arXiv preprints from January 1, 2026 through July 20, 2026 — 00:36:23 EST
Reconstructing the energy profile of DNA-binding proteins along the genome requires an algorithm that quantifies efficiently the binding free energy. We assembled a dataset of protein structures and DNA binding sites, together with their binding energies, and used it to train a machine-learning algorithm that learns a latent invariant...
Polyploidy is defined as the existence of more than two complete sets of homologous chromosomes. Despite it being a widespread phenomenon across the tree of life, its role as either an evolutionary innovation or a dead end is still debated. Here, we investigate how under varying selective pressures the degree of ploidy interacts with...
Electroencephalography (EEG) and magnetoencephalography (MEG) provide noninvasive measurements of brain activity with millisecond temporal resolution, enabling the investigation of functional and effective interactions within large-scale brain networks. This chapter presents a comprehensive overview of the methodological foundations...
Blood transcriptomic profiling enables prognostic modeling by capturing the host immune response at the molecular level. Yet, the within-cohort evaluation strategies employed by many transcriptomic models inadequately reflect deployment across independent hospitals. Outside deployment scenarios introduce a cohort shift that can...
Single-cell and spatial foundation models promise transferable biological representations, yet their generality remains largely untested across modalities, biological domains and analytical tasks. We benchmarked six representative models, Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae, using a harmonised framework...
Part of the excitation energy transfer (EET) characteristics of the photosystem II (PSII) comes from the interconnection between pigments. To understand the correlation between the EET and the pigments' interaction structure, we construct a network from the EET rates, which are related to both the distance between the pigments...
Gene expression is a stochastic process that gives rise to large fluctuations in protein levels leading to phenotypic heterogeneity in clonal cell populations; post-transcriptional regulation plays a crucial role in controlling the level of phenotypic variability within a population, which is directly tied to cell-fate decisions. As...
Accurate kidney failure risk assessment is critical to timely intervention in chronic kidney disease (CKD). Existing equations (e.g. Kidney Failure Risk Equation; KFRE) rely on single laboratory measurements to estimate short- and long-term kidney failure risk, leaving longitudinal laboratory patterns unused. Here we introduce Clalit...
The public goods game serves as a significant paradigm for investigating the emergence and maintenance of cooperation in conflicting situations. In the traditional public goods game, the multiplication factor characterizing the synergy effect of common efforts is typically assumed to be constant. In real-world scenarios, however,...
A fundamental challenge in the science of consciousness is the lack of a universal, predictive framework for motivated behavior. While existing theories excel at describing specific mechanisms, from neural pathways to computational models, they do not provide a foundational principle that explains the consistent direction of conscious...
OBJECTIVES: Vision-language models are increasingly used to interpret medical and everyday images through consumer chat interfaces, yet their ability to read orientation - the single perceptual operation tested by the tumbling-E acuity optotype - is poorly characterized on the surfaces through which they are actually used. METHODS: We...
Many dynamical systems exhibit diverse modes of behavior. In biology, such modes can represent individual or cell fates. While the emergence of multimodality is commonly studied, transient bimodality is much less well understood. Under transient bimodality, a system moving from a well-defined initial to a final state transiently...
Neural activity is widely held to organize on low-dimensional structure embedded in a high-dimensional state space. Persistent homology reads such structure directly from the pattern of pairwise correlations, without assuming in advance which variables are relevant. We apply persistent homology to microelectrode-array (MEA) recordings...
Collective migration of epithelial monolayers emerges from the interplay between mechanical interactions and biochemical signalling. Here, we present a phenomenological mechanobiological framework linking cell-scale orientational interactions to tissue-scale mechanics. We distinguish reversible and irreversible head-on and glancing...
Attempts to quantify biological complexity often consider intrinsic structural properties at a chosen hierarchical level and resolution, such as counts of body parts and their degree of differentiation. These measures are inherently \emph{syntactic}, being concerned with the information needed to specify an arrangement rather than the...
We describe a model of perceptual inference in primary visual cortex (V1) equivalent to a minimal diffusion model whose function can be readily understood from its parameters. The model is based on sparse coding with a non-factorial prior over latent variables in the form of an unconstrained, pairwise interaction matrix, extending...
The primate visual system is typically divided into two streams - the ventral stream, responsible for object recognition, and the dorsal stream, responsible for encoding spatial relations and motion. Recent studies have shown that convolutional neural networks (CNNs) pretrained on object recognition tasks are remarkably effective at...
Standard phylogenetic reconstruction techniques often yield unrooted phylogenetic networks; these are subsequently rooted to infer evolutionary history. A common problem in this process is to determine the structural classes to which the resulting network will belong. In this paper, we investigate unrooted networks in which the choice...
Biomechanical models are used to quantify and optimize human movement in clinical rehabilitation, sports science, and occupational health. Personalizing these models requires accurate identification of anatomical landmarks and body segment parameters, which can be derived from 3D body surface scans. Registering these surfaces to a...
In this paper, we propose a new model to estimate the impact of an intervention on human hosts of a vector-borne infection, such as dengue, which occurs in yearly outbreaks of different magnitudes. The model applies to these outbreaks and, in fact, is independent of their intensity, that is, it does not require the steady-state...
We explore a model of infectious disease spread that incorporates exposure to the pathogen in the classic epidemiological acceptation of the term, i.e., a contact with an infectious individual has taken place but the infection has not necessarily been acquired. The model also includes a (discrete) age of infection structure, allowing...
This study applied a mathematical tool from Topological Data Analysis (TDA), called the Mapper algorithm, to gene expression data from more than 1,000 TCGA-BRCA patients to identify hidden molecular patterns associated with survival. Patients located near high-risk regions of the network showed significantly poorer survival, and...
Deterministic evolutionary game theory makes no distinction between a monomorphic population of individuals all of whom share a mixed evolutionarily stable strategy and a polymorphic population of players of pure strategies present in a ratio that reproduces the mixed strategy on average. The so-called trembling hand hypothesis posits...
Meditative expertise involves sustained attention, rapid recovery from distraction, and coordinated dynamics of large-scale brain networks. We present a computational phenomenology of focused-attention meditation traversing four attractor states: breath focus, mind-wandering, meta-awareness, and redirect attention. Within a...
Processes such as incomplete lineage sorting (ILS) and reticulate evolution (arising, for example, from hybridization and lateral gene transfer (LGT)) are known to cause discordance between gene trees and species trees, complicating phylogenetic inference. While the multispecies coalescent model has led to a rich theoretical...