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This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We begin a systematic study of the enumerative combinatorics of mixed succession rules, which are succession rules such that, in the associated generating tree, the nodes are allowed to produce their sons at several different levels…
Hex-trees are identified as a particular instance of weighted unary-binary trees. The Horton-Strahler numbers of these objects are revisited, and, thanks to a substitution that is not immediately intuitive, explicit results are possible.…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…
New applications of data mining, such as in biology, bioinformatics, or sociology, are faced with large datasetsstructured as graphs. We introduce a novel class of tree-shapedpatterns called tree queries, and present algorithms for…
Building upon the work of Buczy\'nska et al., we study here tensor formats and their corresponding encoding of tensors via two-fold tensor products determined by the combinatorics of a binary tree. The set of all tensors representable by a…
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…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Lifting attempts to speed up probabilistic inference by exploiting symmetries in the model. Exact lifted inference methods, like their propositional counterparts, work by recursively decomposing the model and the problem. In the…
Over the last 10 to 15 years, active inference has helped to explain various brain mechanisms from habit formation to dopaminergic discharge and even modelling curiosity. However, the current implementations suffer from an exponential…
In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
We prove a conjecture of W. Hackbusch about tensor network states related to a perfect binary tree and train track tree. Tensor network states are used to present seemingly complicated tensors in a relatively simple and efficient manner.…
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
The spanning tree heuristic is a commonly adopted procedure in network inference and estimation. It allows one to generalize an inference method developed for trees, which is usually based on a statistically rigorous approach, to a…
A spanning tree of a network or graph is a subgraph that connects all nodes with the least number or weight of edges. The spanning tree is one of the most straightforward techniques for network simplification and sampling, and for…
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…
One of the important features of an interconnection network is its ability to efficiently simulate programs or parallel algorithms written for other architectures. Such a simulation problem can be mathematically formulated as a graph…
Erd\H{o}s and Palka initiated the study of the maximal size of induced trees in random graphs in 1983. They proved that for every fixed $0<p<1$ the size of a largest induced tree in $G_{n,p}$ is concentrated around $2\log_q (np)$ with high…