@article{2970,
abstract = {Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms.},
author = {Kicheva, Anna and Bollenbach, Mark Tobias and Wartlick, Ortrud and Julicher, Frank and Gonzalez Gaitan, Marcos},
journal = {Current Opinion in Genetics & Development},
number = {6},
pages = {527 -- 532},
publisher = {Elsevier},
title = {{Investigating the principles of morphogen gradient formation: from tissues to cells}},
doi = {10.1016/j.gde.2012.08.004},
volume = {22},
year = {2012},
}
@article{2963,
abstract = {Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. },
author = {Jesse, Fabienne and Riebel, Katharina},
journal = {Behavioural Processes},
number = {3},
pages = {262 -- 266},
publisher = {Elsevier},
title = {{Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata}},
doi = {10.1016/j.beproc.2012.09.006},
volume = {91},
year = {2012},
}
@article{3156,
abstract = {Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km.},
author = {Ugelvig, Line V and Andersen, Anne and Boomsma, Jacobus and Nash, David},
journal = {Molecular Ecology},
number = {13},
pages = {3224 -- 3236},
publisher = {Wiley-Blackwell},
title = {{Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion}},
doi = {10.1111/j.1365-294X.2012.05592.x},
volume = {21},
year = {2012},
}
@article{3118,
abstract = {We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.},
author = {Bojsen-Hansen, Morten and Li, Hao and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Tracking surfaces with evolving topology}},
doi = {10.1145/2185520.2185549},
volume = {31},
year = {2012},
}
@article{3120,
abstract = {We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.},
author = {Brown, Gavin and Kerber, Michael and Reid, Miles},
journal = {Compositio Mathematica},
number = {4},
pages = {1171 -- 1194},
publisher = {Cambridge University Press},
title = {{Fano 3 folds in codimension 4 Tom and Jerry Part I}},
doi = {10.1112/S0010437X11007226},
volume = {148},
year = {2012},
}
@inproceedings{3125,
abstract = {We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.},
author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph},
location = {Florence, Italy},
number = {PART 5},
pages = {242 -- 255},
publisher = {Springer},
title = {{Augmented attribute representations}},
doi = {10.1007/978-3-642-33715-4_18},
volume = {7576},
year = {2012},
}
@article{3132,
abstract = {Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony.},
author = {Konrad, Matthias and Pamminger, Tobias and Foitzik, Susanne},
journal = {Naturwissenschaften},
number = {8},
pages = {627 -- 636},
publisher = {Springer},
title = {{Two pathways ensuring social harmony}},
doi = {10.1007/s00114-012-0943-z},
volume = {99},
year = {2012},
}
@article{3245,
abstract = {How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation.},
author = {Behrndt, Martin and Heisenberg, Carl-Philipp J},
journal = {Developmental Cell},
number = {1},
pages = {3 -- 4},
publisher = {Cell Press},
title = {{Spurred by resistance mechanosensation in collective migration}},
doi = {10.1016/j.devcel.2011.12.018},
volume = {22},
year = {2012},
}
@article{3257,
abstract = {Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms.},
author = {Kolmogorov, Vladimir},
journal = {Discrete Applied Mathematics},
number = {4-5},
pages = {416 -- 426},
publisher = {Elsevier},
title = {{Generalized roof duality and bisubmodular functions}},
doi = {10.1016/j.dam.2011.10.026},
volume = {160},
year = {2012},
}
@article{3310,
abstract = {The theory of persistent homology opens up the possibility to reason about topological features of a space or a function quantitatively and in combinatorial terms. We refer to this new angle at a classical subject within algebraic topology as a point calculus, which we present for the family of interlevel sets of a real-valued function. Our account of the subject is expository, devoid of proofs, and written for non-experts in algebraic topology.},
author = {Bendich, Paul and Cabello, Sergio and Edelsbrunner, Herbert},
journal = {Pattern Recognition Letters},
number = {11},
pages = {1436 -- 1444},
publisher = {Elsevier},
title = {{A point calculus for interlevel set homology}},
doi = {10.1016/j.patrec.2011.10.007},
volume = {33},
year = {2012},
}
@article{3168,
abstract = {The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk.},
author = {Feret, Jérôme and Henzinger, Thomas A and Koeppl, Heinz and Petrov, Tatjana},
journal = {Theoretical Computer Science},
pages = {137 -- 164},
publisher = {Elsevier},
title = {{Lumpability abstractions of rule based systems}},
doi = {10.1016/j.tcs.2011.12.059},
volume = {431},
year = {2012},
}
@article{3846,
abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A},
journal = {Journal of Computer and System Sciences},
number = {2},
pages = {394 -- 413},
publisher = {Elsevier},
title = {{A survey of stochastic ω regular games}},
doi = {10.1016/j.jcss.2011.05.002},
volume = {78},
year = {2012},
}
@article{492,
abstract = {Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.},
author = {Galkovskyi, Taras and Mileyko, Yuriy and Bucksch, Alexander and Moore, Brad and Symonova, Olga and Price, Charles and Topp, Chrostopher and Iyer Pascuzzi, Anjali and Zurek, Paul and Fang, Suqin and Harer, John and Benfey, Philip and Weitz, Joshua},
journal = {BMC Plant Biology},
publisher = {BioMed Central},
title = {{GiA Roots: Software for the high throughput analysis of plant root system architecture}},
doi = {10.1186/1471-2229-12-116},
volume = {12},
year = {2012},
}
@article{2848,
abstract = {We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics.},
author = {Chatterjee, Krishnendu and Zufferey, Damien and Nowak, Martin},
journal = {Journal of Theoretical Biology},
pages = {161 -- 173},
publisher = {Elsevier},
title = {{Evolutionary game dynamics in populations with different learners}},
doi = {10.1016/j.jtbi.2012.02.021},
volume = {301},
year = {2012},
}
@inproceedings{2956,
abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and parity objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two-player pushdown games. Finally we also show that all the problems have the same computational complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science},
location = {Dubrovnik, Croatia },
publisher = {IEEE},
title = {{Mean payoff pushdown games}},
doi = {10.1109/LICS.2012.30},
year = {2012},
}
@inproceedings{3341,
abstract = {We consider two-player stochastic games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with \omega-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity gameswith respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition function is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).},
author = {Chatterjee, Krishnendu},
location = {Tallinn, Estonia},
pages = {270 -- 285},
publisher = {Springer},
title = {{Robustness of structurally equivalent concurrent parity games}},
doi = {10.1007/978-3-642-28729-9_18},
volume = {7213},
year = {2012},
}
@inproceedings{3252,
abstract = {We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.},
author = {Chatterjee, Krishnendu and Raman, Vishwanath},
location = {Philadelphia, PA, USA},
pages = {152 -- 168},
publisher = {Springer},
title = {{Synthesizing protocols for digital contract signing}},
doi = {10.1007/978-3-642-27940-9_11},
volume = {7148},
year = {2012},
}
@inproceedings{497,
abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.},
author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
location = {Fontainebleau, France},
pages = {167 -- 182},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster algorithms for alternating refinement relations}},
doi = {10.4230/LIPIcs.CSL.2012.167},
volume = {16},
year = {2012},
}
@misc{5378,
abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.},
author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
issn = {2664-1690},
pages = {21},
publisher = {IST Austria},
title = {{Faster algorithms for alternating refinement relations}},
doi = {10.15479/AT:IST-2012-0001},
year = {2012},
}
@article{2318,
abstract = {We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. },
author = {Seiringer, Robert},
journal = {Journal of Spectral Theory},
number = {3},
pages = {321--328},
publisher = {European Mathematical Society},
title = {{Absence of bound states implies non-negativity of the scattering length}},
doi = {10.4171/JST/31},
volume = {2},
year = {2012},
}