AbstractMetagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the ca…
AbstractMotivationThe statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to…
AbstractProtein sequence not only determines its structure but also provides important clues of its subcellular localization. Although a series of artificial intelligence models have been reported to predict protein subcellular localization, most of th…
AbstractSingle-cell multi-omics technologies have revolutionized the study of cell states and functions by simultaneously profiling multiple molecular layers within individual cells. However, existing methods for integrating these data struggle to pres…
AbstractIn recent years, inspired by the success of large language models (LLMs) for DNA and proteins, several LLMs for RNA have also been developed. These models take massive RNA datasets as inputs and learn, in a self-supervised way, how to represent…
AbstractInvariant molecular representation models provide potential solutions to guarantee accurate prediction of molecular properties under distribution shifts out-of-distribution (OOD) by identifying and leveraging invariant substructures inherent to…
AbstractHuman papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some …
AbstractIn the realm of protein design, the efficient construction of protein sequences that accurately fold into predefined structures has become an important area of research. Although advancements have been made in the study of long-chain proteins, …
AbstractDNA modifications, such as N6-methyladenine (6mA), play important roles in various processes in eukaryotes. Single-molecule, real-time (SMRT) sequencing enables the direct detection of DNA modifications without requiring special sample preparat…
AbstractSynthetic lethality (SL) is a promising gene interaction for cancer therapy. Recent SL prediction methods integrate knowledge graphs (KGs) into graph neural networks (GNNs) and employ attention mechanisms to extract local subgraphs as explanati…