Research use only. Not a medical device. This software was developed in the HEREDITARY project as a research prototype. It has not been assessed or certified under the EU Medical Device Regulation (EU) 2017/745. It must not be used to diagnose, treat, monitor or make any other decision about individual patients.

FactCheck: Knowledge Graph Validation via Large Language Models

📋 Table of Contents

• Overview
• Features
• Installation
• Quick Start
• Datasets
• Methodologies
• Configuration
• Usage Examples
• Results
• Web Platform
• Repository Structure
• Contributing
• Extra Experiments

🎯 Overview

FactCheck is a comprehensive benchmark designed to evaluate Large Language Models (LLMs) capabilities in Knowledge Graph (KG) fact verification. This repository implements multiple verification methodologies and provides extensive evaluation across three real-world KG datasets with over 13,530 facts.

Key Research Questions

FactCheck addresses three fundamental research questions in the domain of LLM-based knowledge graph fact verification:

1. RQ1: Internal Knowledge Assessment: How effective are Large Language Models at knowledge graph fact-checking when relying solely on their internal knowledge representations acquired during pre-training?

2. RQ2: External Evidence Integration: Does augmenting LLMs with external evidence through Retrieval-Augmented Generation (RAG) methodologies improve their capability to verify knowledge graph facts, and at what computational cost?

3. RQ3: Multi-Model Consensus: Does aggregating predictions from multiple LLMs through consensus mechanisms lead to more reliable and robust verification of knowledge graph facts compared to individual model performance?

Main Findings

Our evaluation across three real-world KG datasets (FactBench, YAGO, DBpedia) reveals several critical insights:

Performance Capabilities

• Promising but Limited: While LLMs demonstrate promising fact verification capabilities, they remain insufficient for reliable deployment in real-world KG validation scenarios
• Model Hierarchy: Open-source models achieve competitive performance, with Gemma2 consistently outperforming others (balanced accuracy up to 0.90 on FactBench with RAG)
• Dataset Sensitivity: Performance varies significantly across datasets due to class imbalance and schema complexity

External Evidence Integration

• Inconsistent Improvements: RAG integration provides fluctuating performance gains, offering inconsistent improvements over streamlined internal knowledge approaches
• Computational Trade-offs: External evidence integration increases computational overhead by approximately 10× processing time (0.3s → 2.0s+ per fact)
• Context Dependency: RAG effectiveness is highly dependent on dataset characteristics and retrieval quality

Multi-Model Consensus

• Modest Gains: Consensus strategies provide average 4.5% balanced accuracy improvement over individual models in knowledge-constrained scenarios
• Limited Consistency: "Wisdom of the crowd" approaches fail to consistently outperform individual models across all experimental conditions
• Resource Implications: Consensus methods require 1-1.5× additional computational resources while providing marginal accuracy improvements

Methodological Insights

• Structured Prompting: Few-shot guided iterative verification (GIV-F) consistently outperforms zero-shot approaches
• Evidence Quality: External evidence effectiveness is constrained by retrieval noise and source reliability
• Class Imbalance Challenges: Extreme class imbalance (as in YAGO with 99.2% correct facts) presents significant verification challenges

Research Implications

These findings underscore the urgent need for systematic benchmarking and highlight the complexity of automated KG fact verification, emphasizing that current LLM-based approaches require substantial advancement before practical deployment.

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📊 Detailed Analysis:

• 🔍 For comprehensive ablation study results: Ablation Study Results
• 💰 For token usage analysis and computational cost implications: Token Usage Analysis
• 📊 For dataset-wise analysis of LLM performance: Dataset-wise Analysis

🚀 Features

• Multiple LLM Support: Both open-source (Gemma2, Qwen2.5, Llama3.1, Mistral) and commercial (GPT-4o mini) models
• Diverse Methodologies: Direct Knowledge Assessment (DKA), Guided Iterative Verification (GIV), RAG, and Multi-model Consensus
• Real-world Datasets: FactBench, YAGO, and DBpedia with 13,530 total facts
• RAG Dataset: 2+ million documents specifically curated for KG fact verification
• Mock API: Simulated API for testing and development -- refer to FactCheck MockAPI.
• Interactive Platform: Web-based exploration tool for verification analysis
• Comprehensive Evaluation: Balanced accuracy, F1-macro, efficiency metrics, and cost analysis

📑 Prompt templates

Prompt templates for each methodology are available in the prompts directory.

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📦 Installation

Prerequisites

• Python 3.8+
• Ollama (for open-source models)
• Azure OpenAI API access (for commercial models)

Setup

1. Clone the repository

git clone https://github.com/FactCheck-AI/factcheck-benchmark
cd factcheck-benchmark

2. Install dependencies

pip install -r requirements.txt

3. Install Ollama (for open-source models)

# macOS
brew install ollama

# Linux
curl -fsSL https://ollama.ai/install.sh | sh

# Start Ollama service
ollama serve

4. Download required models

ollama pull gemma2:9b
ollama pull qwen2.5:7b
ollama pull llama3.1:8b
ollama pull mistral:7b

🚀 Quick Start

Basic Fact Verification

python main.py # Run with default configuration in `config.yml`

📊 Datasets

Supported Datasets

Dataset	Facts	Predicates	Gold Accuracy	Description
FactBench	2,800	10	0.54	Systematically generated with balanced true/false distribution
YAGO	1,386	16	0.99	High-quality facts with extreme class imbalance
DBpedia	9,344	1,092	0.85	Diverse schema with extensive predicate coverage

RAG Dataset

• 130,820 questions generated from KG facts
• 2,090,305 documents from Google SERP
• 87.4% text coverage rate
• Similarity scores for question relevance ranking

🔬 Methodologies

1. Direct Knowledge Assessment (DKA)

Basic fact verification using only LLM's internal knowledge without external guidance.

method:
  name: "DKA"

2. Guided Iterative Verification (GIV)

Enhanced verification with structured guidelines and examples.

GIV-Z (Zero-shot):

method:
  name: "GIV-Z"

GIV-F (Few-shot):

method:
  name: "GIV-F"

3. Retrieval-Augmented Generation (RAG)

Verification using external evidence from web search results.

method:
  name: "RAG"

rag:
  embedding_model: 'bge-small-en-v1.5'
  chunking_strategy: 'sliding_window'
  window_size: 3
  similarity_cutoff: 0.3
  top_k: 6

4. Multi-model Consensus

Combines predictions from multiple models using majority voting with tie-breaking.

majority_vote:
  mode: 'commercial'  # Options: commercial, open_source
  final_tie_breaker: 'most_consistent' # Options: least_consistent, most_consistent, Null (for commercial)
  num_votes: 3 # Number of votes for each model
  llms:
    - "mistral:7B"
    - "qwen2.5:7B"
    - "llama3.1:7B"
    - "gemma2:9B"
  higher_parameter_model:
    qwen2.5:7b: 'qwen2.5:7b'
    mistral:7b: 'mistral:7b'
    llama3.1:7b: 'llama3.1:latest'
    gemma2:9b: 'gemma2:9b'
  commercial_model:
    - "gpt-4o-mini"

⚙️ Configuration

Example Configuration (config.yml)

# Dataset configuration
dataset:
  name: "FactBench"  # Options: DBpedia, YAGO, FactBench

# Method configuration
method:
  name: "DKA"  # Options: DKA, GIV-Z, GIV-F, RAG

# LLM configuration
llm:
  mode: "open_source"  # Options: commercial, open_source
  model: "gemma2:9B"
  parameters:
    temperature: 0.75
    top_p: 0.9
    max_tokens: 512

# Evaluation configuration
evaluation:
  metrics:
    accuracy: 'balanced'  # Options: balanced, normal
    f1_score: "macro"     # Options: micro, macro, weighted

# Knowledge Graph configuration
knowledge_graph:
  kg_ids: ['correct_death_00106', 'correct_death_00040']

# Output configuration
output:
  directory: "./results"

Azure OpenAI Configuration

For commercial models, configure Azure OpenAI:

OpenAI:
  azure_endpoint: "https://your-resource.openai.azure.com/"
  api_key: "your-api-key"
  api_version: "2024-02-15-preview"

💻 Usage Examples

1. Single Model Evaluation

python main.py

2. Batch Evaluation

python evaluation.py --file results/factbench_results.json

For full evaluation use --full flag to include all metrics.

python evaluation.py --file results/factbench_results.json --full

3. Majority Vote Consensus

This module is interactive. You can run it as follows:

python consensus.py --dataset FactBench

if you don't specify files it will ask you to enter which files you want to use for the consensus. The output example will be:

Found 3 files for FactBench:
   1. FactBench_open-source_gemma2:9b_rag_20250527-103716.json
      Model: open-source_gemma2:9b, Method: rag
      Facts: 2, Success: 100.0%
   2. FactBench_open-source_qwen2.5:7B_rag_20250527-103404.json
      Model: open-source_qwen2.5:7B, Method: rag
      Facts: 2, Success: 100.0%
   3. FactBench_open-source_qwen2.5:7B_rag_20250527-103603.json
      Model: open-source_qwen2.5:7B, Method: rag
      Facts: 2, Success: 100.0%

How many files do you want to select? (1-3): 

Or you can simply define the files you want to use for the consensus:

python consensus.py --files results/factbench_open-source_gemma2:9b_rag_20250527-103716.json results/factbench_open-source_qwen2.5:7B_rag_20250527-103404.json

🚧 Todo:

• add parallel processing for the consensus

📈 Results

Performance Summary

Method	FactBench BAcc	YAGO BAcc	DBpedia BAcc	Avg Time/Fact
DKA	0.72	0.53	0.64	~0.3s
GIV-F	0.74	0.58	0.65	~0.8s
RAG	0.90	0.56	0.67	~2.3s
Consensus	0.90	0.64	0.68	~1.5s

Key Insights

1. Model Rankings: Gemma2 > Qwen2.5 > Mistral > Llama3.1 > GPT-4o mini
2. Dataset Difficulty: FactBench (easiest) > DBpedia > YAGO (hardest due to class imbalance)
3. Cost-Performance Trade-off: RAG provides best accuracy but 10× computational cost
4. Consensus Benefits: 1-5% improvement over individual models

🌐 Web Platform

Explore verification results interactively at: https://factcheck.dei.unipd.it/

Features:

• Fact Search: Find specific KG triples and their verification results
• Step-by-step Analysis: Inspect RAG pipeline components
• Model Comparison: Compare reasoning patterns across different LLMs
• Error Analysis: Categorized failure analysis with systematic insights
• User Feedback: Collaborative annotation and feedback system

📁 Repository Structure

factcheck-benchmark/
├── config.yml                 # Main configuration file
├── main.py                    # Entry point for experiments
├── config.py                  # Configuration validation and management
├── data_loader.py             # Dataset loading and preprocessing
├── llm_client.py              # LLM client implementations
├── evaluate.py                # Evaluation metrics and analysis
├── requirements.txt           # Python dependencies
├── prompts/                   # Prompt templates for each methodology
├── consensus.py               # Multi-model consensus implementation
├── rag_dataset/              # RAG dataset -- filtered -- for complete dataset refer to mockapi
├── methods/
│   ├── dka.py                 # Direct Knowledge Assessment
│   ├── giv.py                 # Guided Iterative Verification
│   └── rag.py                 # Retrieval-Augmented Generation
├── dataset/
│   ├── FactBench/
│   ├── YAGO/
│   └── DBpedia/
├── results/                   # Output directory for results
└── README.md                  # This file

Key Files

• config.py: Comprehensive configuration validation with support for multiple LLM providers
• evaluate.py: Scikit-learn based evaluation with balanced accuracy and F1-macro metrics
• methods/: Implementation of all verification methodologies
• prompts/: Contains prompt templates for each methodology

📊 Evaluation Metrics

Implemented Metrics

# Balanced Accuracy (addresses class imbalance)
BAcc = (Sensitivity + Specificity) / 2

# F1-Macro Score (unweighted average across classes)  
F1_macro = (1/N) * Σ(2 * Precision_i * Recall_i / (Precision_i + Recall_i))

# Consistency (model agreement)
Consistency = |{f ∈ F | response(m,f) = majorityVote(f)}| / |F|

# Efficiency
Time_per_fact = average_response_time_excluding_outliers

🛠️ Troubleshooting

Common Issues

1. Ollama Connection Error

# Ensure Ollama is running
ollama serve

# Check available models
ollama list

2. Memory Issues

# Reduce batch size or use smaller models
config["llm"]["model"] = "gemma2:2b"  # Instead of 9b

🤝 Contributing

We welcome contributions!

Areas for Contribution

• New Datasets: Integration of additional KG datasets
• Model Support: Adding support for new LLM architectures
• Evaluation Metrics: Implementation of additional evaluation measures
• Optimization: Performance improvements and efficiency enhancements -- important aspect

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🔗 Links

• Paper: EDBT 2026 (edbt:2026.45)
• Dataset: Hugging Face Repository
• Web Platform: https://factcheck.dei.unipd.it/
• Issues: GitHub Issues

👥 Authors

• Farzad Shami - University of Padua - farzad.shami@studenti.unipd.it
• Stefano Marchesin - University of Padua - stefano.marchesin@unipd.it
• Gianmaria Silvello - University of Padua - gianmaria.silvello@unipd.it

Acknowledgments

The work was supported by the HEREDITARY project, as part of the EU Horizon Europe program under Grant Agreement 101137074.

Reference

If you use or extend our work, please cite the following:

@inproceedings{shami_etal-edbt2026,
  title = {Benchmarking Large Language Models for Knowledge Graph Validation},
  author = {F. Shami and S. Marchesin and G. Silvello},
  booktitle = {Proceedings of the 29th International Conference on Extending Database Technology, {EDBT} 2026, Tampere, Finland, March 24-27, 2026},
  pages = {551--565},
  publisher = {OpenProceedings.org},
  year = {2026},
  url = {https://doi.org/10.48786/edbt.2026.45},
  doi = {10.48786/EDBT.2026.45}
}