One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet, the distance between any pair of one-hot vectors is equidistant. This is partic…
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9 results for “k-mers”
nTreeClus clusters categorical sequences using tree-based learners and k-mers.
problem Challenges in clustering categorical and sequential data.
method nTreeClus uses Tree-based Learners, k-mers, and autoregressive models for categorical time series.
result nTreeClus outperformed baseline methods in various validation metrics.
New approach speeds up DNA sequence alignment.
problem Efficiently estimating alignment scores for large sets of reads.
method Rank-one crowdsourcing models and multi-armed bandit algorithm.
result Adaptive algorithm identifies pairs with large alignment scores.
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,…
The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the Set Covering Machine and a k-mer representation of the genomes. We sho…
Unsupervised machine learning framework for discriminating major variants of concern during COVID-19q-bio.OT
Framework uses machine learning to distinguish major COVID-19 variants.
problem Discriminate and visualize associations between major COVID-19 variants based on genome sequences.
method Unsupervised machine learning methods, including k-mer analysis, PCA, t-SNE, UMAP, and agglomerative hierarchical clustering.
result Framework effectively distinguishes between major variants and identifies emerging variants.
Random Fragments Classification of Microbial Marker Clades with Multi-class SVM and N-Best Algorithmq-bio.QM
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific microbial clades within species, a framework of support vector machine (SVM) base…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties …
Motivation: Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificities. Existing methods fall into three classes: Some are based on Convolutional Neural Networks (CNNs), others use Recurrent Neural Networks (RNNs), and others rely on hybrid architectures combinin…