurent","last_name":"Lehmann"},{"last_name":"Linksvayer","full_name":"Linksvayer, Timothy","first_name":"Timothy"},{"last_name":"Lion","full_name":"Lion, Sébastien","first_name":"Sébastien"},{"full_name":"Lyon, Bruce","first_name":"Bruce","last_name":"Lyon"},{"last_name":"Marshall","full_name":"Marshall, James","first_name":"James"},{"first_name":"Richard","full_name":"Mcelreath, Richard","last_name":"Mcelreath"},{"first_name":"Yannis","full_name":"Michalakis, Yannis","last_name":"Michalakis"},{"full_name":"Michod, Richard","first_name":"Richard","last_name":"Michod"},{"full_name":"Mock, Douglas","first_name":"Douglas","last_name":"Mock"},{"full_name":"Monnin, Thibaud","first_name":"Thibaud","last_name":"Monnin"},{"last_name":"Montgomerie","full_name":"Montgomerie, Robert","first_name":"Robert"},{"last_name":"Moore","first_name":"Allen","full_name":"Moore, Allen"},{"first_name":"Ulrich","full_name":"Mueller, Ulrich","last_name":"Mueller"},{"full_name":"Noë, Ronald","first_name":"Ronald","last_name":"Noë"},{"last_name":"Okasha","first_name":"Samir","full_name":"Okasha, Samir"},{"last_name":"Pamilo","full_name":"Pamilo, Pekka","first_name":"Pekka"},{"last_name":"Parker","first_name":"Geoff","full_name":"Parker, Geoff"},{"last_name":"Pedersen","first_name":"Jes","full_name":"Pedersen, Jes"},{"last_name":"Pen","full_name":"Pen, Ido","first_name":"Ido"},{"last_name":"Pfennig","full_name":"Pfennig, David","first_name":"David"},{"first_name":"David","full_name":"Queller, David","last_name":"Queller"},{"first_name":"Daniel","full_name":"Rankin, Daniel","last_name":"Rankin"},{"last_name":"Reece","full_name":"Reece, Sarah","first_name":"Sarah"},{"last_name":"Reeve","full_name":"Reeve, Hudson","first_name":"Hudson"},{"full_name":"Reuter, Max","first_name":"Max","last_name":"Reuter"},{"last_name":"Roberts","first_name":"Gilbert","full_name":"Roberts, Gilbert"},{"first_name":"Simon","full_name":"Robson, Simon","last_name":"Robson"},{"full_name":"Roze, Denis","first_name":"Denis","last_name":"Roze"},{"last_name":"Rousset","full_name":"Rousset, Francois","first_name":"Francois"},{"last_name":"Rueppell","full_name":"Rueppell, Olav","first_name":"Olav"},{"last_name":"Sachs","full_name":"Sachs, Joel","first_name":"Joel"},{"first_name":"Lorenzo","full_name":"Santorelli, Lorenzo","last_name":"Santorelli"},{"first_name":"Paul","full_name":"Schmid Hempel, Paul","last_name":"Schmid Hempel"},{"last_name":"Schwarz","first_name":"Michael","full_name":"Schwarz, Michael"},{"last_name":"Scott Phillips","first_name":"Tom","full_name":"Scott Phillips, Tom"},{"first_name":"Janet","full_name":"Shellmann Sherman, Janet","last_name":"Shellmann Sherman"},{"last_name":"Sherman","first_name":"Paul","full_name":"Sherman, Paul"},{"last_name":"Shuker","full_name":"Shuker, David","first_name":"David"},{"last_name":"Smith","first_name":"Jeff","full_name":"Smith, Jeff"},{"last_name":"Spagna","first_name":"Joseph","full_name":"Spagna, Joseph"},{"first_name":"Beverly","full_name":"Strassmann, Beverly","last_name":"Strassmann"},{"full_name":"Suarez, Andrew","first_name":"Andrew","last_name":"Suarez"},{"last_name":"Sundström","full_name":"Sundström, Liselotte","first_name":"Liselotte"},{"last_name":"Taborsky","first_name":"Michael","full_name":"Taborsky, Michael"},{"first_name":"Peter","full_name":"Taylor, Peter","last_name":"Taylor"},{"last_name":"Thompson","full_name":"Thompson, Graham","first_name":"Graham"},{"full_name":"Tooby, John","first_name":"John","last_name":"Tooby"},{"last_name":"Tsutsui","full_name":"Tsutsui, Neil","first_name":"Neil"},{"full_name":"Tsuji, Kazuki","first_name":"Kazuki","last_name":"Tsuji"},{"full_name":"Turillazzi, Stefano","first_name":"Stefano","last_name":"Turillazzi"},{"last_name":"Úbeda","full_name":"Úbeda, Francisco","first_name":"Francisco"},{"full_name":"Vargo, Edward","first_name":"Edward","last_name":"Vargo"},{"last_name":"Voelkl","first_name":"Bernard","full_name":"Voelkl, Bernard"},{"last_name":"Wenseleers","full_name":"Wenseleers, Tom","first_name":"Tom"},{"first_name":"Stuart","full_name":"West, Stuart","last_name":"West"},{"first_name":"Mary","full_name":"West Eberhard, Mary","last_name":"West Eberhard"},{"last_name":"Westneat","full_name":"Westneat, David","first_name":"David"},{"first_name":"Diane","full_name":"Wiernasz, Diane","last_name":"Wiernasz"},{"first_name":"Geoff","full_name":"Wild, Geoff","last_name":"Wild"},{"full_name":"Wrangham, Richard","first_name":"Richard","last_name":"Wrangham"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"},{"full_name":"Zeh, David","first_name":"David","last_name":"Zeh"},{"last_name":"Zeh","full_name":"Zeh, Jeanne","first_name":"Jeanne"},{"last_name":"Zink","first_name":"Andrew","full_name":"Zink, Andrew"}],"publication_status":"published"},{"arxiv":1,"publisher":"IOP Publishing","publication":"Journal of Physics: Condensed Matter","external_id":{"isi":["000289199800002"],"arxiv":["1101.4240"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.4240"}],"abstract":[{"text":"Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.","lang":"eng"}],"volume":23,"year":"2011","doi":"10.1088/0953-8984/23/15/153102","day":"01","fulldoi":"https://doi.org/10.1088/0953-8984/23/15/153102","date_published":"2011-04-01T00:00:00Z","article_number":"153102","intvolume":"        23","scopus_import":"1","title":"Information transmission in genetic regulatory networks a review","_id":"3374","oa":1,"department":[{"_id":"GaTk"}],"corr_author":"1","date_created":"2018-12-11T12:02:58Z","date_updated":"2025-09-30T08:56:23Z","isi":1,"issue":"15","language":[{"iso":"eng"}],"status":"public","publist_id":"3233","quality_controlled":"1","type":"journal_article","author":[{"first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"},{"full_name":"Walczak, Aleksandra","first_name":"Aleksandra","last_name":"Walczak"}],"publication_status":"published","month":"04","oa_version":"Submitted Version","citation":{"chicago":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2011. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>.","apa":"Tkačik, G., &#38; Walczak, A. (2011). Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>","ieee":"G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15. IOP Publishing, 2011.","ama":"Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. 2011;23(15). doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>","ista":"Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.","short":"G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).","mla":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15, 153102, IOP Publishing, 2011, doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No"},{"date_created":"2018-12-11T12:02:59Z","date_updated":"2025-09-30T08:54:28Z","status":"public","publist_id":"3231","isi":1,"issue":"4","language":[{"iso":"eng"}],"author":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"05","oa_version":"Submitted Version","citation":{"mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>.","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","apa":"Bollenbach, M. T., &#38; Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” <i>Molecular Cell</i>, vol. 42, no. 4. Cell Press, pp. 413–425, 2011.","ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. 2011;42(4):413-425. doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>","chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/"}],"publication":"Molecular Cell","external_id":{"isi":["000291113800005"]},"page":"413 - 425","publisher":"Cell Press","doi":"10.1016/j.molcel.2011.04.016","year":"2011","fulldoi":"https://doi.org/10.1016/j.molcel.2011.04.016","day":"20","acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","abstract":[{"text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.","lang":"eng"}],"volume":42,"scopus_import":"1","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","intvolume":"        42","date_published":"2011-05-20T00:00:00Z","department":[{"_id":"ToBo"}],"oa":1,"_id":"3376"},{"date_published":"2011-06-01T00:00:00Z","intvolume":"        11","scopus_import":"1","title":"Quantifying transversality by measuring the robustness of intersections","_id":"3377","corr_author":"1","oa":1,"department":[{"_id":"HeEd"}],"arxiv":1,"publisher":"Springer","external_id":{"arxiv":["0911.2142"],"isi":["000290038800004"]},"publication":"Foundations of Computational Mathematics","page":"345 - 361","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.2142"}],"volume":11,"abstract":[{"lang":"eng","text":"By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings."}],"acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","day":"01","fulldoi":"https://doi.org/10.1007/s10208-011-9090-8","doi":"10.1007/s10208-011-9090-8","year":"2011","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Morozov, Dmitriy","first_name":"Dmitriy","last_name":"Morozov"},{"full_name":"Patel, Amit","first_name":"Amit","last_name":"Patel","id":"34A254A0-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","citation":{"mla":"Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>.","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.","apa":"Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 345–361, 2011.","ama":"Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. <i>Foundations of Computational Mathematics</i>. 2011;11(3):345-361. doi:<a href=\"https://doi.org/10.1007/s10208-011-9090-8\">10.1007/s10208-011-9090-8</a>","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-011-9090-8\">https://doi.org/10.1007/s10208-011-9090-8</a>."},"month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","date_created":"2018-12-11T12:02:59Z","date_updated":"2025-09-30T08:53:52Z","language":[{"iso":"eng"}],"issue":"3","isi":1,"publist_id":"3230","status":"public"},{"status":"public","publist_id":"3229","isi":1,"issue":"3","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:59Z","date_updated":"2025-09-30T08:53:15Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","month":"06","citation":{"ieee":"P. Bendich and J. Harer, “Persistent intersection homology,” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3. Springer, pp. 305–336, 2011.","apa":"Bendich, P., &#38; Harer, J. (2011). Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>","ama":"Bendich P, Harer J. Persistent intersection homology. <i>Foundations of Computational Mathematics</i>. 2011;11(3):305-336. doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>","chicago":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10208-010-9081-1\">https://doi.org/10.1007/s10208-010-9081-1</a>.","mla":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” <i>Foundations of Computational Mathematics</i>, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:<a href=\"https://doi.org/10.1007/s10208-010-9081-1\">10.1007/s10208-010-9081-1</a>.","short":"P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336.","ista":"Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336."},"oa_version":"None","type":"journal_article","author":[{"last_name":"Bendich","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","full_name":"Bendich, Paul","first_name":"Paul"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"}],"publication_status":"published","quality_controlled":"1","year":"2011","doi":"10.1007/s10208-010-9081-1","day":"01","acknowledgement":"This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007.","fulldoi":"https://doi.org/10.1007/s10208-010-9081-1","abstract":[{"text":"The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology.","lang":"eng"}],"volume":11,"publisher":"Springer","external_id":{"isi":["000290038800002"]},"publication":"Foundations of Computational Mathematics","page":"305 - 336","department":[{"_id":"HeEd"}],"corr_author":"1","_id":"3378","intvolume":"        11","scopus_import":"1","title":"Persistent intersection homology","date_published":"2011-06-01T00:00:00Z"},{"ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"issue":"3","status":"public","publist_id":"3227","date_created":"2018-12-11T12:03:00Z","date_updated":"2026-06-18T18:45:27Z","citation":{"chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>.","ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. 2011;93(3):221-232. doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>","ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” <i>Genetical Research</i>, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011.","apa":"Logeswaran, S., &#38; Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. <i>Genetical Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672311000115\">https://doi.org/10.1017/S0016672311000115</a>","short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” <i>Genetical Research</i>, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:<a href=\"https://doi.org/10.1017/S0016672311000115\">10.1017/S0016672311000115</a>."},"oa_version":"Published Version","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"last_name":"Logeswaran","first_name":"Sayanthan","full_name":"Logeswaran, Sayanthan"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"volume":93,"abstract":[{"text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.","lang":"eng"}],"day":"18","fulldoi":"https://doi.org/10.1017/S0016672311000115","year":"2011","doi":"10.1017/S0016672311000115","publisher":"Cambridge University Press","external_id":{"isi":["000291114300005"]},"page":"221 - 232","publication":"Genetical Research","main_file_link":[{"open_access":"1","url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf"}],"_id":"3380","department":[{"_id":"NiBa"}],"oa":1,"article_type":"original","date_published":"2011-05-18T00:00:00Z","intvolume":"        93","scopus_import":"1","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency"}]