Related papers: A new distance for high level RNA secondary struct…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
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…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
In this work we define a novel edit distance for trees considered with some abstract weights on the edges. The metric is driven by the idea of considering trees as topological summaries in the context of persistence and topological data…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…
RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
Structural pruning of neural networks conventionally relies on identifying and discarding less important neurons, a practice often resulting in significant accuracy loss that necessitates subsequent fine-tuning efforts. This paper…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
Tree-cut width is a parameter that has been introduced as an attempt to obtain an analogue of treewidth for edge cuts. Unfortunately, in spite of its desirable structural properties, it turned out that tree-cut width falls short as an…