Related papers: A consistent least-squares criterion for calibrati…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
We describe a synchronous distributed algorithm which identifies the edge-biconnected components of a connected network. It requires a leader, and uses messages of size O(log |V|). The main idea is to preorder a BFS spanning tree, and then…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Given a polygon representing a transportation network together with a point p in its interior, we aim to extend the network by inserting a line segment, called a feed-link, which connects p to the boundary of the polygon. Once a feed link…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…
Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
We provide an efficient algorithm for determining how a road network has evolved over time, given two snapshot instances from different dates. To allow for such determinations across different databases and even against hand drawn maps, we…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
We consider the problem of estimating the distance, or range, between two locations by measuring the phase of multiple sinusoidal signals transmitted between the locations. Traditional estimators developed for optical interferometry include…
We propose and study a set of algorithms for discovering community structure in networks -- natural divisions of network nodes into densely connected subgroups. Our algorithms all share two definitive features: first, they involve iterative…
Dynamic or temporal networks enable representation of time-varying edges between nodes. Conventional adjacency-based data structures used for storing networks such as adjacency lists were designed without incorporating time and can thus…
A periodic temporal graph, in its simplest form, is a graph in which every edge appears exactly once in the first $\Delta$ time steps, and then it reappears recurrently every $\Delta$ time steps, where $\Delta$ is a given period length.…
Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…
We investigate the evolution rules and degree distribution properties of the Software Heritage dataset, a large-scale growing network linking software source-code versions from open-source communities. The network spans more than 40 years…
Temporal networks model a variety of important phenomena involving timed interactions between entities. Existing methods for machine learning on temporal networks generally exhibit at least one of two limitations. First, time is assumed to…