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Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins.
Language models are few-shot learners
Tom Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared D Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, et al. 2020 · 1901
Earlier work this paper cites.
Rapid and sensitive protein similarity searches
David J Lipman and William R Pearson. 1985 · 1985
Earlier work this paper cites.
Improved tools for biological sequence comparison
William R Pearson and David J Lipman. 1988 · 1988
Earlier work this paper cites.
Smiles, a chemical language and information system. 1. introduction to methodology and encoding rules
David Weininger. 1988 · 1988
Earlier work this paper cites.
Smiles. 2. algorithm for generation of unique smiles notation
David Weininger, Arthur Weininger, and Joseph L Weininger. 1989 · 1989
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Support-vector networks
Corinna Cortes and Vladimir Vapnik. 1995 · 1995
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Random decision forests
Tin Kam Ho. 1995 · 1995
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Long short-term memory
Sepp Hochreiter and Jürgen Schmidhuber. 1997 · 1997
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Machine learning in drug discovery: A review
Suresh Dara, Swetha Dhamercherla, Surender Singh Jadav, Ch Madhu Babu, and Mohamed Jawed Ahsan. 2022 · 1999
Earlier work this paper cites.
Prediction of membrane protein types based on the hydrophobic index of amino acids
Zhi-Ping Feng and Chun-Ting Zhang. 2000 · 2000
Earlier work this paper cites.
Reoptimization of mdl keys for use in drug discovery
Joseph L Durant, Burton A Leland, Douglas R Henry, and James G Nourse. 2002 · 2002
Earlier work this paper cites.
Bleu: a method for automatic evaluation of machine translation
Kishore Papineni, Salim Roukos, Todd Ward, and Wei-Jing Zhu. 2002 · 2002
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Rouge: A package for automatic evaluation of summaries
Chin-Yew Lin. 2004 · 2004
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METEOR: an automatic metric for MT evaluation with improved correlation with human judgments
Satanjeev Banerjee and Alon Lavie. 2005 · 2005
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Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities
Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson. 2007 · 2007
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Uniref: comprehensive and non-redundant uniprot reference clusters
Baris E Suzek, Hongzhan Huang, Peter McGarvey, Raja Mazumder, and Cathy H Wu. 2007 · 2007
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Detection of IUPAC and iupac-like chemical names
Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich. 2008 · 2008
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Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, and Minoru Kanehisa. 2008 · 2008
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Levenshtein distance: Information theory, computer science, string (computer science), string metric, damerau? levenshtein distance, spell checker, hamming distance
Frederic P Miller, Agnes F Vandome, and John McBrewster. 2009 · 2009
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Chemberta: Large-scale self-supervised pretraining for molecular property prediction
Seyone Chithrananda, Gabriel Grand, and Bharath Ramsundar. 2020 · 2010
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Extended-connectivity fingerprints
David Rogers and Mathew Hahn. 2010 · 2010
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Pubmed: the bibliographic database
Kathi Canese and Sarah Weis. 2013 · 2013
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Improving compound–protein interaction prediction by building up highly credible negative samples
Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng, and Shuigeng Zhou. 2015 · 2015
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An introduction to convolutional neural networks
Keiron O’Shea and Ryan Nash. 2015 · 2015
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Harnessing computational biology for exact linear b-cell epitope prediction: a novel amino acid composition-based feature descriptor
Vijayakumar Saravanan and Namasivayam Gautham. 2015 · 2015
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Get your atoms in order - an open-source implementation of a novel and robust molecular canonicalization algorithm
Nadine Schneider, Roger A. Sayle, and Gregory A. Landrum. 2015 · 2015
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Deep residual learning for image recognition
Kaiming He, Xiangyu Zhang, Shaoqing Ren, and Jian Sun. 2016 · 2016
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin. 2017 · 2017
Cited alongside, same era.
Sentencepiece: A simple and language independent subword tokenizer and detokenizer for neural text processing
Taku Kudo and John Richardson. 2018 · 2018
Cited alongside, same era.
Fréchet chemnet distance: A metric for generative models for molecules in drug discovery
Kristina Preuer, Philipp Renz, Thomas Unterthiner, Sepp Hochreiter, and Günter Klambauer. 2018 · 2018
Cited alongside, same era.
Moleculenet: a benchmark for molecular machine learning
Zhenqin Wu, Bharath Ramsundar, Evan N Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S Pappu, Karl Leswing, and Vijay Pande. 2018 · 2018
Cited alongside, same era.
Pubchem 2019 update: improved access to chemical data
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, et al. 2019 · 2019
Cited alongside, same era.
Lora: Low-rank adaptation of large language models
Edward J. Hu, Yelong Shen, Phillip Wallis, Zeyuan Allen-Zhu, Yuanzhi Li, Shean Wang, Lu Wang, and Weizhu Chen. 2022 · 2022
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Language models of protein sequences at the scale of evolution enable accurate structure prediction
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, et al. 2022 · 2022
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Pre-training molecular graph representation with 3d geometry
Shengchao Liu, Hanchen Wang, Weiyang Liu, Joan Lasenby, Hongyu Guo, and Jian Tang. 2022 · 2022
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A molecular multimodal foundation model associating molecule graphs with natural language
Bing Su, Dazhao Du, Zhao Yang, Yujie Zhou, Jiangmeng Li, Anyi Rao, Hao Sun, Zhiwu Lu, and Ji-Rong Wen. 2022 · 2022
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Bern2: an advanced neural biomedical named entity recognition and normalization tool
Mujeen Sung, Minbyul Jeong, Yonghwa Choi, Donghyeon Kim, Jinhyuk Lee, and Jaewoo Kang. 2022 · 2022
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DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences
Ingoo Lee, Jongsoo Keum, and Hojung Nam. 2019 · 2019
Cited alongside, same era.
Decoupled weight decay regularization
Ilya Loshchilov and Frank Hutter. 2019 · 2019
Cited alongside, same era.
biorxiv: the preprint server for biology
Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, and John R Inglis. 2019 · 2019
Cited alongside, same era.
Transformercpi: improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments
Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, and Mingyue Zheng. 2020 · 2020
Cited alongside, same era.
Zinc20—a free ultralarge-scale chemical database for ligand discovery
John J Irwin, Khanh G Tang, Jennifer Young, Chinzorig Dandarchuluun, Benjamin R Wong, Munkhzul Khurelbaatar, Yurii S Moroz, John Mayfield, and Roger A Sayle. 2020 · 2020
Cited alongside, same era.
Self-referencing embedded strings (selfies): A 100% robust molecular string representation
Mario Krenn, Florian Häse, AkshatKumar Nigam, Pascal Friederich, and Alan Aspuru-Guzik. 2020 · 2020
Cited alongside, same era.
Exploring the limits of transfer learning with a unified text-to-text transformer
Colin Raffel, Noam Shazeer, Adam Roberts, Katherine Lee, Sharan Narang, Michael Matena, Yanqi Zhou, Wei Li, and Peter J Liu. 2020 · 2020
Cited alongside, same era.
Later among the works it cites.
Galactica: A large language model for science
Ross Taylor, Marcin Kardas, Guillem Cucurull, Thomas Scialom, Anthony Hartshorn, Elvis Saravia, Andrew Poulton, Viktor Kerkez, and Robert Stojnic. 2022 · 2022
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Molecular contrastive learning of representations via graph neural networks
Yuyang Wang, Jianren Wang, Zhonglin Cao, and Amir Barati Farimani. 2022 · 2022
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Peer: a comprehensive and multi-task benchmark for protein sequence understanding
Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Ma Chang, Runcheng Liu, and Jian Tang. 2022 · 2022
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A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals
Zheni Zeng, Yuan Yao, Zhiyuan Liu, and Maosong Sun. 2022 · 2022
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Prot2text: Multimodal protein’s function generation with GNNs and transformers
Hadi Abdine, Michail Chatzianastasis, Costas Bouyioukos, and Michalis Vazirgiannis. 2023 · 2023
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The impact of large language models on scientific discovery: a preliminary study using gpt-4
Microsoft Research AI4Science and Microsoft Azure Quantum. 2023 · 2023
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Interpretable bilinear attention network with domain adaptation improves drug–target prediction
Peizhen Bai, Filip Miljković, Bino John, and Haiping Lu. 2023 · 2023
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He Cao, Zijing Liu, Xingyu Lu, Yuan Yao, and Yu Li. 2023 · 2023
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Vicuna: An open-source chatbot impressing gpt-4 with 90%* chatgpt quality
Wei-Lin Chiang, Zhuohan Li, Zi Lin, Ying Sheng, Zhanghao Wu, Hao Zhang, Lianmin Zheng, Siyuan Zhuang, Yonghao Zhuang, Joseph E. Gonzalez, Ion Stoica, and Eric P. Xing. 2023 · 2023
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Unifying molecular and textual representations via multi-task language modelling
Dimitrios Christofidellis, Giorgio Giannone, Jannis Born, Ole Winther, Teodoro Laino, and Matteo Manica. 2023 · 2023
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GLM-130b: An open bilingual pre-trained model
Aohan Zeng et.al. 2023 · 2023
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Mol-instructions: A large-scale biomolecular instruction dataset for large language models
Yin Fang, Xiaozhuan Liang, Ningyu Zhang, Kangwei Liu, Rui Huang, Zhuo Chen, Xiaohui Fan, and Huajun Chen. 2023 · 2023
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Goat: Fine-tuned llama outperforms GPT-4 on arithmetic tasks
Tiedong Liu and Bryan Kian Hsiang Low. 2023 · 2023
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Molxpt: Wrapping molecules with text for generative pre-training
Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, and Tie-Yan Liu. 2023c · 2023
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MolCA: Molecular graph-language modeling with cross-modal projector and uni-modal adapter
Zhiyuan Liu, Sihang Li, Yanchen Luo, Hao Fei, Yixin Cao, Kenji Kawaguchi, Xiang Wang, and Tat-Seng Chua. 2023d · 2023
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OpenAI. 2023 · 2023
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BioT5: Enriching cross-modal integration in biology with chemical knowledge and natural language associations
Qizhi Pei, Wei Zhang, Jinhua Zhu, Kehan Wu, Kaiyuan Gao, Lijun Wu, Yingce Xia, and Rui Yan. 2023 · 2023
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Stanford alpaca: An instruction-following llama model
Rohan Taori, Ishaan Gulrajani, Tianyi Zhang, Yann Dubois, Xuechen Li, Carlos Guestrin, Percy Liang, and Tatsunori B. Hashimoto. 2023 · 2023
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Uni-mol: A universal 3d molecular representation learning framework
Gengmo Zhou, Zhifeng Gao, Qiankun Ding, Hang Zheng, Hongteng Xu, Zhewei Wei, Linfeng Zhang, and Guolin Ke. 2023 · 2023
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Empowering molecule discovery for molecule-caption translation with large language models: A chatgpt perspective
Jiatong Li, Yunqing Liu, Wenqi Fan, Xiao-Yong Wei, Hui Liu, Jiliang Tang, and Qing Li. 2024 · 2024
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Leveraging biomolecule and natural language through multi-modal learning: A survey
Qizhi Pei, Lijun Wu, Kaiyuan Gao, Jinhua Zhu, Yue Wang, Zun Wang, Tao Qin, and Rui Yan. 2024 · 2024
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