14 papers · ranked by Valyu relevance
Sebastian Schmidt, Jarno N. Alanko
A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e. without k-mer repetitions and in plain…
Yu Huo, Hongpei Li, Xiao Wang, Xiaochen Du + 1 more
When analysing two-dimensional data sets, scientists are often interested in regions where one variable depends linearly on the other. Typically they use an ad hoc method to do so. Here we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a data set into contiguous piece-wise…
Marijn van Vliet, Riitta Salmelin
Linear machine learning models “learn” a data transformation by being exposed to examples of input with the desired output, forming the basis for a variety of powerful techniques for analyzing neuroimaging data. However, their ability to learn the desired transformation is limited by the quality and size of the example…
David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M Novak + 3 more
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of…
Md. Hasin Abrar, Paul Medvedev
Understanding structural properties of k-mer multisets is crucial to designing space-efficient indices to query them. A potentially novel source of structure can be found in the rank function of a k-mer multiset. In particular, the rank function of a k-mer multiset can be approximated by a piece-wise linear function…
Peter L. Bartlett, Chris Junchi Li, Jingfeng Wu, Bin Yu
In the field of optimization, developing accelerated methods for solving minimax and fixed-point problems remains a fundamental challenge. This paper presents a novel family of dual accelerated algorithms that achieve optimal convergence rates for both minimax and fixed-point problems. By exploring new anchoring…
Chirag Jain, Daniel Gibney, Sharma V. Thankachan
Co-linear chaining has proven to be a powerful technique for finding approximately optimal alignments and approximating edit distance. It is used as an intermediate step in numerous mapping tools that follow seed-and-extend strategy. Despite this popularity, subquadratic time algorithms for the case where chains…
David Brust, Johannes J. Brust
Grouping samples with low prevalence of positives into pools and testing these pools can achieve considerable savings in testing resources compared with individual testing in the context of COVID-19. We review published pooling matrices, which encode the assignment of samples into pools and describe decoding…
Pencho Yordanov, Jörg Stelling
Kirchhoff polynomials are central for deriving symbolic steady-state expressions of models whose dynamics are governed by linear diffusion on graphs. In biology, such models have been unified under a common linear framework subsuming studies across areas such as enzyme kinetics, G-protein coupled receptors, ion…
Patrick Kunzmann
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all…
Ragnar Groot Koerkamp, Igor Martayan
Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular…
Yuexuan Wang, Andreas Futschik, Ritabrata Dutta
Our topic is the reconstruction of the unknown matrices S and ω for the multivariate linear model Y = Sω + ε under the assumption that the entries of S are drawn from the finite alphabet 𝔄 = 0, 1 and ω is a weight matrix. While a frequentist method has recently been proposed for this purpose, a Bayesian approach seems…
Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence…
Minindu Weerakoon, Christopher T Saunders, Haynes Heaton
Most multiple sequence alignment and string-graph alignment algorithms focus on global alignment, but many applications exist for semi-global and local string-graph alignment. Long reads require enormous amounts of memory and runtime to fill out large dynamic programming tables. Effective algorithms for finding the…