@article{1171, author = {Tkacik, Gasper}, journal = {Physics of Life Reviews}, pages = {166 -- 167}, publisher = {Elsevier}, title = {{Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.}}, doi = {10.1016/j.plrev.2016.06.005}, volume = {17}, year = {2016}, } @article{1172, abstract = {A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.}, author = {Sachdeva, Himani and Barma, Mustansir and Rao, Madan}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae}}, doi = {10.1038/srep38840}, volume = {6}, year = {2016}, } @article{1177, abstract = {Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.}, author = {Kamath Hosdurg, Chethan and Chatterjee, Sanjit}, journal = {Algorithmica}, number = {4}, pages = {1321 -- 1362}, publisher = {Springer}, title = {{A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound}}, doi = {10.1007/s00453-015-9997-6}, volume = {74}, year = {2016}, } @inproceedings{1179, abstract = {Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another. Such chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.) A variable X has k bits of HILL entropy of quality (ϵ,s) if there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ by distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists. We first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s) , then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2) in circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality). The chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s) , then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.}, author = {Pietrzak, Krzysztof Z and Maciej, Skorski}, location = {Beijing, China}, pages = {183 -- 203}, publisher = {Springer}, title = {{Pseudoentropy: Lower-bounds for chain rules and transformations}}, doi = {10.1007/978-3-662-53641-4_8}, volume = {9985}, year = {2016}, } @article{1181, abstract = {This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.}, author = {Dwyer, Noelle and Chen, Bin and Chou, Shen and Hippenmeyer, Simon and Nguyen, Laurent and Ghashghaei, Troy}, journal = {Journal of Neuroscience}, number = {45}, pages = {11394 -- 11401}, publisher = {Society for Neuroscience}, title = {{Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity}}, doi = {10.1523/JNEUROSCI.2359-16.2016}, volume = {36}, year = {2016}, } @inproceedings{1182, abstract = {Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Tkadlec, Josef}, location = {New York, NY, USA}, pages = {172 -- 179}, publisher = {AAAI Press}, title = {{Robust draws in balanced knockout tournaments}}, volume = {2016-January}, year = {2016}, } @inproceedings{11834, abstract = {We present a deterministic incremental algorithm for exactly maintaining the size of a minimum cut with ~O(1) amortized time per edge insertion and O(1) query time. This result partially answers an open question posed by Thorup [Combinatorica 2007]. It also stays in sharp contrast to a polynomial conditional lower-bound for the fully-dynamic weighted minimum cut problem. Our algorithm is obtained by combining a recent sparsification technique of Kawarabayashi and Thorup [STOC 2015] and an exact incremental algorithm of Henzinger [J. of Algorithm 1997]. We also study space-efficient incremental algorithms for the minimum cut problem. Concretely, we show that there exists an O(n log n/epsilon^2) space Monte-Carlo algorithm that can process a stream of edge insertions starting from an empty graph, and with high probability, the algorithm maintains a (1+epsilon)-approximation to the minimum cut. The algorithm has ~O(1) amortized update-time and constant query-time.}, author = {Goranci, Gramoz and Henzinger, Monika H and Thorup, Mikkel}, booktitle = {24th Annual European Symposium on Algorithms}, isbn = {978-3-95977-015-6}, issn = {1868-8969}, location = {Aarhus, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Incremental exact min-cut in poly-logarithmic amortized update time}}, doi = {10.4230/LIPICS.ESA.2016.46}, volume = {57}, year = {2016}, } @inproceedings{11835, abstract = {During the last 10 years it has become popular to study dynamic graph problems in a emergency planning or sensitivity setting: Instead of considering the general fully dynamic problem, we only have to process a single batch update of size d; after the update we have to answer queries. In this paper, we consider the dynamic subgraph connectivity problem with sensitivity d: We are given a graph of which some vertices are activated and some are deactivated. After that we get a single update in which the states of up to $d$ vertices are changed. Then we get a sequence of connectivity queries in the subgraph of activated vertices. We present the first fully dynamic algorithm for this problem which has an update and query time only slightly worse than the best decremental algorithm. In addition, we present the first incremental algorithm which is tight with respect to the best known conditional lower bound; moreover, the algorithm is simple and we believe it is implementable and efficient in practice.}, author = {Henzinger, Monika H and Neumann, Stefan}, booktitle = {24th Annual European Symposium on Algorithms}, isbn = {978-3-95977-015-6}, issn = {1868-8969}, location = {Aarhus, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Incremental and fully dynamic subgraph connectivity for emergency planning}}, doi = {10.4230/LIPICS.ESA.2016.48}, volume = {57}, year = {2016}, } @inproceedings{11836, abstract = {Given a graph where vertices are partitioned into k terminals and non-terminals, the goal is to compress the graph (i.e., reduce the number of non-terminals) using minor operations while preserving terminal distances approximately. The distortion of a compressed graph is the maximum multiplicative blow-up of distances between all pairs of terminals. We study the trade-off between the number of non-terminals and the distortion. This problem generalizes the Steiner Point Removal (SPR) problem, in which all non-terminals must be removed. We introduce a novel black-box reduction to convert any lower bound on distortion for the SPR problem into a super-linear lower bound on the number of non-terminals, with the same distortion, for our problem. This allows us to show that there exist graphs such that every minor with distortion less than 2 / 2.5 / 3 must have Omega(k^2) / Omega(k^{5/4}) / Omega(k^{6/5}) non-terminals, plus more trade-offs in between. The black-box reduction has an interesting consequence: if the tight lower bound on distortion for the SPR problem is super-constant, then allowing any O(k) non-terminals will not help improving the lower bound to a constant. We also build on the existing results on spanners, distance oracles and connected 0-extensions to show a number of upper bounds for general graphs, planar graphs, graphs that exclude a fixed minor and bounded treewidth graphs. Among others, we show that any graph admits a minor with O(log k) distortion and O(k^2) non-terminals, and any planar graph admits a minor with 1 + epsilon distortion and ~O((k/epsilon)^2) non-terminals.}, author = {Cheung, Yun Kuen and Goranci, Gramoz and Henzinger, Monika H}, booktitle = {43rd International Colloquium on Automata, Languages, and Programming}, isbn = {978-3-95977-013-2}, issn = {1868-8969}, location = {Rome, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Graph minors for preserving terminal distances approximately - lower and upper bounds}}, doi = {10.4230/LIPICS.ICALP.2016.131}, volume = {55}, year = {2016}, } @article{1184, abstract = {Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival.}, author = {Metzler, Sina and Heinze, Jürgen and Schrempf, Alexandra}, journal = {Ecology and Evolution}, number = {24}, pages = {8903 -- 8906}, publisher = {Wiley-Blackwell}, title = {{Mating and longevity in ant males}}, doi = {10.1002/ece3.2474}, volume = {6}, year = {2016}, } @article{1185, abstract = {The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk.}, author = {Cucinotta, Mara and Manrique, Silvia and Guazzotti, Andrea and Quadrelli, Nadia and Mendes, Marta and Benková, Eva and Colombo, Lucia}, journal = {Development}, number = {23}, pages = {4419 -- 4424}, publisher = {Company of Biologists}, title = {{Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development}}, doi = {10.1242/dev.143545}, volume = {143}, year = {2016}, } @article{1186, abstract = {The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.}, author = {Gutierrez-Fernandez, Javier and Saleh, Malek and Alcorlo, Martín and Gómez Mejóa, Alejandro and Pantoja Uceda, David and Treviño, Miguel and Vob, Franziska and Abdullah, Mohammed and Galán Bartual, Sergio and Seinen, Jolien and Sánchez Murcia, Pedro and Gago, Federico and Bruix, Marta and Hammerschmidt, Sven and Hermoso, Juan}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis}}, doi = {10.1038/srep38094}, volume = {6}, year = {2016}, } @inproceedings{11866, abstract = {We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the CONGEST model); here n is the number of nodes in the network and D is its (hop) diameter. This is the first non-trivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al. STOC 2011] modulo some lower-order terms, thus essentially settling the status of this problem which was raised at least a decade ago [Elkin SIGACT News 2004]. It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for approximating a network’s weighted diameter which almost matches the lower bound by Holzer et al. [PODC 2012]. In achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic, construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these techniques with many distributed algorithmic techniques, some of which from problems that are not directly related to shortest paths, e.g. ruling sets [Goldberg et al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC 2014]. The second result partially answers an open problem raised by McGregor in 2006 [
sublinear.info
, Problem 14].}, author = {Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, booktitle = {48th Annual ACM SIGACT Symposium on Theory of Computing}, isbn = {978-145034132-5}, issn = {0737-8017}, location = {Cambridge, MA, United States}, pages = {489 -- 498}, publisher = {Association for Computing Machinery}, title = {{A deterministic almost-tight distributed algorithm for approximating single-source shortest paths}}, doi = {10.1145/2897518.2897638}, year = {2016}, } @inproceedings{11867, abstract = {We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a (2+є)-approximate maximum matching in general graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an αK approximation of the value of the maximum matching with O(n2/K) update time in bipartite graphs, for every sufficiently large constant positive integer K. Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the first deterministic algorithm that can maintain an o(logn)-approximate maximum matching with polylogarithmic update time, improving the seminal result of Onak et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS 2011]. Result (2) achieves a better-than-two approximation with arbitrarily small polynomial update time on bipartite graphs. Previously the best update time for this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current number of edges in the graph.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon}, booktitle = {48th Annual ACM SIGACT Symposium on Theory of Computing}, isbn = {978-145034132-5}, issn = {0737-8017}, location = {Cambridge, MA, United States}, pages = {398 -- 411}, publisher = {Association for Computing Machinery}, title = {{New deterministic approximation algorithms for fully dynamic matching}}, doi = {10.1145/2897518.2897568}, year = {2016}, } @article{1188, abstract = {We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. In the asymptotic regime of slow diffusion, that coincides with the relevant experimental range, the resulting non-linear Fokker–Planck equation is solved for the steady state in the WKB approximation that maps it into the ground state of a quantum particle in an Airy potential plus a centrifugal term. We retrieve scaling laws for growth rate fluctuations and time response with respect to the distance from the maximum growth rate suggesting that suboptimal populations can have a faster response to perturbations.}, author = {De Martino, Daniele and Masoero, Davide}, journal = { Journal of Statistical Mechanics: Theory and Experiment}, number = {12}, publisher = {IOP Publishing}, title = {{Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth}}, doi = {10.1088/1742-5468/aa4e8f}, volume = {2016}, year = {2016}, } @phdthesis{1189, abstract = {Within the scope of this thesis, we show that a driven-dissipative system with few ultracold atoms can exhibit dissipatively bound states, even if the atom-atom interaction is purely repulsive. This bond arises due to the dipole-dipole inter- action, which is restricted to one of the lower electronic energy states, resulting in the distance-dependent coherent population trapping. The quality of this al- ready established method of dissipative binding is improved and the application is extended to higher dimensions and a larger number of atoms. Here, we simu- late two- and three-atom systems using an adapted approach to the Monte Carlo wave-function method and analyse the results. Finally, we examine the possi- bility of finding a setting allowing trimer states but prohibiting dimer states. In the context of open quantum systems, such a three-body bound states corre- sponds to the driven-dissipative analogue of a Borromean state. These states can be detected in modern experiments with dipolar and Rydberg-dressed ultracold atomic gases. }, author = {Jochum, Clemens}, pages = {94}, publisher = {Technical University Vienna}, title = {{Dissipative Few-Body Quantum Systems}}, year = {2016}, } @article{11891, abstract = {We study dynamic (1+𝜖)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected 𝑛-node 𝑚-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp. 670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of 𝑂(𝑚𝑛2) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of 𝑂̃ (𝑛5/2/𝜖) and constant query time that has an additive error of 2 in addition to the 1+𝜖 multiplicative error. This beats the previous 𝑂̃ (𝑚𝑛/𝜖) time when 𝑚=Ω(𝑛3/2). Note that the additive error is unavoidable since, even in the static case, an 𝑂(𝑛3−𝛿)-time (a so-called truly subcubic) combinatorial algorithm with 1+𝜖 multiplicative error cannot have an additive error less than 2−𝜖, unless we make a major breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick, SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems [V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm can also be turned into a (2+𝜖)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3+𝜖)-approximation algorithm with 𝑂̃ (𝑛5/2+𝑂(log(1/𝜖)/log𝑛√)) running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and a query time of 𝑂(loglog𝑛). The algorithm has a multiplicative error of 1+𝜖 and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic algorithm can be turned into a deterministic fully dynamic (1+𝜖)-approximation with an amortized update time of 𝑂̃ (𝑚𝑛/(𝜖𝑡)) and a query time of 𝑂̃ (𝑡) for every 𝑡≤𝑛√. In order to achieve our results, we introduce two new techniques: (i) A monotone Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called a locally persevering emulator. (ii) A derandomization technique based on moving Even--Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest.}, author = {Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {3}, pages = {947--1006}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization}}, doi = {10.1137/140957299}, volume = {45}, year = {2016}, } @inproceedings{1193, abstract = {We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.}, author = {Kolmogorov, Vladimir}, booktitle = {Proceedings - Annual IEEE Symposium on Foundations of Computer Science}, location = {New Brunswick, NJ, USA }, publisher = {IEEE}, title = {{Commutativity in the algorithmic Lovasz local lemma}}, doi = {10.1109/FOCS.2016.88}, volume = {2016-December}, year = {2016}, } @article{1195, abstract = {The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. }, author = {Franssen, Susan and Barton, Nicholas H and Schlötterer, Christian}, journal = {Molecular Biology and Evolution}, number = {1}, pages = {174 -- 184}, publisher = {Oxford University Press}, title = {{Reconstruction of haplotype-blocks selected during experimental evolution.}}, doi = {10.1093/molbev/msw210}, volume = {34}, year = {2016}, } @article{1197, abstract = {Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.}, author = {Prentice, Jason and Marre, Olivier and Ioffe, Mark and Loback, Adrianna and Tkacik, Gasper and Berry, Michael}, journal = {PLoS Computational Biology}, number = {11}, publisher = {Public Library of Science}, title = {{Error-robust modes of the retinal population code}}, doi = {10.1371/journal.pcbi.1005148}, volume = {12}, year = {2016}, }