Quantitative Biology
Self-supervised learning (SSL) leverages vast unannotated medical datasets, yet steep technical barriers limit adoption by clinical researchers. We introduce Vision Foundry, a code-free, HIPAA-compliant platform that democratizes…
Chemical reaction networks are widely used to model stochastic dynamics in chemical kinetics, systems biology and epidemiology. Solving the chemical master equation that governs these systems poses a significant challenge due to the large…
Artificial intelligence (AI) is reshaping computational and network biology by enabling new approaches to decode cellular communication networks. We introduce Hierarchical Molecular Language Models (HMLMs), a novel framework that models…
Hirschsprung Disease is characterized by the absence of ganglion cells in the myenteric plexus. Therefore, the correct identification of ganglion cells is crucial for diagnosing Hirschsprung disease. We introduce a three-stage analysis…
As epithelial development or wound closure approaches completion, cell proliferation progressively slows via contact inhibition of proliferation (CIP) - a mechanism understood as being strictly local. Here we report the discovery of…
Quantum-like modeling (QLM) - quantum theory applications outside of physics - are intensively developed with applications in biology, cognition, psychology, and decision-making. For cognition, QLM should be distinguished from quantum…
In early childhood education, accurately detecting collaborative and behavioral engagement is essential to foster meaningful learning experiences. This paper presents an AI driven approach that leverages Vision Transformers (ViTs) to…
Decades of scientific inquiry have sought to understand how evolution fosters cooperation, a concept seemingly at odds with the belief that evolution should produce rational, self-interested individuals. Most previous work has focused on…
Understanding how biological organisms make decisions is of fundamental importance in understanding behavior. Such an understanding within evolutionary game theory so far has been sought by appealing to bounded rationality. Here, we present…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Noise plays a crucial role in the regulation of cellular and organismal function and behavior. Exploring noise's impact is key to understanding fundamental biological processes, such as gene expression, signal transduction, and the…
Multimodal MRI offers complementary multi-scale information to characterize the brain structure. However, it remains challenging to effectively integrate multimodal MRI while achieving neuroscience interpretability. Here we propose to use…
Rapid advancements in technology have led to an increased use of artificial intelligence (AI) technologies in medicine and bioinformatics research. In anticipation of this, the National Institutes of Health (NIH) assembled the Bridge to…
Introduction: The blood-brain barrier (BBB) protects the central nervous system but prevents most neurotherapeutics from reaching effective concentrations in the brain. BBB-penetrating peptides (BBBPs) offer a promising strategy for brain…
Protein S (PS) is a notable anticoagulant implicated in both bleeding and thrombotic disorders, making it a promising drug target. Importantly, PS enhances the anticoagulant function of TFPI$\alpha$, likely circulating in the bloodstream…
Mitigation measures are essential for controlling the spread of infectious diseases during pandemics and epidemics, but they impose considerable societal, individual, and economic costs. We developed a general optimization framework to…
HIV pre-exposure prophylaxis (PrEP) drastically reduces the risk of HIV infection if taken as prescribed, providing almost perfect protection even during unprotected sexual intercourse. Although this has been transformative in reducing new…
Endangered populations often experience limited growth ability at low densities, a phenomenon described by the Allee effect. In this thesis, we investigate a predator-prey model incorporating the Allee effect within a two-dimensional…
Agave villalobosii sp. nov. (sect. Ditepalae, Agavaceae, Asparagales) from the Mexican central plain in Aguascalientes and southern Zacatecas, Mexico, is described and illustrated. It resembles A. flexispina in terms of color and the…
Honey bees play a crucial role in pollination, contributing significantly to global agriculture and ecosystems. Accurately estimating hive populations is essential for understanding the effects of environmental factors on bee colonies, yet…