Related papers: FM-index of Alignment with Gaps

This paper investigates the problem of recovering missing samples using methods based on sparse representation adapted especially for image signals. Instead of $l_2$-norm or Mean Square Error (MSE), a new perceptual quality measure is used…

The matched filter (MF) is one of the most popular and reliable techniques to the detect signals of known structure and amplitude smaller than the level of the contaminating noise. Under the assumption of stationary Gaussian noise, MF…

This paper introduces Latent Relational Analysis (LRA), a method for measuring relational similarity. LRA has potential applications in many areas, including information extraction, word sense disambiguation, machine translation, and…

In this paper, we present a compressed data structure for moving object trajectories in a road network, which are represented as sequences of road edges. Unlike existing compression methods for trajectories in a network, our method supports…

In this paper we consider alignment of sparse graphs, for which we introduce the Neighborhood Tree Matching Algorithm (NTMA). For correlated Erd\H{o}s-R\'{e}nyi random graphs, we prove that the algorithm returns -- in polynomial time -- a…

Feedback Alignment (FA) methods are biologically inspired local learning rules for training neural networks with reduced communication between layers. While FA has potential applications in distributed and privacy-aware ML, limitations in…

Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions…

We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…

Language models are trained mainly on massive text data from the Internet, and it becomes increasingly important to understand this data source. Exact-match search engines enable searching in large text corpora - counting string appearances…

We propose a new sparse estimation method, termed MIC (Minimum approximated Information Criterion), for generalized linear models (GLM) in fixed dimensions. What is essentially involved in MIC is the approximation of the $\ell_0$-norm with…

Millimeter wave (mmWave) systems can enable high data rates if the link between the transmitting and receiving radios is configured properly. Fast configuration of mmWave links, however, is challenging due to the use of large antenna arrays…

Recent advancements in retrieval-augmented generation (RAG) have enhanced large language models in question answering by integrating external knowledge. However, challenges persist in achieving global understanding and aligning responses…

We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on…

Large language models (LLMs) struggle with compositional generalisation, limiting their ability to systematically combine learned components to interpret novel inputs. While architectural modifications, fine-tuning, and data augmentation…

We study the cosine similarity of sentence transformer embeddings and observe that they are well modeled by gamma mixtures. From a fixed corpus, we measure similarities between all document embeddings and a reference query embedding.…

This letter proposes a novel hybrid automatic repeat request with chase combining assisted sparse code multiple access (HARQ-CC-SCMA) scheme. Depending on whether the same superimposed packet are retransmitted, synchronous and asynchronous…

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…

This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…

We consider sparse array beamfomer design achieving maximum signal-to interference plus noise ratio (MaxSINR). Both array configuration and weights are attuned to the changing sensing environment. This is accomplished by simultaneously…

In pattern matching on strings, a locate query asks for an enumeration of all the occurrences of a given pattern in a given text. The r-index [Gagie et al., 2018] is a recently presented compressed self index that stores the text and…