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Search · four archives
13 papers · ranked by Valyu relevance
Raima Carol Appaw, Matthew J Silk, Julie Rushmore, Kimberly VanderWaal + 2 more
Detecting patterns in animal social behaviour and movement is complicated by the diversity of ecological, evolutionary, environmental, and biological drivers of these behaviours such as migration, foraging, assortative mixing, socio-ecological factors, and human influence. Addressing these complexities requires a…
Fernando Alcalde Cuesta, Gustavo Guerberoff, Álvaro Lozano Rojo
In this paper, we study the absorption and fixation times for evolutionary processes on graphs, under different updating rules. While in Moran process a single neighbour is randomly chosen to be replaced, in proliferation processes other neighbours can be replaced using Bernoulli or binomial draws depending on 0 < p ≤…
Ata Kalirad, Ralf J. Sommer
Ecological drift, the random fluctuation of abundance in communities, can drastically affect the possibility of coexistence. However, ecological drift has mostly been considered at the macro-ecological scale, whereas its potential contribution to short-term ecological dynamics remains underexplored. Here, we propose a…
Tusharkanti Ghosh, Debashis Ghosh
Identifying spatially variable genes (SVGs), genes whose expression varies coherently across tissue space, is a central analytic goal in spatially resolved transcriptomics. Current methods rank spatially variable genes using either significance probabilities from parametric models or effect sizes such as the proportion…
Maram Alqarni, Mark Cooper, Diane Donovan, James Lefevre
Does higher clustering shorten attractor periods? We examine whether the global clustering coefficient C, a direct measure of triangle density, predicts attractor lengths in synchronous, signed-threshold Boolean networks on Watts-Strogatz (WS) graphs. We generate 330 directed, signed WS networks spanning sizes N =…
Deniz Sezer, Erdal Toprak
Time-resolved sequencing of pooled mutants is widely used to track their frequencies under selection pressure, thereby revealing variants that are enriched or depleted. Here, we address how to quantify variant growth rates by analyzing the temporal dimension of the counts data through a model of growth. For exponential…
Moussa Djioua
This study presents improvements to the Hodgkin-Huxley (HH) models of ionic conductance and action potential generation. Sodium and potassium conductances are expressed by a single analytical formula describing the impulse response of a convolution of exponential distributions within a short-memory integration space.…
Marco Stock, Florin Ratajczak, Paul Bertin, Eva Hoermanseder + 6 more
Accurate reconstruction of gene regulatory networks (GRNs) from single-cell transcriptomic data remains a major methodological challenge. Recent machine learning approaches, particularly graph neural networks and graph autoencoders, have reported improved performance, yet these gains do not consistently translate to…
Daniel M. Gonçalves, André Patrício, Rafael S. Costa, Rui Henriques
The growing availability and complexity of omics data have driven the development of specialized algorithms for modeling molecular systems. Although graph-based learning methods effectively represent biological interactions, they often neglect the statistical information embedded in node and edge annotations. To…
Baoyin Yuan, Feng Jiao
Understanding extinction probabilities in branching processes is pivotal for epidemiology and population dynamics. Traditional models often assume a fixed generation time, resulting in extinction probabilities determined solely by offspring distributions and remaining unchanged over time. By contrast, our study…
S. Gholami, C.S. Korosec, Q. Su, M.I. Betti + 4 more
Understanding how viruses replicate and spread within a host is fundamental to predicting disease progression, timing, and dosage of effective therapeutic and prophylactic interventions. A target-cell limited approach is often used to model within-host viral kinetics to characterize disease infection dynamics. The…
Qichen Huang, Haoyang Guo
Cellular automata and graph reaction–diffusion systems encode local spatial interactions in different mathematical forms. We develop a cochain-operator calculus for these two settings. Over a finite field F_q_, every local rule on a finite neighborhood has a unique reduced polynomial representative. On an oriented…
Luis J Ponce, Esther Li Wen Choo, Diyar Mailepessov, Somya Bansal + 3 more
Estimating the effective reproduction number is crucial for understanding and managing infectious disease outbreaks. For vector-borne diseases like dengue, transmission depends on environmental and spatial conditions: temperature affects the extrinsic incubation period in mosquitoes, altering transmission timing, while…