相关论文: Efficient Construction of a Complete Index for Pan…
We propose BS-tree, an in-memory implementation of the B+-tree that adopts the structure of the disk-based index (i.e., a balanced, multiway tree), setting the node size to a memory block that can be processed fast and in parallel using…
Previous authors have shown how to build FM-indexes efficiently in external memory, but querying them efficiently remains an open problem. Searching na\"{i}vely for a pattern $P$ requires (\Theta (|P|)) random access. In this paper we show…
Matrix factorization (MF) has been widely used to discover the low-rank structure and to predict the missing entries of data matrix. In many real-world learning systems, the data matrix can be very high-dimensional but sparse. This poses an…
The paper discusses the construction of high dimensional spatial discretizations for arbitrary multivariate trigonometric polynomials, where the frequency support of the trigonometric polynomial is known. We suggest a construction based on…
We address the problem of building an index for a set $D$ of $n$ strings, where each string location is a subset of some finite integer alphabet of size $\sigma$, so that we can answer efficiently if a given simple query string (where each…
The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers…
Configuring databases for efficient querying is a complex task, often carried out by a database administrator. Solving the problem of building indexes that truly optimize database access requires a substantial amount of database and domain…
Structured distributions, i.e. distributions over combinatorial spaces, are commonly used to learn latent probabilistic representations from observed data. However, scaling these models is bottlenecked by the high computational and memory…
In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…
We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization -…
The data made available for analysis are becoming more and more complex along several directions: high dimensionality, number of examples and the amount of labels per example. This poses a variety of challenges for the existing machine…
We introduce a method to reduce constituent parsing to sequence labeling. For each word w_t, it generates a label that encodes: (1) the number of ancestors in the tree that the words w_t and w_{t+1} have in common, and (2) the nonterminal…
Similarity search is a fundamental operation for analyzing data series (DS), which are ordered sequences of real values. To enhance efficiency, summarization techniques are employed that reduce the dimensionality of DS. SAX-based approaches…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…