| Challenge: | Existing approaches to enzyme–reaction retrieval suffer from poor generalization across tasks and distributions . TIGER is a text-informed generalized enzyme-reaction retrieval framework that bridges enzymes and biochemical reactions. |
| Approach: | They propose a text-informed generalized enzyme-reaction retrieval framework that leverages protein-to-text generation models to distill textual knowledge from enzyme sequences. |
| Outcome: | The proposed framework outperforms state-of-the-art methods in enzyme–reaction retrieval tasks and distributions. |
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Ming Zhong, Siru Ouyang, Yizhu Jiao, Priyanka Kargupta, Leo Luo, Yanzhen Shen, Bobby Zhou, Xianrui Zhong, Xuan Liu, Hongxiang Li, Jinfeng Xiao, Minhao Jiang, Vivian Hu, Xuan Wang, Heng Ji, Martin Burke, Huimin Zhao, Jiawei Han
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| Challenge: | Recent studies have focused on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment. |
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BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning (2024.findings-acl)
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Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
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Predictive Chemistry Augmented with Text Retrieval (2023.emnlp-main)
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| Challenge: | TextReact is a new method to augment predictive chemistry with text descriptions retrieved from the literature. |
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ProtT3: Protein-to-Text Generation for Text-based Protein Understanding (2024.acl-long)
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| Challenge: | Language Models excel in understanding textual descriptions of proteins, but struggle to process texts. |
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Show, Write, and Retrieve: Entity-aware Article Generation and Retrieval (2023.findings-emnlp)
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| Challenge: | Prior work typically encodes all tokens in articles using pre-trained language models, however, many named entities are difficult to accurately recognize and predict by language models. |
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Cross-Task Knowledge Transfer for Query-Based Text Summarization (D19-58)
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ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision (2023.findings-acl)
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| Challenge: | Structured chemical reaction information is a vital tool for chemists engaged in laboratory work and advanced endeavors such as computer-aided drug design. |
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BioReader: a Retrieval-Enhanced Text-to-Text Transformer for Biomedical Literature (2022.emnlp-main)
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| Challenge: | Recent research has equipped language models with the ability to attend over relevant and factual information from non-parametric external sources, drawing a complementary path to architectural scaling. |
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G3R: A Graph-Guided Generate-and-Rerank Framework for Complex and Cross-domain Text-to-SQL Generation (2023.findings-acl)
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| Challenge: | Existing approaches to complex and cross-domain Text-to-SQL generation lack domain knowledge . domain knowledge is not incorporated to enhance their ability to generalise to unseen databases. |
| Approach: | They propose a framework called G3R for complex and cross-domain Text-to-SQL generation . they propose re-ranking SQL queries based on domain knowledge and a graph-guided SQL generator . |
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