Wenhao Lin

Jiahao Li, Zhourun Wu, Wenhao Lin et al.

Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the performance of enhancer identification, they cannot learn position-related multiscale contextual information from raw DNA sequences. Results: In this article, we propose a novel enhancer identification method (iEnhancer-ELM) based on BERT-like enhancer language models. iEnhancer-ELM tokenizes DNA sequences with multi-scale k-mers and extracts contextual information of different scale k-mers related with their positions via an multi-head attention mechanism. We first evaluate the performance of different scale k-mers, then ensemble them to improve the performance of enhancer identification. The experimental results on two popular benchmark datasets show that our model outperforms stateof-the-art methods. We further illustrate the interpretability of iEnhancer-ELM. For a case study, we discover 30 enhancer motifs via a 3-mer-based model, where 12 of motifs are verified by STREME and JASPAR, demonstrating our model has a potential ability to unveil the biological mechanism of enhancer. Availability and implementation: The models and associated code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Zirui Wang, Shaoming Duan, Chengyue Wu et al. · cmu

Swarm learning (SL) is an emerging promising decentralized machine learning paradigm and has achieved high performance in clinical applications. SL solves the problem of a central structure in federated learning by combining edge computing and blockchain-based peer-to-peer network. While there are promising results in the assumption of the independent and identically distributed (IID) data across participants, SL suffers from performance degradation as the degree of the non-IID data increases. To address this problem, we propose a generative augmentation framework in swarm learning called SL-GAN, which augments the non-IID data by generating the synthetic data from participants. SL-GAN trains generators and discriminators locally, and periodically aggregation via a randomly elected coordinator in SL network. Under the standard assumptions, we theoretically prove the convergence of SL-GAN using stochastic approximations. Experimental results demonstrate that SL-GAN outperforms state-of-art methods on three real world clinical datasets including Tuberculosis, Leukemia, COVID-19.