add drugchat

data/tabular/drugchat_liang_zhang_et_al/meta.yaml

@@ -0,0 +1,57 @@
+---
+name: drugchat_liang_zhang_et_al
+description: |-
+    Instruction tuning dataset used for the LLM component of DrugChat.
+    10,834 compounds (3,8962  from ChEMBL and 6,942 from  PubChem) containing
+    descriptive drug information were collected. 143,517 questions were generated
+    using the molecules' classification, properties and descriptions from ChEBI, LOTUS & YMDB.
+targets:
+    - id: answ
+      description: answer to the question about the SMILES
+      type: string
+identifiers:
+    - id: SMILES
+      type: SMILES
+      description: SMILES
+    - id: quest
+      type: string
+      description: Question about SMILES
+license: BSD-3-Clause
+links:
+    - url: https://www.techrxiv.org/articles/preprint/DrugChat_Towards_Enabling_ChatGPT-Like_Capabilities_on_Drug_Molecule_Graphs/22945922
+      description: corresponding publication
+    - url: https://github.com/UCSD-AI4H/drugchat
+      description: rep & data source
+num_points: 143,517
+bibtex:
+    - |-
+      @article{Liang2023,
+      author = "Youwei Liang and Ruiyi Zhang and Li Zhang and Pengtao Xie",
+      title = "{DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs}",
+      year = "2023",
+      month = "5",
+      url = "https://www.techrxiv.org/articles/preprint/DrugChat_Towards_Enabling_ChatGPT-Like_Capabilities_on_Drug_Molecule_Graphs/22945922",
+      doi = "10.36227/techrxiv.22945922.v1"}
+templates:
+    - |-
+      Task: Please answer the following question about the molecule with {SMILES__description} {SMILES#}.
+      {#Description|Question|Request!}: {quest#}
+      {#Result|Answer|Completion!}: {answ#}
+    - |-
+      {#Question|Q!}: {quest#}
+      {#Constraint:|Description:|!} The {#Molecule|Compound|Chemical!} {#has the|can be represented with the!} {SMILES__description} {SMILES#}.
+      {#Answer|Result|Answer!}: {answ#}
+    - |-
+      User: I have a question about the {#molecule|chemical|compound!} with {SMILES__description} {SMILES#}.
+      Assistant: {#Sure, what is your question?|How can I help?|That sounds interesting, how can I help?|Interesting, how can I help?!}
+      User: {quest#}
+      Assistant: {#The answer is |!}{answ#}
+    - |-
+      User: I want to know more about the {#molecule|chemical|compound!} with {SMILES__description} {SMILES#}.
+      Assistant: {#Sure, what is your question?|How can I help?|That sounds interesting, how can I help?|Interesting, how can I help?!}
+      User: {quest#}
+      Assistant: {#The answer is |!}{answ#}
+    - |-
+      Task: Answer the following question about the molecule with {SMILES__description} {SMILES#}.
+      {#Description|Question|Request!}: {quest#}
+      {#Result|Answer|Completion!}: {answ#}

data/tabular/drugchat_liang_zhang_et_al/transform.py

@@ -0,0 +1,54 @@
+from datasets import concatenate_datasets, load_dataset
+
+PUBCHEM_DATASET = "alxfgh/PubChem_Drug_Instruction_Tuning"
+CHEMBL_DATASET = "alxfgh/ChEMBL_Drug_Instruction_Tuning"
+
+
+if __name__ == "__main__":
+    # Load the two datasets
+    dataset1 = load_dataset(PUBCHEM_DATASET)
+    dataset2 = load_dataset(CHEMBL_DATASET)
+
+    # Verify that the datasets have the same schema (i.e., the same fields)
+    assert (
+        dataset1["train"].features == dataset2["train"].features
+    ), "Datasets do not have the same schema"
+
+    # Concatenate the 'train' split of dataset2 to the 'train' split of dataset1
+    combined_dataset = concatenate_datasets([dataset1["train"], dataset2["train"]])
+
+    # Define the fractions for train/test/valid split
+    train_fraction = 0.8
+    test_fraction = 0.1
+    # The remaining part will be the validation fraction
+
+    # Generate the train/test/valid splits
+    train_test_valid_datasets = combined_dataset.train_test_split(
+        test_size=test_fraction, shuffle=True
+    )
+    train_valid_datasets = train_test_valid_datasets["train"].train_test_split(
+        test_size=(1 - train_fraction) / (1 - test_fraction), shuffle=True
+    )
+
+    final_datasets = {
+        "train": train_valid_datasets["train"],
+        "test": train_test_valid_datasets["test"],
+        "valid": train_valid_datasets["test"],
+    }
+
+    # Add the 'split' column to each dataset
+    for split in final_datasets:
+        final_datasets[split] = final_datasets[split].add_column(
+            "split", [split] * len(final_datasets[split])
+        )
+
+    # Concatenate all splits again
+    all_datasets = concatenate_datasets(
+        [final_datasets[split] for split in final_datasets]
+    )
+    df = all_datasets.to_pandas()
+
+    df.rename(columns={"Answer": "answ", "Question": "quest"}, inplace=True)
+
+    # Save the combined dataset as a CSV file
+    df.to_csv("data_clean.csv", index=False)