arXiv preprints from January 1, 2026 through September 22, 2026 — 02:16:30 EST
One of the central challenges in evolutionary dynamics is understanding why some species combinations persist while others disappear. Although cyclic-interaction models have provided fundamental insights into biodiversity maintenance, much less is known about how hierarchical competitive interactions shape long-term community...
Hi-M combines fluorescence in situ hybridization (FISH), automated microfluidics, sequential imaging, and computational chromatin tracing to measure the three-dimensional organization of selected genomic regions in single cells. This chapter describes a Hi-M workflow adapted for cryosections of adult Drosophila melanogaster brains,...
Dimensional attention in learning is often implemented as a globally shared attention vector, where each stimulus dimension corresponds to a single scalar. These scalars are learned by models through gradient-descent on error, where predictive features acquire more salience. We show that under multi-outcome learning, where models...
Cancer remains a major global health concern due to chemotherapy resistance and toxicity from high-dose treatments. To overcome these challenges, new therapeutic strategies targeting key proteins in cancer progression are essential. This study evaluates two phytochemicals, Carpaine (Car) and Rutin (Rut), from Carica papaya leaves, for...
Electroencephalography (EEG) microstate analysis commonly converts each scalp topography into a winner-take-all hard label and summarises the resulting sequence using duration, occurrence, coverage, transitions, and symbolic complexity. Although interpretable, this readout discards evidence strength, assignment ambiguity, and...
Predicting protein dynamics is a long-standing problem in computational structural biology. Often, protein function critically depends on local directed motions, such as hinge movements, catalytic loop rearrangements and domain reorientations, which can be characterized by directional flexibility and correlated structural motions of...
In molecular discovery, molecule size is coupled to composition, structure, and other target properties. Yet most 3D generators require molecule size to be specified before generation. Here, we introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage generative framework that relies entirely on a single...
Understanding why individuals respond differently to psilocybin requires modeling the drug's transcriptional perturbation signature at the cell-type level. I present a Transformer-based delta expression encoder that learns to classify differential gene expression status - upregulated, downregulated, or neutral - from single-nucleus...
Protein-conditioned 3D molecule generation is a central challenge in structure-based drug design, requiring a balance between pocket compatibility, molecular properties, and physical geometry. We propose \textbf{PocketVE}, a protein-pocket-conditioned variance-exploding (VE) diffusion framework that couples stable coordinate denoising...
Objective: To develop and evaluate an AI-assisted MRI method for quantitative knee cartilage morphometry in a multicenter phase III knee osteoarthritis trial. Methods: AI pre-segmentation used 3D full-resolution nnU-Net. Version 1.0 used separate femorotibial- and patellar-cartilage models, whereas version 2.0 used a unified...
The brain uses discrete spikes for dynamic computation, yet, how neural microcircuits (NMCs) solve temporal credit assignment using local spike timing remains a fundamental open question. Dominant spiking neural network (SNN) approaches circumvent this by approximating backpropagation through surrogate gradients, decoupling learning...
Acidophilic proteins that remain stable and functional under highly acidic conditions, are important for industrial biocatalysis, acid-related bioprocessing, and the discovery of acid-stable enzymes. However, their identification relies heavily on time-consuming experimental screening methods. With the rapid growth of protein sequence...
DNA replication requires the coordination of origin firing and fork progression to ensure the entire genome is timely duplicated before cell division. Yet origin firing is stochastic, giving rise to the classical random completion problem of how probabilistic local events can nevertheless ensure reliable genome duplication. Although...
Automated prediction of Enzyme Commission (EC) numbers plays a central role in functional annotation and computational drug discovery. However, standard multi-label machine learning pipelines frequently rely on default decision thresholds (t=0.50), assuming balanced prior distributions across target heads. In this study, we present a...
Normative age models are trained to predict chronological age in a nominally healthy cohort. Applied to patients, they deviate, and the gap between predicted and chronological age is read as disease risk. Here, we attribute the disease-related effect size of the age gap directly to individual training samples, rather than using a...
Motor control research involves the study of movement kinematics derived from the positional trajectories that complex motions describe. In natural, unconstrained motions requiring cognitive and memory processes in real time, the temporal speed profiles are not bell-shaped, may have multiple maxima and the peaks distribution is best...
Critical phenomena are widespread across many disciplines and have recently become a topic of deep interest in the study of biological and artificial neural networks. A distinct signature of criticality is the emergence of avalanches with power-law-distributed sizes and durations. However, empirically estimating the critical exponents...
Continuous-time multi-type branching processes are fundamental models for expanding and migrating populations with cancer evolution being a prototypical example. Inferring model parameters, like mutation and growth rates, from time-series count data requires efficient computation of population size distributions. Existing methods are...
A common formalization of homeostasis is the free energy principle, a framework that defines a set of desired observation values, or critical states, that the agent should reach or remain close to. Under the free energy principle, an agent should act to maximize the probability of receiving the desired observations. Here we revisit...
The evolution of DNA sequences can be viewed as stochastic dynamics on a high-dimensional discrete space, but it is unclear when empirical transition biases reduce to an effective energy landscape versus retain irreducible non-equilibrium circulation. Human context-dependent mutation probabilities offer a direct test: every...
Reservoir computing provides a controlled setting for studying how recurrent network architectureshapes computation: input signals are projected into a high-dimensional state space by a fixed nonlinear dynamical system, and only the readout is trained. However, reservoir performance can be dependent on hyperparameters; this paper asks...
Infectious diseases may interact by competing for the same hosts or by facilitating subsequent infections. Understanding the dynamics of such multi-pathogen systems, particularly those subject to endemic seasonality and mitigation, is essential for designing robust public health interventions. We propose a three-stage modeling...
We test whether the Kuramoto model quantitatively describes spatial synchronization in regional epidemic waves, using daily COVID-19 incidence for 400 German \emph{Kreise} (2021--2023) and weekly ILI rates for 12 European countries (ECDC, 2021--2026). Bandpass filtering and Hilbert-transform phase extraction yield high global order...
High-resolution volumetric medical imaging is critical for clinical diagnosis, yet acquisition is often limited by scanner hardware, scan time, and for CT, radiation dose. Medical 3D Super-Resolution (Med3DSR) offers a computational alternative, but existing methods commonly rely on per-subject optimization, pretrained priors, or...
We define the variance swap delta as the sensitivity of the price of variance to a change in underlying price. We use Carr-Madan spanning formulas to analyze this sensitivity when the implied volatility smile curve may depend on the underlying price. We show that the variance swap total delta is zero for the class of smile curves that...