Publications

(MMLI researchers in bold) 


Daniel Campos and Heng Ji. December 2021. "IMG2SMI: Translating Molecular Structure Images to Simplified Molecular-input Line-entry System." NeurIPS 2021. Accepted  


Xuan Wang, Vivian Hu, Xiangchen Song, Shweta Garg, Jinfeng Xiao, and Jiawei Han. November 2021. "ChemNER: Fine-Grained Chemistry Named Entity Recognition with Ontology-Guided Distant Supervision." EMNLP 2021. 


Carl Edwards, ChengXiang Zhai, and Heng Ji. November 2021. "Text2Mol: Cross-Modal Molecule Retrieval with Natural Language Queries." EMNLP 2021. 


Chenkai Sun, Weijiang Li, Jinfeng Xiao, Nikolaus Nova Parulian, ChengXiang Zhai, and Heng Ji. "Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation." EMNLP 2021.


Tuan Lai, Heng Ji, and ChengXiang Zhai. "BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks." EMNLP 2021. 


Yunan Luo, Guangde Jiang, Tianhao Yu, Yang Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao, and Jian Peng. September 30, 2021. "ECNet is an evolutionary context-integrated machine learning framework for protein engineering.Nature Communications DOI: 10.1038/s41467-021-25976-8.


Lin Wang, Vikas Upadhyay, and Costas D. Maranas. September 27, 2021. "dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design." PLOS Computational Biology DOI: 10.1371/journal.pcbi.1009448.


Ayush Kumar Shah, Abhisek Dey, and Richard Zanibbi. September 2021. "A Math Formula Extraction and Evaluaition Framework for PDF Documents." ICDAR 2021.


Xiaotao Gu, Zihan Wang, Zhenyu Bi, Yu Meng, Liyuan Liu, Jiawei Han, and Jingbo Shang. August 2021. "UCPhrase: Unsupervised Context-aware Quality Phrase Tagging." Proc. of 2021 ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 


Yu Meng, Jiaxin Huang, Yu Zhang, and Jiawei Han. "On the Power of Pre-Trained Text Representations: Models and Applications in Text Mining." Proc. of 2021 ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 


Tuan Lai, Heng Ji, ChengXiang Zhai, and Quan Hung Tran. August 2021. "Joint Biomedical Entity and Relation Extraction with Knowledge-Enhanced Collective Inference." ACL-IJCNLP 2021.


Zixuan Zhang, Nikolaus Parulian, Heng Ji, Ahmed S. Elsayed, Skatje Myers, and Martha Palmer. August 2021. "Fine-grained Information Extraction from Biomedical Literature based on Knowledge-enriched Abstract Meaning Representation." ACL-IJCNLP 2021.


Xuan Wang, Xiangchen Song, Bandzheng Li, Kang Zhou, Qi Li, and Jiawei Han. December 2020. "Fine-Grained Named Entity Recognition with Distant Supervision in COVID-19 Literature." IEEE International Conference on Bioinformatics and Biomedicine.


Xuan Wang, Yu Zhang, Aabhas Chauhan, Qi Li, and Jiawei Han. December 2020. "Textual Evidence Mining via Spherical Heterogenous Information Network Embedding." IEEE International Conference on Big Data. 


Xuan Wang, Yingjun Guan, Yu Zhang, Qi Li, and Jiawei Han. December 2020. "Pattern-enhanced Named Entity Recognition with Distant Supervision." IEEE International Conference on Big Data.