Related papers: FM-index of Alignment with Gaps
Index is an important component in database systems. Learned indexes have been shown to outperform traditional tree-based index structures for fixed-sized integer or floating point keys. However, the application of the learned solution to…
With the rapid growth of the Internet of Things ecosystem, Automatic Modulation Classification (AMC) has become increasingly paramount. However, extended signal lengths offer a bounty of information, yet impede the model's adaptability,…
In this work, based on the local phase information of images, an objective index, called the feature similarity index for tone-mapped images (FSITM), is proposed. To evaluate a tone mapping operator (TMO), the proposed index compares the…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data…
Audio-to-score alignment is an important pre-processing step for in-depth analysis of classical music. In this paper, we apply novel transposition-invariant audio features to this task. These low-dimensional features represent local pitch…
Making large language models (LLMs) more efficient in memory, latency, and serving cost is crucial for edge deployment, interactive applications, and sustainable inference at scale. Pruning is a promising technique, but existing pruning…
We give some new results on sparse signal recovery in the presence of noise, for weighted spaces. Traditionally, were used dictionaries that have the norm equal to 1, but, for random dictionaries this condition is rarely satisfied.…
The Lattice String Approximation algorithm (or LSA algorithm) of M. L. Lapidus and M. van Frankenhuijsen is a procedure that approximates the complex dimensions of a nonlattice self-similar fractal string by the complex dimensions of a…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
In this paper, the task-related fMRI problem is treated in its matrix factorization formulation, focused on the Dictionary Learning (DL) approach. The new method allows the incorporation of a priori knowledge associated both with the…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
Low-rank matrix approximation (LRMA) is a powerful technique for signal processing and pattern analysis. However, its potential for data compression has not yet been fully investigated in the literature. In this paper, we propose sparse…
Large language models (LLMs) are increasingly used to assist ideation in research, but evaluating the quality of LLM-generated research proposals remains difficult: novelty and soundness are hard to measure automatically, and large-scale…
Low-rank matrix approximation (LRMA) has been arisen in many applications, such as dynamic MRI, recommendation system and so on. The alternating direction method of multipliers (ADMM) has been designed for the nuclear norm regularized least…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…