Related papers: On Minimizers of Minimum Density
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
The k-means++ seeding algorithm is one of the most popular algorithms that is used for finding the initial $k$ centers when using the k-means heuristic. The algorithm is a simple sampling procedure and can be described as follows: Pick the…
Maximizing submodular functions under cardinality constraints lies at the core of numerous data mining and machine learning applications, including data diversification, data summarization, and coverage problems. In this work, we study this…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
In many estimation problems, e.g. linear and logistic regression, we wish to minimize an unknown objective given only unbiased samples of the objective function. Furthermore, we aim to achieve this using as few samples as possible. In the…
We consider sets in $\mathbb R^N$ which minimise, for fixed volume, the sum of the perimeter and a non-local term given by the double integral of a kernel $g:\mathbb R^N\setminus\{0\}\to \mathbb R^+$. We establish some general existence and…
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…
Minwise hashing is a fundamental and one of the most successful hashing algorithm in the literature. Recent advances based on the idea of densification~\cite{Proc:OneHashLSH_ICML14,Proc:Shrivastava_UAI14} have shown that it is possible to…
We study the use of sampling for efficiently mining the top-K frequent itemsets of cardinality at most w. To this purpose, we define an approximation to the top-K frequent itemsets to be a family of itemsets which includes (resp., excludes)…
The k-means++ seeding algorithm is one of the most popular algorithms that is used for finding the initial $k$ centers when using the k-means heuristic. The algorithm is a simple sampling procedure and can be described as follows: {quote}…
In this work, we propose a novel optimization model termed "sum-of-minimum" optimization. This model seeks to minimize the sum or average of $N$ objective functions over $k$ parameters, where each objective takes the minimum value of a…
Finding a sparse representation of a possibly noisy signal can be modeled as a variational minimization with l_q-sparsity constraints for q less than one. Especially for real-time, on-line, or iterative applications, in which problems of…
We consider the graph $k$-partitioning problem under the min-max objective, termed as Minmax $k$-cut. The input here is a graph $G=(V,E)$ with non-negative edge weights $w:E\rightarrow \mathbb{R}_+$ and an integer $k\geq 2$ and the goal is…
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…
Universal hitting sets are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between universal hitting sets and minimizers schemes, where…
We present a study on how to effectively reduce the dimensions of the $k$-means clustering problem, so that provably accurate approximations are obtained. Four algorithms are presented, two \textit{feature selection} and two \textit{feature…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
This paper considers the problem of maintaining statistic aggregates over the last W elements of a data stream. First, the problem of counting the number of 1's in the last W bits of a binary stream is considered. A lower bound of…
The $k$-center problem for a point set~$P$ asks for a collection of $k$ congruent balls (that is, balls of equal radius) that together cover all the points in $P$ and whose radius is minimized. The $k$-center problem with outliers is…
We consider the minimum vertex cover problem in hypergraphs in which every hyperedge has size k (also known as minimum hitting set problem, or minimum set cover with element frequency k). Simple algorithms exist that provide…