9 papers · ranked by Valyu relevance
Denis Kleverov, Ekaterina Aladyeva, Alexey Serdyukov, Maxim N. Artyomov
Non-negative matrix factorization (NMF) is one of the most powerful linear algebra tools, which has found application in various areas of data analysis, including computational biology. Despite numerous optimization methods devised for NMF, our comprehension of the inherent topological structure within factorizable…
Colin Lynch, Kaitlin Baudier, Douglas Montgomery, Meghan Barrett
Animal nutritionists seek to understand how animals regulate the intake and balance of multiple nutrients, yet the design and analysis of such experiments are often limited by how nutrient spaces are represented. The geometric framework for nutrition (GFN) provides a powerful means to visualize nutrient interactions…
Haoyu Cheng, Han Qu, Sean McKenzie, Katherine R. Lawrence + 4 more
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally challenging to obtain and are thus often unavailable for samples without established…
Haoyu Cheng, Han Qu, Sean McKenzie, Katherine R. Lawrence + 4 more
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally challenging to obtain and are thus often unavailable for samples without established…
Yi Fu, Tianxiao Zhao, Finnegan Clark, Sofia Nomikou + 2 more
The transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is…
Michael W. Reimann, Daniela Egas-Santander
Neuronal connectivity has been characterized at various scales and with respect to various structural aspects. In models of connectivity, it has so far remained difficult to match all of them at once, in particular the higher-order structure appears to be elusive. Here we introduce a new type of graph model that…
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…
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…
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…