Sun, Siqi

22 publications

NeurIPS 2025 Bidirectional Representations Augmented Autoregressive Biological Sequence Generation Xiang Zhang, Jiaqi Wei, Zijie Qiu, Sheng Xu, Zhi Jin, ZhiQiang Gao, Nanqing Dong, Siqi Sun

ICML 2025 Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing Xiang Zhang, Jiaqi Wei, Zijie Qiu, Sheng Xu, Nanqing Dong, Zhiqiang Gao, Siqi Sun

AAAI 2025 PriFold: Biological Priors Improve RNA Secondary Structure Predictions Chenchen Yang, Hao Wu, Tao Shen, Kai Zou, Siqi Sun

NeurIPS 2025 Retrieval Is Not Enough: Enhancing RAG Through Test-Time Critique and Optimization Jiaqi Wei, Hao Zhou, Xiang Zhang, Di Zhang, Zijie Qiu, Noah Wei, Jinzhe Li, Wanli Ouyang, Siqi Sun

NeurIPS 2025 Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning Yuhao Zhou, Yiheng Wang, Xuming He, Ruoyao Xiao, Zhiwei Li, Qiantai Feng, Zijie Guo, Yuejin Yang, Hao Wu, Wenxuan Huang, Jiaqi Wei, Dan Si, Yao Xiuqi, Jia Bu, Haiwen Huang, Tianfan Fu, Shixiang Tang, Ben Fei, Dongzhan Zhou, Fenghua Ling, Yan Lu, Siqi Sun, Chenhui Li, Guanjie Zheng, Jiancheng Lv, Wenlong Zhang, Lei Bai

ICML 2025 Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing Zijie Qiu, Jiaqi Wei, Xiang Zhang, Sheng Xu, Kai Zou, Zhi Jin, Zhiqiang Gao, Nanqing Dong, Siqi Sun

NeurIPS 2024 BEACON: Benchmark for Comprehensive RNA Tasks and Language Models Yuchen Ren, Zhiyuan Chen, Lifeng Qiao, Hongtai Jing, Yuchen Cai, Sheng Xu, Peng Ye, Xinzhu Ma, Siqi Sun, Hongliang Yan, Dong Yuan, Wanli Ouyang, Xihui Liu

AAAI 2024 Causal Representation Learning via Counterfactual Intervention Xiutian Li, Siqi Sun, Rui Feng

AAAI 2024 ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing Zhi Jin, Sheng Xu, Xiang Zhang, Tianze Ling, Nanqing Dong, Wanli Ouyang, Zhiqiang Gao, Cheng Chang, Siqi Sun

AAAI 2024 CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues Linglin Jing, Sheng Xu, Yifan Wang, Yuzhe Zhou, Tao Shen, Zhigang Ji, Hui Fang, Zhen Li, Siqi Sun

NeurIPS 2024 MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun

IJCAI 2022 Human Parity on CommonsenseQA: Augmenting Self-Attention with External Attention Yichong Xu, Chenguang Zhu, Shuohang Wang, Siqi Sun, Hao Cheng, Xiaodong Liu, Jianfeng Gao, Pengcheng He, Michael Zeng, Xuedong Huang

AAAI 2022 RetGen: A Joint Framework for Retrieval and Grounded Text Generation Modeling Yizhe Zhang, Siqi Sun, Xiang Gao, Yuwei Fang, Chris Brockett, Michel Galley, Jianfeng Gao, Bill Dolan

AAAI 2021 FILTER: An Enhanced Fusion Method for Cross-Lingual Language Understanding Yuwei Fang, Shuohang Wang, Zhe Gan, Siqi Sun, Jingjing Liu

ICLR 2020 FreeLB: Enhanced Adversarial Training for Natural Language Understanding Chen Zhu, Yu Cheng, Zhe Gan, Siqi Sun, Tom Goldstein, Jingjing Liu

AISTATS 2017 Learning Nonparametric Forest Graphical Models with Prior Information Yuancheng Zhu, Zhe Liu, Siqi Sun

ECML-PKDD 2016 AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling Sheng Wang, Siqi Sun, Jinbo Xu

ECML-PKDD 2016 Graphical Model Sketch Branislav Kveton, Hung Bui, Mohammad Ghavamzadeh, Georgios Theocharous, S. Muthukrishnan, Siqi Sun

AISTATS 2015 Inferring Block Structure of Graphical Models in Exponential Families Siqi Sun, Hai Wang, Jinbo Xu

ICML 2015 Learning Scale-Free Networks by Dynamic Node Specific Degree Prior Qingming Tang, Siqi Sun, Jinbo Xu

NeurIPS 2015 Learning Structured Densities via Infinite Dimensional Exponential Families Siqi Sun, Mladen Kolar, Jinbo Xu

AISTATS 2014 Adaptive Variable Clustering in Gaussian Graphical Models Siqi Sun, Yuancheng Zhu, Jinbo Xu