Jun Zhang

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.

Sirui Liu, Jun Zhang, Haotian Chu et al.

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. To the best of our knowledge, the existing open source datasets are far less to satisfy the needs of modern protein sequence-structure related research. To solve this problem, we present the first million-level protein structure prediction dataset with high coverage and diversity, named as PSP. This dataset consists of 570k true structure sequences (10TB) and 745k complementary distillation sequences (15TB). We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset. We validate the utility of this dataset for training by participating CAMEO contest in which our model won the first place. We hope our PSP dataset together with the training benchmark can enable a broader community of AI/biology researchers for AI-driven protein related research.

Zeyuan Ma, Hongshu Guo, Yue-Jiao Gong et al.

In this survey, we introduce Meta-Black-Box-Optimization~(MetaBBO) as an emerging avenue within the Evolutionary Computation~(EC) community, which incorporates Meta-learning approaches to assist automated algorithm design. Despite the success of MetaBBO, the current literature provides insufficient summaries of its key aspects and lacks practical guidance for implementation. To bridge this gap, we offer a comprehensive review of recent advances in MetaBBO, providing an in-depth examination of its key developments. We begin with a unified definition of the MetaBBO paradigm, followed by a systematic taxonomy of various algorithm design tasks, including algorithm selection, algorithm configuration, solution manipulation, and algorithm generation. Further, we conceptually summarize different learning methodologies behind current MetaBBO works, including reinforcement learning, supervised learning, neuroevolution, and in-context learning with Large Language Models. A comprehensive evaluation of the latest representative MetaBBO methods is then carried out, alongside an experimental analysis of their optimization performance, computational efficiency, and generalization ability. Based on the evaluation results, we meticulously identify a set of core designs that enhance the generalization and learning effectiveness of MetaBBO. Finally, we outline the vision for the field by providing insight into the latest trends and potential future directions. Relevant literature will be continuously collected and updated at https://github.com/MetaEvo/Awesome-MetaBBO.