[{"status":"public","publication_status":"published","publisher":"IST Austria","type":"technical_report","date_updated":"2025-04-15T08:11:41Z","doi":"10.15479/AT:IST-2016-523-v1-1","alternative_title":["IST Austria Technical Report"],"pubrep_id":"523","related_material":{"record":[{"status":"public","relation":"later_version","id":"1604"}]},"has_accepted_license":"1","page":"33","_id":"5445","year":"2016","oa_version":"Published Version","day":"31","abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. "}],"ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:22Z","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:58Z","date_published":"2016-03-31T00:00:00Z","title":"Quantitative interprocedural analysis","month":"03","file":[{"file_name":"IST-2016-523-v1+1_main.pdf","creator":"system","file_id":"5513","checksum":"cef516fa091925b5868813e355268fb4","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:52Z","content_type":"application/pdf","file_size":1012204}],"oa":1,"department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>","ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p."}},{"_id":"5446","page":"26","oa_version":"Published Version","year":"2016","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the\r\neffectiveness of our approach."}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","date_updated":"2020-07-14T23:05:05Z","publication_status":"published","publisher":"IST Austria","status":"public","type":"technical_report","alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","pubrep_id":"618","file_date_updated":"2020-07-14T12:46:58Z","title":"Termination and worst-case analysis of recursive programs","date_published":"2016-07-15T00:00:00Z","oa":1,"file":[{"file_size":686241,"content_type":"application/pdf","date_created":"2019-05-10T13:27:24Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","checksum":"689069a7abbb34b21516164cbee9e0df","file_id":"6403","creator":"dernst","file_name":"popl2017a.pdf"},{"file_name":"author_names.txt","file_id":"6404","creator":"dernst","checksum":"fc08022bfbaac07bac047a9407c0bbb3","date_created":"2019-05-10T13:27:31Z","access_level":"closed","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","content_type":"text/plain","file_size":258}],"month":"07","citation":{"short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis of Recursive Programs, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Termination and worst-case analysis of recursive programs</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Termination and worst-case analysis of recursive programs</i>. IST Austria.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria; 2016."},"date_created":"2018-12-12T11:39:23Z","language":[{"iso":"eng"}],"author":[{"last_name":"Anonymous","first_name":"1","full_name":"Anonymous, 1"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"first_name":"3","last_name":"Anonymous","full_name":"Anonymous, 3"}],"publication_identifier":{"issn":["2664-1690"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"abstract":[{"lang":"eng","text":"We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase\r\nbounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms."}],"day":"15","page":"20","_id":"5447","year":"2016","oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"pubrep_id":"619","has_accepted_license":"1","status":"public","type":"technical_report","publisher":"IST Austria","publication_status":"published","date_updated":"2020-07-14T23:05:06Z","month":"07","oa":1,"file":[{"creator":"dernst","checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb","file_id":"6406","access_level":"closed","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:32:16Z","file_name":"listofauthors.txt","content_type":"text/plain","file_size":281},{"file_name":"popl2017b.pdf","checksum":"7bdd94ba13aa0dec9c46887fcf13870b","creator":"dernst","file_id":"6407","date_created":"2019-05-10T13:32:16Z","date_updated":"2020-07-14T12:46:58Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":563642}],"citation":{"short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria; 2016.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria."},"file_date_updated":"2020-07-14T12:46:58Z","date_published":"2016-07-15T00:00:00Z","title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","language":[{"iso":"eng"}],"author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"}],"publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:23Z"},{"publication_status":"published","publisher":"IST Austria","type":"technical_report","status":"public","date_updated":"2025-05-20T09:45:08Z","pubrep_id":"620","related_material":{"record":[{"id":"5456","relation":"later_version","status":"public"},{"id":"10417","relation":"later_version","status":"public"}]},"has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"year":"2016","oa_version":"Published Version","page":"20","_id":"5448","ddc":["000"],"day":"15","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:23Z","arxiv":1,"external_id":{"arxiv":["1610.01188"]},"publication_identifier":{"issn":["2664-1690"]},"author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"full_name":"Anonymous, 2","last_name":"Anonymous","first_name":"2"},{"full_name":"Anonymous, 3","first_name":"3","last_name":"Anonymous"},{"first_name":"4","full_name":"Anonymous, 4","last_name":"Anonymous"}],"language":[{"iso":"eng"}],"date_published":"2016-07-15T00:00:00Z","title":"Data-centric dynamic partial order reduction","file_date_updated":"2020-07-14T12:46:58Z","citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2016.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, &#38; Anonymous, 4. (2016). <i>Data-centric dynamic partial order reduction</i>. IST Austria.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic partial order reduction, IST Austria, 20p."},"month":"07","oa":1,"file":[{"file_size":538881,"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:58Z","relation":"main_file","date_created":"2018-12-12T11:53:45Z","file_id":"5506","creator":"system","checksum":"1d69252d66bcdf782615ddfb911d2957","file_name":"IST-2016-620-v1+1_main.pdf"},{"creator":"dernst","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","file_id":"6405","date_created":"2019-05-10T13:30:40Z","relation":"main_file","access_level":"closed","date_updated":"2020-07-14T12:46:58Z","file_name":"authornames.txt","content_type":"text/plain","file_size":121}]},{"_id":"5449","page":"22","oa_version":"Updated Version","year":"2016","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"ddc":["519"],"day":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-09-18T09:50:09Z","publisher":"IST Austria","type":"technical_report","status":"public","publication_status":"published","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2016-648-v1-1","has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"512"}]},"pubrep_id":"648","file_date_updated":"2020-07-14T12:46:58Z","title":"Amplification on undirected population structures: Comets beat stars","date_published":"2016-11-09T00:00:00Z","oa":1,"file":[{"file_size":1264221,"content_type":"application/pdf","file_name":"IST-2016-648-v1+1_tr.pdf","date_created":"2018-12-12T11:54:07Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:58Z","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","creator":"system","file_id":"5529"}],"month":"11","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>."},"department":[{"_id":"KrCh"}],"date_created":"2018-12-12T11:39:24Z","author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]}},{"date_created":"2018-12-12T11:39:24Z","publication_identifier":{"issn":["2664-1690"]},"author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"language":[{"iso":"eng"}],"date_published":"2016-12-30T00:00:00Z","title":"Strong amplifiers of natural selection","file_date_updated":"2020-07-14T12:46:59Z","department":[{"_id":"KrCh"}],"citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p."},"month":"12","oa":1,"file":[{"file_name":"IST-2016-728-v1+1_main.pdf","date_created":"2018-12-12T11:53:04Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:59Z","creator":"system","checksum":"7b8bb17c322c0556acba6ac169fa71c1","file_id":"5465","file_size":1014732,"content_type":"application/pdf"}],"publisher":"IST Austria","status":"public","type":"technical_report","publication_status":"published","date_updated":"2023-02-23T12:27:05Z","pubrep_id":"728","has_accepted_license":"1","doi":"10.15479/AT:IST-2016-728-v1-1","alternative_title":["IST Austria Technical Report"],"year":"2016","oa_version":"Published Version","page":"34","_id":"5451","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30"},{"publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:25Z","citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. 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Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>"},"month":"12","article_processing_charge":"No","date_created":"2021-08-10T08:22:52Z","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"first_name":"Youann","full_name":"Anciaux, Youann","last_name":"Anciaux"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"day":"14","_id":"9864","year":"2016","oa_version":"Published Version","doi":"10.6084/m9.figshare.4315652.v1","related_material":{"record":[{"id":"1077","status":"public","relation":"used_in_publication"}]},"status":"public","publisher":"The Royal Society","type":"research_data_reference","date_updated":"2025-07-10T11:49:59Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"article_processing_charge":"No","month":"12","oa":1,"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."},"date_published":"2016-12-14T00:00:00Z","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","author":[{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A"},{"full_name":"de Vladar, Harold","last_name":"de Vladar","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612"}],"date_created":"2021-08-10T08:29:47Z"},{"author":[{"full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"first_name":"Bartłomiej","full_name":"Wacław, Bartłomiej","last_name":"Wacław"}],"date_created":"2021-08-10T08:37:20Z","month":"12","article_processing_charge":"No","citation":{"ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>."},"department":[{"_id":"AnKi"}],"title":"ZIP-archived directory containing all data and computer programs","date_published":"2016-12-09T00:00:00Z","doi":"10.1371/journal.pcbi.1005218.s009","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1167"}]},"date_updated":"2025-09-22T09:53:16Z","type":"research_data_reference","publisher":"Public Library of Science","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"09","_id":"9866","oa_version":"Published Version","year":"2016"},{"date_created":"2021-08-10T08:42:00Z","author":[{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Kristin","full_name":"Hagel, Kristin","last_name":"Hagel"},{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"}],"title":"Experimental game instructions","article_processing_charge":"No","month":"10","department":[{"_id":"KrCh"}],"citation":{"apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016)."},"type":"research_data_reference","status":"public","publisher":"Public Library of Science","date_updated":"2025-09-22T08:27:00Z","doi":"10.1371/journal.pone.0163867.s008","related_material":{"record":[{"id":"1322","status":"public","relation":"used_in_publication"}]},"_id":"9867","year":"2016","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"day":"04"},{"_id":"9868","year":"2016","oa_version":"Published Version","abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"day":"04","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","type":"research_data_reference","status":"public","date_updated":"2025-09-22T08:27:00Z","doi":"10.1371/journal.pone.0163867.s009","related_material":{"record":[{"id":"1322","relation":"used_in_publication","status":"public"}]},"date_published":"2016-10-04T00:00:00Z","title":"Experimental data","month":"10","article_processing_charge":"No","department":[{"_id":"KrCh"}],"citation":{"chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","ama":"Hilbe C, Hagel K, Milinski M. 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Milinski, (2016)."},"date_created":"2021-08-10T08:45:00Z","author":[{"first_name":"Christian","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"full_name":"Hagel, Kristin","first_name":"Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}]},{"date_created":"2021-08-10T08:53:48Z","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"title":"Error bound on an estimator of position","date_published":"2016-09-27T00:00:00Z","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"department":[{"_id":"GaTk"}],"article_processing_charge":"No","month":"09","date_updated":"2025-09-22T08:46:14Z","publisher":"Public Library of Science","type":"research_data_reference","status":"public","related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pone.0163628.s001","oa_version":"Published Version","year":"2016","_id":"9869","abstract":[{"text":"A lower bound on the error of a positional estimator with limited positional information is derived.","lang":"eng"}],"day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"citation":{"apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"department":[{"_id":"GaTk"}],"article_processing_charge":"No","month":"09","title":"Computation of positional information in an Ising model","date_published":"2016-09-27T00:00:00Z","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"date_created":"2021-08-10T09:23:45Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"day":"27","oa_version":"Published Version","year":"2016","_id":"9870","related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pone.0163628.s002","date_updated":"2025-09-22T08:46:14Z","type":"research_data_reference","publisher":"Public Library of Science","status":"public"}]