Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general rates-across-sites models. Our results imply, in particular, that large phylogenies are typically identifiable under rate variation. We also derive sequence-length requirements for high-probability reconstruction. Our main contribution is a novel algorithm that clusters sites according to their mutation rate. Following this site clustering step, standard reconstruction techniques can be used to recover the phylogeny. Our results rely on a basic insight: that, for large trees, certain site statistics experience concentration-of-measure phenomena.
The proof of our main results relies on the construction of a site clustering statistic that discriminates between different rates. A similar statistic was also used in @cite_4 in a different context. However, in contrast to @cite_4 , our main reconstruction result requires that a site clustering statistic be constructed based only on data generated by the mixture---that is, without prior knowledge of the model.
@cite_4
2143557214 2139280638 2147256592 2962699510
Server side measurements from several Wi-Fi hot-spots deployed in a nationwide network over different types of venues from small coffee shops to large enterprises are used to highlight differences in traffic volumes and patterns. We develop a common modeling framework for the number of simultaneously present customers. Our approach has many novel elements: (a) We combine statistical clustering with Poisson regression from Generalized Linear Models to fit a non-stationary Poisson process to the arrival counts and demonstrate its remarkable accuracy; (b) We model the heavy tailed distribution of connection durations through fitting a Phase Type distribution to its logarithm so that not only the tail but also the overall distribution is well matched; (c) We obtain the distribution of the number of simultaneously present customers from an M t G ∞ queuing model using a novel regenerative argument that is transparent and avoids the customarily made assumption of the queue starting empty at an infinite past; (d) Most importantly, we validate our models by comparison of their predictions and confidence intervals against test data that is not used in fitting the models. We explore the idea of evidence accumulation (EAC) for combining the results of multiple clusterings. First, a clustering ensemble?a set of object partitions, is produced. Given a data set (n objects or patterns in d dimensions), different ways of producing data partitions are: 1) applying different clustering algorithms and 2) applying the same clustering algorithm with different values of parameters or initializations. Further, combinations of different data representations (feature spaces) and clustering algorithms can also provide a multitude of significantly different data partitionings. We propose a simple framework for extracting a consistent clustering, given the various partitions in a clustering ensemble. According to the EAC concept, each partition is viewed as an independent evidence of data organization, individual data partitions being combined, based on a voting mechanism, to generate a new n n similarity matrix between the n patterns. The final data partition of the n patterns is obtained by applying a hierarchical agglomerative clustering algorithm on this matrix. We have developed a theoretical framework for the analysis of the proposed clustering combination strategy and its evaluation, based on the concept of mutual information between data partitions. Stability of the results is evaluated using bootstrapping techniques. A detailed discussion of an evidence accumulation-based clustering algorithm, using a split and merge strategy based on the K-means clustering algorithm, is presented. Experimental results of the proposed method on several synthetic and real data sets are compared with other combination strategies, and with individual clustering results produced by well-known clustering algorithms. Our goal in this paper is to develop a practical framework for obtaining a uniform sample of users in an online social network (OSN) by crawling its social graph. Such a sample allows to estimate any user property and some topological properties as well. To this end, first, we consider and compare several candidate crawling techniques. Two approaches that can produce approximately uniform samples are the Metropolis-Hasting random walk (MHRW) and a re-weighted random walk (RWRW). Both have pros and cons, which we demonstrate through a comparison to each other as well as to the "ground truth." In contrast, using Breadth-First-Search (BFS) or an unadjusted Random Walk (RW) leads to substantially biased results. Second, and in addition to offline performance assessment, we introduce online formal convergence diagnostics to assess sample quality during the data collection process. We show how these diagnostics can be used to effectively determine when a random walk sample is of adequate size and quality. Third, as a case study, we apply the above methods to Facebook and we collect the first, to the best of our knowledge, representative sample of Facebook users. We make it publicly available and employ it to characterize several key properties of Facebook. In this paper, we consider the cluster estimation problem under the stochastic block model. We show that the semidefinite programming (SDP) formulation for this problem achieves an error rate that decays exponentially in the signal-to-noise ratio. The error bound implies weak recovery in the sparse graph regime with bounded expected degrees as well as exact recovery in the dense regime. An immediate corollary of our results yields error bounds under the censored block model. Moreover, these error bounds are robust, continuing to hold under heterogeneous edge probabilities and a form of the so-called monotone attack. Significantly, this error rate is achieved by the SDP solution itself without any further pre- or post-processing and improves upon existing polynomially decaying error bounds proved using the Grothendieck’s inequality. Our analysis builds on two key ingredients: 1) showing that the graph has a well-behaved spectrum, even in the sparse regime, after discounting an exponentially small number of edges and 2) an order-statistics argument that governs the final error rate. Both arguments highlight the implicit regularization effect of the SDP formulation.