arXiv preprints from January 1, 2026 through September 5, 2026 — 09:15:40 EST
Decoding visual semantic representations from human brain activity is a significant challenge. While recent zero-shot decoding approaches have improved performance by leveraging aligned image-text datasets, they overlook a fundamental aspect of human cognition: semantic understanding is inherently anchored in the auditory modality of...
Continuous attractor networks (CANs) are a well-established class of models for representing low-dimensional continuous variables such as head direction, spatial position, and phase. In canonical spatial domains, transitions along the attractor manifold are driven by continuous displacement signals, such as angular velocity-provided...
Bacteria regulate their motility through a variety of mechanisms, including quorum sensing (QS) and other density-dependent responses mediated by diffusible signals. While nonlinear density-dependent motility is well known in active-matter theory to generate nonequilibrium spatial patterns, its consequences for the coexistence of...
Aortic valve opening (AO) events are crucial for detecting frequency and rhythm disorders, especially in real-world settings where seismocardiography (SCG) signals collected via consumer smartphones are subject to noise, motion artifacts, and variability caused by device heterogeneity. In this work, we present a robust deep-learning...
Mooney images are high-contrast, two-tone visual stimuli, created by thresholding photographic images. They allow researchers to separate image content from image understanding, making them valuable for studying visual perception. An ideal Mooney image for this purpose achieves a specific balance: it initially appears unrecognizable...
Perturbation screens hold the potential to systematically map regulatory processes at single-cell resolution, yet modeling and predicting transcriptome-wide responses to perturbations remains a major computational challenge. Existing methods often underperform simple baselines, fail to disentangle measurement noise from biological...
Precision psychiatry aspires to elucidate brain-based biomarkers of psychopathology to bolster disease risk assessment and treatment development. To this end, functional magnetic resonance imaging (fMRI) has helped triangulate brain circuits whose functional features are correlated with or even predictive of forms of psychopathology....
The maintenance of diversity in complex ecological communities despite unpredictable dynamics and competitive exclusion is thought to require continual influx of new species or competitive advantages that accrue as species become rare. We examine isolated planktonic microbial communities under permanent ice cover in Antarctic lakes,...
Complex systems with nonreciprocal interactions are often stratified into layers. Ecosystems are a prime example, where species at one trophic level grow by consuming those at another. Yet the dynamical consequences of such stratified nonreciprocity -- where the correlation between growth and consumption differs across trophic levels...
Many biological systems exhibit multiscale dynamics, where some species occur in high copy numbers while others remain rare. This heterogeneity necessitates hybrid modelling approaches: deterministic models are computationally efficient but inaccurate for low-count species, while fully stochastic simulations are accurate but...
Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To...
Pigmentation abnormalities, ranging from hypo- to hyperpigmentation, can serve as biomarkers of developmental disruption in fish exposed to environmental contaminants. However, the mechanistic pathways underlying these alterations remain poorly understood. Studies have shown that pattern formation in fish development requires specific...
Background: Conventional electrocardiogram (ECG) analysis faces a persistent dichotomy: expert-driven features ensure interpretability but lack sensitivity to latent patterns, while deep learning offers high accuracy but functions as a black box with high data dependency. We introduce ECGomics, a systematic paradigm and open-source...
The use of multi-centric analyses is crucial for obtaining sufficient sample sizes and representative clinical populations in experimental studies. In this setting, data harmonization techniques are typically employed to address systematic biases and ensure the interoperability of the data. State-of-the-art harmonisation approaches...
Background: Being born very or extreme preterm is a major source of cerebral anomalies and neurodevelopmental disorders, whose occurrence depends on many perinatal factors. A better understanding of these factors could be provided by cerebral Magnetic Resonance Imaging (MRI) at term-equivalent age (TEA). Objective: To investigate,...
Cognitive processes are realized across an extraordinary range of natural, artificial, and hybrid systems, yet there is no unified framework for comparing their forms, limits, and unrealized possibilities. Here, we propose a cognition space approach that replaces narrow, substrate-dependent definitions with a comparative...
Evolutionary accumulation models (EvAMs) are an emerging class of machine learning methods designed to infer the evolutionary pathways by which features are acquired. Applications include cancer evolution (accumulation of mutations), anti-microbial resistance (accumulation of drug resistances), genome evolution (organelle gene...
Across neuroscience, artificial intelligence, and related fields, dominant models of intelligence typically privilege convergence: uncertainty is reduced, competing explanations are eliminated, and behaviour is governed by the optimisation of a single objective or policy. While this framing has proved powerful in many settings, it...
Biological neural networks self-organize according to local synaptic modifications to produce stable computations. How modifications at the synaptic level give rise to such computations at the network level remains an open question. Pehlevan et al. [Neur. Comp. 27 (2015), 1461--1495] proposed a model of a self-organizing neural...
Many biochemical measurements define state spaces that are bounded, absorbing, and physically irreversible, yet are routinely analysed using linear and Euclidean frameworks that assume global invertibility, symmetry, and translation invariance. This mismatch can irretrievably obscure biological structure, independent of data quality,...
Existing methods in nanoscale connectomics are at present too slow to map entire mammalian brains. As an emerging approach, expansion microscopy (ExM) has enormous promise, yet it still suffers from throughput limitations. Mapping the human brain and even mapping nonhuman primate brains therefore remain distant goals. While ExM...
Diseases originating from wildlife pose a significant threat to global health, causing human and economic losses each year. The transmission of disease from animals to humans occurs at the interface between humans, livestock, and wildlife reservoirs, influenced by abiotic factors and ecological mechanisms. Although evidence suggests...
Understanding how the brain represents the multifaceted properties of words in context is essential for explaining the neural architecture of human language. Here, we combine large-scale psycholinguistic modeling with naturalistic fMRI to uncover the latent structure of word properties and their neural representations during narrative...
OBJECTIVES: The grandmother hypothesis proposes that ancestral women ceased reproduction midlife to instead provision their grandchildren. An alternative two-sex account proposes that the high energetic burden of caring for slow-developing offspring was met with biparental investment. Menopause evolved because the physiological costs...
Motivation: Opioid use disorder (OUD) often arises after prescription opioid exposure and follows transitions among onset, remission, and relapse. Linked EHR-survey resources such as the All of Us Research Program enable stage-specific risk modeling and connection to intervention options. Results: We built a multi-stage framework to...