CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes
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arXiv
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| Format: | Preprint |
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2024
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| author | Yang, Jason Mora, Ariane Liu, Shengchao Wittmann, Bruce J. Anandkumar, Anima Arnold, Frances H. Yue, Yisong |
| author_facet | Yang, Jason Mora, Ariane Liu, Shengchao Wittmann, Bruce J. Anandkumar, Anima Arnold, Frances H. Yue, Yisong |
| contents | Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2406_15669 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes Yang, Jason Mora, Ariane Liu, Shengchao Wittmann, Bruce J. Anandkumar, Anima Arnold, Frances H. Yue, Yisong Biomolecules Machine Learning Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/. |
| title | CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes |
| topic | Biomolecules Machine Learning |
| url | https://arxiv.org/abs/2406.15669 |