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--- |
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license: llama3.1 |
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datasets: |
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- BAAI/OPI |
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language: |
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- en |
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pipeline_tag: text-generation |
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tags: |
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- Life Science |
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- AI4Science |
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- Biology |
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- Protein |
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- LLM |
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- Instruction |
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base_model: meta-llama/Meta-Llama-3.1-8B-Instruct |
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--- |
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# Model Card of OPI-Llama-3.1-8B-Instruct |
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OPI-Llama-3.1-8B-Instruct was fine-tuned from the Meta-Llama-3.1-8B-Instruct model using the complete OPI training set (i.e.,[OPI_full_1.61M_train.json](https://huggingface.co/datasets/BAAI/OPI/blob/main/OPI_DATA/OPI_full_1.61M_train.json)). |
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For more details of training and testing, please visit [https://github.com/baaihealth/opi](https://github.com/baaihealth/opi). |
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# Evaluation of OPI-Llama-3.1-8B-Instruct on 9 tasks |
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Each testing result is derived from the Meta-Llama-3.1-8B-Instruct model that has been fine-tuned using [OPI_full_1.61M.json](https://huggingface.co/datasets/BAAI/OPI/blob/main/OPI_DATA/OPI_full_1.61M_train.json) and subsequently evaluated on the respective testing set for each specific task. |
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<table border="1" style="text-align:center; border-collapse:collapse; width: 100%;"> |
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<thead> |
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<tr> |
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<th style="text-align:center;">Task Type</th> |
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<th style="text-align:center;">Task Name</th> |
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<th style="text-align:center;">Testing file</th> |
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<th style="text-align:center;">Accuracy</th> |
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<th style="text-align:center;">Precision</th> |
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<th style="text-align:center;">Recall</th> |
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<th style="text-align:center;">F1</th> |
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<th style="text-align:center;">Rouge-L</th> |
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</tr> |
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</thead> |
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<tbody> |
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<tr> |
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<td rowspan="6">Sequence Understanding</td> |
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<td rowspan="2">EC Number Prediction (split100)</td> |
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<td>CLEAN_EC_number_new_test</td> |
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<td>-</td> |
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<td>0.3724</td> |
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<td>0.3374</td> |
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<td>0.3468</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>CLEAN_EC_number_price_test</td> |
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<td>-</td> |
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<td>0.0738</td> |
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<td>0.0738</td> |
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<td>0.0738</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td rowspan="3">Fold Type Prediction</td> |
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<td>fold_type_test_Fold_Holdout</td> |
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<td>0.1045</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>fold_type_test_Superfamily_Holdout</td> |
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<td>0.1507</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>fold_type_test_Family_Holdout</td> |
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<td>0.6145</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>Subcellular Localization Prediction</td> |
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<td>subcell_loc_test</td> |
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<td>0.4214</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td rowspan="9">Annotation Prediction</td> |
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<td rowspan="3">Function Keywords Prediction</td> |
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<td>CASPSimilarSeq_keywords_test</td> |
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<td>-</td> |
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<td>0.4202</td> |
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<td>0.5057</td> |
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<td>0.4385</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>IDFilterSeq_keywords_test</td> |
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<td>-</td> |
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<td>0.6762</td> |
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<td>0.6905</td> |
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<td>0.6650</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>UniProtSeq_keywords_test</td> |
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<td>-</td> |
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<td>0.7606</td> |
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<td>0.7489</td> |
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<td>0.7374</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td rowspan="3">Gene Ontology(GO) Terms Prediction</td> |
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<td>CASPSimilarSeq_go_terms_test</td> |
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<td>-</td> |
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<td>0.1113</td> |
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<td>0.0936</td> |
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<td>0.099</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>IDFilterSeq_go_terms_test</td> |
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<td>-</td> |
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<td>0.6686</td> |
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<td>0.6287</td> |
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<td>0.6304</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>UniProtSeq_go_terms_test</td> |
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<td>-</td> |
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<td>0.7150</td> |
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<td>0.6897</td> |
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<td>0.6849</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td rowspan="3">Function Description Prediction</td> |
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<td>CASPSimilarSeq_function_test</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>0.7524</td> |
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</tr> |
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<tr> |
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<td>IDFilterSeq_function_test</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>0.4786</td> |
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</tr> |
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<tr> |
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<td>UniProtSeq_function_test</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>-</td> |
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<td>0.5144</td> |
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</tr> |
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<tr> |
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<td rowspan="3">Knowledge Mining</td> |
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<td>Tissue Location Prediction from Gene Symbol</td> |
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<td>gene_symbol_to_tissue_test</td> |
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<td>-</td> |
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<td>0.4002</td> |
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<td>0.9356</td> |
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<td>0.5466</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>Cancer Prediction from Gene Symbol</td> |
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<td>gene_symbol_to_cancer_test</td> |
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<td>-</td> |
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<td>0.2890</td> |
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<td>0.2701</td> |
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<td>0.2664</td> |
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<td>-</td> |
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</tr> |
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<tr> |
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<td>Cancer Prediction from Gene Name</td> |
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<td>gene_name_to_cancer_test</td> |
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<td>-</td> |
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<td>0.2786</td> |
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<td>0.2707</td> |
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<td>0.2659</td> |
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<td>-</td> |
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</tr> |
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</tbody> |
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</table> |
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# Prediction comparison with SOTA mdoels |
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