Related papers: FM-index of Alignment with Gaps
Sparse sensor arrays offer a cost effective alternative to uniform arrays. By utilizing the co-array, a sparse array can match the performance of a filled array, despite having significantly fewer sensors. However, even sparse arrays can…
Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate…
This paper proposes a general framework for matching similar subsequences in both time series and string databases. The matching results are pairs of query subsequences and database subsequences. The framework finds all possible pairs of…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Similarity searching finds application in a wide variety of domains including multilingual databases, computational biology, pattern recognition and text retrieval. Similarity is measured in terms of a distance function, edit distance, in…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
Aligning large language models (LLMs) to diverse human preferences is fundamentally challenging since criteria can often conflict with each other. Inference-time alignment methods have recently gained popularity as they allow LLMs to be…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
Computational approaches in historical linguistics have been increasingly applied during the past decade and many new methods that implement parts of the traditional comparative method have been proposed. Despite these increased efforts,…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
The compact directed acyclic word graph (CDAWG) is the minimal compact automaton that recognizes all the suffixes of a string. Classically the CDAWG has been implemented as an index of the string it recognizes, requiring $o(n)$ space for a…
We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
We show that the maximization of the sum degrees-of-freedom for the static flat-fading multiple-input multiple-output (MIMO) interference channel is equivalent to a rank constrained rank minimization problem (RCRM), when the signal spaces…