FLAWS: Fault Localization Across Writing in Science

This repository provides the benchmark dataset, automated error insertion pipeline, and error identification & evaluation framework for the paper FLAWS: A Benchmark for Error Identification and Localization in Scientific Papers. The code allows you to:

1. Evaluate LLMs on their ability to identify errors in scientific papers.
2. Insert claim-specific errors into research papers using their LaTeX source to create examples similar to those in this dataset.

Set up the environment with:

cd FLAWS
conda env create -f environment.yml
conda activate llm_error

IMPORTANT: for ghostscript (used for PDF compression), windows users may need to download it from https://www.ghostscript.com/releases/gsdnld.html.

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A. Benchmark

The benchmark datasets are hosted on Hugging Face. Download and unzip them, and place the ALL_GEMINI and ALL_OPENAI folders in another folder data the same level as src:

• FLAWS Dataset

The current benchmark includes 713 papers:

• 265 unique papers, each with one error inserted using GPT 5
• 448 unique papers, each with one error inserted using Gemini 2.5 Pro

Five frontier LLMs have been evaluated on this benchmark. Models are ranked using a logistic regression coefficient β_j, which measures performance in identifying errors. This ranking accounts for differences in errors inserted by the two insertion models, not just raw accuracy. For more details about how this score is calculated, refer to the paper.

To evaluate other models by these 5 model providers - anthropic, deepseek, gemini, openai, xai - go to src/evaluate_llm.py and modify the following parameters to test different models:

# CHANGE THE IDENTIFICATION MODELS
model_family_identification = "deepseek"  # Options: anthropic, deepseek, gemini, openai, xai
model_identification = "deepseek-reasoner"  # Specific model name

To run the evaluation code on all the paper-error pairs, use

python -m src.evaluate_llm

this will produce a JSON results file and print out the identification accuracy. If you only wish to evaluate you model on a subset of paper-error pairs, modify this section:

with open(file, "r") as f:
    valid_errors = json.load(f)
identification_dict = defaultdict(list)

# if you only want to evaluate k examples, use replace with this line
# for paper, c in list(valid_errors.items())[:k]:
for paper, c in valid_errors.items():
    ...

To add a new model provider, update src/utils/llm_calls.py:

def completion_response(model_family: str, model: str, prompt: str, pdf_path: str | None) -> str:
    completion_mapping = {
        "anthropic": get_completion_anthropic,
        "deepseek": get_completion_deepseek,
        "gemini": get_completion_gemini,
        "openai": get_completion_openai,
        "xai": get_completion_grok,
        ## create a new function and add it here
    }
    completion = completion_mapping[model_family]
    llm_output = completion(prompt=prompt, model=model, file=pdf_path)
    return llm_output

Contribute Your Model Evaluations

We welcome contributions from the research community! If you have evaluted a model and would like to include it on the FLAWS leaderboard, please follow these steps to contribute your results:

1. Create a PR for the modified code.
2. Submit this google form: https://forms.gle/BaB49pxyBU3HcPKx7.
3. Once we verify your results, we will include your model into the leaderboard and merge the PR.

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B. Frameworks

To insert an error into a paper and evaluate an LLM's ability to identify it:

1. Place your LaTeX source folder in data/papers/
2. Add your API keys to src/utils/llm_calls.py for single error insertion, or to the batch pipeline scripts for batch insertion:
   • src/pipeline/batch_process/batching_pipeline_gemini.py
   • src/pipeline/batch_process/batching_pipeline_openai.py

1. Single Error Insertion

Entry Point: To run the error insertion for a single paper, modify the following in src/pipeline/single_process/single_error_insertion.py:

# Version control for results
version_control = "test"

# Specify paper and claim index
paper = "Matchmaker"  # LaTeX folder name in data/papers
ind = 0  # Claim index (0-indexed)

Then, use the following command

python -m src.pipeline.single_process.single_error_insertion

Pipeline Steps: By running the insertion pipeline, it will perform the following steps sequentially:

1. Extract claims from the paper.
2. Generate an error for the specified claim.
3. Filter the error out if it is invalid or trivial.
4. If the error is not filtered out, insert it into the original LaTeX source.
5. Localize all of the text excerpts related to the error.
6. Perform self-identification using the same LLM to further filter out the error if it is too easy to identify.
7. Compile a modified PDF if the error is not filtered out.

2. Single Error Identification (+ Evaluation)

Entry Point: To run the error identification and evaluation for a single paper-error pair, modify the following in src/pipeline/single_process/single_error_identification.py:

# Ensure these variable names match the insertion pipeline
# Version control for results
version_control = "test"

# Specify papers and claim indices
papers = ["Matchmaker"]  # List of LaTeX folders
ind = [0]  # Corresponding claim indices

Then, you can run:

python -m src.pipeline.single_process.single_error_identification

3. Batch Processing

The previous modules process one paper-error pair at a time, but insertion can be batched using the following modules:

python -m src.pipeline.batch_process.batching_pipeline_gemini
python -m src.pipeline.batch_process.batching_pipeline_openai

Similarly, before running you may modify the following:

# Version control for batch results
version_control = "test_batch"

# Papers to process
papers = get_papers("data/papers/")  # Returns all folder names in data/papers

The batch pipelines also run identification and evaluation after insertion.

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C. Other

To download papers from a specific conference using OpenReview, edit and then run src/download_papers.py:

# OpenReview credentials
username = ""
password = ""

# Venue ID (e.g., ICML 2025)
venue_id = "ICML.cc/2025/Conference"

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Citation

If you use FLAWS in your research, please cite our paper:

@misc{xi2025,
      title={FLAWS: A Benchmark for Error Identification and Localization in Scientific Papers}, 
      author={Sarina Xi and Vishisht Rao and Justin Payan and Nihar B. Shah},
      year={2025},
      eprint={2511.21843},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2511.21843}, 
}