@article{550,
abstract = {For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.},
author = {Alt, Johannes},
issn = {1083589X},
journal = {Electronic Communications in Probability},
publisher = {Institute of Mathematical Statistics},
title = {{Singularities of the density of states of random Gram matrices}},
doi = {10.1214/17-ECP97},
volume = {22},
year = {2017},
}
@inproceedings{551,
abstract = {Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. },
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Nowak, Martin},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs}},
doi = {10.4230/LIPIcs.MFCS.2017.61},
volume = {83},
year = {2017},
}
@inproceedings{552,
abstract = {Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Svozil, Alexander},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster algorithms for mean payoff parity games}},
doi = {10.4230/LIPIcs.MFCS.2017.39},
volume = {83},
year = {2017},
}
@inproceedings{553,
abstract = {We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. },
author = {Chatterjee, Krishnendu and Hansen, Kristofer and Ibsen-Jensen, Rasmus},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Strategy complexity of concurrent safety games}},
doi = {10.4230/LIPIcs.MFCS.2017.55},
volume = {83},
year = {2017},
}
@misc{5559,
abstract = {Strong amplifiers of natural selection},
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak , Martin},
keywords = {natural selection},
publisher = {IST Austria},
title = {{Strong amplifiers of natural selection}},
doi = {10.15479/AT:ISTA:51},
year = {2017},
}
@misc{5560,
abstract = {This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity".
The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.
Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.},
author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C},
keywords = {single cell microscopy, mother machine microfluidic device, AcrAB-TolC pump, multi-drug efflux, Escherichia coli},
publisher = {IST Austria},
title = {{Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity}},
doi = {doi:10.15479/AT:ISTA:53},
year = {2017},
}
@misc{5561,
abstract = {Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. },
author = {Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Meyers, Gene},
keywords = {graph matching, feature matching, QAP, MAP-inference},
publisher = {IST Austria},
title = {{Graph matching problems for annotating C. Elegans}},
doi = {10.15479/AT:ISTA:57},
year = {2017},
}
@misc{5562,
abstract = {This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:
[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.},
author = {Marre, Olivier and Tkacik, Gasper and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael},
keywords = {multi-electrode recording, retinal ganglion cells},
publisher = {IST Austria},
title = {{Multi-electrode array recording from salamander retinal ganglion cells}},
doi = {10.15479/AT:ISTA:61},
year = {2017},
}
@misc{5563,
abstract = {MATLAB code and processed datasets available for reproducing the results in:
Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.
*equal contributions},
author = {Lukacisin, Martin},
publisher = {IST Austria},
title = {{MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'}},
doi = {10.15479/AT:ISTA:64},
year = {2017},
}
@misc{5564,
abstract = {Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.},
author = {Steinrück, Magdalena and Guet, Calin C},
publisher = {IST Austria},
title = {{Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection"}},
doi = {10.15479/AT:ISTA:65},
year = {2017},
}