Related papers: Multiple Sequence Alignment is not a Solved Proble…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Process mining leverages event data extracted from IT systems to generate insights into the business processes of organizations. Such insights benefit from explicitly considering the frequency of behavior in business processes, which is…
A central question in computational vision is whether human-like visual representations are better explained by discriminative or generative learning. Existing comparisons, however, often confound the learning objective with architecture,…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Cross-domain knowledge alignment is essential for integrating heterogeneous medical systems, yet existing approaches typically treat entity alignment as a static matching problem, ignoring query context and cross-system asymmetry. This…
Multimodal geometry reasoning requires models to jointly understand visual diagrams and perform structured symbolic inference, yet current vision--language models struggle with complex geometric constructions due to limited training data…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Multiobjective optimization problems with heterogeneous objectives are defined as those that possess significantly different types of objective function components (not just incommensurable in units or scale). For example, in a…
Techniques for coordination of multi-agent systems are vast and varied, often utilizing purpose-built solvers or controllers with tight coupling to the types of systems involved or the coordination goal. In this paper, we introduce a…
Joint object matching, also known as multi-image matching, namely, the problem of finding consistent partial maps among all pairs of objects within a collection, is a crucial task in many areas of computer vision. This problem subsumes…
We use the reconfiguration framework to analyze problems that involve the rearrangement of items among groups. In various applications, a group of items could correspond to the files or jobs assigned to a particular machine, and the goal of…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
Comparing observed behavior (event data generated during process executions) with modeled behavior (process models), is an essential step in process mining analyses. Alignments are the de-facto standard technique for calculating conformance…
Biological and physical systems often exhibit distinct structures at different spatial/temporal scales. Persistent homology is an algebraic tool that provides a mathematical framework for analyzing the multi-scale structures frequently…