10 papers · ranked by Valyu relevance
Mahmudur Rahman Hera, David Koslicki, Conrado Martínez
With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k-mers, and summarize large k-mer sets into compact…
Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An + 2 more
Plate Design is a necessary and time-consuming operation for GC/LC-MS based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a significant impact on the final analysis results. For researchers without programming skills, a stable and…
Filip Milisav, Vincent Bazinet, Richard F. Betzel, Bratislav Misic
Scientific discovery in connectomics relies on the use of network null models. To systematically evaluate the prominence of brain network features, empirical measures are compared against null statistics computed in randomized networks. Modern imaging and tracing technologies provide an increasingly rich repertoire of…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the minimal k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Mohamed Abdelnaby, Marmar R. Moussa
Principal Component Analysis (PCA) has long been a cornerstone in dimensionality reduction for high-dimensional data, including single-cell RNA sequencing (scRNA-seq). However, PCA’s performance typically degrades with increasing data size, can be sensitive to outliers, and assumes linearity. Recently, Random…
Martin Papenberg, Cheng Wang, Maïgane Diop, Syed Hassan Bukhari + 13 more
High throughput sequencing is a powerful tool for processing large amounts of DNA and RNA samples in batches. Proper experimental design and statistical methods are required to mitigate systematic technical factors due to differences in batches (“batch effects”), as data variation due to these non-biological factors…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the smallest k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Olena Doroshenko
Pathfinding in complex topographies poses a challenge with applications extending from urban planning to autonomous navigation. While numerous algorithms offer potential solutions, their comparative efficiency and reliability when confronted with nonlinear terrains remain to be systematically evaluated. This study…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…