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Multiple Set Membership Testing (MSMT) is a well-known problem in a variety of search and query applications. Given a dataset of K different sets and a query q, it aims to find all of the sets containing the query. Trivially, an MSMT…
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…
This thesis aims to invent new approaches for making inferences with the k-means algorithm. k-means is an iterative clustering algorithm that randomly assigns k centroids, then assigns data points to the nearest centroid, and updates…
Large Language Models(LLMs) have had a profound impact on AI applications, particularly in the domains of long-text comprehension and generation. KV Cache technology is one of the most widely used techniques in the industry. It ensures…
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…
The k-means algorithm is one of the most common clustering algorithms and widely used in data mining and pattern recognition. The increasing computational requirement of big data applications makes hardware acceleration for the k-means…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
A Bloom filter is a method for reducing the space (memory) required for representing a set by allowing a small error probability. In this paper we consider a \emph{Sliding Bloom Filter}: a data structure that, given a stream of elements,…
Clustering is an important tool in data analysis, with K-means being popular for its simplicity and versatility. However, it cannot handle non-linearly separable clusters. Kernel K-means addresses this limitation but requires a large kernel…
This work proposes a clusterization algorithm called k-Morphological Sets (k-MS), based on morphological reconstruction and heuristics. k-MS is faster than the CPU-parallel k-Means in worst case scenarios and produces enhanced…
k-means has recently been recognized as one of the best algorithms for clustering unsupervised data. Since k-means depends mainly on distance calculation between all data points and the centers, the time cost will be high when the size of…
Clustering samples according to an effective metric and/or vector space representation is a challenging unsupervised learning task with a wide spectrum of applications. Among several clustering algorithms, k-means and its kernelized version…
In this paper, we consider non-coherent detection for molecular communication systems in the presence of inter-symbol-interference. In particular, we study non-coherent detectors based on memory-bits-based thresholds in order to achieve low…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its analysis. In this…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
The K-means algorithm is arguably the most popular data clustering method, commonly applied to processed datasets in some "feature spaces", as is in spectral clustering. Highly sensitive to initializations, however, K-means encounters a…
Clustering is a widely used and powerful machine learning technique, but its effectiveness is often limited by the need to specify the number of clusters, k, or by relying on thresholds that implicitly determine k. We introduce k*-means, a…