arXiv preprints from January 1, 2026 through September 19, 2026 — 02:35:56 EST
AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural boundary remains poorly understood. We analyze per-residue activations from the Pairformer trunk and...
Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs. However, their predictive performance is often constrained by limited dataset scale and insufficient coverages of cancer and chemical spaces. In addition,...
To be conscious is to have an experience - not a collection of phenomenal atoms, but a structured whole composed of distinctions and the relations that bind them. Integrated Information Theory (IIT) identifies the essential properties of every experience (axioms), formulates them operationally as postulates that a substrate must...
Predicting how molecular changes affect large-scale brain activity is a difficult task because of the lack of appropriate methods to link scales. In this perspective, we review a class of mean-field models that can integrate biophysical details such as synaptic receptors or membrane ion channels. This leads to a multi-scale modeling...
Representational similarity analysis (RSA) is increasingly used to ask which learning rules give convolutional networks brain-like representations. Because biologically plausible rules such as feedback alignment, predictive coding and STDP do not scale, studies that include them train small networks on small images (typically 32x32...
Reproductive hormones regulate a wide range of physiological processes throughout the human lifespan. Estrogen, in particular, varies substantially across the menstrual cycle and is widely used in contraceptives and hormone replacement therapies. Despite its physiological importance, few experimental studies and even fewer...
Neural tracking - the time-locking of neural responses to continuous stimuli such as speech, music, and video - is widely used to study how the brain processes natural input. Tracking strength is typically quantified as the correlation between the recorded neural response and the stimulus, decoded and/or encoded through data-driven...
A key issue in using AI for pathology diagnosis is what image information should be given to the AI and how limited analysis resources should be used. This study compares two ways of processing different types of images under limited resources. The first is WSI-AI, in which AI automatically compresses information from the whole slide...
Environmental sharing changes the value of diversification even when the marginal statistics experienced by each lineage remain unchanged. A minimal model of cell division couples this effect to the inheritance of a conserved protective reserve. Each mother partitions its reserve between two daughters, and each fixed partition policy...
Brains and large language models (LLMs) are fundamentally different memory systems, but they can be compared through shared functional questions: where memory-related information is represented, how partial cues recover broader associations, how new information is written or updated, and how memory-related states can be perturbed. In...
Genome-scale modelling methods primarily predict reaction fluxes, whereas established high throughput experimental technologies primarily measure molecular species concentrations. This apparently paradoxical situation has arisen because implementing the non-linear constraints that represent reaction kinetic rate equations is...
Muscle redundancy can be formulated as a constrained selection on a time-varying convex set of feasible activations. We introduce Torque Fiber Proximal Dynamics (TFPD), where activation evolves as the Euclidean projection of the previous state onto a convex polytope defined by torque equality and physiological bounds. TFPD is...
LLMs are widely regarded as alien intelligences, systems whose cognitive operations are fundamentally unlike our own. Apparent similarities to human cognition are therefore often seen as the result of anthropomorphic projection. We argue that this framing is mistaken. LLMs clearly differ from humans in important respects, including...
Patient-reported pain location is diagnostically decisive for some presentations and nearly uninformative for others. The prevailing account treats this as a single gradient of diagnostic utility governed by anatomical complexity. That explanation conflates three epistemically distinct failures of localization, each with its own...
Four centuries ago Francis Bacon warned against the anticipations of nature, hasty generalization that wins assent on a few facts, and set against it the table of absence: checking that a property fails to appear where it should not. The demand was that looking convincing should not, on its own, count as evidence. Science has...
Despite the variability in gene regulation and environmental conditions, development of an organism occurs through a sequence of highly coordinated patterning processes. Cells integrate different signals to accurately infer their position in order to adopt an appropriate identity. Using a model of epigenetic landscape originally...
Dynamics of reaction networks is often modelled by parameterised polynomials and describing the set of parameters for which the system attains multiple positive equilibrium states is a challenging problem. In the full parameter space, determined by the reaction rate constants and the total concentrations, the existing methods can give...
Biological systems often synchronize their dynamics with periodic environmental and intracellular signals. Whether such periodic coordination can also improve performance, however, remains unclear. Here, we study this question in the ribosome flow model, a nonlinear dynamical model of ribosome movement along an mRNA transcript during...
Genome-scale modelling methods primarily predict reaction fluxes, whereas established high throughput experimental technologies primarily measure molecular species concentrations.This apparently paradoxical situation has arisen because implementing the non-linear constraints that represent reaction kinetic rate equations is...
Predicting how tightly two biomolecules bind remains a major challenge, in part because different interaction classes present dissimilar interfaces, from compact metal-coordinated pockets to broad, featureless protein surfaces. We introduce persistent manifold learning (PML), a novel computational framework that describes a binding...
mRNA translation in the cell requires efficient allocation of shared and limited resources including free ribosomes, tRNA molecules, and initiation factors across multiple transcripts. Using a network of dynamic mathematical models for ribosome flow along the mRNA, we pose the problem of maximizing the total steady-state protein...
Muscle redundancy can be formulated as a constrained selection on a time-varying convex set of feasible activations. We introduce Torque Fiber Proximal Dynamics (TFPD), where activation evolves as the Euclidean projection of the previous state onto a convex polytope defined by torque equality and physiological bounds. TFPD is...
Biological neurons combine excitatory and inhibitory (E/I) activity on branched dendrites through shunting, in which inhibition divisively attenuates excitation. Whether this improves population readout over additive E/I integration of the same nonnegative inputs remains unclear. We introduce DendriNet, a trainable framework that...
It has been proposed (Richerson and Boyd, 2008) that human intelligence is underpinned by a ratchet-like process called Cultural Evolution in which ideas, originated by individuals, can selectively spread by social learning and replace older, less fruitful ones. Useful ideas can thus accumulate beyond the lifetime of individuals....
Resting-state functional connectivity (FC) is altered in Alzheimer's disease (AD), widely regarded as a distributed network process; whether its signature reduces to a few focal sites has not been tested causally, a question central to targeted neuromodulation. We fit subject-specific, cross-subject-identifiable models whose...