Related papers: External memory BWT and LCP computation for sequen…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

Recent years has witnessed dramatic progress of neural machine translation (NMT), however, the method of manually guiding the translation procedure remains to be better explored. Previous works proposed to handle such problem through…

Attention mechanisms, especially self-attention, have played an increasingly important role in deep feature representation for visual tasks. Self-attention updates the feature at each position by computing a weighted sum of features using…

Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…

This study introduces bifurcated attention, a method designed to enhance language model inference in shared-context batch decoding scenarios. Our approach addresses the challenge of redundant memory IO costs, a critical factor contributing…

Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…

This thesis introduces PEMS2, an improvement to PEMS (Parallel External Memory System). PEMS executes Bulk-Synchronous Parallel (BSP) algorithms in an External Memory (EM) context, enabling computation with very large data sets which exceed…

Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external…

We study the problem of list ranking in the parallel external memory (PEM) model. We observe an interesting dual nature for the hardness of the problem due to limited information exchange among the processors about the structure of the…

We investigate a recurrent neural network model with common external and bias inputs that can retrieve branching sequences. Retrieval of memory sequences is one of the most important functions of the brain. A lot of research has been done…

Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…

Memory is identified as a crucial human faculty that allows for the retention of visual and linguistic information within the hippocampus and neurons in the brain, which can subsequently be retrieved to address real-world challenges that…

Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural…

We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…

In this paper, we develop semi-external and external memory algorithms for graph partitioning and clustering problems. Graph partitioning and clustering are key tools for processing and analyzing large complex networks. We address both…

This paper introduces an Enhanced Boolean version of the Correlation Matrix Memory (CMM), which is useful to work with binary memories. A novel Boolean Orthonormalization Process (BOP) is presented to convert a non-orthonormal Boolean…

Concurrent data structures often require additional memory for handling synchronization issues in addition to memory for storing elements. Depending on the amount of this additional memory, implementations can be more or less…

External sorting is at the core of many operations in large-scale database systems, such as ordering and aggregation queries for large result sets, building indexes, sort-merge joins, duplicate removal, sharding, and record clustering.…

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…

The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…