arXiv preprints from January 1, 2026 through September 5, 2026 — 00:31:59 EST
Here we present the Active Visual Semantics (AVS) dataset, a large-scale collection of magnetoencephalography (MEG) and eye-tracking data recorded while five participants freely explored 4,080 natural scenes over 10 sessions each, yielding more than 200,000 fixation epochs in total. Unlike existing neuroimaging datasets that rely on...
Geometric eigenmodes provide a compact and biologically grounded representation of large-scale neural activity. Previous work demonstrated that they can mitigate the underdetermined nature of electroencephalographic (EEG) and magnetoencephalographic (MEG) source localisation, an ill-posed inverse problem in which neural activity is...
Many natural and engineered systems are large complex networks of interacting components, and external perturbations drive them along different dynamical paths. Identifying which perturbation occurred matters for diagnosis, control, and prediction. Yet often times only a few components can be jointly monitored. Which components should...
Single-cell studies are typically initiated from predefined research questions, leaving much of the biological information encoded within existing data unexplored. We formalize open-ended discovery as an analytical paradigm, in which data-derived signals are identified before biological context is interrogated and subsequently...
Like pairwise distances, quartets can be highly redundant and correlated on a phylogenetic tree, and their number grows on the order of n^4 rather than n^2. I explore BME-like weights for reweighting quartet scores before summing them to score a full tree. Three weights are considered on an unrooted binary tree:...
The corticothalamic circuit supports rhythms with timescales that differ by orders of magnitude: sleep spindles, the sigma-band events of non-rapid-eye-movement (NREM) sleep, and infra-slow fluctuations near 0.02Hz that organize when spindles occur. Because the anatomy is the same in both cases, architecture alone cannot determine...
RNA molecules perform diverse biological functions by dynamically exploring multiple conformational states rather than adopting a single static structure. Capturing these ensembles is a challenge in molecular biology. Recent advances in cryoEM are now transforming this landscape by enabling the visualization of RNA molecules across a...
Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing...
Canonical neural circuit motifs are usually described functionally: divisive normalization rescales population activity by a pooled signal, and winner-take-all competition selects one pattern through recurrent excitation and shared inhibition. We represent them, and their compositions, algebraically as finite transformation systems...
Scientific progress depends not only on finding solutions, but on learning the rules that explain why they work and using that understanding to design better experiments. We introduce science sandboxes, a framework for studying this capability in AI agents through repeated cycles of experimentation, feedback, and hypothesis revision....
Relative-frequency trajectories are often used to infer selective advantage in competing biological populations. A common empirical approach is to fit a linear function to the logit-transformed frequency of an invading type and interpret the slope as the relative advantage. Here we test how this estimator is affected when the...
Disordered dynamical systems comprising many interacting units, from ecological communities to neural circuits, are ubiquitous, and understanding how connectivity shapes their collective behavior is a central theoretical challenge. One long-recognized feature of neural circuits is local connectivity balance, in which the excitatory...
Planar cell polarity is preceded by the clustering of polarity proteins into discrete, low-turnover membrane subdomains (puncta), yet the minimal interactions that nucleate puncta, set their number, and segregate opposite orientations remain unclear. We address these questions with a mass-conserving reaction-diffusion model in which...
We propose a neurobiologically plausible model of cognition that combines the advantages of connectionist and symbolic systems, and that can explain a wide range of cognitive phenomena. This model, called Rate-Coding Bundle Memory (RCBM), is based on the Symbolic Subsystem Hypothesis, which posits that the brain implements a symbolic...
40-Hz ASSR is reduced in schizophrenia, but it is unclear if this reflects altered auditory input or cortical E/I dynamics. We hypothesized that similar group differences could arise via distinct model mechanisms. EEG gamma% and ITPC from 21 HC and 21 SCZ constrained an auditory front-end coupled to a Wilson-Cowan E/I model. We...
Cocaine Use Disorder (CUD) is associated with widespread alterations in large-scale functional brain networks, yet the mechanisms contributing to these changes and their relationship to clinical and cognitive outcomes remain poorly understood. To address this gap, we introduce a framework to extract structurally informed dynamic...
Batch integration is a central preprocessing step in single-cell genomics, where datasets collected across experiments, donors, and protocols must be combined despite pervasive technical batch effects. The leading integration methods produce a shared low-dimensional embedding, which discards the corrected gene-expression values that...
Cryo-electron microscopy (cryo-EM) determines the structures of proteins and macromolecular assemblies at near-atomic resolution, and the final 3D reconstruction depends on extracting a clean particle stack from noisy micrographs. This extraction decomposes into three sub-tasks, namely particle picking, contamination removal, and 2D...
Cryo-electron microscopy (cryo-EM) is crucial for analyzing 3D biological structures, in which automated particle picking is essential for the workflow. However, fully supervised methods require extensive manual annotations. While few-shot learning offers a potential solution, existing approaches struggle to handle the diverse...
As human missions to Mars move from concept to planning to reality, a systematic quantitative health risk assessment of martian regolith exposure has become critically important. This study presents a comprehensive multi-element, multi-pathway health hazard analysis of martian regolith for a 70 kg adult astronaut on an 18-month...
AlphaFold 3 (AF3) enables structure prediction of biomolecular complexes through co-folding multiple interacting molecules, making it increasingly useful for de novo protein design and for large-scale studies of protein-protein, protein-peptide, and other biomolecular interactions. However, systematic co-folding experiments can...
Vision neuroscience has experienced a surge in the collection and use of large-scale datasets of brain responses to naturalistic images. However, static images lack the temporal dimension essential for understanding how vision is solved in the brain during dynamic real life settings. To facilitate the study of the neural correlates of...
By analyzing a stochastic Lotka-Volterra (LV) equation, we show that the underlying logic behind the diversity-stability debate in ecology can be framed as a dimensionality-induced critical phase transition, that is, a transition separating the regime dominated by statistical averaging and a systemic tipping point. This phase...
Deep neural networks are high-dimensional dynamical systems whose function depends on the stable propagation of activity and perturbations across many layers. Maintaining suitable dynamical regimes may therefore be essential for robust learning and for preventing dynamical instabilities during training. Here, we show that the global...
Linking individual-level processes, such as survival and reproduction, to ecosystem dynamics is challenging due to interactions among populations and species. These interactions depend on organism traits, such as age, body size, and mass, and are influenced by fluctuations in population structure. Integral projection models (IPMs)...