Related papers: Family-joining: A fast distance-based method for c…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
Relation classification (RC) task is one of fundamental tasks of information extraction, aiming to detect the relation information between entity pairs in unstructured natural language text and generate structured data in the form of…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Clustering is a fundamental approach to understanding data patterns, wherein the intuitive Euclidean distance space is commonly adopted. However, this is not the case for implicit cluster distributions reflected by qualitative attribute…
Model structure and complexity selection remains a challenging problem in system identification, especially for parametric non-linear models. Many Evolutionary Algorithm (EA) based methods have been proposed in the literature for estimating…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
We consider a distributed detection system with communication constraints, where several nodes are arranged in an arbitrary tree topology, under the assumption of conditionally independent observations. We propose a cyclic design procedure…
In this paper, we will analyze the behavior of the Neighbor Joining algorithm on five taxa and we will show that the partition of the sample (data) space for estimation of a tree topology with five taxa into subspaces, within each of which…
Variations in complex traits are influenced by multiple genetic variants, environmental risk factors, and their interactions. Though substantial progress has been made in identifying single genetic variants associated with complex traits,…
Exact inference in Bayesian networks is intractable and has an exponential dependence on the size of the largest clique in the corresponding clique tree (CT), necessitating approximations. Factor based methods to bound clique sizes are more…
We say that a family $\mathcal F$ of $k$-element sets is a {\it $j$-junta} if there is a set $J$ of size $j$ such that, for any $F$, its presence in $\mathcal F$ depends on its intersection with $J$ only. Approximating arbitrary families by…
We propose a new graph metric and study its properties. In contrast to the standard distance in connected graphs, it takes into account all paths between vertices. Formally, it is defined as d(i,j)=q_{ii}+q_{jj}-q_{ij}-q_{ji}, where q_{ij}…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
Generalized linear and additive models are very efficient regression tools but the selection of relevant terms becomes difficult if higher order interactions are needed. In contrast, tree-based methods also known as recursive partitioning…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
The theory of complex trees is introduced as a new approach to study a broad class of self-similar sets. Systems of equations encoded by complex trees tip-to-tip equivalence relations are used to obtain one-parameter families of connected…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…