Papers with PubChem
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning (2024.findings-acl)
Copied to clipboard
Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
| Challenge: | BioT5+ is an extension of the BioT5, but lacked a nuanced understanding of molecular structures. |
| Approach: | They propose a new bio-entity modeling framework, BioT5+, which integrates IUPAC names and molecule data. |
| Outcome: | The proposed model bridges the gap between molecular representations and textual descriptions and improves the grounded reasoning of bio-text and bio-sequences. |
MolXPT: Wrapping Molecules with Text for Generative Pre-training (2023.acl-short)
Copied to clipboard
| Challenge: | Experimental results show that Generative pre-trained Transformers (GPT) have great success in natural language processing. |
| Approach: | They propose a unified language model of text and molecules pre-trained on SMILES wrapped by text. |
| Outcome: | The proposed model outperforms strong baselines of molecular property prediction on MoleculeNet and performs comparably to the best model in text-molecule translation while using less than half of its parameters. |
Learning to Describe for Predicting Zero-shot Drug-Drug Interactions (2023.emnlp-main)
Copied to clipboard
| Challenge: | Existing computational methods for DDI prediction fail to capture interactions for new drugs due to the lack of knowledge. |
| Approach: | They propose a problem setup as zero-shot DDI prediction that deals with the case of new drugs by using textual information from online databases. |
| Outcome: | The proposed method improves on several settings including zero-shot and few-shot DDI prediction and the selected texts are semantically relevant. |