8 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…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…
Sumedh S Nagrale, Alik S Widge
The use of Deep Brain Stimulation (DBS) on the ventral capsule/ventral striatum (VCVS) has therapeutic potential for patients with refractory psychiatric disorders, but clinical success is impeded by the need for a time-consuming and trial-and-error process when setting the parameters, this process relying on…
Niklas Neubrand, Timo Rachel, Tim Litwin, Jens Timmer + 2 more
Systems biology strives to unravel the complex dynamics of cellular processes, often with the help of ordinary differential equations (ODEs). However, the sparsity of measured data and the strong non-linearity of common ODEs introduce severe numerical problems in typical modeling tasks. This gave rise to the…
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…
Daisy Fry Brumit, Alicia A. Sorgen, Anthony Fodor
Beta diversity quantifies pairwise differences between two or more communities through matrix transformations, which are either naïve to phylogeny or phylogenetically aware. Methods have recently been introduced that also consider compositionality and sparsity and that display an increased magnitude of pseudo-F scores…
Kagari Yamada, Kazushi Tsutsui, Kazutoshi Kudo
Human intuition about randomness is systematically biased. When asked to generate random sequences, people systematically generate too many alternations. At the same time, game-theoretic analyses of competitive interactions prescribe truly random mixed strategies as the unique way to remain unpredictable to an…
Ryo Tsuchihashi, Misaki Kinoshita
Cyclic peptides have emerged as a pivotal modality for next-generation therapeutics, due to their superior biocompatibility, high selectivity, and structural stability. While AI-driven peptide design has advanced rapidly, conventional optimization algorithms are often constrained by initialization biases, which impede…