@article{2944, abstract = {We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.}, author = {Aeschbacher, Simon and Futschik, Andreas and Beaumont, Mark}, journal = {Molecular Ecology}, number = {4}, pages = {987 -- 1002}, publisher = {Wiley-Blackwell}, title = {{Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. }}, doi = {10.1111/mec.12165}, volume = {22}, year = {2013}, } @inproceedings{2948, abstract = {Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.}, author = {Tommasi, Tatiana and Quadrianto, Novi and Caputo, Barbara and Lampert, Christoph}, location = {Daejeon, Korea}, pages = {1 -- 15}, publisher = {Springer}, title = {{Beyond dataset bias: Multi-task unaligned shared knowledge transfer}}, doi = {10.1007/978-3-642-37331-2_1}, volume = {7724}, year = {2013}, } @inproceedings{2973, abstract = {Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip. Implementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. In this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols.}, author = {Bangerter, Endre and Barzan, Stefania and Stephan Krenn and Sadeghi, Ahmad-Reza and Schneider, Thomas and Tsay, Joe-Kai}, editor = {Christianson, Bruce and Malcolm, James A. and Matyas, Vashek and Roe, Michael}, pages = {51 -- 62}, publisher = {Springer}, title = {{Bringing Zero-Knowledge Proofs of Knowledge to Practice}}, doi = {10.1007/978-3-642-36213-2_9}, volume = {7028}, year = {2013}, } @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}, } @article{331, abstract = {We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents.}, author = {Li, Wenhua and Zamani, Reza and Rivera Gil, Pilar and Pelaz, Beatriz and Ibáñez, Maria and Cadavid, Doris and Shavel, Alexey and Alvarez Puebla, Ramon and Parak, Wolfgang and Arbiol, Jordi and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {19}, pages = {7098 -- 7101}, publisher = {ACS}, title = {{CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents}}, doi = {10.1021/ja401428e}, volume = {135}, 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{342, abstract = {Morphology is a key parameter in the design of novel nanocrystals and nanomaterials with controlled functional properties. Here, we demonstrate the potential of foreign metal ions to tune the morphology of colloidal semiconductor nanoparticles. We illustrate the underlying mechanism by preparing copper selenide nanocubes in the presence of Al ions. We further characterize the plasmonic properties of the obtained nanocrystals and demonstrate their potential as a platform to produce cubic nanoparticles with different composition by cation exchange. © 2013 American Chemical Society.}, author = {Li, Wenhua and Zamani, Reza and Ibáñez, Maria and Cadavid, Doris and Shavel, Alexey and Morante, Joan and Arbiol, Jordi and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {12}, pages = {4664 -- 4667}, publisher = {American Chemical Society}, title = {{Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes}}, doi = {10.1021/ja400472m}, volume = {135}, year = {2013}, } @article{13405, abstract = {We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance.}, author = {Ely, Tal and Das, Sanjib and Li, Wenjie and Kundu, Pintu and Tirosh, Einat and Cahen, David and Vilan, Ayelet and Klajn, Rafal}, issn = {1437-2096}, journal = {Synlett}, keywords = {Organic Chemistry}, number = {18}, pages = {2370--2374}, publisher = {Georg Thieme Verlag}, title = {{Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol}}, doi = {10.1055/s-0033-1340087}, volume = {24}, year = {2013}, } @article{13406, abstract = {Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli.}, author = {Das, Sanjib and Ranjan, Priyadarshi and Maiti, Pradipta Sankar and Singh, Gurvinder and Leitus, Gregory and Klajn, Rafal}, issn = {0935-9648}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {3}, pages = {422--426}, publisher = {Wiley}, title = {{Dual-responsive nanoparticles and their self-assembly}}, doi = {10.1002/adma.201201734}, volume = {25}, year = {2013}, } @inproceedings{1374, abstract = {We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.}, author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël}, booktitle = {22nd EACSL Annual Conference on Computer Science Logic}, location = {Torino, Italy}, pages = {181 -- 196}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Infinite-state games with finitary conditions}}, doi = {10.4230/LIPIcs.CSL.2013.181}, volume = {23}, year = {2013}, } @inproceedings{1376, abstract = {We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Pavlogiannis, Andreas}, booktitle = {13th International Conference on Formal Methods in Computer-Aided Design}, location = {Portland, OR, United States}, pages = {18 -- 25}, publisher = {IEEE}, title = {{Distributed synthesis for LTL fragments}}, doi = {10.1109/FMCAD.2013.6679386}, year = {2013}, } @inproceedings{1385, abstract = {It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.}, author = {Hofferek, Georg and Gupta, Ashutosh and Könighofer, Bettina and Jiang, Jie and Bloem, Roderick}, booktitle = {2013 Formal Methods in Computer-Aided Design}, location = {Portland, OR, United States}, pages = {77 -- 84}, publisher = {IEEE}, title = {{Synthesizing multiple boolean functions using interpolation on a single proof}}, doi = {10.1109/FMCAD.2013.6679394}, year = {2013}, } @inproceedings{1387, abstract = {Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.}, author = {Boker, Udi and Kuperberg, Denis and Kupferman, Orna and Skrzypczak, Michał}, location = {Riga, Latvia}, number = {PART 2}, pages = {89 -- 100}, publisher = {Springer}, title = {{Nondeterminism in the presence of a diverse or unknown future}}, doi = {10.1007/978-3-642-39212-2_11}, volume = {7966}, year = {2013}, } @phdthesis{1405, abstract = {Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency. First, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point.}, author = {Zufferey, Damien}, issn = {2663-337X}, pages = {134}, publisher = {Institute of Science and Technology Austria}, title = {{Analysis of dynamic message passing programs}}, doi = {10.15479/at:ista:1405}, year = {2013}, } @phdthesis{1406, abstract = {Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading.}, author = {Campinho, Pedro}, issn = {2663-337X}, pages = {123}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading}}, year = {2013}, } @article{1442, abstract = {We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties.}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Annals of Mathematics}, number = {3}, pages = {1147 -- 1168}, publisher = {Princeton University Press}, title = {{Positivity for Kac polynomials and DT-invariants of quivers}}, doi = {10.4007/annals.2013.177.3.8}, volume = {177}, year = {2013}, } @inbook{1443, abstract = {Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory.}, author = {Tamas Hausel}, booktitle = {Handbook of Moduli: Volume II}, pages = {29 -- 70}, publisher = {International Press}, title = {{Global topology of the Hitchin system}}, volume = {25}, year = {2013}, } @article{1469, abstract = {We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups.}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Advances in Mathematics}, pages = {85 -- 128}, publisher = {Academic Press}, title = {{Arithmetic harmonic analysis on character and quiver varieties II}}, doi = {10.1016/j.aim.2012.10.009}, volume = {234}, year = {2013}, } @article{1470, abstract = {We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena.}, author = {De Cataldo, Mark A and Tamas Hausel and Migliorini, Luca}, journal = {Journal of Singularities}, pages = {23 -- 38}, publisher = {Worldwide Center of Mathematics}, title = {{Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces}}, doi = {10.5427/jsing.2013.7c}, volume = {7}, year = {2013}, }