相关论文: Taxonomic classification with maximal exact matche…

Decision forests are widely used for classification and regression tasks. A lesser known property of tree-based methods is that one can construct a proximity matrix from the tree(s), and these proximity matrices are induced kernels. While…

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…

We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…

Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…

In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…

Extreme learning machine (ELM) is an extremely fast learning method and has a powerful performance for pattern recognition tasks proven by enormous researches and engineers. However, its good generalization ability is built on large numbers…

We study the problem of column selection in large-scale kernel canonical correlation analysis (KCCA) using the Nystr\"om approximation, where one approximates two positive semi-definite kernel matrices using "landmark" points from the…

Minimizer schemes, or just minimizers, are a very important computational primitive in sampling and sketching biological strings. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a total order…

In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection and Reconnection) distance…

We study the CONNECTED \eta-TREEDEPTH DELETION problem where the input instance is an undireted graph G = (V, E) and an integer k. The objective is to decide if G has a set S \subseteq V(G) of at most k vertices such that G - S has…

Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…

Kernel-based clustering algorithm can identify and capture the non-linear structure in datasets, and thereby it can achieve better performance than linear clustering. However, computing and storing the entire kernel matrix occupy so large…

The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…

The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…

Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…

This paper presents how to perform minimax optimal classification, regression, and density estimation based on fixed-$k$ nearest neighbor (NN) searches. We consider a distributed learning scenario, in which a massive dataset is split into…

Discovering fine-grained categories from coarsely labeled data is a practical and challenging task, which can bridge the gap between the demand for fine-grained analysis and the high annotation cost. Previous works mainly focus on…

Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…

Consider an input text string T[1,N] drawn from an unbounded alphabet. We study partial computation in suffix-based problems for Data Compression and Text Indexing such as (I) retrieve any segment of K<=N consecutive symbols from the…