Related papers: Ordered Leaf Attachment (OLA) Vectors can Identify…
Motivated by the problem of maintaining data structures for a large sets of points that are evolving over the course of time, we consider the problem of maintaining a set of labels assigned to the vertices of a tree, where the locations of…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we obtain two combinatorial results on the number…
The degree distribution of an ordered tree $T$ with $n$ nodes is $\vec{n} = (n_0,\ldots,n_{n-1})$, where $n_i$ is the number of nodes in $T$ with $i$ children. Let $\mathcal{N}(\vec{n})$ be the number of trees with degree distribution…
We present a classification method with incremental capabilities based on the Optimum-Path Forest classifier (OPF). The OPF considers instances as nodes of a fully-connected training graph, arc weights represent distances between two…
One of the main concerns of silviculture and forest management focuses on finding fast, cost-efficient and non-destructive ways of measuring wood properties in standing trees. This paper presents an R package \verb+fiberLD+ that provides…
This paper introduces Weighted Optimal Classification Forests (WOCFs), a new family of classifiers that takes advantage of an optimal ensemble of decision trees to derive accurate and interpretable classifiers. We propose a novel…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
Speculative decoding accelerates Large Language Models via draft-then-verify, where verification can be framed as an Optimal Transport (OT) problem. Existing approaches typically handle multi-draft and multi-step aspects in isolation,…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
In the present work we propose an unsupervised ensemble method consisting of oblique trees that can address the task of auto-encoding, namely Oblique Forest AutoEncoders (briefly OF-AE). Our method is a natural extension of the eForest…
Let $\mathcal{O}_n$ be the set of ordered labeled trees on ${0,...,n}$. A maximal decreasing subtree of an ordered labeled tree is defined by the maximal ordered subtree from the root with all edges being decreasing. In this paper, we study…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively…
In mathematical phylogenetics, labeled histories describe the sequences by which sets of labeled lineages coalesce to a shared ancestral lineage. We study labeled histories for at-most-$r$-furcating trees. Consider a rooted leaf-labeled…