相关论文: Compressing and Indexing Aligned Readsets
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
Neural information retrieval architectures based on transformers such as BERT are able to significantly improve system effectiveness over traditional sparse models such as BM25. Though highly effective, these neural approaches are very…
The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…
We investigate properties of the bijective Burrows-Wheeler transform (BBWT). We show that for any string $w$, a bidirectional macro scheme of size $O(r_B)$ can be induced from the BBWT of $w$, where $r_B$ is the number of maximal character…
This paper presents an approach to parsing humans when there is significant occlusion. We model humans using a graphical model which has a tree structure building on recent work [32, 6] and exploit the connectivity prior that, even in…
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…
JSON Lines (JSONL) is widely used for managing large collections of semi-structured data, ranging from large language model (LLM) prompts to chemical compound records and geospatial datasets. A key operation is substructure search, which…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Supervised machine learning often requires large training sets to train accurate models, yet obtaining large amounts of labeled data is not always feasible. Hence, it becomes crucial to explore active learning methods for reducing the size…
The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…
Constrained counting is a fundamental problem in artificial intelligence. A promising new algebraic approach to constrained counting makes use of tensor networks, following a reduction from constrained counting to the problem of…
Decompilation is the procedure of transforming binary programs into a high-level representation, such as source code, for human analysts to examine. While modern decompilers can reconstruct and recover much information that is discarded…
We focus on the task of unsupervised lemmatization, i.e. grouping together inflected forms of one word under one label (a lemma) without the use of annotated training data. We propose to perform agglomerative clustering of word forms with a…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…