论文发表Publications

Direction 1: Representation Learning & Biomolecular Mechanisms

My current research leverages state-of-the-art Deep Learning techniques to decipher complex biological systems. I focus on overcoming the limitations of traditional bioinformatics by introducing novel inductive biases and representation strategies. My work spans protein structure prediction, protein design, and molecular dynamics, aiming to provide robust, high-throughput tools for the life sciences.

1. Wang, Y., Cai, M., Dong, Y., Ma, Y., & Wei, K. (2025). From Signal to Symphony: Exploring 2D Sequence Representations for Protein Function Prediction. Journal of Chemical Information and Modeling, 65(23), 12723-12736. (SCI, JCR Q1, CAS Q2 Top, IF 5.3, First author). [PDF]

2. Wang, Y.*, Cai, M., Ma, Y., & Wei, K. (2025). Sequence-context-aware decoding enables robust reconstruction of protein dynamics from crystallographic B-factors. bioRxiv, 2025.12.05.692009. (First & corresponding author).

3. Wang, Y.†, Ma, Y.†, Chang, Y., Yan, J., Zhang, J., Cai, M., & Wei, K. (2025). Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules versus Therapeutic Peptides. Biology, 14(12), 1665. (SCI, JCR Q1, CAS Q2, Co-first author). [PDF]

4. Wang, X.†, Wang, Y.†*, Huang, T. Y., Dong, Y., Deng, J., Xu, L., ..., & He, R. (2025). Octopus Inspired Optimization (OIO): A Hierarchical Framework for Navigating Protein Fitness Landscapes. In 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 6897-6904). IEEE. (CCF-B, EI, Co-first & corresponding author). [PDF]

5. Cai, M., Lei, H., Zhang, Y., Zou, J., Cao, W., Wang, Y.*, ..., & Alzheimer's Disease Neuroimaging Initiative. (2025). APOE ε4-Associated Hippocampal Atrophy Trajectories Across the Alzheimer's Disease Continuum: A Systematic Review, Meta-Analysis, and Longitudinal Validation. medRxiv, 2025.12.08.25341534. (Corresponding author).

6. Wang, Y.*, Cai, M., & Huang, T. Y. (2025). AI for disease prediction: Performance insights and key limitations. Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia, 138, 111360. (SCI, JCR Q3, CAS Q4, IF 1.8, letter, First & corresponding author). [PDF]

Direction 2: First-Principles of Biological Complexity Based on Mathematical Physics

While Deep Learning provides powerful approximations, my ultimate goal is to find the analytical ground truths of biological systems. I am transitioning from purely data-driven approaches to physics-informed theories. I aim to use Condensed Matter Physics, Topology, Manifold Learning, and Differential Geometry to describe the energy landscapes of proteins and the thermodynamic essence of life.

1. Wang, Y. (2026). Structural barriers of the discrete Hasimoto map applied to protein backbone geometry. arXiv preprint arXiv:2602.13160. (Sole author). [arXiv]

Direction 3: Interdisciplinary Explorations & Collaborative Synergies

My research journey is fueled by broad curiosity. I have collaborated with experts in linguistics, computer vision, cryptography, and operations research. These diverse experiences have equipped me with a unique toolkit—allowing me to transfer methodologies and tackle problems from orthogonal perspectives.

1. Wang, Y.*, Chang, Y., Zhang, J., Cai, M., Yan, J., Zhao, H., & Alzheimer's Disease Neuroimaging Initiative. (2026). Geometric Fragility in Alzheimer's Disease: Probing the Loss of Hippocampal Hierarchical Abstraction via Contrastive Point Cloud Modeling. bioRxiv, 2026.01.31.702997. (First & corresponding author).

2. Wang, Y., Liu, Z., Zai, J., Chen, J., & Sabir, E. (2026). Resilient AI Infrastructure by Design: A Spatially-Aware Framework for Tolerating Clustered Failures. In 4th Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE). (First author). [PDF]

3. Wang, Y.*, Cai, M., Zhang, J., Chang, Y., & Yan, J. (2026). Adaptive Decision-Making in Multi-Stage Production: A Framework for Cost Optimization under Sampling Uncertainty. Applied Operations and Analytics, 2(1), 1-23. (First & corresponding author). [PDF]

4. Wang, X.†, Wang, Y.†, & Huang, T. Y.† (2025). Crypto-ncRNA: Non-coding RNA (ncRNA) Based Encryption Algorithm. ICLR 2025 Workshop on AI for Nucleic Acids. (Co-first author). [PDF]

5. Wang, X., Wang, F., & Wang, Y. (2025). DIALOGUES BETWEEN ADAM AND EVE: EXPLORATION OF UNKNOWN CIVILIZATION LANGUAGE BY LLM. ICLR 2025 Workshop on World Models: Understanding, Modelling and Scaling.

6. Wang, X.†, Wang, Y.†*, & Pan, J. (2025). Digital Art Creation and Copyright Protection in Pollock Style Using GANs, Fractal Analysis, and NFT Generation. The 1st Workshop on GenAI Watermarking (ICLR 2025). (Co-first & corresponding author). [PDF]

7. Wang, X., Huang, T. Y., Wang, Y., & Yuan, Y. (2025). StrucTrace: Fourier Watermarking for Traceable Bio-molecular Assets. bioRxiv, 2025-10.

8. Wang, Y., Huang, T. Y., Gao, Q., & Zhang, J. (2025). HeDA: AI Driven Discovery of Bio-Ecological Mediation in Cascading Heatwave Risks. arXiv preprint arXiv:2509.25112. (First author). [PDF]

9. Zhao, H., Shi, W., Liu, C., & Wang, Y. (2025). Boundary Box-Guided Targeted Adversarial Attacks with Semantic Perturbation. In 2025 IEEE International Conference on Systems, Man, and Cybernetics (SMC) (pp. 1604-1609). IEEE. (CCF-C, EI).

10. Zuo, J., Wang, Y., Pan, Y., & Yibulayin, X. (2025). Construction and educational application of a linguistically grounded dependency treebank for Uyghur. arXiv preprint arXiv:2507.21536.

11. Wang, Y.*, Wang, J., Huang, T. Y., Yang, J., & Xu, Z. (2025). STGCN-LSTM for Olympic Medal Prediction: Dynamic Power Modeling and Causal Policy Optimization. arXiv preprint arXiv:2501.17711. (First & corresponding author).

12. Luo, Z.†, Wang, X.†, Wang, Y.†, Zhang, H., & Li, Z. (2024). A personalized MOOC learning group and course recommendation method based on graph neural network and social network analysis. arXiv preprint arXiv:2410.10658. (Co-first author).

13. Wang, Y.*, Zhang, J., & Chang, Y. (2024). A probability prediction model for flood disasters based on Multi-layer Perceptron. Journal of Physics: Conference Series, 2905(1), 012003. (EI, First & corresponding author). [PDF]

14. Wang, J., & Wang, Y.* (2024). Multi-stage Crop Planting Strategy Optimization Model Based on PSO Algorithm. In 2024 3rd International Conference on Electronics and Information Technology (EIT) (pp. 915-919). IEEE. (EI, Corresponding author).

15. Wang, G., Wang, Y., & Li, W. (2024). Research on Travel Route Planning Problems Based on Greedy Algorithm. In 2024 4th International Conference on Electronic Information Engineering and Computer Science (EIECS) (pp. 755-758). IEEE. (EI).