Related papers: FM-index of Alignment with Gaps
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
Little research explores the correlation between the expressive ability and generalization ability of the low-rank adaptation (LoRA). Sharpness-Aware Minimization (SAM) improves model generalization for both Convolutional Neural Networks…
The alignment of two similar graphs from different domains is a well-studied problem. In many practical usages, there is no reliable information or labels over the vertices or edges, leaving structural similarity as the only information…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
Many large-scale Web applications that require ranked top-k retrieval such as Web search and online advertising are implemented using inverted indices. An inverted index represents a sparse term-document matrix, where non-zero elements…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…
In partial multi-label learning (PML), each instance is associated with a set of candidate labels containing both ground-truth and noisy labels. The presence of noisy labels disrupts the correspondence between features and labels, degrading…
Approximate matching (AM) is a concept in digital forensics to determine the similarity between digital artifacts. An important use case of AM is the reliable and efficient detection of case-relevant data structures on a blacklist, if only…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation,…
In this paper, we propose a novel variable selection approach in the framework of sparse high-dimensional GLARMA models. It consists in combining the estimation of the autoregressive moving average (ARMA) coefficients of these models with…
Aggregating multi-subject functional magnetic resonance imaging (fMRI) data is indispensable for generating valid and general inferences from patterns distributed across human brains. The disparities in anatomical structures and functional…
Strings in the real world are often encoded with some level of uncertainty. In the character-level uncertainty model, an uncertain string $X$ of length $n$ on an alphabet $\Sigma$ is a sequence of $n$ probability distributions over…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
Motivated by recent interest in permutation arrays, we introduce and investigate the more general concept of frequency permutation arrays (FPAs). An FPA of length n=m lambda and distance d is a set T of multipermutations on a multiset of m…
Motivation: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate…