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Update src/about.py

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  1. src/about.py +31 -6
src/about.py CHANGED
@@ -105,8 +105,6 @@ CITATION_BUTTON_LABEL = "Copy the following snippet to cite these results"
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  CITATION_BUTTON_TEXT = r"""Unsal, S., Atas, H., Albayrak, M., Turhan, K., Acar, A. C., & Doğan, T. (2022). Learning functional properties of proteins with language models. *Nature Machine Intelligence, 4*(3), 227-245.
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  """
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- TASK_INFO = ["similarity", "function", "family", "affinity"]
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-
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  CSV_RESULT_PATH = "./src/data/results.csv"
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  LEADERBOARD_INTRODUCTION = """
@@ -126,10 +124,37 @@ If you find PROBE useful, please consider citing our work:
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  Unsal, S., Atas, H., Albayrak, M., Turhan, K., Acar, A. C., & Doğan, T. (2022). Learning functional properties of proteins with language models. *Nature Machine Intelligence, 4*(3), 227-245.
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  """
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- similarity_tasks_options = ["sparse", "200", "500"]
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- function_prediction_aspect_options = ["MF", "BP", "CC", "All_Aspects"]
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- function_prediction_dataset_options = ["High", "Middle", "Low", "All_Data_Sets"]
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- family_prediction_dataset_options = ["nc", "uc50", "uc30", "mm15"]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  benchmark_specific_metrics = {
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  'similarity': ['sparse_MF_correlation', 'sparse_BP_correlation', 'sparse_CC_correlation', 'sparse_Ave_correlation',
 
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  CITATION_BUTTON_TEXT = r"""Unsal, S., Atas, H., Albayrak, M., Turhan, K., Acar, A. C., & Doğan, T. (2022). Learning functional properties of proteins with language models. *Nature Machine Intelligence, 4*(3), 227-245.
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  """
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  CSV_RESULT_PATH = "./src/data/results.csv"
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  LEADERBOARD_INTRODUCTION = """
 
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  Unsal, S., Atas, H., Albayrak, M., Turhan, K., Acar, A. C., & Doğan, T. (2022). Learning functional properties of proteins with language models. *Nature Machine Intelligence, 4*(3), 227-245.
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  """
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+ TASK_INFO = ["Semantic Similarity", "GO-Based Function Prediction", "Target Protein Family Prediction", "Protein Protein Binding Affinity"]
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+ similarity_tasks_options = ["Sparse Uniform", "Well Annotated 200", "Well Annotated 500"]
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+ function_prediction_aspect_options = ["Molecular Function", "Biological Process", "Celular Components", "All Aspects"]
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+ family_prediction_dataset_options = ["Not-clustered", "UniClust50", "UniClust30", "MM-seqs15"]
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+
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+ benchmark_type_map = {
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+ "Semantic Similarity": "similarity",
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+ "GO-Based Function Prediction": "function",
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+ "Target Protein Family Prediction": "family",
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+ "Protein Protein Binding Affinity": "affinity",
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+ }
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+
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+ similarity_tasks_map = {
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+ "Sparse Uniform": "sparse",
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+ "Well Annotated 200": "200",
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+ "Well Annotated 500": "500",
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+ }
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+
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+ function_prediction_aspect_map = {
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+ "Molecular Function": "MF",
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+ "Biological Process": "BP",
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+ "Celular Components": "CC",
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+ "All Aspects": "All_Aspects",
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+ }
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+
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+ family_prediction_dataset_map = {
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+ "Not-clustered": "nc",
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+ "UniClust50": "uc50",
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+ "UniClust30": "uc30",
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+ "MM-seqs15": "mm15",
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+ }
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  benchmark_specific_metrics = {
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  'similarity': ['sparse_MF_correlation', 'sparse_BP_correlation', 'sparse_CC_correlation', 'sparse_Ave_correlation',