Quantitative Biology
Designing functional protein sequences that satisfy multiple desired properties is a core research focus of protein engineering. Prior methods struggle with inability or inefficiency when dealing with numerous, often conflicting,…
We study the geometry of the mean fitness surface of replicator systems and its relationship to evolutionary trajectory dynamics. Using the symmetric--antisymmetric decomposition of the fitness landscape matrix, we derive an explicit…
We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
Intrinsic channel noise is fundamental to neural processing, yet its state-dependent nature, when constrained by strict Feller boundary conditions, is often overlooked. Here, we demonstrate that this bounded multiplicative noise is not…
Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas. GPTCelltype-style one-shot prompting allows large language…
Diabetic foot ulcers (DFUs) are a severe complication of diabetes associated with significant morbidity, amputation risk, and healthcare burden. Developing effective continuous monitoring frameworks requires first establishing reliable…
Spatial structure and species interactions jointly shape the dynamics and biodiversity of ecological systems, yet most theoretical models either neglect spatial heterogeneity or sacrifice analytical tractability. Here, we provide a unified…
Mutualisms are key for structuring ecological communities, but they are sensitive to environmental change and fluctuations in population size. Consequently, how mutualisms achieve stability remains an open question in ecological theory.…
We investigate a model for a mosquito-borne epidemic in which human hosts may adopt protective behaviour against vector bites in response to information on both past and current disease prevalence. Assuming that mosquitoes can also feed on…
The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides and cofactors. At the origin of metabolism there were no enzymes--how did it start? Empirical…
Advances in brain-to-image reconstruction are enabling us to externalize the subjective visual experiences encoded in the brain as images. A key challenge in this task is data scarcity: a translator that maps brain activity to latent image…
Managing patients with respiratory failure increasingly involves noninvasive respiratory support (NIRS) strategies to support respiration, often preventing the need for invasive mechanical ventilation. However, despite the rapidly expanding…
Inferring structural connectivity from observed dynamics remains a fundamental open problem in complex systems, particularly for nonlinear networks where direct measurements are unavailable, and existing methodological approaches each incur…
Computational cognitive models discovered using large language models have so far relied solely on behavioral data. However, it is well-known that models produced from the behavioral trajectory alone are typically under-determined. In this…
Failing to account for ecological processes such as dispersal and connectivity when modeling distributions can lead to biased inference about environmental drivers and reduced predictive performance. Spatial dynamic occupancy models are…
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progress, computational modeling of TCR-peptide specificity remains…
Cross-frequency interactions are fundamental brain mechanisms for integrating information across temporal scales. However, accurate identification of these couplings is hindered by complex multi-frequency nonlinearities and by spurious,…
The Great Filter hypothesis proposes that the emergence of technological societies capable of interstellar travel depends on a small number of exceptionally hard and highly improbable steps. Traditional versions of this hypothesis enumerate…
Deep convolutional neural networks (DCNNs) have rivaled humans on many visual tasks, yet they remain vulnerable to near-imperceptible perturbations generated by adversarial attacks. Recent work shows that aligning DCNN representations with…