Automatic Inter-document Multi-hop Scientific QA Generation
Organizations: Yonsei University, Seoul, Republic of Korea · OnomaAI, Seoul, Republic of Korea
Abstract
Existing automatic scientific question generation studies mainly focus on single-document factoid QA, overlooking the inter-document reasoning crucial for scientific understanding. We present AIM-SciQA, an automated framework for generating multi-document, multi-hop scientific QA datasets. AIM-SciQA extracts single-hop QAs using large language models (LLMs) with machine reading comprehension and constructs cross-document relations based on embedding-based semantic alignment while selectively leveraging citation information. Applied to 8,211 PubMed Central papers, it produced 411,409 single-hop and 13,672 multi-hop QAs, forming the IM-SciQA dataset. Human and automatic validation confirmed high factual consistency, and experimental results demonstrate that IM-SciQA effectively differentiates reasoning capabilities across retrieval and QA stages, providing a realistic and interpretable benchmark for retrieval-augmented scientific reasoning. We further extend this framework to construct CIM-SciQA, a citation-guided variant achieving comparable performance to the Oracle setting, reinforcing the dataset's validity and generality.
Figures & tables
| Dataset | M Hop | M Doc | #QA | QA Gen | Free-form | Domain | Source |
| PubMedQA | X | X | 211k | Human | X | Biomedical | PubMed |
| SciQAG-24D | X | X | 180k | LLM | O | Scientific Literature | Scientific Literature |
| WikiHop | O | O | 51k | Rule-based | X | General/Wiki | Wiki |
| HotpotQA | O | O | 113k | Human | O | General/Wiki | Wiki |
| DocHop-QA | O | O | 11k | LLM | X | Biomedical/Scientific | PubMed |
| M3SciQA | O | O | 1.4k | Human | X | NLP Papers | NLP Papers (+cited) |
| Item | Value |
| Count | 411,409 |
| Avg. Question Length | 88.75 |
| Avg. Answer Length | 126.92 |
| Avg. QA per Paper | 55.67 |
| Avg. QA per Section | 10.49 |
| Item | Dev | Test |
| Count | 13,372 | 300 |
| Avg. Retrieval Q Length | 15.05 | 15.16 |
| Avg. Inter-doc Q Length | 28.68 | 28.65 |
| Avg. Combined Q Length | 48.52 | 49.21 |
| Avg. Inter-doc A Length | 28.13 | 29.98 |
| Avg. Combined A Length | 43.00 | 45.33 |
| Criterion | Description |
| Fluency | Whether the Complete QA is grammatically correct and naturally written. |
| Completeness | Whether the Complete QA can be answered solely based on the provided QA pair. |
| Cross-reference Necessity | Whether both papers are essential to answer the Complete QA. |
| Relational Appropriateness | Whether the two papers are conceptually suitable to be combined into a single QA. |
| Overall Decision | Synthesizes the above four criteria to make the final decision. |
| Evidence (E) | For instance, the U.S. CDC N1 assay had a recall of 99.0% and the U.S. CDC N2 assay had a 99.2% recall. |
| Meta | PMC10021650 |
| Q1 | What was the recall rate for the U.S. CDC N1 assay? |
| A1 | The recall rate for the U.S. CDC N1 assay was 99.0%. |
| Q2 | What was the recall rate for the U.S. CDC N2 assay? |
| A2 | The recall rate for the U.S. CDC N2 assay was 99.2%. |
| Model | Paper Cluster (N=30) | Random Cluster (N=30) | Full Papers (N=8211) | ||||||
| Hit@1 | Hit@3 | MRR@5 | Hit@1 | Hit@3 | MRR@5 | Hit@1 | Hit@50 | MRR@50 | |
| GritLM-7B Muennighoff et al. (2024) | 0.220 | 0.353 | 0.306 | 0.177 | 0.303 | 0.248 | 0.010 | 0.130 | 0.023 |
| Jina-v2-base-en Günther et al. (2023) | 0.197 | 0.350 | 0.280 | 0.183 | 0.340 | 0.266 | 0.020 | 0.117 | 0.030 |
| e5-base-v2 Wang et al. (2022) | 0.273 | 0.493 | 0.395 | 0.307 | 0.537 | 0.428 | 0.017 | 0.157 | 0.028 |
| e5-mistral-7b-instruct Wang et al. (2023) | 0.300 | 0.473 | 0.390 | 0.273 | 0.430 | 0.356 | 0.030 | 0.203 | 0.058 |
| Qwen3-Embedding-8B Zhang et al. (2025) | 0.407 | 0.597 | 0.554 | 0.483 | 0.607 | 0.555 | 0.080 | 0.397 | 0.136 |
| Model | Oracle Setting | Realistic Setting | ||||||
| Acc | F1 | ROUGE | BERTScore | Acc | F1 | ROUGE | BERTScore | |
| Human Expert | 0.975 | 0.324 | 0.319 | 0.447 | – | – | – | – |
| gemma-3-1b-it Team et al. (2025) | 0.265 | 0.337 | 0.301 | 0.340 | 0.260 | 0.332 | 0.292 | 0.328 |
| Llama-3.2-3B-it Grattafiori et al. (2024) | 0.57 | 0.421 | 0.403 | 0.435 | 0.515 | 0.399 | 0.380 | 0.403 |
| gemma-3-4b-it Team et al. (2025) | 0.590 | 0.430 | 0.403 | 0.465 | 0.515 | 0.418 | 0.390 | 0.453 |
| gemma-3-27b-it Team et al. (2025) | 0.750 | 0.517 | 0.495 | 0.556 | 0.670 | 0.483 | 0.461 | 0.519 |
| Model | Acc | F1 | ROUGE | BERTScore |
| gemma-3-1b-it Team et al. (2025) | 0.446 | 0.330 | 0.295 | 0.366 |
| gemma-3-4b-it Team et al. (2025) | 0.635 | 0.366 | 0.329 | 0.405 |
| Llama-3.2-3B-it Grattafiori et al. (2024) | 0.608 | 0.367 | 0.339 | 0.379 |
| gemma-3-27b-it Team et al. (2025) | 0.798 | 0.427 | 0.402 | 0.449 |
| DeepSeek-R1 Guo et al. (2025) | 0.784 | 0.131 | 0.205 | 0.110 |
| Qwen3-30B-A3B-it Yang et al. (2025) | 0.824 | 0.425 | 0.392 | 0.439 |
Scientific QA
Scientific question answering develops systems that answer research and domain-science questions using reliable evidence from papers, data, and figures.
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