@article{3116, abstract = {Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC.}, author = {Chatterjee, Krishnendu and De Alfaro, Luca and Faella, Marco and Majumdar, Ritankar and Raman, Vishwanath}, journal = {Formal Methods in System Design}, number = {2}, pages = {142 -- 174}, publisher = {Springer}, title = {{Code aware resource management}}, doi = {10.1007/s10703-012-0170-4}, volume = {42}, year = {2013}, } @article{3261, abstract = {Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.}, author = {Dubuis, Julien and Tkacik, Gasper and Wieschaus, Eric and Gregor, Thomas and Bialek, William}, journal = {PNAS}, number = {41}, pages = {16301 -- 16308}, publisher = {National Academy of Sciences}, title = {{Positional information, in bits}}, doi = {10.1073/pnas.1315642110}, volume = {110}, year = {2013}, } @misc{3321, author = {Quadrianto, Novi and Lampert, Christoph}, booktitle = {Encyclopedia of Systems Biology}, editor = {Dubitzky, Werner and Wolkenhauer, Olaf and Cho, Kwang and Yokota, Hiroki}, pages = {1069 -- 1069}, publisher = {Springer}, title = {{Kernel based learning}}, doi = {10.1007/978-1-4419-9863-7_604}, volume = {3}, year = {2013}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @inproceedings{10897, abstract = {Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.}, author = {Edelsbrunner, Herbert}, booktitle = {Graph-Based Representations in Pattern Recognition}, isbn = {9783642382208}, issn = {1611-3349}, location = {Vienna, Austria}, pages = {182--183}, publisher = {Springer Nature}, title = {{Persistent homology in image processing}}, doi = {10.1007/978-3-642-38221-5_19}, volume = {7877}, year = {2013}, } @inproceedings{10898, abstract = {A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.}, author = {Haas, Andreas and Lippautz, Michael and Henzinger, Thomas A and Payer, Hannes and Sokolova, Ana and Kirsch, Christoph M. and Sezgin, Ali}, booktitle = {Proceedings of the ACM International Conference on Computing Frontiers - CF '13}, isbn = {978-145032053-5}, location = {Ischia, Italy}, number = {5}, publisher = {ACM Press}, title = {{Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation}}, doi = {10.1145/2482767.2482789}, year = {2013}, } @inbook{10899, author = {Barton, Nicholas H}, booktitle = {Encyclopedia of Biodiversity}, isbn = {978-0-12-384720-1}, keywords = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation}, pages = {508--515}, publisher = {Elsevier}, title = {{Differentiation}}, doi = {10.1016/b978-0-12-384719-5.00031-9}, year = {2013}, } @inbook{10900, abstract = {Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.}, author = {Weber, Michele and Sixt, Michael K}, booktitle = {Chemokines}, editor = {Cardona, Astrid and Ubogu, Eroboghene}, isbn = {9781627034258}, issn = {1940-6029}, pages = {215--226}, publisher = {Humana Press}, title = {{Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations}}, doi = {10.1007/978-1-62703-426-5_14}, volume = {1013}, year = {2013}, } @inproceedings{10902, abstract = {We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language.}, author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Rubin, Sasha}, booktitle = {7th International Conference on Language and Automata Theory and Applications}, isbn = {9783642370632}, issn = {1611-3349}, location = {Bilbao, Spain}, pages = {214--225}, publisher = {Springer Nature}, title = {{How to travel between languages}}, doi = {10.1007/978-3-642-37064-9_20}, volume = {7810}, year = {2013}, } @article{827, abstract = {As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.}, author = {O'Brien, José and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Cytokinin cross talking during biotic and abiotic stress responses}}, doi = {10.3389/fpls.2013.00451}, volume = {4}, year = {2013}, } @article{828, abstract = {The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.}, author = {Cuesta, Candela and Wabnik, Krzysztof T and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Systems approaches to study root architecture dynamics}}, doi = {10.3389/fpls.2013.00537}, volume = {4}, year = {2013}, } @inproceedings{2000, abstract = {In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.}, author = {Reiter, Johannes and Božić, Ivana and Chatterjee, Krishnendu and Nowak, Martin}, booktitle = {Proceedings of 25th Int. Conf. on Computer Aided Verification}, location = {St. Petersburg, Russia}, pages = {101 -- 106}, publisher = {Springer}, title = {{TTP: Tool for tumor progression}}, doi = {10.1007/978-3-642-39799-8_6}, volume = {8044}, year = {2013}, } @article{2009, abstract = {Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.}, author = {Uhler, Caroline and Slavkovic, Aleksandra and Fienberg, Stephen}, journal = {Journal of Privacy and Confidentiality }, number = {1}, pages = {137 -- 166}, publisher = {Carnegie Mellon University}, title = {{Privacy-preserving data sharing for genome-wide association studies}}, doi = {10.29012/jpc.v5i1.629}, volume = {5}, year = {2013}, } @article{2010, abstract = {Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.}, author = {Uhler, Caroline and Raskutti, Garvesh and Bühlmann, Peter and Yu, Bin}, journal = {The Annals of Statistics}, number = {2}, pages = {436 -- 463}, publisher = {Institute of Mathematical Statistics}, title = {{Geometry of the faithfulness assumption in causal inference}}, doi = {10.1214/12-AOS1080}, volume = {41}, year = {2013}, } @inproceedings{2181, abstract = {There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all "legal" sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Payer, Hannes and Sezgin, Ali and Sokolova, Ana}, booktitle = {Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language}, isbn = {978-1-4503-1832-7}, location = {Rome, Italy}, pages = {317 -- 328}, publisher = {ACM}, title = {{Quantitative relaxation of concurrent data structures}}, doi = {10.1145/2429069.2429109}, year = {2013}, } @inproceedings{2182, abstract = {We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed.}, author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun}, booktitle = {Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language}, location = {Rome, Italy}, pages = {115 -- 128}, publisher = {ACM}, title = {{Quantitative abstraction refinement}}, doi = {10.1145/2429069.2429085}, year = {2013}, } @inproceedings{2209, abstract = {A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985. }, author = {Biedl, Therese and Held, Martin and Huber, Stefan}, location = {St. Petersburg, Russia}, pages = {37 -- 46}, publisher = {IEEE}, title = {{Recognizing straight skeletons and Voronoi diagrams and reconstructing their input}}, doi = {10.1109/ISVD.2013.11}, year = {2013}, } @inproceedings{2210, abstract = {A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model.}, author = {Biedl, Therese and Held, Martin and Huber, Stefan}, booktitle = {29th European Workshop on Computational Geometry}, location = {Braunschweig, Germany}, pages = {95 -- 98}, publisher = {TU Braunschweig}, title = {{Reconstructing polygons from embedded straight skeletons}}, year = {2013}, } @inproceedings{2237, abstract = {We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation.}, author = {Blanc, Régis and Gupta, Ashutosh and Kovács, Laura and Kragl, Bernhard}, location = {Stellenbosch, South Africa}, pages = {173 -- 181}, publisher = {Springer}, title = {{Tree interpolation in Vampire}}, doi = {10.1007/978-3-642-45221-5_13}, volume = {8312}, year = {2013}, } @inproceedings{2238, abstract = {We study the problem of achieving a given value in Markov decision processes (MDPs) with several independent discounted reward objectives. We consider a generalised version of discounted reward objectives, in which the amount of discounting depends on the states visited and on the objective. This definition extends the usual definition of discounted reward, and allows to capture the systems in which the value of different commodities diminish at different and variable rates. We establish results for two prominent subclasses of the problem, namely state-discount models where the discount factors are only dependent on the state of the MDP (and independent of the objective), and reward-discount models where they are only dependent on the objective (but not on the state of the MDP). For the state-discount models we use a straightforward reduction to expected total reward and show that the problem whether a value is achievable can be solved in polynomial time. For the reward-discount model we show that memory and randomisation of the strategies are required, but nevertheless that the problem is decidable and it is sufficient to consider strategies which after a certain number of steps behave in a memoryless way. For the general case, we show that when restricted to graphs (i.e. MDPs with no randomisation), pure strategies and discount factors of the form 1/n where n is an integer, the problem is in PSPACE and finite memory suffices for achieving a given value. We also show that when the discount factors are not of the form 1/n, the memory required by a strategy can be infinite. }, author = {Chatterjee, Krishnendu and Forejt, Vojtěch and Wojtczak, Dominik}, location = {Stellenbosch, South Africa}, pages = {228 -- 242}, publisher = {Springer}, title = {{Multi-objective discounted reward verification in graphs and MDPs}}, doi = {10.1007/978-3-642-45221-5_17}, volume = {8312}, year = {2013}, }