Selected Publications
2025
- Liu P, Tao J, Zhixiang Ren*. A self-feedback knowledge elicitation approach for chemical reaction predictions[J]. Engineering Applications of Artificial Intelligence, 2025. [Full text]
- Mingqing Wang, Zhiwei Nie, Yonghong He, Athanasios V Vasilakos, Qiang Shawn Cheng, Zhixiang Ren*. Deep learning methods for protein representation and function prediction: A comprehensive overview[J]. Engineering Applications of Artificial Intelligence, 2025. [Full text]
- Zhiwei Nie, Daixi Li, Yutian Liu, Fan Xu, Hongyu Zhang, Xiansong Huang, Xudong Liu, Zhennan Wang, Yiming Ma, Yuxin Ye, Feng Yin, Wen-Bin Zhang, Zhixiang Ren*, Zhihong Liu, Zigang Li, Jie Chen. A Unified Peptide Generative Framework via a Weakly Order-Dependent Autoregressive Language Model and Lifelong Learning[J]. Journal of Chemical Information and Modeling, 2025. [Full text]
- Shuang Ge, Shuqing Sun, Huan Xu, Qiang Cheng, Zhixiang Ren*. A multi-modal genomic knowledge distillation framework for drug response prediction[J]. Applied Intelligence, 2025. [Full text]
- Zhiwei Nie, Yiming Ma, Yutian Liu, Xiansong Huang, Zhihong Liu, Peng Yang, Fan Xu, Feng Yin, Zigang Li, Jie Fu, Zhixiang Ren*, Wen-Bin Zhang, Jie Chen. Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence[J]. Briefings in Bioinformatics, 2025. [Full text]
- Wang M, Z Nie, He Y, AV Vasilakos, Zhixiang Ren*. Aligning sequence and structure representations leveraging protein domains for function prediction[J]. Expert Systems with Applications, Volume 278, 10, June 2025, 127246. [Full text]
- Zhao T, Zhou Y, Shi R, Xu P, Cao Z, Zhixiang Ren*. Compact binary coalescence gravitational wave signal counting and separation[J]. Phys. Rev. D 111, 104028. [Full text]
- Liu X, Nie Z, Si H, Shen X, Liu Y, Huang X, Dong T, Xu F, Zhixiang Ren*, Zhou P, Chen J. Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution[J]. Briefings in Bioinformatics, Volume 26, Issue 3, May 2025, bbaf276. [Full text]
- Kuang T, Ma Q, AV Vasilakos, Wang Y, Zhixiang Ren*. Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation[J]. arXiv preprint arXiv:2503.08160, 2025. [Full text]
- Zhixiang Ren, Y Ren, P Liu, Q Shu, H Ma, H Xu, Yang Y. Discovery of Bioactive Constituents for Colitis from Traditional Chinese Medicine Prescription via Deep Neural Network[J]. IEEE Transactions on Computational Biology and Bioinformatics ( Volume: 22, Issue: 2, March-April 2025). [Full text]
- Ge S, Sun S, Xu H, Cheng Q, Zhixiang Ren*. Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective[J]. Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf136. [Full text]
- Shi R, Zhou Y, Zhao T, Wang Z, Zhixiang Ren*, Cao Z. Rapid eccentric spin-aligned binary black hole waveform generation based on deep learning[J]. Phys. Rev. D 111, 044016. [Full text]
- Liu P, Tao J, Zhixiang Ren*. A quantitative analysis of knowledge-learning preferences in large language models in molecular science[J]. Nature Machine Intelligence volume 7, pages 315–327 (2025). [Full text]
- T Zhao, R Shi, Y Zhou, Z Cao, Zhixiang Ren*. Dawning of a new era in gravitational wave data analysis: Unveiling cosmic mysteries via artificial intelligence — A systematic review[J]. arXiv preprint arXiv:2311.15585, 2023. [Full text]
2024
- Zhao T, Zhou Y, Shi R, Cao Z, Zhixiang Ren*. GWAI: Artificial intelligence platform for enhanced gravitational wave data analysis[J]. SoftwareX, 2024, 28: 101930. [Full text]
- Zhixiang Ren, Ren Y, Li Z, Xu H. TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations[J]. Computational and Structural Biotechnology Journal, 2024, 23: 1619-1630. [Full text]
- Kuang T, Ren Y, Zhixiang Ren*. 3D-mol: A novel contrastive learning framework for molecular property prediction with 3D information[J]. Pattern Analysis and Applications, 2024, 27(3): 71. [Full text]
- Kuang T, Liu P, Zhixiang Ren*. Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey[J]. Big Data Mining and Analytics, 2024, 7(3): 858-888. [Full text]
- Chen K, Zhou Y, Ding M, Wang Y, Zhixiang Ren*, Yang Y*. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction[J]. Briefings in Bioinformatics, 2024, 25(3): bbae163. [Full text]
- Zhao T, Zhou Y, Shi R, Cao Z, Zhixiang Ren*. Dilated convolutional neural network for detecting extreme-mass-ratio inspirals[J]. Physical Review D, 2024, 109(8): 084054. [Full text]
- Shi R, Zhou Y, Zhao T, Cao Z, Zhixiang Ren*. Compact binary systems waveform generation with a generative pretrained transformer[J]. Physical Review D, 2024, 109(8): 084017. [Full text]
- Zhixiang Ren, Ren Y, Liu P, Xu H. Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification[J]. Computational Biology and Chemistry, 2024, 109: 108025. [Full text]
- Wang H, Zhou Y, Cao Z, Guo Z, Zhixiang Ren*. WaveFormer: transformer-based denoising method for gravitational-wave data[J]. Machine Learning: Science and Technology, 2024, 5(1): 015046. [Full text]
- Liu P, Ren Y, Tao J, Zhixiang Ren*. Git-mol: A multi-modal large language model for molecular science with graph, image, and text[J]. Computers in biology and medicine, 2024, 171: 108073. [Full text]
2023
- Zhixiang Ren, Zhao T, Cao Z, et al. Taiji data challenge for exploring gravitational wave universe[J]. Frontiers of Physics, 2023, 18(6): 64302. [Full text]
- Zhao T, Lyu R, Wang H, Cao Z, Zhixiang Ren*. Space-based gravitational wave signal detection and extraction with deep neural network[J]. Communications Physics, 2023, 6(1): 212. [Full text]
2021
- Wang H, Cao Z, Zhou Y, Guo ZK, Zhixiang Ren*. Sampling with prior knowledge for high-dimensional gravitational wave data analysis[J]. Big Data Mining and Analytics, 2021, 5(1): 53-63. [Full text]
- Zhixiang Ren*, Liu Y, Shi T, et al. AIPerf: Automated machine learning as an AI-HPC benchmark[J]. Big Data Mining and Analytics, 2021, 4(3): 208-220. [Full text]