EpiQwen2.5-7B

EpiQwen2.5-7B: Fine-tuned Qwen for Epidemiological Information Extraction

Model Description

EpiQwen2.5-7B is a fine-tuned version of Qwen/Qwen2.5-7B-Instruct specialized for extracting structured epidemiological information from unstructured disease outbreak reports. The model was trained on the WHO Disease Outbreak News (DONs) curated database (Carlson et al., 2023) to automatically extract key epidemiological features including disease classification, geographical locations, case counts, temporal information, and outbreak characteristics.

Model Details

• Base Model: Qwen/Qwen2.5-7B-Instruct
• Base Model License: Apache License 2.0
• Model Type: Causal Language Model (Decoder-only Transformer)
• Fine-tuning Method: Parameter-Efficient Fine-Tuning (PEFT) with LoRA (Low-Rank Adaptation)
• Adapter Weights License: CC0-1.0 (Public Domain Dedication) - Note: Only the LoRA adapter weights are released under CC0. The base model weights remain under Apache 2.0.
• Training Data: WHO Disease Outbreak News curated database (3,338 records through 2019)
• Language: English
• Application Domain: Public health surveillance, epidemic intelligence, epidemiological information extraction

License

Licensing Information

This repository contains LoRA adapter weights only, not the full model weights.

• Base Model (Qwen 2.5 7B): Licensed under Apache License 2.0

  • Copyright (c) Alibaba Cloud
  • Permissive open-source license allowing commercial use, modification, and distribution
  • Requires preservation of copyright and license notices

• LoRA Adapter Weights: Released under CC0 1.0 Universal (Public Domain Dedication)

  • The adapter weights can be used without restriction
  • To use these adapters, you must have access to the base Qwen 2.5 7B model (available under Apache 2.0)

Attribution: When using this model, please include appropriate attribution:

Qwen 2.5 is licensed under the Apache License 2.0,
Copyright (c) Alibaba Cloud.

EpiQwen2.5-7B LoRA adapter weights are released under CC0 1.0 Universal (Public Domain).

Distribution Notes

• This repository distributes only the fine-tuned LoRA adapter parameters
• Base model weights are unchanged and must be obtained separately from Alibaba Cloud/Hugging Face
• Users benefit from Apache 2.0's permissive terms for the base model
• The LoRA adapters are applied on top of the base model weights at inference time

Performance

The model achieved the following results on the evaluation set:

These scores represent overall performance across 5-fold stratified cross-validation, demonstrating high accuracy in extracting structured epidemiological information from unstructured outbreak reports.

Training Summary

• Best Training Step: 5,330 (final)
• Final Training Loss: 0.5623
• Initial Training Loss: 1.7273
• Total Improvement: 1.1650
• Total Training Steps: 5,330
• Training Epochs: 10

Intended Uses & Limitations

Intended Uses

This model is designed for:

• Automated extraction of epidemiological information from disease outbreak reports
• Public health surveillance systems requiring structured data from unstructured sources
• Epidemic intelligence pipelines for rapid outbreak detection and monitoring
• Research purposes in computational epidemiology and public health informatics

Limitations

• The model is trained specifically on WHO DONs format and may require adaptation for other report formats
• Performance on diseases not well-represented in the training data may vary
• The model extracts information present in the text and does not generate or infer missing data
• Designed for English-language outbreak reports only
• Should be used as a decision-support tool, with human verification for critical public health decisions

Extracted Features

The model extracts the following structured epidemiological information:

Disease Information:

• DiseaseLevel1 (primary disease classification)
• DiseaseLevel2 (disease subtype/variant)

Geographical Information:

• Country
• ISO country code
• OutbreakEpicenter (specific location within country)

Case Counts:

• CasesTotal
• CasesSuspected
• CasesProbable
• CasesConfirmed
• Deaths

Temporal Information:

• Outbreak start date (year, month, day)
• Outbreak detection date (year, month, day)
• Outbreak verification date (year, month, day)
• Outbreak end date and status

Training Procedure

Training Data

The model was trained on the WHO Disease Outbreak News curated database (Carlson et al., 2023), which contains:

• 3,338 structured records of disease outbreaks (data through 2019)
• Curated epidemiological information manually extracted from WHO DONs reports
• Standardized format for disease classifications, geographical locations, case counts, and temporal data

Training Approach

The training followed an instruction-tuning paradigm where unstructured outbreak report text is paired with structured JSON output containing extracted epidemiological features. The prompt format used was:

Below is an instruction that describes a task, paired with an input that provides further context. 
Write a response that appropriately completes the request.

### Instruction:
Extract disease outbreak information from the given text and format it as JSON.
Return a list containing one JSON object per outbreak mentioned.
Use "None" for missing information. Never invent or guess data.

### Input:
[Outbreak report text]

### Response:
[Extracted JSON with epidemiological features]

Fine-tuning Configuration

LoRA (Low-Rank Adaptation) Parameters:

• Rank (r): 16
• Alpha (α): 16
• Target modules: q_proj, k_proj, v_proj, o_proj, gate_proj, up_proj, down_proj
• Dropout: 0.05
• Task type: CAUSAL_LM

Training Hyperparameters:

• Learning rate: 1e-5 (with linear decay)
• Optimizer: AdamW (8-bit paged)
• Training batch size: 4 per device (8 GPUs)
• Gradient accumulation steps: 4
• Number of epochs: 10
• Warmup steps: Adaptive (10% of training steps, max 10)
• FP16 mixed precision training
• Weight decay: 0.01
• LR scheduler: Linear
• Seed: 41

Evaluation Strategy:

• 5-fold stratified cross-validation
• Evaluation metric: Training loss (model selection based on lowest training loss)
• Early stopping: After 6 consecutive evaluations without improvement
• Logging steps: 10
• Save steps: Adaptive (10% of training steps)

Hardware:

• Infrastructure: JRC Big Data Analytics Platform
• System: Linux cluster, Ubuntu 22.04.5 LTS
• CPU: Intel Xeon Platinum 8470 (208 CPUs)
• RAM: 1TB
• GPUs: 8x NVIDIA H100
• Training time: ~20-22 hours per fold

Quantization

The model uses 8-bit quantization with LoRA during training:

• Load in 8-bit: True
• Quantization type: Standard 8-bit
• Compute dtype: bfloat16

Usage

Installation

pip install transformers==4.52.4
pip install torch==2.3.1
pip install peft==0.12.0
pip install accelerate==1.7.0
pip install bitsandbytes==0.43.3

Basic Usage

Note: You need access to the base Qwen 2.5 7B model (available under Apache 2.0) to use these adapter weights.

import torch
from transformers import AutoTokenizer, AutoModelForCausalLM
from peft import PeftModel

# Load base model (Apache 2.0 licensed)
base_model_id = "Qwen/Qwen2.5-7B-Instruct"
adapter_model_id = "jrc-ai/EpiQwen2.5-7B"  # LoRA adapters
device = "cuda" if torch.cuda.is_available() else "cpu"

# Load tokenizer from base model
tokenizer = AutoTokenizer.from_pretrained(base_model_id, trust_remote_code=True)

# Load base model
base_model = AutoModelForCausalLM.from_pretrained(
    base_model_id,
    device_map="auto",
    torch_dtype=torch.bfloat16,
)

# Load and apply LoRA adapters
model = PeftModel.from_pretrained(base_model, adapter_model_id)

# Example outbreak report
outbreak_text = """
WHO has reported 3 suspected cases of yellow fever in Maryland county, 
in the south-eastern part of the country. One case with disease onset on 
1 August has been confirmed (IgM positive) by the Institut Pasteur in 
Abidjan, Côte d'Ivoire. All three cases have died.
"""

# Format prompt
prompt = f"""Below is an instruction that describes a task, paired with an input that provides further context. Write a response that appropriately completes the request.

### Instruction:
Extract disease outbreak information from the given text and format it as JSON.
Return a list containing one JSON object per outbreak mentioned.
Always return a list of JSON objects, even for single outbreaks.
Use "None" for missing information. If no outbreak information is found, return an empty list [].
Never invent or guess data.

### Input:
{outbreak_text}

### Response:
"""

# Tokenize and generate
inputs = tokenizer(prompt, return_tensors="pt", truncation=True).to(device)

with torch.no_grad():
    outputs = model.generate(
        **inputs,
        max_new_tokens=600,
        temperature=0.1,
        do_sample=False,
        pad_token_id=tokenizer.eos_token_id
    )

# Decode output
extracted_info = tokenizer.decode(outputs[0], skip_special_tokens=True)
print(extracted_info)

Expected Output Format

[{
  "DiseaseLevel1": "Yellow fever",
  "DiseaseLevel2": "",
  "Country": "Liberia",
  "ISO": "LBR",
  "OutbreakEpicenter": "Maryland county",
  "CasesTotal": 3,
  "CasesSuspected": 2,
  "CasesProbable": null,
  "CasesConfirmed": 1,
  "Deaths": 3,
  "OutbreakStartYear": 2001,
  "OutbreakStartMonth": 8,
  "OutbreakStartDay": 1,
  "OutbreakDetectionYear": null,
  "OutbreakDetectionMonth": null,
  "OutbreakDetectionDay": null,
  "OutbreakVerificationYear": null,
  "OutbreakVerificationMonth": null,
  "OutbreakVerificationDay": null,
  "OutbreakEnd": null,
  "OutbreakEndYear": null,
  "OutbreakEndMonth": null,
  "OutbreakEndDay": null
}]

Comparison with Other Approaches

In-Context Learning vs Fine-Tuning

This fine-tuned model significantly outperforms in-context learning (iCL) approaches:

Performance gain from fine-tuning: ~10 percentage points across all ROUGE metrics.

Comparison with Other Fine-tuned Models

All pairwise comparisons are statistically significant (p < 0.001, Nemenyi post-hoc test with Bonferroni correction).

Key Advantage: EpiQwen 2.5-7B achieves performance within 0.019-0.032 points of the much larger EpiLLaMA 3.3-70B (70B parameters) while being 10× smaller, making it ideal for resource-constrained deployment scenarios.

Citation

If you use this model in your research, please cite:

@article{consoli2026generative,
  title={Generative AI for Structured Epidemiological Information Extraction: Comparing In-Context Learning and Fine-Tuning Approaches},
  author={Consoli, Sergio and Bertolini, Lorenzo and Stefanovitch, Nicolas and Spagnolo, Luigi and Espinosa, Laura and Stilianakis, Nikolaos I.},
  journal={PLoS Digital Health},
  volume={submitted, currently under revision},
  year={2026}
}

Please also acknowledge the base model:

@article{qwen2.5,
  title={Qwen2.5: A Party of Foundation Models},
  author={Qwen Team},
  year={2024},
  url={https://qwenlm.github.io/blog/qwen2.5/}
}

Ethical Considerations & Dual-Use Implications

Upon evaluation, we identified no dual-use implications for this model. The model is designed specifically for public health surveillance and epidemic intelligence applications to support global health initiatives.

Important Notes:

• The model should be used as a decision-support tool with appropriate human oversight
• Extracted information should be verified by public health professionals before making critical decisions
• The model does not replace human expertise in epidemiological analysis
• Privacy and data protection regulations should be followed when processing outbreak reports

Acknowledgments

We acknowledge:

• Alibaba Cloud for developing and releasing Qwen 2.5 7B under the Apache License 2.0
• The GPT@JRC initiative for providing access to LLMs
• The JRC Big Data Analytics Platform for computational infrastructure
• The WHO Epidemic Intelligence from Open Sources (EIOS) initiative for support
• Colleagues at the European Commission Joint Research Centre (JRC) and the European Centre for Disease Prevention and Control (ECDC)

Framework Versions

• Transformers: 4.52.4
• PyTorch: 2.3.1
• PEFT: 0.12.0
• Accelerate: 1.7.0
• BitsAndBytes: 0.43.3
• Datasets: 2.20.0

<!-- ## Contact For questions or issues regarding this model, please contact: - Sergio Consoli ([email protected]) - Joint Research Centre (JRC), European Commission -->

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Disclaimer: The views expressed are purely those of the authors and may not in any circumstance be regarded as stating an official position of the European Commission.