arXiv preprints from January 1, 2026 through September 5, 2026 — 08:17:19 EST
Gene expression is a stochastic process that allows for fluctuations in protein levels that can give rise to phenotypic heterogeneity within a population of genetically identical cells. Thus, there is great interest in quantifying how natural variation (noise) in gene expression is impacted by cellular control mechanisms, such as the...
Food webs have been extensively studied from both ecological and mathematical aspects. However, most of the models studied in this area do not capture the effects of infectious diseases simultaneously. Recently, the idea of including an infectious disease in a food web model has been investigated. We study and simulate a small food...
Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored. We ask how much biosecurity-relevant signal is linearly accessible in these representations by training minimal linear and attention probes on frozen Evo 2 layer-26 activations, without...
Transient synaptic memory has emerged as a potential mechanism for maintaining short-term information even in the absence of persistent neuronal activity. However, it remains unclear whether the hidden synaptic state alone contains sufficient information to predict the future evolution of neuronal networks after activity has ceased....
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional clustering problems, biological sequence clustering faces unique challenges due to the lack of direct...
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of each metabolite are balanced. This assumption imposes linear constraints on the fluxes of...
Excessive consumption of dietary sugars is a major contributor to metabolic disorders, driving global interest in finding alternative sweeteners with reduced caloric impact. Natural sweet proteins, such as brazzein, offer exceptional sweetness intensity with little caloric contribution. However, their widespread use is limited by...
A central challenge in developing Multimodal Large Language Models (MLLMs) is effectively integrating heterogeneous inputs into a cohesive reasoning engine. Current paradigms predominantly rely on modular architectures that introduce modality-specific encoders and cross-modal fusion mechanisms. However, these designs are fundamentally...
In the wake of the SARS-CoV-2 pandemic, there has been heightened interest from applied mathematicians in infectious disease modelling. Modelling efforts often focus on predicting whether diseases are likely to be eliminated or, instead, (re-)emerge, especially as a result of control measures.This tipping point between elimination and...
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence prediction tasks but are usually evaluated under i.i.d. assumptions, even though real...
This paper investigates the classification capability of small-scale spiking neural networks based on the Leaky Integrate-and-Fire (LIF) neuron model. We analyze the relationship between classification accuracy and three factors: the number of neurons, the number of stimulus nodes, and the number of classification categories. Notably,...
Collective movement is observed widely in nature, where individuals interact locally to produce globally ordered, coherent motion. In typical models of collective motion, each individual takes the average direction of multiple neighbors, resulting in ordered movement. In small flocks, noise induced order can also emerge with...
Cortical gamma ($γ$)-band activity reflects local excitation-inhibition (E/I) balance. In schizophrenia (SCZ), reduced task-evoked gamma suggests altered E/I dynamics, but it is unclear whether differences stem from input properties or systematic shifts in E/I operating point and gain. We coupled a cochlear-inspired speech front end...
Understanding the population dynamics of ecological systems is crucial for predicting shifts in biodiversity and ensuring the protection of these systems. Established models often focus on pairwise species interactions, yet recent studies have highlighted the importance of higher-order interactions (HOIs) in shaping community...
Tree balance has received considerable attention in recent years, both in phylogenetics and in other areas. Numerous (im)balance indices have been proposed to quantify the (im)balance of rooted trees. A recent comprehensive survey summarized this literature and showed that many existing indices are based on similar underlying...
We consider a SIRD epidemic model for a population composed of two groups of individuals with asymmetric interactions, where the force of infection depends on the active (alive) population in each group, rather than on the total population, as in the classical formulation. We prove that the final state for susceptible individuals is...
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to decipher emergent multi-cellular behaviors. In particular agent-based (or cell-based) models that...
We study the ChorHendySnir2006 evolutionary model, which consists of a rooted phylogenetic tree with three leaves, subject to the Jukes--Cantor (JC69) molecular evolutionary model and molecular clock. We show that the likelihood function associated with this model has a unique maximum which depends analytically of the parameters (as...
This study presents the first large-scale empirical evaluation of quantum machine learning for predicting antibiotic resistance in clinical urine cultures. Antibiotic resistance is amongst the top threats to humanity, and inappropriate antibiotic use is a main driver of resistance. We developed a Quantum Projective Learning (QPL)...
Strong, correlated noise in recurrent neural circuits often passes through nonlinear transfer functions, complicating dynamical mean-field analyses of complex phenomena such as transients and bifurcations. We introduce a method that replaces nonlinear functions of Ornstein-Uhlenbeck (OU) noise with a Gaussian-equivalent process...
Neural coupling in both neuroscience and artificial intelligence emerges as dynamic oscillatory patterns that encode abstract concepts. To this end, we hypothesize that a deeper understanding of the neural mechanisms governing brain rhythms can inspire next-generation design principles for machine learning algorithms, leading to...
This research explores how total mortality figures relate to age-standardized death rates within the United States, using the complete historical record of national mortality statistics. Through a detailed investigation of both all-cause and cause-specific mortality trends, the study evaluates the impact of demographic standardization...
Hepatitis A severity increases sharply with age, while Korea is experiencing a cohort shift in which low seroprevalence adult cohorts are aging into older, higher fatality age groups. This demographic and immunological transition creates an urgent policy question regarding how adult vaccination should be prioritized under resource...
Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and elucidating the molecular mechanisms of bioactive compounds. Despite its critical role, reverse screening remains challenging because accurately capturing...
During infectious disease epidemics, pathogen transmission occurs in host populations made up of interacting subpopulations. Using stochastic simulation and analytical approximations, we examine how outbreak sizes in networked populations depend on network architecture, subpopulation sizes and the strength of coupling between...