# RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

arXiv: https://arxiv.org/abs/2505.23823 · HTML: https://mlsanity.com/paper/2505.23823/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 31 references that are in the map.
- First posted on arXiv 28 May 2025.

## Builds on (most cited first, 13 of 13)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [FActScore: Fine-grained Atomic Evaluation of Factual Precision in Long Form Text Generation](https://mlsanity.com/paper/2305.14251/) (2023)
- [Generalization through Memorization: Nearest Neighbor Language Models](https://mlsanity.com/paper/1911.00172/) (2019)
- [Passage Re-ranking with BERT](https://mlsanity.com/paper/1901.04085/) (2019)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [Tx-LLM: A Large Language Model for Therapeutics](https://mlsanity.com/paper/2406.06316/) (2024)
- [Understand the Dynamic World: An End-to-End Knowledge Informed Framework for Open Domain Entity State Tracking](https://mlsanity.com/paper/2304.13854/) (2023)
- [GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration](https://mlsanity.com/paper/2501.16382/) (2025)

## Abstract (arXiv)

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.