arXiv preprints from January 1, 2026 through September 19, 2026 — 20:29:57 EST
Protein-protein interaction (PPI) databases do not faithfully reflect biological realities. Instead, they are influenced by study and technical biases that distort certain protein and interaction attributes. Machine learning models can exploit these as learning shortcuts if the negative dataset is not constructed with care. So far,...
Scientific agents can move beyond automated model building by using accumulated evidence to revise both their questions and experimental strategies. The challenge is sustaining this adaptation across heterogeneous tasks without overfitting decisions to internal validation. Absorption, distribution, metabolism, excretion and toxicity...
Stochastic switching between gene expression states, coupled with production and degradation dynamics, governs the accumulation of mRNA and proteins in cells. The concentrations of these accumulated entities dictate the phenotypic distribution of genetically identical cells. The underlying accumulation dynamics are well-captured by a...
Manual counting and classification of bacterial colonies are critical yet labor-intensive tasks in microbiology, prone to human error particularly on densely populated plates. This work proposes a multi-task deep learning framework trained on the Annotated Germs for Automated Recognition (AGAR) dataset (18,000 images; 9,202 training /...
How cultural repertoires maintain diversity under selection is a fundamental question in cultural evolution. We address this using thirteen years of weekly popularity data for approximately 20,000 Irish traditional tunes, fitting ecological birth-process models under neutral, frequency-dependent, and per-tune selection hypotheses. We...
Periodic impulsive interventions arise naturally in the management of biological populations, including chemotherapy, pesticide application, and infectious-disease treatment. We develop general conditions for permanence in n-species population models subject to periodic multiplicative pulse disturbances. Our main result provides a...
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,...
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...
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...
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...
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...
Physical equations in protein modeling appear to have been replaced by generative models trained directly on structure data. By learning a mapping from noise to data, sampling de novo protein structures has become much more efficient. However, such models can also learn non-physical features and break down with out-of-distribution...
Foundation models are beginning to reshape brain-signal analysis by moving the field beyond task-specific decoding pipelines toward reusable models pretrained on broad neural datasets. Magnetoencephalography (MEG) is a compelling but still underdeveloped target for this shift: it captures human cortical dynamics at millisecond...
Alzheimer's disease is a progressive neurodegenerative disorder characterized by memory loss, cognitive decline, and behavioral changes, primarily affecting the elderly. Current treatments focus on symptom management as no therapies effectively halt or reverse disease progression. Newer therapies targeting BACE1, a key enzyme in...