mRNA2vec: mRNA Embedding with Language Model in the 5'UTR-CDS for mRNA Design

Messenger RNA (mRNA)-based vaccines are accelerating the discovery of new drugs and revolutionizing the pharmaceutical industry. However, selecting particular mRNA sequences for vaccines and therapeutics from extensive mRNA libraries is costly. Effective mRNA therapeutics require carefully designed sequences with optimized expression levels and stability. This paper proposes a novel contextual language model (LM)-based embedding method: mRNA2vec. In contrast to existing mRNA embedding approaches, our method is based on the self-supervised teacher-student learning framework of data2vec. We jointly use the 5' untranslated region (UTR) and coding sequence (CDS) region as the input sequences. We adapt our LM-based approach specifically to mRNA by 1) considering the importance of location on the mRNA sequence with probabilistic masking, 2) using Minimum Free Energy (MFE) prediction and Secondary Structure (SS) classification as additional pretext tasks. mRNA2vec demonstrates significant improvements in translation efficiency (TE) and expression level (EL) prediction tasks in UTR compared to SOTA methods such as UTR-LM. It also gives a competitive performance in mRNA stability and protein production level tasks in CDS such as CodonBERT.

StarGraph: A Coarse-to-Fine Representation Method for Large-Scale Knowledge Graph

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector, ignoring the rich information contained in neighbor entities. We propose a method named StarGraph, which gives a novel way to utilize the neighborhood information for large-scale knowledge graphs to get better entity representations. The core idea is to divide the neighborhood information into different levels for sampling and processing, where the generalized coarse-grained information and unique fine-grained information are combined to generate an efficient subgraph for each node. In addition, a self-attention network is proposed to process the subgraphs and get the entity representations, which are used to replace the entity embeddings in conventional methods. The proposed method achieves the best results on the ogbl-wikikg2 dataset, which validates the effectiveness of it. The code is now available at https://github.com/hzli-ucas/StarGraph