Related papers: Counting, generating and sampling tree alignments
We describe an new algorithm for visualizing an alignment of biological sequences according to a probabilistic model of evolution. The resulting data array is readily interpreted by the human eye and amenable to digital image techniques. We…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
We define a class of properties on random plane trees, which we call subtree additive properties, inspired by the combinatorics of certain biologically-interesting properties in a plane tree model of RNA secondary structure. The class of…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
Dealing with datasets of very high dimension is a major challenge in machine learning. In this paper, we consider the problem of feature selection in applications where the memory is not large enough to contain all features. In this…
Semantic matching is of central importance to many natural language tasks \cite{bordes2014semantic,RetrievalQA}. A successful matching algorithm needs to adequately model the internal structures of language objects and the interaction…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
We consider the rooted trees which not have isomorphic representation and introduce a conception of complexity a natural number also. The connection between quantity such trees with $n$ edges and a complexity of natural number $n$ is…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
Decision trees and their ensembles are popular in machine learning as easy-to-understand models. Several techniques have been proposed in the literature for learning tree-based classifiers, with different techniques working well for data…
Quasi-trees generalize trees in that the unique "path" between two nodes may be infinite and have any countable order type. They are used to define the rank-width of a countable graph in such a way that it is equal to the least upper-bound…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
As alignment links are not given between English sentences and Abstract Meaning Representation (AMR) graphs in the AMR annotation, automatic alignment becomes indispensable for training an AMR parser. Previous studies formalize it as a…
The ternary betweenness relation of a tree, B(x,y,z) expresses that y is on the unique path between x and z. This notion can be extended to order-theoretic trees defined as partial orders such that the set of nodes larger than any node is…
Packing graphs is a combinatorial problem where several given graphs are being mapped into a common host graph such that every edge is used at most once. In the planar tree packing problem we are given two trees T1 and T2 on n vertices and…
Tree-structured neural networks encode a particular tree geometry for a sentence in the network design. However, these models have at best only slightly outperformed simpler sequence-based models. We hypothesize that neural sequence models…
Tree ensembles (TEs) find a multitude of practical applications. They represent one of the most general and accurate classes of machine learning methods. While they are typically quite concise in representation, their operation remains…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
A probabilistic representation for initial value semilinear parabolic problems based on generalized random trees has been derived. Two different strategies have been proposed, both requiring generating suitable random trees combined with a…