Bo Chen

Bo Chen (陈波)
allanchen224 [at] gmail [dot] com

I am now a fourth year PhD student at Knowledge Engineering Group(KEG), Department of Computer Science and Technology of Tsinghua University, under the surpervision of Prof. Jie Tang. My research interests include data mining, large language model, and AI for science.

News

on October, 2024, Our paper xTrimoPGLM-100B has been accepted by Nature Methods'24 (To Appear)!
on September, 2024, Our paper PLM Scaling Law has been accepted by NeurIPS'24 (Spotlight)!
on September, 2024, Our paper MSAGPT has been accepted by NeurIPS'24 (Poster)!
on January, 2024, Our paper BOND has been accepted by WWW'24!
on May, 2023, Our paper WhoIsWho has been accepted by KDD'23!
on May, 2023, Our paper ESMPair has been accepted by Briefings in Bioinformatics'23!
on August, 2022, Our paper GraphCAD has been accepted by IEEE TKDE'22!
on March, 2022, Our paper CODE has been accepted by AAAI'22!
on December, 2021, Our regular WhoIsWho benchmark & competition website is avaliable now! We honestly invite all the researchers of interest to attend our competition!
on May, 2021, We will hold the third name disambiguation competition at IJCAI'21 Competition Track based on the newly-released version(na-v3) of WhoIsWho dataset.

Preprints

Publications

xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein
Bo Chen, Xingyi Cheng, Yangli-ao Geng, Shen Li, Xin Zeng, Boyan Wang, Jing Gong, Chiming Liu, Aohan Zeng, Yuxiao Dong, Jie Tang, and Le Song
Nature Methods (To Appear), 2024

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
Bo Chen, Zhilei Bei, Xingyi Cheng, Pan Li, Jie Tang, and Le Song
NeurIPS 2024 (poster), also at ICML 2024 Workshop AI4Science, 2024, [Github]

Training Compute-Optimal Protein Language Models
Xingyi Cheng*, Bo Chen*, Pan Li, Jing Gong, Jie Tang, and Le Song
NeurIPS 2024 (Spotlight), also at ICML 2024 Workshop AI4Science (Spotlight), 2024

	OAG-Bench: A Human-Curated Benchmark for Academic Graph Mining Fanjin Zhang, Shijie Shi, Yifan Zhu, Bo Chen, Yukuo Cen, Jifan Yu, Yelin Chen, Lulu Wang, Qingfei Zhao, Yuqing Cheng, Tianyi Han, Yuwei An, Dan Zhang, Weng Lam Tam, Kun Cao, Yunhe Pang, Xinyu Guan, Huihui Yuan, Jian Song, Xiaoyan Li, Yuxiao Dong, and Jie Tang 30TH ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2024
	BOND: Bootstrapping From-Scratch Name Disambiguation with Multi-task Promoting Yuqing Cheng, Bo Chen, Fanjin Zhnag*, and Jie Tang The 2024 ACM Web Conference (WWW), 2024
	Web-Scale Academic Name Disambiguation: the WhoIsWho Benchmark, Leaderboard, and Toolkit Bo Chen, Jing Zhang, Fanjin Zhang, Tianyi Han, Yuqing Cheng, Xiaoyan Li, Yuxiao Dong, and Jie Tang 29TH ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2023, [Github]
	Improved the Heterodimer Protein Complex Prediction with Protein Language Models Bo Chen, Ziwei Xie, Jiezhong Qiu, Zhaofeng Ye, Jinbo Xu, and Jie Tang Briefings in Bioinformatics , 2023
	Graph Contrastive Learning for Anomaly Detection Bo Chen, Jing Zhang, Xiaokang Zhang, Yuxiao Dong, Jian Song, Peng Zhang, Kaibo Xu, Evgeny Kharlamov, and Jie Tang IEEE Transaction on Knowledge and Data Engineering (TKDE), 2022, [Github]
	CODE: Contrastive Pre-training with Adversarial Fine-tuning for Zero-shot Expert Linking Bo Chen, Jing Zhang, Xiaokang Zhang, Xiaobin Tang, Lingfan Cai, Cuiping Li, Hong Chen, Peng Zhang, Jie Tang AAAI Conference on Artificial Intelligence (AAAI), 2022, [Github] (Full Paper, acceptance rate: 15%)
	Neural, Symbolic and Neural-Symbolic Reasoning on Knowledge Graphs Jing Zhang, Bo Chen, Lingxi Zhang, Xirui Ke, Haipeng Ding AI Open Journal, 2021
	CONNA: Addressing Name Disambiguation on The Fly Bo Chen, Jing Zhang, Jie Tang, Lingfan Cai, Zhaoyu Wang, Shu Zhao, Hong Chen and Cuiping Li. IEEE Transaction on Knowledge and Data Engineering (TKDE), 2020, [Github]
	BERT-INT:A BERT-based Interaction Model For Knowledge Graph Alignment Xiaobin Tang, Jing Zhang, Bo Chen, Yang Yang, Hong Chen, Cuiping Li International Joint Conference on Artificial Intelligence (IJCAI), 2020, [Github] (Full Paper, acceptance rate: 12.6%)
	JarKA: Modeling Attribute Interactions for Cross-lingual Knowledge Alignment Bo Chen, Jing Zhang, Xiaobin Tang, Hong Chen, and Cuiping Li Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), 2020, [Github] (Full Paper, acceptance rate: 21%)
	Hierarchical Reinforcement Learning for Course Recommendation in MOOCs Jing Zhang, Bowen Hao, Bo Chen, Cuiping Li, Hong Chen and Jimeng Sun AAAI Conference on Artificial Intelligence (AAAI), 2019, [Github] (Full Paper, acceptance rate: 16.2%)
	MEgo2Vec: Embedding Matched Ego Networks for User Alignment Across Social Networks Jing Zhang, Bo Chen, Xianming Wang, Hong Chen, Cuiping Li, Fengmei Jin, Guojie Sone, Yutao Zhang International Conference on Information and Knowledge Management (CIKM), 2018, [Github] (Full Paper, acceptance rate: 17%)
*=equal contributions.

Projects

These are some open-sourced projects.

WhoIsWho

WhoIsWho is the world’s largest manually-labeled paper name disambiguation(NA) benchmark up to now, which consists about 900,000+ papers belonging to 70,000+ authors, 1,000+ names, and we also comprehensively define two basic tasks, Continuous Name Disambiguation and Name disambiguation from Scatch in NA domain with corresponding SOTA baselines. (see deatils WhoIsWho).

Education

September, 2013 - June, 2017, Bachelor, Department of Computer Science and Technology, Information School, Renmin University of China.
September, 2017 - June, 2020, Master, Department of Computer Science and Technology, Information School, Renmin University of China, under the surpervision of Associate Prof. Jing Zhang and Prof. Hong Chen.
September, 2021 - , PhD, Department of Computer Science and Technology, Tsinghua University, under the surpervision of Prof. Jie Tang.

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