DNA Motif Knowledge Extraction and Distillation from Big Deep Learning Models in Regulatory Genomics

Project: Research

1 - 12 out of 12Page size: 20

Research Output

  1. 2024
  2. Published

    AutoCancer as an automated multimodal framework for early cancer detection

    Liu, L., Xiong, Y., Zheng, Z., Huang, L., Song, J., Lin, Q., Tang, B., & 1 othersWong, K., 19 Jul 2024, In: iScience. 27, 7, 110183.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  3. Published

    TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation

    Chen, N., Yu, J., Liu, Z., Wang, F., Li, X. & Wong, K., Jul 2024, In: Briefings in Bioinformatics. 25, 4, bbae308.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  4. Published

    DeepSeq2Drug: An expandable ensemble end-to-end anti-viral drug repurposing benchmark framework by multi-modal embeddings and transfer learning

    Xie, W., Yu, J., Huang, L., For, L. S., Zheng, Z., Chen, X., Wang, Y., & 3 othersLiu, Z., Peng, C. & Wong, K., Jun 2024, In: Computers in Biology and Medicine. 175, 108487.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  5. Published

    TransPTM: A transformer-based model for non-histone acetylation site prediction

    Meng, L., Chen, X., Cheng, K., Chen, N., Zheng, Z., Wang, F., Sun, H., & 1 othersWong, K., May 2024, In: Briefings in Bioinformatics. 25, 3, 10 p., bbae219.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  6. Online published

    A unified conditional diffusion framework for dual protein targets based bioactive molecule generation

    Huang, L., Yuan, Z., Yan, H., Sheng, R., Liu, L., Wang, F., Xie, W., & 5 othersChen, N., Huang, F., Huang, S., Wong, K. & Zhang, Y., 11 Apr 2024, (Online published) In: IEEE Transactions on Artificial Intelligence.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  7. Online published

    Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation

    Chen, N., Yu, J., Liu, Z., Meng, L., Li, X. & Wong, K., 4 Apr 2024, (Online published) In: Nucleic Acids Research. gkae210.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  8. Online published

    scGREAT: Transformer-Based Deep-Language Model for Gene Regulatory Network Inference from Single-Cell Transcriptomics

    Wang, Y., Chen, X., Zheng, Z., Huang, L., Xie, W., Wang, F., Zhang, Z., & 1 othersWong, K., 28 Feb 2024, (Online published) In: iScience.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  9. Published

    A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets

    Huang, L., Xu, T., Yu, Y., Zhao, P., Chen, X., Han, J., Xie, Z., & 4 othersLi, H., Zhong, W., Wong, K. & Zhang, H., 2024, In: Nature Communications. 15, 2657.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 5
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  10. Published

    Unsupervised Gene-Cell Collective Representation Learning with Optimal Transport

    Yu, J., Chen, N., Gao, M., Li, X. & Wong, K., 2024, Proceedings of the 38th AAAI Conference on Artificial Intelligence. Dy, J., Natarajan, S. & Wooldridge, M. (eds.). Washington, DC: AAAI Press, p. 356-364 (Proceedings of the AAAI Conference on Artificial Intelligence; vol. 38, no. 1).

    Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

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  11. 2023
  12. Published

    LncRNA-Top: Controlled Deep Learning Approaches for LncRNA Gene Regulatory Relationship Annotations across Different Platforms

    Xie, W., Chen, X., Zheng, Z., Wang, F., Zhu, X., Lin, Q., Sun, Y., & 1 othersWong, K., 17 Nov 2023, In: iScience. 26, 11, 108197.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  13. Online published

    Construction of Immune Infiltration-Related LncRNA Signatures Based on Machine Learning for the Prognosis in Colon Cancer

    Liu, Z., Petinrin, O. O., Toseef, M., Chen, N. & Wong, K., 4 Oct 2023, (Online published) In: Biochemical Genetics.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 1
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  14. Published

    Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results

    Toseef, M., Petinrin, O. O., Wang, F., Rahaman, S., Liu, Z., LI, X. & WONG, K., Jul 2023, In: Briefings in Bioinformatics. 24, 4, bbad254.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 3
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