Related papers: Comparing RNA structures using a full set of biolo…
Automated program analysis is a pivotal research domain in many areas of Computer Science -- Formal Methods and Artificial Intelligence, in particular. Due to the undecidability of the problem of program equivalence, comparing two programs…
We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
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,…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…
Arc permutations, which were originally introduced in the study of triangulations and characters, have recently been shown to have interesting combinatorial properties. The first part of this paper continues their study by providing signed…
Rhetorical Structure Theory implies no single discourse interpretation of a text, and the limitations of RST parsers further exacerbate inconsistent parsing of similar structures. Therefore, it is important to take into account that the…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
It is a major open problem whether the $(\min,+)$-product of two $n\times n$ matrices has a truly sub-cubic (i.e. $O(n^{3-\epsilon})$ for $\epsilon>0$) time algorithm, in particular since it is equivalent to the famous…
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
We consider the classical tree edit distance between ordered labeled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit…
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…
Almost 30 years ago, Zhang and Shasha (1989) published a seminal paper describing an efficient dynamic programming algorithm computing the tree edit distance, that is, the minimum number of node deletions, insertions, and replacements that…
Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs, in terms of the minimum-cost edit sequence that transforms one graph to the other. However, the exact computation of GED is NP-Hard, which has recently…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
The edit distance between strings classically assigns unit cost to every character insertion, deletion, and substitution, whereas the Hamming distance only allows substitutions. In many real-life scenarios, insertions and deletions…
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…