Related papers: Fast Iteration of Spaced k-mers
Hidden Markov models (HMMs) are one of the most widely used statistical methods for analyzing sequence data. However, the reporting of output from HMMs has largely been restricted to the presentation of the most-probable (MAP) hidden state…
We study the $k$-means problem for a set $\mathcal{S} \subseteq \mathbb{R}^d$ of $n$ segments, aiming to find $k$ centers $X \subseteq \mathbb{R}^d$ that minimize $D(\mathcal{S},X) := \sum_{S \in \mathcal{S}} \min_{x \in X} D(S,x)$, where…
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}…
Efficient text indexing data structures have enabled large-scale genomic sequence analysis and are used to help solve problems ranging from assembly to read mapping. However, these data structures typically assume that the underlying…
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…
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…
The k-means clustering algorithm is a popular algorithm that partitions data into k clusters. There are many improvements to accelerate the standard algorithm. Most current research employs upper and lower bounds on point-to-cluster…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
We present several generative and predictive algorithms based on the RKHS (reproducing kernel Hilbert spaces) methodology, which, most importantly, are scale up efficiently with large datasets or high-dimensional data. It is well recognized…
This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and…
Deep learning self-supervised algorithms that can segment an image in a fixed number of hard labels such as the k-means algorithm and relying only on deep learning techniques are still lacking. Here, we introduce the k-textures algorithm…
Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. This paper introduces SpecPCM, an in-memory computing (IMC) accelerator designed to…
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…
The discovery of disease subtypes is an essential step for developing precision medicine, and disease subtyping via omics data has become a popular approach. While promising, subtypes obtained from existing approaches are not necessarily…
Summary: Counting all k-mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k-mer databases.…
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…
The problem of constrained clustering has attracted significant attention in the past decades. In this paper, we study the balanced $k$-center, $k$-median, and $k$-means clustering problems where the size of each cluster is constrained by…
This paper presents a recursive secret sharing technique that distributes k-1 secrets of length b each into n shares such that each share is effectively of length (n/(k-1))*b and any k pieces suffice for reconstructing all the k-1 secrets.…
A number of concurrent, relaxed priority queues have recently been proposed and implemented. Results are commonly reported for a throughput benchmark that uses a uniform distribution of keys drawn from a large integer range, and mostly for…
Though nearest neighbor Machine Translation ($k$NN-MT) \citep{khandelwal2020nearest} has proved to introduce significant performance boosts over standard neural MT systems, it is prohibitively slow since it uses the entire reference corpus…