相关论文: Compressing and Indexing Aligned Readsets
Given a text, rank and select queries return the number of occurrences of a character up to a position (rank) or the position of a character with a given rank (select). These queries have applications in, e.g., compression, computational…
We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
When trained on language data, do transformers learn some arbitrary computation that utilizes the full capacity of the architecture or do they learn a simpler, tree-like computation, hypothesized to underlie compositional meaning systems…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Machine learning-based multi-label medical text classifications can be used to enhance the understanding of the human body and aid the need for patient care. We present a broad study on clinical natural language processing techniques to…
The idea of "stratified medicine" is an important driver of methodological research on the identification of predictive biomarkers. Most methods proposed so far for this purpose have been developed for the use on randomized data only.…
Suffix Array (SA) is a cardinal data structure in many pattern matching applications, including data compression, plagiarism detection and sequence alignment. However, as the volumes of data increase abruptly, the construction of SA is not…
This paper describes our submission to the First Workshop on Reordering for Statistical Machine Translation. We have decided to build a reordering system based on tree-to-string model, using only publicly available tools to accomplish this…
Text generation from AMR requires mapping a semantic graph to a string that it annotates. Transformer-based graph encoders, however, poorly capture vertex dependencies that may benefit sequence prediction. To impose order on an encoder, we…
We study the problem of using (partial) constituency parse trees as syntactic guidance for controlled text generation. Existing approaches to this problem use recurrent structures, which not only suffer from the long-term dependency problem…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
This paper presents trainable methods for generating letter to sound rules from a given lexicon for use in pronouncing out-of-vocabulary words and as a method for lexicon compression. As the relationship between a string of letters and a…
Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
This article describes lossless compression algorithms for multisets of sequences, taking advantage of the multiset's unordered structure. Multisets are a generalisation of sets where members are allowed to occur multiple times. A multiset…
Many large-scale Web applications that require ranked top-k retrieval such as Web search and online advertising are implemented using inverted indices. An inverted index represents a sparse term-document matrix, where non-zero elements…
Any Boolean function corresponds with a complete full binary decision tree. This tree can in turn be represented in a maximally compact form as a direct acyclic graph where common subtrees are factored and shared, keeping only one copy of…
We reduce phrase-representation parsing to dependency parsing. Our reduction is grounded on a new intermediate representation, "head-ordered dependency trees", shown to be isomorphic to constituent trees. By encoding order information in…