@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},
}
@article{2902,
abstract = {We present an algorithm for simplifying linear cartographic objects and results obtained with a computer program implementing this algorithm. },
author = {Edelsbrunner, Herbert and Musin, Oleg and Ukhalov, Alexey and Yakimova, Olga and Alexeev, Vladislav and Bogaevskaya, Victoriya and Gorohov, Andrey and Preobrazhenskaya, Margarita},
journal = {Modeling and Analysis of Information Systems},
number = {6},
pages = {152 -- 160},
publisher = {Technische Universität Darmstadt},
title = {{Fractal and computational geometry for generalizing cartographic objects}},
volume = {19},
year = {2012},
}
@inproceedings{2825,
abstract = {We study the problem of maximum marginal prediction (MMP) in probabilistic graphical models, a task that occurs, for example, as the Bayes optimal decision rule under a Hamming loss. MMP is typically performed as a two-stage procedure: one estimates each variable's marginal probability and then forms a prediction from the states of maximal probability. In this work we propose a simple yet effective technique for accelerating MMP when inference is sampling-based: instead of the above two-stage procedure we directly estimate the posterior probability of each decision variable. This allows us to identify the point of time when we are sufficiently certain about any individual decision. Whenever this is the case, we dynamically prune the variables we are confident about from the underlying factor graph. Consequently, at any time only samples of variables whose decision is still uncertain need to be created. Experiments in two prototypical scenarios, multi-label classification and image inpainting, show that adaptive sampling can drastically accelerate MMP without sacrificing prediction accuracy.},
author = {Lampert, Christoph},
location = {Lake Tahoe, NV, United States},
pages = {82 -- 90},
publisher = {Neural Information Processing Systems},
title = {{Dynamic pruning of factor graphs for maximum marginal prediction}},
volume = {1},
year = {2012},
}
@article{2849,
author = {Edelsbrunner, Herbert and Strelkova, Nataliya},
journal = {Russian Mathematical Surveys},
number = {6},
pages = {1167 -- 1168},
publisher = {IOP Publishing Ltd.},
title = {{On the configuration space of Steiner minimal trees}},
doi = {10.1070/RM2012v067n06ABEH004820},
volume = {67},
year = {2012},
}
@article{2945,
abstract = {In search of foreign antigens, lymphocytes recirculate from the blood, through lymph nodes, into lymphatics and back to the blood. Dendritic cells also migrate to lymph nodes for optimal interaction with lymphocytes. This continuous trafficking of immune cells into and out of lymph nodes is essential for immune surveillance of foreign invaders. In this article, we review our current understanding of the functions of high endothelial venules (HEVs), stroma and lymphatics in the entry, positioning and exit of immune cells in lymph nodes during homeostasis, and we highlight the unexpected role of dendritic cells in the control of lymphocyte homing through HEVs.},
author = {Girard, Jean and Moussion, Christine and Förster, Reinhold},
journal = {Nature Reviews Immunology},
number = {11},
pages = {762 -- 773},
publisher = {Nature Publishing Group},
title = {{HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes}},
doi = {10.1038/nri3298},
volume = {12},
year = {2012},
}
@article{2938,
abstract = {Social insects have a very high potential to become invasive pest species. Here, we explore how their social lifestyle and their interaction with parasites may contribute to this invasive success. Similar to solitary species, parasite release followed by the evolution of increased competitive ability can promote establishment of introduced social insect hosts in their introduced range. Genetic bottlenecks during introduction of low numbers of founder individuals decrease the genetic diversity at three levels: the population, the colony and the individual, with the colony level being specific to social insects. Reduced genetic diversity can affect both the individual immune system and the collective colony-level disease defences (social immunity). Still, the dual immune system is likely to make social insects more robust to parasite attack. Changes in social structure from small, family-based, territorially aggressive societies in native populations towards huge networks of cooperating nests (unicoloniality) occur in some invasive social insects, for example, most invasive ants and some termites. Unicoloniality is likely to affect disease dynamics in multiple ways. The free exchange of individuals within the population leads to an increased genetic heterogeneity among individuals of a single nest, thereby decreasing disease transmission. However, the multitude of reproductively active queens per colony buffers the effect of individual diseased queens and their offspring, which may result in a higher level of vertical disease transmission in unicolonial societies. Lastly, unicoloniality provides a competitive advantage over native species, allowing them to quickly become the dominant species in the habitat, which in turn selects for parasite adaptation to this common host genotype and thus eventually a high parasite pressure. Overall, invasions by insect societies are characterized by general features applying to all introduced species, as well as idiosyncrasies that emerge from their social lifestyle. It is important to study these effects in concert to be able to develop efficient management and biocontrol strategies. © 2012 British Ecological Society.},
author = {Ugelvig, Line V and Cremer, Sylvia},
journal = {Functional Ecology},
number = {6},
pages = {1300 -- 1312},
publisher = {Wiley-Blackwell},
title = {{Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies}},
doi = {10.1111/1365-2435.12013},
volume = {26},
year = {2012},
}
@article{2952,
abstract = {Body axis elongation represents a common and fundamental morphogenetic process in development. A key mechanism triggering body axis elongation without additional growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing and extension. Both collective cell migration and cell intercalation are thought to drive CE and are used to different degrees in various species as they elongate their body axis. Here, we provide an overview of CE as a general strategy for body axis elongation and discuss conserved and divergent mechanisms underlying CE among different species.},
author = {Tada, Masazumi and Heisenberg, Carl-Philipp J},
journal = {Development},
number = {21},
pages = {3897 -- 3904},
publisher = {Company of Biologists},
title = {{Convergent extension Using collective cell migration and cell intercalation to shape embryos}},
doi = {10.1242/dev.073007},
volume = {139},
year = {2012},
}
@article{2969,
abstract = {The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic
opening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal
granule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker
ω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced
mIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,
suggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor
agonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.
},
author = {Goswami, Sarit and Bucurenciu, Iancu and Jonas, Peter M},
journal = {Journal of Neuroscience},
number = {41},
pages = {14294 -- 14304},
publisher = {Society for Neuroscience},
title = {{Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling}},
doi = {10.1523/JNEUROSCI.6104-11.2012},
volume = {32},
year = {2012},
}
@inproceedings{2971,
abstract = {We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. },
author = {Zankl, Georg and Haxhimusa, Yll and Ion, Adrian},
location = {Graz, Austria},
pages = {11 -- 20},
publisher = {Springer},
title = {{Interactive labeling of image segmentation hierarchies}},
doi = {10.1007/978-3-642-32717-9_2},
volume = {7476},
year = {2012},
}
@inproceedings{3119,
abstract = {We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.
},
author = {Raveendran, Karthik and Thuerey, Nils and Wojtan, Christopher J and Turk, Greg},
booktitle = {Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation},
location = {Aire-la-Ville, Switzerland},
pages = {255 -- 264},
publisher = {ACM},
title = {{Controlling liquids using meshes}},
year = {2012},
}