Related papers: Reconstructing Trees from Traces

This paper contains a classification of countable lower 1-transitive linear orders. The notion of lower 1-transitivity generalises that of 1-transitivity for linear orders, and is essential for the structure theory of 1-transitive trees.…

The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…

Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…

Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…

We consider the classical sparse regression problem of recovering a sparse signal $x_0$ given a measurement vector $y = \Phi x_0+w$. We propose a tree search algorithm driven by the deep neural network for sparse regression (TSN). TSN…

The need to learn from positive and unlabeled data, or PU learning, arises in many applications and has attracted increasing interest. While random forests are known to perform well on many tasks with positive and negative data, recent PU…

Reconstructing complex networks from measurable data is a fundamental problem for understanding and controlling collective dynamics of complex networked systems. However, a significant challenge arises when we attempt to decode structural…

Various modifications of decision trees have been extensively used during the past years due to their high efficiency and interpretability. Tree node splitting based on relevant feature selection is a key step of decision tree learning, at…

This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…

Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…

We introduce a cluster evaluation technique called Tree Index. Our Tree Index algorithm aims at describing the structural information of the clustering rather than the quantitative format of cluster-quality indexes (where the representation…

We introduce an approach for updating older tree inventories with geographic coordinates using street-level panorama images and a global optimization framework for tree instance matching. Geolocations of trees in inventories until the early…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

Model trees provide an appealing way to perform interpretable machine learning for both classification and regression problems. In contrast to ``classic'' decision trees with constant values in their leaves, model trees can use linear…

We frame the task of predicting a semantic labeling as a sparse reconstruction procedure that applies a target-specific learned transfer function to a generic deep sparse code representation of an image. This strategy partitions training…

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…

Complex networks datasets often come with the problem of missing information: interactions data that have not been measured or discovered, may be affected by errors, or are simply hidden because of privacy issues. This Element provides an…

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…

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…

It is known that the stationary distribution of the random walk process is dependent on the structure of the network. This could provide us a solution of the network reconstruction. However, the stationary distribution of the random walk…