arXiv preprints from January 1, 2026 through September 19, 2026 — 19:28:55 EST
Non-tuberculous mycobacterial (NTM) infections are a clinical challenge in cystic fibrosis (CF), where impaired mucociliary clearance and altered mucus rheology promote bacterial colonization despite host immune responses. Understanding how bacterial growth, immune cell dynamics, and mucus transport regulate infection progression is...
Co-folding models have advanced rapidly, yet no single model consistently performs best across all biomolecular complexes. This raises the question of whether independently trained co-folding models encode complementary information that can be transferred across co-folding models. We introduce SoupFold, which improves co-folding...
Traumatic brain injury (TBI) often leads to subtle white matter damage that remains undetected on conventional MRI. Diffusion kurtosis imaging (DKI), an extension of diffusion tensor imaging (DTI), provides complementary information on non-Gaussian water diffusion and is sensitive to complex white-matter microstructure. With the...
Animal activity often consists of intermittent bursts separated by prolonged periods of inactivity. Here, we describe this behavior using a two-state telegraph process with extrinsically fluctuating transition rates. We derived analytical expressions for the stationary behavior of the system and characterized how stationary...
We study the evolution of the speed of life history in populations competing for a single growth-limiting resource subject to demographic stochasticity and mass mortality events. We focus on a quasi-neutral regime in which competing types have equal resource-use efficiency but differ in life-history speed. In the...
In many biological contexts selection is strong relative to genetic drift. Working under the diffusion approximation, we define $R = 2N_{e}|s|$, where $N_{e}$ is the effective population size and $s$ is the selection coefficient associated with a focal allele. Strong selection corresponds to $R \gg1$ and can occur for relatively...
Deep learning now underpins structure-based drug design, from complex and affinity prediction to ligand ranking and pose generation. Recent co-folding models reportedly approach free-energy-perturbation accuracy at far lower cost. Yet standard evaluation, a single held-out correlation or pooled pose-success rate, cannot separate...
Classical theories of random neural networks typically assume independent connectivity, overlooking the local motif structures prevalent in biological circuits. Here, we investigate how four second-order synaptic motifs (chain, reciprocal, convergent, and divergent) shape the dynamics of nonlinear firing-rate networks. While previous...
Single-cell foundation models (scFMs) are transforming computational biology by enabling generalizable, task-agnostic representations for versatile single-cell analysis. Despite their progress in facilitating rapid deployment for downstream tasks, off-the-shelf scFMs still have some overlooked concerns: (I) (Pretraining Cost.)...
Efferocytosis, the clearance of dying cells typically by macrophages, is essential for tissue homeostasis and the resolution of inflammation. Previous experiments by Ford et al. (Proc. R. Soc. B, 2019) showed that cannibalistic efferocytosis redistributes endogenous lipid from dying macrophages into the surviving population, but...
The BabyLM challenge measures how much language a model can learn from developmentally-plausible, child-scale data rather than internet-scale corpora, yet prior language models forgo the biological constraints of the neural circuitry that acquires human language: spiking neurons separated into excitatory and inhibitory populations...
How can a neural circuit rhythmically burst when none of its constituent neurons can endogenously do so? We address this question through a bottom-up reconstruction of a 4-cell neural circuit modeled after the swim central pattern generator (CPG) of the sea slug \textit{Dendronotus iris}. We first map the intrinsic regimes of a swim...
The basic reproduction number $R_0$ is the central dimensionless quantity in mathematical epidemiology, characterizing the threshold for disease outbreak and the early growth rate of an epidemic. The algebraic form of $R_0$ varies widely across models of distinct transmission mechanisms, and its interpretation can yield further...
Purpose: To develop and validate a deep learning-based method for the automated identification and volumetric segmentation of microaneurysms (MAs) in diabetic retinopathy (DR) using OCT. Participants: A total of 125 participants were enrolled, including 20 healthy eyes, 27 with mild NPDR, 30 with moderate NPDR, 30 with severe NPDR,...
Computational models supporting mechanistic understanding of (complex) biological systems, systems behaviour prediction, and experimental design are becoming more and more embedded in research on complex biological systems. Reuse and refinement of models, rather than continuous reinvention, is becoming increasingly important as...
Many biological discovery problems require experiments to be selected sequentially under constrained budgets. CRISPR screening is a prominent example, as exhaustive perturbation testing is often infeasible and candidate perturbations must instead be prioritized over multiple experimental rounds. Despite the importance of this problem,...
Groups that search collectively often exploit what they find by recruiting: one member directs others to a site it has found. Recruitment raises the number of members foraging at a known site, but the return per forager may fall as that number grows, so there is an intermediate optimal recruitment rate. In addition, a site may be used...
The analysis of neuronal avalanches offers insights into brain dynamics utilizing the framework of criticality, but the reproducibility and comparability of studies are limited by the use of fragmented, lab-specific scripts. To address this issue, we introduce pyAvalanches, an open-source Python package providing a standardized,...
Motor control has described the surplus of solutions available to the nervous system as redundancy, a term that names duplication: interchangeable elements, robust to loss but incapable of differential adaptation. Biology has had a second term for twenty-five years. Degeneracy names elements that are not interchangeable and are...
We propose the Platonic brain bridge hypothesis: omni models, which process video, audio and text jointly like the brain, converge on brain-like representations, and the correspondence is bidirectional. From model to brain, brain-likeness of seven omni models is stable across participants, and our encoding models on their internal...
Parkinson's disease is clinically and biologically heterogeneous, yet its spatiotemporal progression remains poorly characterized. We present a connectome-constrained disease progression model that jointly estimates subject-specific disease time and data-driven subtypes from longitudinal morphometry. Applied to 85 imaging and clinical...
Whether human motor and brain lateralization arises from fundamentally distinct neural architectures or emerges from conserved network dynamics remains a central question at the intersection of network science and neurobiology. Conventional measures of cortical activation often fail to resolve how directed information exchange adapts...
Longitudinal single cell atlases now capture matched pre treatment and post treatment states from responders and non responders, presenting an opportunity to mechanistically explain why two patients on the same drug diverge. We introduce scDEFT (single cell Drug EFfect Transducer), which treats a drug as a conditioning operator on...
Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry, it requires determining whether that geometry is compatible with the sequence. We introduce SIRGE, a sequence-informed geometric evaluator that conditions...
Scientific agents can move beyond automated model building by using accumulated evidence to revise both their questions and experimental strategies. The challenge is sustaining this adaptation across heterogeneous tasks without overfitting decisions to internal validation. Absorption, distribution, metabolism, excretion and toxicity...