Related papers: Fast Circular Pattern Matching
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
Temporal Pattern Mining (TPM) is the problem of mining predictive complex temporal patterns from multivariate time series in a supervised setting. We develop a new method called the Fast Temporal Pattern Mining with Extended Vertical Lists.…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
We consider several types of internal queries, that is, questions about fragments of a given text $T$ specified in constant space by their locations in $T$. Our main result is an optimal data structure for Internal Pattern Matching (IPM)…
Data replication is used in distributed systems to maintain up-to-date copies of shared data across multiple computers in a network. However, despite decades of research, algorithms for achieving consistency in replicated systems are still…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…
Cumulative probability models (CPMs) are a robust alternative to linear models for continuous outcomes. However, they are not feasible for very large datasets due to elevated running time and memory usage, which depend on the sample size,…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
Protein circular permutations are crucial for understanding protein evolution and functionality. Traditional detection methods, sequence-based or structure-based, struggle with accuracy and computational efficiency, the latter also limited…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…
We present a finite-order system of recurrence relations for a permanent of circulant matrices containing a band of k any-value diagonals on top of a uniform matrix (for k = 1, 2, and 3) as well as the method for deriving such recurrence…
DNA replication fidelity is a critical issue in molecular biology. Biochemical experiments have provided key insights on the mechanism of fidelity control by DNAP in the past decades, whereas systematic theoretical studies on this issue…
Nowadays, frequent pattern mining (FPM) on large graphs receives increasing attention, since it is crucial to a variety of applications, e.g., social analysis. Informally, the FPM problem is defined as finding all the patterns in a large…
In several multiobjective decision problems Pairwise Comparison Matrices (PCM) are applied to evaluate the decision variants. The problem that arises very often is the inconsistency of a given PCM. In such a situation it is important to…
In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest…