定量生物学
Protein language models (PLMs) have enabled advances in structure prediction and de novo protein design, yet they frequently collapse into pathological repetition during generation. Unlike in text, where repetition merely reduces…
Identifying minimal and informative feature sets is a central challenge in data analysis, particularly when few data points are available. Here we present a theoretical analysis of an unsupervised feature selection pipeline based on the…
Handwriting literacy is an important skill for learning and communication in school-age children. In the digital age, handwriting has been largely replaced by typing, leading to a decline in handwriting proficiency, particularly in…
Predicting critical transitions in complex systems, such as epileptic seizures in the brain, represents a major challenge in scientific research. The high-dimensional characteristics and hidden critical signals further complicate…
Neural coupling in both neuroscience and artificial intelligence emerges as dynamic oscillatory patterns that encode abstract concepts. To this end, we hypothesize that a deeper understanding of the neural mechanisms governing brain rhythms…
Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration…
Objective: In randomized clinical trials, prediction models can be used to explore the relationships between patients' variables (e.g., clinical, pathological, or lifestyle variables, and also biomarker or genomic data) and treatment effect…
The generalized Lotka-Volterra (GLV) equations with quenched random interactions have been extensively used to investigate the stability and dynamics of complex ecosystems. However, the standard linear interaction model suffers from…
Zero-one reaction networks are pivotal to cellular signaling, and establishing the equivalence of such networks represents a foundational computational challenge in the realm of chemical reaction network research. Herein, we propose a…
Enzyme-catalyzed protein cleavage is essential for many biological functions. Accurate prediction of cleavage sites can facilitate various applications such as drug development, enzyme design, and a deeper understanding of biological…
Spatiotemporal flows of neural activity, such as traveling waves, have been observed throughout the brain since the earliest recordings; yet there is still little consensus on their functional role. Recent experiments and models have linked…
In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the…
Multispecific antibodies offer transformative therapeutic potential by engaging multiple epitopes simultaneously, yet their efficacy is an emergent property governed by complex molecular architectures. Rational design is often bottlenecked…
Tactile localization is the seemingly simple ability to 'tell' where a touch has occurred. However, how this ability is assessed, and what conclusions are drawn from experiments, depends on the theoretical ideas that inspire the research.…
Microbes constantly interact with their environment by depleting and transforming food sources. Theoretical studies have mainly focused on Lotka-Volterra models, which do not account for food source dynamics. In contrast, consumer-resource…
Recent advances in metagenomics have revealed macroecological patterns or "laws" describing robust statistical regularities across microbial communities. Stochastic logistic models (SLMs), which treat species as independent -- akin to ideal…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
The efficacy of anti-cancer therapies is severely limited by the emergence of drug resistance. While genetic drivers are well-characterized, growing evidence suggests that non-genetic mechanisms, particularly those involving drug-tolerant…
Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms…
Generative modeling of peptide sequences requires navigating a discrete and highly constrained space in which many intermediate states are chemically implausible or unstable. Existing discrete diffusion and flow-based methods rely on…