@inproceedings{1691,
abstract = {We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment.},
author = {Svoreňová, Mária and Chmelik, Martin and Leahy, Kevin and Eniser, Hasan and Chatterjee, Krishnendu and Cěrná, Ivana and Belta, Cǎlin},
booktitle = {Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control},
location = {Seattle, WA, United States},
pages = {233 -- 238},
publisher = {ACM},
title = {{Temporal logic motion planning using POMDPs with parity objectives: Case study paper}},
doi = {10.1145/2728606.2728617},
year = {2015},
}
@inproceedings{1658,
abstract = {Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space.},
author = {Bogomolov, Sergiy and Henzinger, Thomas A and Podelski, Andreas and Ruess, Jakob and Schilling, Christian},
location = {Nantes, France},
pages = {77 -- 89},
publisher = {Springer},
title = {{Adaptive moment closure for parameter inference of biochemical reaction networks}},
doi = {10.1007/978-3-319-23401-4_8},
volume = {9308},
year = {2015},
}
@inproceedings{1836,
abstract = {In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools.},
author = {Cerny, Pavol and Henzinger, Thomas A and Kovács, Laura and Radhakrishna, Arjun and Zwirchmayr, Jakob},
location = {London, United Kingdom},
pages = {105 -- 131},
publisher = {Springer},
title = {{Segment abstraction for worst-case execution time analysis}},
doi = {10.1007/978-3-662-46669-8_5},
volume = {9032},
year = {2015},
}
@inproceedings{1610,
abstract = {The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1,L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to pushdown automata is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Otop, Jan},
location = {Kyoto, Japan},
number = {Part II},
pages = {121 -- 133},
publisher = {Springer},
title = {{Edit distance for pushdown automata}},
doi = {10.1007/978-3-662-47666-6_10},
volume = {9135},
year = {2015},
}
@inproceedings{1603,
abstract = {For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.
The key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Fellner, Andreas and Kretinsky, Jan},
location = {San Francisco, CA, United States},
pages = {158 -- 177},
publisher = {Springer},
title = {{Counterexample explanation by learning small strategies in Markov decision processes}},
doi = {10.1007/978-3-319-21690-4_10},
volume = {9206},
year = {2015},
}
@article{1855,
abstract = {Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.},
author = {Mcmahon, Dino and Fürst, Matthias and Caspar, Jesicca and Theodorou, Panagiotis and Brown, Mark and Paxton, Robert},
journal = {Journal of Animal Ecology},
number = {3},
pages = {615 -- 624},
publisher = {Wiley},
title = {{A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees}},
doi = {10.1111/1365-2656.12345},
volume = {84},
year = {2015},
}
@article{1812,
abstract = {We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.
},
author = {Lahrz, Martin and Lemeshko, Mikhail and Mathey, Ludwig},
journal = {New Journal of Physics},
number = {4},
publisher = {IOP Publishing Ltd.},
title = {{Exotic roton excitations in quadrupolar Bose–Einstein condensates }},
doi = {10.1088/1367-2630/17/4/045005},
volume = {17},
year = {2015},
}
@misc{5441,
abstract = {We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Goharshady, Amir and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {24},
publisher = {IST Austria},
title = {{Algorithms for algebraic path properties in concurrent systems of constant treewidth components}},
doi = {10.15479/AT:IST-2015-340-v1-1},
year = {2015},
}
@inproceedings{1595,
abstract = {A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.},
author = {Fulek, Radoslav and Pelsmajer, Michael and Schaefer, Marcus},
location = {Los Angeles, CA, USA},
pages = {99 -- 110},
publisher = {Springer},
title = {{Hanani-Tutte for radial planarity}},
doi = {10.1007/978-3-319-27261-0_9},
volume = {9411},
year = {2015},
}
@article{1709,
abstract = {The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.},
author = {Reiter, Johannes and Kanodia, Ayush and Gupta, Raghav and Nowak, Martin and Chatterjee, Krishnendu},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1812},
publisher = {Royal Society},
title = {{Biological auctions with multiple rewards}},
doi = {10.1098/rspb.2015.1041},
volume = {282},
year = {2015},
}
@article{1665,
abstract = {Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome.},
author = {Landau, Dan and Tausch, Eugen and Taylor Weiner, Amaro and Stewart, Chip and Reiter, Johannes and Bahlo, Jasmin and Kluth, Sandra and Božić, Ivana and Lawrence, Michael and Böttcher, Sebastian and Carter, Scott and Cibulskis, Kristian and Mertens, Daniel and Sougnez, Carrie and Rosenberg, Mara and Hess, Julian and Edelmann, Jennifer and Kless, Sabrina and Kneba, Michael and Ritgen, Matthias and Fink, Anna and Fischer, Kirsten and Gabriel, Stacey and Lander, Eric and Nowak, Martin and Döhner, Hartmut and Hallek, Michael and Neuberg, Donna and Getz, Gad and Stilgenbauer, Stephan and Wu, Catherine},
journal = {Nature},
number = {7574},
pages = {525 -- 530},
publisher = {Nature Publishing Group},
title = {{Mutations driving CLL and their evolution in progression and relapse}},
doi = {10.1038/nature15395},
volume = {526},
year = {2015},
}
@article{1848,
abstract = {The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.},
author = {Schwamb, Bettina and Pick, Robert and Fernández, Sara and Völp, Kirsten and Heering, Jan and Dötsch, Volker and Bösser, Susanne and Jung, Jennifer and Beinoravičiute Kellner, Rasa and Wesely, Josephine and Zörnig, Inka and Hammerschmidt, Matthias and Nowak, Matthias and Penzel, Roland and Zatloukal, Kurt and Joos, Stefan and Rieker, Ralf and Agaimy, Abbas and Söder, Stephan and Reid Lombardo, Kmarie and Kendrick, Michael and Bardsley, Michael and Hayashi, Yujiro and Asuzu, David and Syed, Sabriya and Ördög, Tamás and Zörnig, Martin},
journal = {International Journal of Cancer},
number = {6},
pages = {1318 -- 1329},
publisher = {Wiley},
title = {{FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors}},
doi = {10.1002/ijc.29498},
volume = {137},
year = {2015},
}
@inproceedings{1672,
abstract = {Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol.},
author = {Alwen, Joel F and Ostrovsky, Rafail and Zhou, Hongsheng and Zikas, Vassilis},
location = {Santa Barbara, CA, United States},
pages = {763 -- 780},
publisher = {Springer},
title = {{Incoercible multi-party computation and universally composable receipt-free voting}},
doi = {10.1007/978-3-662-48000-7_37},
volume = {9216},
year = {2015},
}
@misc{5439,
abstract = {The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata. },
author = {Boker, Udi and Henzinger, Thomas A and Otop, Jan},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{The target discounted-sum problem}},
doi = {10.15479/AT:IST-2015-335-v1-1},
year = {2015},
}