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Random forests are widely used in regression. However, the decision trees used as base learners are poor approximators of linear relationships. To address this limitation we propose RaFFLE (Random Forest Featuring Linear Extensions), a…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
We consider the parameterized version of the maximum internal spanning tree problem, which, given an $n$-vertex graph and a parameter $k$, asks for a spanning tree with at least $k$ internal vertices. Fomin et al. [J. Comput. System Sci.,…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
We present sublinear-time (randomized) algorithms for finding simple cycles of length at least $k\geq 3$ and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being…
We present a detailed analysis of the class of regression decision tree algorithms which employ a regulized piecewise-linear node-splitting criterion and have regularized linear models at the leaves. From a theoretic standpoint, based on…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
The Steiner tree problem is one of the most prominent problems in network design. Given an edge-weighted undirected graph and a subset of the vertices, called terminals, the task is to compute a minimum-weight tree containing all terminals…
We introduce the concept of Random Sequential Renormalization (RSR) for arbitrary networks. RSR is a graph renormalization procedure that locally aggregates nodes to produce a coarse grained network. It is analogous to the (quasi-)parallel…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…