相关论文: Compressing and Indexing Aligned Readsets

Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…

We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…

Recent analyses suggest that encoders pretrained for language modeling capture certain morpho-syntactic structure. However, probing frameworks for word vectors still do not report results on standard setups such as constituent and…

Column-oriented indexes-such as projection or bitmap indexes-are compressed by run-length encoding to reduce storage and increase speed. Sorting the tables improves compression. On realistic data sets, permuting the columns in the right…

Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are…

In this study, we present a method for generating automated anatomy segmentation datasets using a sequential process that involves nnU-Net-based pseudo-labeling and anatomy-guided pseudo-label refinement. By combining various fragmented…

A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…

We consider the problem of {\em restructuring} compressed texts without explicit decompression. We present algorithms which allow conversions from compressed representations of a string $T$ produced by any grammar-based compression…

Compressed inverted indices in use today are based on the idea of gap compression: documents pointers are stored in increasing order, and the gaps between successive document pointers are stored using suitable codes which represent smaller…

Inverted indexes are vital in providing fast key-word-based search. For every term in the document collection, a list of identifiers of documents in which the term appears is stored, along with auxiliary information such as term frequency,…

We introduce BOURBON, a log-structured merge (LSM) tree that utilizes machine learning to provide fast lookups. We base the design and implementation of BOURBON on empirically-grounded principles that we derive through careful analysis of…

We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…

We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…

Extreme multi-label text classification (XMTC) is a task for tagging a given text with the most relevant labels from an extremely large label set. We propose a novel deep learning method called APLC-XLNet. Our approach fine-tunes the…

Many common sequential data sources, such as source code and natural language, have a natural tree-structured representation. These trees can be generated by fitting a sequence to a grammar, yielding a hierarchical ordering of the tokens in…

We report on a method for compiling decision trees into weighted finite-state transducers. The key assumptions are that the tree predictions specify how to rewrite symbols from an input string, and the decision at each tree node is…

This paper revisits cluster-based retrieval that partitions the inverted index into multiple groups and skips the index partially at cluster and document levels during online inference using a learned sparse representation. It proposes an…

We address unsupervised discontinuous constituency parsing, where we observe a high variance in the performance of the only previous model in the literature. We propose to build an ensemble of different runs of the existing discontinuous…

We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…

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…