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We present an automated approach for identifying and annotating motifs and domains in protein sequences, using pretrained Protein Language Models (PLMs) and Concept Activation Vectors (CAVs), adapted from interpretability research in…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is…
This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understanding the distinct…
DNA motif discovery is an important issue in gene research, which aims to identify transcription factor binding sites (i.e., motifs) in DNA sequences to reveal the mechanisms that regulate gene expression. However, the phenomenon of data…
Sequential pattern mining (SPM) is an important technique of pattern mining, which has many applications in reality. Although many efficient sequential pattern mining algorithms have been proposed, there are few studies can focus on target…
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…
The discovery of motifs underlying gene expression is a challenging one. Some of these motifs are known transcription factors, but sequence inspection often provides valuable clues, even discovery of novel motifs with uncharacterized…
Network motif provides a way to uncover the basic building blocks of most complex networks. This task usually demands high computer processing, specially for motif with 5 or more vertices. This paper presents an extended methodology with…
Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…
A natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are $k$ background sequences, and each character in a background sequence is a random…
Motifs are the most repetitive/frequent patterns of a time-series. The discovery of motifs is crucial for practitioners in order to understand and interpret the phenomena occurring in sequential data. Currently, motifs are searched among…
Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…
Scaling laws have allowed Pre-trained Language Models (PLMs) into the field of causal reasoning. Causal reasoning of PLM relies solely on text-based descriptions, in contrast to causal discovery which aims to determine the causal…
The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
Background: The computation of the statistical properties of motif occurrences has an obviously relevant practical application: for example, patterns that are significantly over- or under-represented in the genome are interesting candidates…
In this paper we describe two simple, fast, space-efficient algorithms for finding all matches of an indeterminate pattern $p = p[1..m]$ in an indeterminate string $x = x[1..n]$, where both $p$ and $x$ are defined on a "small" ordered…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
The Spatial Pattern Matching (SPM) query allows for the retrieval of Points of Interest (POIs) based on spatial patterns defined by keywords and distance criteria. However, it does not consider the connectivity between POIs. In this study,…