定量生物学
Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue…
Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core…
How can cognitive science build generalizable theories that span the full scope of natural situations and behaviors? We argue that progress in Artificial Intelligence (AI) offers timely opportunities for cognitive science to embrace…
Endothelial cells form the linchpin of vascular and lymphatic systems, creating intricate networks that are pivotal for angiogenesis, controlling vessel permeability, and maintaining tissue homeostasis. Despite their critical roles, there…
The semantic knowledge stored in our brains can be accessed from different stimulus modalities. For example, a picture of a cat and the word "cat" both engage similar conceptual representations. While existing research has found evidence…
Understanding the environmental drivers of forest transpiration is critical for improving global predictions of water availability and ecosystem health. Due to many competing controls on plant water stress and ecosystem transpiration,…
The phase of Quasi-Linkage Equilibrium (QLE) in evolutionary populations is analogous to the thermal equilibrium state in statistical mechanics, a concept pioneered by Kimura in 1965 for two-locus two-allele models. QLE describes a…
It is widely accepted that the brain operates near a critical state, characterized by neural avalanches that follow power-law distributions. However, the functional rationale for why neural systems attain criticality remains unclear. Here,…
Non-pharmaceutical interventions (NPIs), including mask-wearing, physical distancing, and hygiene measures, provide the primary means of reducing transmission in the early stages of an epidemic. Individuals adopt one of two…
Processing sequential inputs is a fundamental brain function, underlying tasks such as sensory perception, language, and motor control. A challenge in sequence processing is to represent not only the order of events, but also their precise…
Highly pathogenic avian influenza A(H5N1) has expanded geographically and ecologically, affecting wild birds, mammalian wildlife, domestic animals, and humans. Wildlife surveillance provides critical early warning for One Health…
We present an investigation of the applicability of topological data analysis (TDA) to the study of high-resolution confocal microscopy images of fibrin network structures from patients with oesophageal cancer undergoing intended curative…
We give a Hasse-diagram characterization of when a clustering system $\mathcal C$ on a finite taxa set $X$ is the hardwired clustering system $C_N$ of a rooted level-$k$ network. For each non-trivial block $B$ of $H=\mathcal H[\mathcal C]$,…
Phylogenetic trees are hybrid objects: branch lengths vary continuously, while topologies change discretely through edge contractions and expansions. Billera-Holmes-Vogtmann (BHV) tree space provides a canonical geometry for this structure,…
We investigate how key epidemiological parameters shape both seasonal epidemics and the persistence of dengue transmission. Our findings confirm known mechanistic drivers of epidemic variability and introduce a ranking of parameter…
Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…
Polygenic risk scores (PRSs) aggregate genetic effect estimates to predict disease susceptibility, yet clinical deployment often exposes raw genotype data to third-party compute infrastructure. Prior homomorphic-encryption approaches, still…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…
Computational functionalism about consciousness is often criticized for relying on observer-relative interpretations of physical systems. This paper proposes a mathematical refinement of functionalism that avoids this problem. The central…
Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely…