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@flexpa/llm-fhir-eval

Important

This is an early preview release. All evaluations are experimental. Follow the development progress on FHIR Chat.

Overview

@flexpa/llm-fhir-eval is a preview of an evaluation framework designed to benchmark the performance of LLMs on FHIR-specific tasks including generation, validation, and extraction. This framework aims to systematically test and validate the capabilities of LLMs in handling various healthcare-interoperability related tasks, ensuring they meet the standards required for effective FHIR implementations. It implements evaluations from prior art such as FHIR-GPT. We are seeking feedback on the benchmark and its evaluations.

Benchmark

@flexpa/llm-fhir-eval benchmarks FHIR-specific tasks including:

  1. FHIR Resource Generation:

    • Generate accurate FHIR resources such as Patient, Observation, MedicationStatement, etc.
    • Test the ability to create complex resource relationships and validate terminology bindings.

  2. FHIR Resource Validation:

    • Validate FHIR resources using operations like $validate.
    • Check for schema compliance, required field presence, and value set binding verification.

  3. Summarization:

    • Summarize clinical notes into FHIR-compliant resources.
    • Evaluate the proficiency of LLMs in generating concise and accurate summaries.

  4. FHIR Path Evaluation:

    • Assess the ability of models to evaluate complex FHIR Path expressions.
    • Validate extraction accuracy and handle nested data structures.

Configuration

The evaluation benchmark is configured using a YAML file. See promptfooconfig.yaml for an example.

Evaluations

Important

The tests for each evaluation are placeholders in this preview release. They may require a separate process to execute or may have distribution restrictions.

  1. Structured FHIR Data Extraction (extract-structured.yaml)

    • Description: Evaluates the ability to extract specific information from structured FHIR resources.
    • Tests: Includes demographic extraction, nested data extraction, and interpretation-based extraction.

  2. Unstructured Encounter Profile Extraction (extract-unstructured-encounter-profile-first-experiment.yaml)

    • Description: Success at extracting US Core Encounter Profile from clinical notes.
    • Tests: Validates JSON output and checks for the presence of an Encounter FHIR resource.

  3. Unstructured Data Extraction (extract-unstructured.yaml)

    • Description: Extracts structured FHIR-compliant data from clinical notes.
    • Tests: Ensures JSON output includes specific FHIR resources like Patient, Observation, and MedicationRequest.

  4. FHIR Path Evaluation (fhir-path.yaml)

    • Description: Tests the ability to extract data using FHIR Path expressions.
    • Tests: Includes extraction from nested arrays, date manipulation, and boolean logic.

  5. Tool Use Validation (tool-use-validator.yaml)

    • Description: Validates FHIR resources using tool functions.
    • Tests: Includes basic validation, terminology validation, and profile-based validation.

This preview release also includes an implementation of the FHIR-GPT prompt as prior art:

  1. FHIR-GPT Prompt Evaluation (fhir-gpt.yaml)
  • Description: Focuses on extracting medication data, specifically the drug route, from narratives.
  • Tests: Validates JSON output and checks for correct SNOMED code extraction.

Commands to Run Evaluations

Assuming you have Bun installed, copy the .env.template file to .env and supply your OpenAI and Anthropic API keys.

Then, run the following command to execute an evaluation:

bun run eval -c evals/extract-unstructured.yaml

The evaluation will print its performance metrics to the console.

Roadmap

The framework is continuously evolving, with ongoing efforts to expand its capabilities:

  • Model Comparison: Expand model coverage to support HealthSage Llama fine-tune.