skimgpt 2.0.0

Biomedical Knowledge Mining with co-occurrence modeling and LLMs

Evaluating hypotheses using SKiM-GPT (Note: Must be on Mir-81)

This repository provides tools to SKIM through PubMed abstracts to evalaute hypotheses.

Requirements

• Python 3.9^
• Libraries specified in requirements.txt
• OpenAI API key
• Pubmed API key
• CHTC auth token
• Rstewart2 access

Getting Started

1. Setup: Clone the repository to your machine and change to its top level directory.

   git clone <repository_url>
   cd <repository_directory>
   

2. Install Dependencies (with conda) Install the required packages using pip:

   conda create --name {myenv} python=3.9
   conda activate {myenv}
   pip install -r requirements.txt
   

3. Environment Variables Before running the script, ensure you have set up your environment variables. We recommend setting in your shell profile. You must source your shell profile after setting the environment variables (Jack has our OpenAI and Pubmed keys in his .bashrc on the server FYI):

```bash
  export OPENAI_API_KEY=your_api_key_here
  export PUBMED_API_KEY=your_api_key_here
 ```

4. Configuring Parameters The config.json file includes global parameters as well as several job types, each with unique paramenters. Please view the [config Module Overview] (#config-overview) to help set up your job.

5. Running the script

   python main.py
   

---

config Module Overview

This configuration file contains various settings for different job types. Below are descriptions of each parameter:

General Parameters

• JOB_TYPE: Specifies the type of job to be executed, e.g., km_with_gpt or skim_with_gpt.
• KM_hypothesis: Hypothesis template for KM analysis, using f-string format like {a_term} and {b_term} (e.g., "Treatment with {b_term} will have no effect on {a_term} patient outcomes.").
• SKIM_hypotheses: A dictionary of hypothesis templates for SKIM analysis (Must use f-string format).
  • AB: Relevance hypothesis between {a_term} and {b_term} (e.g., "There exists an interaction between the organ {a_term} and the gene {b_term}.").
  • BC: Relevance hypothesis between{c_term} and {b_term} (e.g., "There exists an interaction between the disease {c_term} and the gene {b_term}.").
  • rel_AC: Relevance hypothesis between {c_term} and {a_term} (e.g., "There exists an interaction between the disease {c_term} and the organ {a_term}.").
  • ABC: Evaluation hypothesis (e.g., "The gene {b_term} links the organ {a_term} to the disease {c_term}.").
  • AC: Evaluation hypothesis (e.g., "The gene {a_term} influences the disease {c_term}.").

Global Settings

• A_TERM: The primary term of interest, such as an organ (e.g., "Thymus").
• A_TERM_SUFFIX: Optional suffix for the A_TERM (e.g., "").
• TOP_N_ARTICLES_MOST_CITED: Number of top-cited articles to consider (e.g., 50).
• TOP_N_ARTICLES_MOST_RECENT: Number of most recent articles to consider (e.g., 50).
• POST_N: Number of articles to process after relevance filtering (e.g., 5).
• MIN_WORD_COUNT: Minimum word count for an abstract to be considered (e.g., 98).
• MODEL: Machine learning model used for processing (e.g., "o3").
• RATE_LIMIT: Maximum number of requests allowed per time unit (e.g., 3).
• DELAY: Time in seconds to wait before making a new request (e.g., 10).
• MAX_RETRIES: Maximum number of retry attempts after a failed request (e.g., 10).
• RETRY_DELAY: Delay in seconds before retrying a failed request (e.g., 5).
• LOG_LEVEL: Logging level (e.g., "INFO").
• OUTDIR_SUFFIX: Suffix for the output directory (e.g., "").
• iterations: Number of iterations for processing (e.g., 3).
• DCH_MIN_SAMPLING_FRACTION: Minimum sampling fraction for DCH (e.g., 0.06).
• DCH_SAMPLE_SIZE: Sample size for DCH (e.g., 50).
• TRITON_MAX_WORKERS: Maximum number of workers for Triton (e.g., 10).
• TRITON_SHOW_PROGRESS: Boolean to show progress for Triton (e.g., true).
• TRITON_BATCH_CHUNK_SIZE: Batch chunk size for Triton (e.g., null).

Relevance Filter Settings

• SERVER_URL: URL for the Triton server (e.g., "https://xdddev.chtc.io/triton").
• MODEL_NAME: Model name for relevance filtering (e.g., "porpoise").
• TEMPERATURE: Sampling temperature for model inference (e.g., 0).
• TOP_P: Cumulative probability for nucleus sampling (e.g., 0.95).
• MAX_COT_TOKENS: Maximum tokens for Chain-of-Thought reasoning (e.g., 500).
• DEBUG: Boolean flag to enable debug mode (e.g., false).
• TEST_LEAKAGE: Boolean flag to test for data leakage (e.g., false).
• TEST_LEAKAGE_TYPE: Type of data leakage test (e.g., "empty").

Job-Specific Settings

km_with_gpt

• position: Boolean flag to consider positional data (e.g., false).
• A_TERM_LIST: Boolean to indicate if a list of A terms is used (e.g., false).
• A_TERMS_FILE: File path for the A terms list (e.g., "../input_lists/test/km_a.txt").
• B_TERMS_FILE: File path for the B terms list (e.g., "../input_lists/hpv.txt").
• is_dch: Boolean flag for DCH mode (e.g., false).
• SORT_COLUMN: Column used for sorting A-B relationships (e.g., "ab_sort_ratio").
• ab_fet_threshold: Fisher Exact Test threshold for A-B relationships (e.g., 1).
• censor_year_upper: Upper bound year for data censoring (e.g., 1980).
• censor_year_lower: Lower bound year for data censoring (e.g., 0).

skim_with_gpt

• position: Boolean flag to consider positional data (e.g., false).
• A_TERM_LIST: Boolean to indicate if a list of A terms is used (e.g., true).
• A_TERMS_FILE: File path for the A terms list (e.g., "../input_lists/exercise3/skim_a.txt").
• B_TERMS_FILE: File path for the B terms list (e.g., "../input_lists/exercise3/skim_b.txt").
• C_TERMS_FILE: File path for the C terms list (e.g., "../input_lists/exercise3/skim_c.txt").
• SORT_COLUMN: Column used for sorting B-C relationships (e.g., "bc_sort_ratio").
• ab_fet_threshold: Fisher Exact Test threshold for A-B relationships (e.g., 0.1).
• bc_fet_threshold: Fisher Exact Test threshold for B-C relationships (e.g., 0.5).
• censor_year_upper: Upper bound year for data censoring (e.g., 2024).
• censor_year_lower: Lower bound year for data censoring (e.g., 0).

This configuration is critical for tailoring the behavior of the system to specific job types and requirements. Ensure all file paths and parameters are correctly set before execution to avoid runtime errors.

Contributions

Feel free to contribute to this repository by submitting a pull request or opening an issue for suggestions and bugs.