Zilan Yu

Guangyan Zhang, Ziru Liu, Jichen Dai et al.

Motivation: Since long non-coding RNAs (lncRNAs) have involved in a wide range of functions in cellular and developmental processes, an increasing number of methods have been proposed for distinguishing lncRNAs from coding RNAs. However, most of the existing methods are designed for lncRNAs in animal systems, and only a few methods focus on the plant lncRNA identification. Different from lncRNAs in animal systems, plant lncRNAs have distinct characteristics. It is desirable to develop a computational method for accurate and robust identification of plant lncRNAs. Results: Herein, we present a plant lncRNA identification method ItLnc-BXE, which utilizes multiple features and the ensemble learning strategy. First, a diversity of lncRNA features is collected and filtered by feature selection to represent RNA transcripts. Then, several base learners are trained and further combined into a single meta-learner by ensemble learning, and thus an ItLnc-BXE model is constructed. ItLnc-BXE models are evaluated on datasets of six plant species, the results show that ItLnc-BXE outperforms other state-of-the-art plant lncRNA identification methods, achieving better and robust performances (AUC>95.91%). We also perform some experiments about cross-species lncRNA identification, and the results indicate that dicots-based and monocots-based models can be used to accurately identify lncRNAs in lower plant species, such as mosses and algae. Availability: source codes are available at https://github.com/BioMedicalBigDataMiningLab/ItLnc-BXE. Contact: zhangwen@mail.hzau.edu.cn (or) zhangwen@whu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Yafeng Zhang, Zilan Yu, Yuang Huang et al.

Few-shot Named Entity Recognition (NER), the task of identifying named entities with only a limited amount of labeled data, has gained increasing significance in natural language processing. While existing methodologies have shown some effectiveness, such as enriching label semantics through various prompting modes or employing metric learning techniques, their performance exhibits limited robustness across diverse domains due to the lack of rich knowledge in their pre-trained models. To address this issue, we propose CLLMFS, a Contrastive Learning enhanced Large Language Model (LLM) Framework for Few-Shot Named Entity Recognition, achieving promising results with limited training data. Considering the impact of LLM's internal representations on downstream tasks, CLLMFS integrates Low-Rank Adaptation (LoRA) and contrastive learning mechanisms specifically tailored for few-shot NER. By enhancing the model's internal representations, CLLMFS effectively improves both entity boundary awareness ability and entity recognition accuracy. Our method has achieved state-of-the-art performance improvements on F1-score ranging from 2.58\% to 97.74\% over existing best-performing methods across several recognized benchmarks. Furthermore, through cross-domain NER experiments conducted on multiple datasets, we have further validated the robust generalization capability of our method. Our code will be released in the near future.