Related papers: Partitioning the Sample Space on Five Taxa for the…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
The Neighbor Joining Algorithm is among the most fundamental algorithmic results in computational biology. However, its definition and correctness proof are not straightforward. In particular, ''the question ''what does the NJ method seek…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this article we propose a new method, which we name 'quartet neighbor joining', or 'quartet-NJ', to infer an unrooted species tree on a given set of taxa T from empirical distributions of unrooted quartet gene trees on all four-taxon…
The problem of community detection in networks is usually formulated as finding a single partition of the network into some "correct" number of communities. We argue that it is more interpretable and in some regimes more accurate to…
Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry…
A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a…
Real bipartite networks combine degree-constrained random mixing with structured, locality-like rules. We introduce a statistical filter that benchmarks node-level bipartite clustering against degree-preserving randomizations to classify…
The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is ``optimal'' when the algorithm…
This paper gives a new algorithm for sampling tree-weighted partitions of a large class of planar graphs. Formally, the tree-weighted distribution on $k$-partitions of a graph weights $k$-partitions proportional to the product of the number…
Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
Considering a clique as a conservative definition of community structure, we examine how graph partitioning algorithms interact with cliques. Many popular community-finding algorithms partition the entire graph into non-overlapping…
This paper introduces the Partition Tree Weighting technique, an efficient meta-algorithm for piecewise stationary sources. The technique works by performing Bayesian model averaging over a large class of possible partitions of the data…
Graph sampling allows mining a small representative subgraph from a big graph. Sampling algorithms deploy different strategies to replicate the properties of a given graph in the sampled graph. In this study, we provide a comprehensive…
In many domains, data measurements can naturally be associated with the leaves of a tree, expressing the relationships among these measurements. For example, companies belong to industries, which in turn belong to ever coarser divisions…
Bipartite networks manifest as a stream of edges that represent transactions, e.g., purchases by retail customers. Many machine learning applications employ neighborhood-based measures to characterize the similarity among the nodes, such as…
The topological information of a network can be retrieved equivalently from its complement consisting of the same nodes but complementary edges. Hence the partition of a network into certain substructures based on given criteria should be…