@article{1357, author = {Barton, Nicholas H}, journal = {Genetics}, number = {3}, pages = {865 -- 866}, publisher = {Genetics Society of America}, title = {{Richard Hudson and Norman Kaplan on the coalescent process}}, doi = {10.1534/genetics.116.187542}, volume = {202}, year = {2016}, } @article{1359, abstract = {The role of gene interactions in the evolutionary process has long been controversial. Although some argue that they are not of importance, because most variation is additive, others claim that their effect in the long term can be substantial. Here, we focus on the long-term effects of genetic interactions under directional selection assuming no mutation or dominance, and that epistasis is symmetrical overall. We ask by how much the mean of a complex trait can be increased by selection and analyze two extreme regimes, in which either drift or selection dominate the dynamics of allele frequencies. In both scenarios, epistatic interactions affect the long-term response to selection by modulating the additive genetic variance. When drift dominates, we extend Robertson ’ s [Robertson A (1960) Proc R Soc Lond B Biol Sci 153(951):234 − 249] argument to show that, for any form of epistasis, the total response of a haploid population is proportional to the initial total genotypic variance. In contrast, the total response of a diploid population is increased by epistasis, for a given initial genotypic variance. When selection dominates, we show that the total selection response can only be increased by epistasis when s ome initially deleterious alleles become favored as the genetic background changes. We find a sim- ple approximation for this effect and show that, in this regime, it is the structure of the genotype - phenotype map that matters and not the variance components of the population.}, author = {Paixao, Tiago and Barton, Nicholas H}, journal = {PNAS}, number = {16}, pages = {4422 -- 4427}, publisher = {National Academy of Sciences}, title = {{The effect of gene interactions on the long-term response to selection}}, doi = {10.1073/pnas.1518830113}, volume = {113}, year = {2016}, } @article{1360, abstract = {We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. }, author = {Akopyan, Arseniy and Balitskiy, Alexey and Karasev, Roman and Sharipova, Anastasia}, journal = {Proceedings of the American Mathematical Society}, number = {10}, pages = {4501 -- 4513}, publisher = {American Mathematical Society}, title = {{Elementary approach to closed billiard trajectories in asymmetric normed spaces}}, doi = {10.1090/proc/13062}, volume = {144}, year = {2016}, } @inproceedings{1361, abstract = {We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.}, author = {Da, Fang and Hahn, David and Batty, Christopher and Wojtan, Christopher J and Grinspun, Eitan}, location = {Anaheim, CA, USA}, number = {4}, publisher = {ACM}, title = {{Surface only liquids}}, doi = {10.1145/2897824.2925899}, volume = {35}, year = {2016}, } @inproceedings{1363, abstract = {When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.}, author = {Bojsen-Hansen, Morten and Wojtan, Christopher J}, location = {Anaheim, CA, USA}, number = {4}, publisher = {ACM}, title = {{Generalized non-reflecting boundaries for fluid re-simulation}}, doi = {10.1145/2897824.2925963}, volume = {35}, year = {2016}, } @inproceedings{1364, abstract = {We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.}, author = {Miguel Villalba, Eder and Lepoutre, Mathias and Bickel, Bernd}, location = {Anaheim, CA, USA}, number = {4}, publisher = {ACM}, title = {{Computational design of stable planar-rod structures}}, doi = {10.1145/2897824.2925978}, volume = {35}, year = {2016}, } @inproceedings{1365, abstract = {A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.}, author = {Alwen, Joel F and Blocki, Jeremiah}, location = {Santa Barbara, CA, USA}, pages = {241 -- 271}, publisher = {Springer}, title = {{Efficiently computing data-independent memory-hard functions}}, doi = {10.1007/978-3-662-53008-5_9}, volume = {9815}, year = {2016}, } @inproceedings{1366, abstract = {We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.}, author = {Gazi, Peter and Tessaro, Stefano}, location = {Vienna, Austria}, pages = {87 -- 116}, publisher = {Springer}, title = {{Provably robust sponge-based PRNGs and KDFs}}, doi = {10.1007/978-3-662-49890-3_4}, volume = {9665}, year = {2016}, } @article{1368, abstract = {Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.}, author = {Wysokiński, Marcin and Kaczmarczyk, Jan and Spałek, Jozef}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {2}, publisher = {American Physical Society}, title = {{Correlation driven d wave superconductivity in Anderson lattice model: Two gaps}}, doi = {10.1103/PhysRevB.94.024517}, volume = {94}, year = {2016}, } @inproceedings{1369, abstract = {We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.}, author = {Kolesnikov, Alexander and Lampert, Christoph}, location = {Amsterdam, The Netherlands}, pages = {695 -- 711}, publisher = {Springer}, title = {{Seed, expand and constrain: Three principles for weakly-supervised image segmentation}}, doi = {10.1007/978-3-319-46493-0_42}, volume = {9908}, year = {2016}, } @article{1370, abstract = {We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.}, author = {Barzanjeh, Shabir and Vitali, David}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {3}, publisher = {American Physical Society}, title = {{Phonon Josephson junction with nanomechanical resonators}}, doi = {10.1103/PhysRevA.93.033846}, volume = {93}, year = {2016}, } @article{1371, abstract = {Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.}, author = {Martin, Olivier and Krzywicki, André and Zagórski, Marcin P}, journal = {Physics of Life Reviews}, pages = {124 -- 158}, publisher = {Elsevier}, title = {{Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function}}, doi = {10.1016/j.plrev.2016.06.002}, volume = {17}, year = {2016}, } @article{1372, abstract = {Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.}, author = {Pernisová, Markéta and Prat, Tomas and Grones, Peter and Haruštiaková, Danka and Matonohova, Martina and Spíchal, Lukáš and Nodzyński, Tomasz and Friml, Jirí and Hejátko, Jan}, journal = {New Phytologist}, number = {2}, pages = {497 -- 509}, publisher = {Wiley-Blackwell}, title = {{Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis}}, doi = {10.1111/nph.14049}, volume = {212}, year = {2016}, } @article{1373, author = {Martin, Olivier and Zagórski, Marcin P}, journal = {Physics of Life Reviews}, pages = {168 -- 171}, publisher = {Elsevier}, title = {{Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"}}, doi = {10.1016/j.plrev.2016.06.006}, volume = {17}, year = {2016}, } @article{1377, abstract = {We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.}, author = {Kolmogorov, Vladimir and Pock, Thomas and Rolinek, Michal}, journal = {SIAM Journal on Imaging Sciences}, number = {2}, pages = {605 -- 636}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Total variation on a tree}}, doi = {10.1137/15M1010257}, volume = {9}, year = {2016}, } @inproceedings{1378, abstract = {We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M.}, author = {Dotterrer, Dominic and Kaufman, Tali and Wagner, Uli}, location = {Medford, MA, USA}, pages = {35.1 -- 35.10}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On expansion and topological overlap}}, doi = {10.4230/LIPIcs.SoCG.2016.35}, volume = {51}, year = {2016}, } @inproceedings{1379, abstract = {We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.}, author = {Burton, Benjamin and De Mesmay, Arnaud N and Wagner, Uli}, location = {Medford, MA, USA}, pages = {24.1 -- 24.15}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Finding non-orientable surfaces in 3-manifolds}}, doi = {10.4230/LIPIcs.SoCG.2016.24}, volume = {51}, year = {2016}, } @article{1380, abstract = {We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.}, author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James}, journal = {Journal of the ACM}, number = {3}, publisher = {ACM}, title = {{On the complexity of the orbit problem}}, doi = {10.1145/2857050}, volume = {63}, year = {2016}, } @inproceedings{1381, abstract = {Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.}, author = {Mabillard, Isaac and Wagner, Uli}, location = {Medford, MA, USA}, pages = {51.1 -- 51.12}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range}}, doi = {10.4230/LIPIcs.SoCG.2016.51}, volume = {51}, year = {2016}, } @article{1382, abstract = {Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.}, author = {Ellis, Thomas and Field, David}, journal = {Annals of Botany}, number = {7}, pages = {1133 -- 1140}, publisher = {Oxford University Press}, title = {{Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae}}, doi = {10.1093/aob/mcw043}, volume = {117}, year = {2016}, }