Related papers: On Minimizers of Minimum Density
We propose a new finding $k$-minima algorithm and prove that its query complexity is $\mathcal{O}(\sqrt{kN})$, where $N$ is the number of data indices. Though the complexity is equivalent to that of an existing method, the proposed is…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
Most sequence sketching methods work by selecting specific $k$-mers from sequences so that the similarity between two sequences can be estimated using only the sketches. Estimating sequence similarity is much faster using sketches than…
Reduced k-means clustering is a method for clustering objects in a low-dimensional subspace. The advantage of this method is that both clustering of objects and low-dimensional subspace reflecting the cluster structure are simultaneously…
Though mostly used as a clustering algorithm, k-means are originally designed as a quantization algorithm. Namely, it aims at providing a compression of a probability distribution with k points. Building upon [21, 33], we try to investigate…
Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…
Clustering is an important technique for identifying structural information in large-scale data analysis, where the underlying dataset may be too large to store. In many applications, recent data can provide more accurate information and…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
The running maximum-minimum (max-min) filter computes the maxima and minima over running windows of size w. This filter has numerous applications in signal processing and time series analysis. We present an easy-to-implement online…
Minimum sum-of-squares clustering (MSSC) is a widely used clustering model, of which the popular K-means algorithm constitutes a local minimizer. It is well known that the solutions of K-means can be arbitrarily distant from the true MSSC…
In this paper we study the problem of minimizing a submodular function $f : 2^V \rightarrow \mathbb{R}$ that is guaranteed to have a $k$-sparse minimizer. We give a deterministic algorithm that computes an additive $\epsilon$-approximate…
We consider the problem of identifying, from its first $m$ noisy moments, a probability distribution on $[0,1]$ of support $k<\infty$. This is equivalent to the problem of learning a distribution on $m$ observable binary random variables…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial…
We present a local density estimator based on first order statistics. To estimate the density at a point, $x$, the original sample is divided into subsets and the average minimum sample distance to $x$ over all such subsets is used to…
When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…
We consider the minimal k-grouping problem: given a graph G=(V,E) and a constant k, partition G into subgraphs of diameter no greater than k, such that the union of any two subgraphs has diameter greater than k. We give a silent…
The minimum spanning tree clustering algorithm is capable of detecting clusters with irregular boundaries. In this paper we propose two minimum spanning trees based clustering algorithm. The first algorithm produces k clusters with center…
We define the min-min expectation selection problem (resp. max-min expectation selection problem) to be that of selecting k out of n given discrete probability distributions, to minimize (resp. maximize) the expectation of the minimum value…
We study the problem of finding global minimizers of $V(x):\mathbb{R}^d\rightarrow\mathbb{R}$ approximately via sampling from a probability distribution $\mu_{\sigma}$ with density $p_{\sigma}(x)=\dfrac{\exp(-V(x)/\sigma)}{\int_{\mathbb…