Publications

2025

• Liu P, Tao J, Ren Z*. A self-feedback knowledge elicitation approach for chemical reaction predictions[J]. Engineering Applications of Artificial Intelligence, Volume 156, Part C, 15, September 2025, 111112. [Full text]
• Nie Z, Zhang H, Jiang H, Liu Y, Huang X, Xu F, Fu J, Ren Z, Tian Y, Zhang W, Chen J. OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning[J]. arXiv preprint arXiv:2506.17963, 2025. [Full text]
• Wang M, Z Nie, He Y, AV Vasilakos, Ren Z*. 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, Ren Z*. 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, Ren Z*, 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, Ren Z*. Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation[J]. arXiv preprint arXiv:2503.08160, 2025. [Full text]
• Z 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, Ren Z*. 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, Ren Z, 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, Ren Z*. 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, Ren Z*. 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, Ren Z*. GWAI: Artificial intelligence platform for enhanced gravitational wave data analysis[J]. SoftwareX, 2024, 28: 101930. [Full text]
• Ren Z, 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, Ren Z*. 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, Ren Z*. 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]
• Wang M, Nie Z, He Y, Ren Z*. ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception[J]. arXiv preprint arXiv:2405.15158, 2024. [Full text]
• Fang Y, Luo M, Ren Z, Wei L, Wei DQ. CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction[J]. Briefings in Bioinformatics, 2024, 25(4). [Full text]
• Chen K, Zhou Y, Ding M, Wang Y, Ren Z, 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, Ren Z*. Dilated convolutional neural network for detecting extreme-mass-ratio inspirals[J]. Physical Review D, 2024, 109(8): 084054. [Full text]
• Liu P, Tao J, Ren Z*. A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions[J]. arXiv preprint arXiv:2404.09606, 2024. [Full text]
• Shi R, Zhou Y, Zhao T, Cao Z, Ren Z*. Compact binary systems waveform generation with a generative pretrained transformer[J]. Physical Review D, 2024, 109(8): 084017. [Full text]
• Ren Z, 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, Ren Z*. 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, Ren Z*. 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]
• Dou F, Xu L, Zhao D, Ren Z*. A Multibranch Deep Neural Network for the Superresolution of Solar Magnetograms[J]. The Astrophysical Journal Supplement Series, 2024, 271(1): 9. [Full text]
• Liu P, Tao J, Ren Z*. Scientific language modeling: A quantitative review of large language models in molecular science[J]. arXiv preprint arXiv:2402.04119, 2024. [Full text]
• Zhao T, Zhou Y, Shi R, Cao Z, Ren Z*. GWAI: Harnessing Artificial Intelligence for Enhancing Gravitational Wave Data Analysis[J]. arXiv preprint arXiv:2402.02825, 2024. [Full text]
• Nie Z, Ma Y, Chen J, Ren Z, et al. Towards anchoring evolutionary fitness for protein stability with virtual chemical environment recovery[J]. bioRxiv, 2024: 2024.04. 22.590665. [Full text]
• Ge S, Sun S, Ren Y, Xu H, Ren Z*. MetaSCDrug: Meta-Transfer Learning for Single-Cell-Level Drug Response Prediction from Transcriptome and Molecular Representations[J]. bioRxiv, 2024: 2024.04. 25.591050. [Full text]

2023

• Fang Y, Jiang Y, Wei L, Ma Q, Ren Z*, Yuan Q, Wei DQ. DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model[J]. Bioinformatics, 2023, 39(12): btad718. [Full text]
• Ren Z, 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, Shi R, Zhou Y, Cao Z, Ren Z*. 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]
• Chen J, Nie Z, Wang Y, Ren Z, et al. Running ahead of evolution—AI-based simulation for predicting future high-risk SARS-CoV-2 variants[J]. The International Journal of High Performance Computing Applications, 2023, 37(6): 650-665. [Full text]
• Zhao T, Lyu R, Wang H, Cao Z, Ren Z*. Space-based gravitational wave signal detection and extraction with deep neural network[J]. Communications Physics, 2023, 6(1): 212. [Full text]
• Zhang X, Xu L, Ren Z, Xu X, Li J. Attention-Based Deep Learning Model for Image Desaturation of SDO/AIA[J]. Research in Astronomy and Astrophysics, 2023, 23(8): 085004. [Full text]
• Zhao Z, Xu L, Zhu X, Ren Z, et al. A large-scale dataset of three-dimensional solar magnetic fields extrapolated by nonlinear force-free method[J]. Scientific Data, 2023, 10(1): 178. [Full text]
• Schäfer M B, Zelenka O, Nitz A H, Ren Z, et al. First machine learning gravitational-wave search mock data challenge[J]. Physical Review D, 2023, 107(2): 023021. [Full text]
• Ren Z, Ren Y, Liu P, Shu Q, Ma H, Xu H. Identification of bioactive constituents for colitis from traditional Chinese medicine prescription via deep neural network[J]. bioRxiv, 2023: 2023.05. 31.542690. [Full text]

2022

• Albert A, Alfaro R, Alvarez C, Ren Z, et al. Constraints on the very high energy gamma-ray emission from short GRBs with HAWC[J]. The Astrophysical Journal, 2022, 936(2): 126. [Full text]
• Dou F, Xu L, Ren Z, Zhao D, Zhang X. Super-resolution of solar magnetograms using deep learning[J]. Research in Astronomy and Astrophysics, 2022, 22(8): 085018. [Full text]
• Yu X, Xu L, Ren Z, Zhao D, Sun W. Image desaturation for SDO/AIA using mixed convolution network[J]. Research in Astronomy and Astrophysics, 2022, 22(6): 065009. [Full text]

2021

• Wang H, Cao Z, Zhou Y, Guo ZK, Ren Z*. Sampling with prior knowledge for high-dimensional gravitational wave data analysis[J]. Big Data Mining and Analytics, 2021, 5(1): 53-63. [Full text]
• Ren Z, 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]
• Abeysekara A U, Albert A, Alfaro R, Ren Z, et al. HAWC observations of the acceleration of very-high-energy cosmic rays in the Cygnus Cocoon[J]. Nature Astronomy, 2021, 5(5): 465-471. [Full text]