Related papers: A new distance for high level RNA secondary struct…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Topological structures such as the merge tree provide an abstract and succinct representation of scalar fields. They facilitate effective visualization and interactive exploration of feature-rich data. A merge tree captures the topology of…
The measurement of the similarity of RNA secondary structures, and in general of contact structures, of a fixed length has several specific applications. For instance, it is used in the analysis of the ensemble of suboptimal secondary…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
Many natural language processing (NLP) applications require the computation of similarities between pairs of syntactic or semantic trees. Many researchers have used tree edit distance for this task, but this technique suffers from the…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
We present an unusual algorithm involving classification trees where two trees are grown in opposite directions so that they are matched at their leaves. This approach finds application in a new data mining task we formulate, called…
In this work we define a metric structure to compare functions defined on different merge trees. The metric introduced possesses some stability properties, which we illustrate within a standard topological data analysis (TDA) framework, and…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…