Related papers: SPRISS: Approximating Frequent $k$-mers by Samplin…
We present a new algorithm for finding a near optimal low-rank approximation of a matrix $A$ in $O(nnz(A))$ time. Our method is based on a recursive sampling scheme for computing a representative subset of $A$'s columns, which is then used…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…
Clustering is one of the most fundamental tools in the artificial intelligence area, particularly in the pattern recognition and learning theory. In this paper, we propose a simple, but novel approach for variance-based k-clustering tasks,…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
Recent advancements in Artificial Neural Networks have significantly improved human activity recognition using multiple time-series sensors. While employing numerous sensors with high-frequency sampling rates usually improves the results,…
Given a point set S and an unknown metric d on S, we study the problem of efficiently partitioning S into k clusters while querying few distances between the points. In our model we assume that we have access to one versus all queries that…
In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…
Kernel $k$-means clustering is a powerful tool for unsupervised learning of non-linearly separable data. Since the earliest attempts, researchers have noted that such algorithms often become trapped by local minima arising from…
Representative subset selection (RSS) is an important tool for users to draw insights from massive datasets. Existing literature models RSS as the submodular maximization problem to capture the "diminishing returns" property of the…
Given a point set S and an unknown metric d on S, we study the problem of efficiently partitioning S into k clusters while querying few distances between the points. In our model we assume that we have access to one versus all queries that…
Objective: Spike sorting is a fundamental step in analysing extracellular recordings, enabling the isolation of single-neuron activity. However, it remains a challenging problem because extracellular traces mix overlapping spikes from…
Subset selection from massive data with noised information is increasingly popular for various applications. This problem is still highly challenging as current methods are generally slow in speed and sensitive to outliers. To address the…
Fast coverage of k-space is a major concern to speed up data acquisition in Magnetic Resonance Imaging (MRI) and limit image distortions due to long echo train durations. The hardware gradient constraints (magnitude, slew rate) must be…
The analysis of continously larger datasets is a task of major importance in a wide variety of scientific fields. In this sense, cluster analysis algorithms are a key element of exploratory data analysis, due to their easiness in the…
We generalise the results of Bhattacharya et al. (Journal of Computing Systems, 62(1):93-115, 2018) for the list-$k$-means problem defined as -- for a (unknown) partition $X_1, ..., X_k$ of the dataset $X \subseteq \mathbb{R}^d$, find a…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
The $k$-$\mathtt{means}$++ seeding algorithm (Arthur & Vassilvitskii, 2007) is widely used in practice for the $k$-means clustering problem where the goal is to cluster a dataset $\mathcal{X} \subset \mathbb{R} ^d$ into $k$ clusters. The…
The Nyquist-Shannon theorem states that the information accessible by discrete Fourier protocols saturates when the sampling rate reaches twice the bandwidth of the detected continuous time signal. This maximum rate (the NS-limit) plays a…
In this article, we develop efficient sampling algorithms for random surjections from $[n]$ to $[k]$ for all $n \geq k$. We make no assumption about $n$ and $k$. In particular, we do not make the common assumption that the ratio…