Preprocessing

Use preprocessing scripts in data_processing to preprocess raw datasets that are in data/raw. The preprocessed datasets are in data/processed.

Prompts

Sample prompt for CDR dataset:

Your task is to extract all chemical-disease relations from a text in which the chemical/drug induces the disease. Note that the chemical or disease names should have appeared in the original input text.
The output should be saved as per the following format:
{'relations':
[
  {
    "chemical": "chemical1",
    "disease": "disease1"
  },
  {
    "chemical": "chemical2",
    "disease": "disease2"
  },
  ...
]
}
The output will be {'relations':[]} if there are no chemical-disease pairs in which the chemical induces the disease expressed in the input text.
With this format, a hypothetical example output for a biomedical text could be the following:
{'relations':
[
  {
    "chemical": "Lidocaine",
    "disease": "cardiac asystole"
  },
  {
    "gene": "daunorubicin",
    "disease": "neutropenia"
  }
]
}

Templates

Template should be a class satisfying either OpenAI function calling (schema) or json mode feature. The schema Template should be look like:

class Template_schema:
        
    <entity1> = {
            "type": "string",
            "description": "<description>"
        }
    <entity2> = {
            "type": "string",
            "description": "<description>"
        }
    
    items = {
        "type": "object",
        "properties": {
            "<entity1>": ,
            "<entity2>": 
            },
        "description": "<description>"
        }
    
    relations = {
        "type": "array",
        "items": items,
        "required": ["<entity1>", "<entity2>"],
        "description": "<description>"
        }
    
    parameters = {
            "type": "object",
            "properties": {
                "relations": relations
            }
        }

    schema = {
        "name": "extract_relations",
        "description": "Extracts a list of relations from a text.",
        "parameters": parameters,
        "required": ["relations"]
    }

    @classmethod
    def extract_relations(cls, relation_list):
        <YOUR CODE>
        return relations
    
    @classmethod
    def make_prompt(cls, example):
        
        system_content = system_prompt
        
        user_content = f'Title: {example.title}\n\nAbstract: {example.text}'
        
        system = {'role': 'system',
                  'content': system_content}
        
        user = {'role': 'user',
                'content': user_content}
        
        messages = [system, user]

        return messages

The json Template should be look like:

class Template_json:

    @classmethod
    def extract_relations(cls, relation_list):
        <YOUR CODE>
        return relations
    
    @classmethod
    def make_prompt(cls, example):
        
        system_content = system_prompt
        user_content = f'Title: {example.title}\n\nAbstract: {example.text}'
        system = {'role': 'system',
                  'content': "You are a helpful assistant designed to output JSON." + system_content}
        user = {'role': 'user',
                'content': user_content}
        messages = [system, user]

        return messages

Run scripts

python main.py run
--model {'gpt-4-1106-preview' | 'o1' | 'openai/gpt-oss-120b'}
--dataset_name {ADE | DCE | ChemProt | DDI | CDR | GDA | BioRED}
--split {train | valid | test}
--openai_key {Your API key}
--max_examples 100
--normalized {True | False}
--template {CDRTemplate_json | CDRTemplate_schema | ...}
--save_dir {Directory of output files}
--max_tokens {4096 | 8192}
--temperatures {0.7}
--data_seed {0}

Arguments:

--model: GPT models.

--normalized: Evaluated on entity level (True) or mention level (False).

--template: dataset_name + Template_json (inferred models) or Template_schema (explicit models).

--max_examples: Maxmium number of examples run by GPT. Set None to run on the whole train/valid/test dataset.

--openai_key: An OpenAI API key is required for gpt-4-1106-preview and o1 models, while a HuggingFace API key is required for openai/gpt-oss-120b model.