# CrossTrace: A Cross-Domain Dataset of Grounded Scientific Reasoning Traces for Hypothesis Generation

arXiv: https://arxiv.org/abs/2603.28924 · HTML: https://mlsanity.com/paper/2603.28924/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Knowledge- and tool-augmented reasoning, one of 17 directions in LLM reasoning.
- Builds on 13 of its 25 references that are in the map.
- First posted on arXiv 30 Mar 2026.

## Placed in

- LLM reasoning / [Knowledge- and tool-augmented reasoning](https://mlsanity.com/lr/knowledge-and-tool-augmented-reasoning/)

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

- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [The AI Scientist-v2: Workshop-Level Automated Scientific Discovery via Agentic Tree Search](https://mlsanity.com/paper/2504.08066/) (2025)
- [DiscoveryBench: Towards Data-Driven Discovery with Large Language Models](https://mlsanity.com/paper/2407.01725/) (2024)
- [SciAgents: Automating scientific discovery through multi-agent intelligent graph reasoning](https://mlsanity.com/paper/2409.05556/) (2024)
- [Hypothesis Generation with Large Language Models](https://mlsanity.com/paper/2404.04326/) (2024)
- [ResearchBench: Benchmarking LLMs in Scientific Discovery via Inspiration-Based Task Decomposition](https://mlsanity.com/paper/2503.21248/) (2025)
- [Robin: A multi-agent system for automating scientific discovery](https://mlsanity.com/paper/2505.13400/) (2025)
- [MegaScience: Pushing the Frontiers of Post-Training Datasets for Science Reasoning](https://mlsanity.com/paper/2507.16812/) (2025)
- [HypoBench: Towards Systematic and Principled Benchmarking for Hypothesis Generation](https://mlsanity.com/paper/2504.11524/) (2025)
- [How Does Code Pretraining Affect Language Model Task Performance?](https://mlsanity.com/paper/2409.04556/) (2024)
- [Sparks of Science: Hypothesis Generation Using Structured Paper Data](https://mlsanity.com/paper/2504.12976/) (2025)
- [ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding](https://mlsanity.com/paper/2408.11363/) (2024)
- [Scientific Hypothesis Generation and Validation: Methods, Datasets, and Future Directions](https://mlsanity.com/paper/2505.04651/) (2025)

## Abstract (arXiv)

Scientific hypothesis generation is a critical bottleneck in accelerating research, yet existing datasets for training and evaluating hypothesis-generating models are limited to single domains and lack explicit reasoning traces connecting prior knowledge to novel contributions. I introduce CrossTrace, a dataset of 1,389 grounded scientific reasoning traces spanning biomedical research (518), AI/ML (605), and cross-domain work (266). Each trace captures the structured reasoning chain from established knowledge through intermediate logical steps to a novel hypothesis, with every step grounded in source paper text. I define an Input/Trace/Output schema that extends the Bit-Flip-Spark framework of HypoGen with step-level verification, a taxonomy of eight discovery patterns, and multi-domain coverage. Fine-tuning Qwen2.5-7B-Instruct on CrossTrace via QLoRA yields substantial improvements over the untuned baseline: IAScore rises from 0.828 to 0.968 (GPT-4o judge) and from 0.716 to 0.888 (Claude Opus 4.5), structural compliance improves from 0% to 100%, and spark cosine similarity increases from 0.221 to 0.620. Balanced cross-domain training (biomedical + AI/ML + CS) outperforms single-domain training, providing evidence that scientific reasoning patterns transfer across disciplines. Human validation of 150 stratified records confirms 99.7% step-level grounding accuracy and a 0.0% fabrication rate. To my knowledge, CrossTrace is the first large-scale, cross-domain dataset with step-level grounded reasoning traces for hypothesis generation, and my results demonstrate that such traces are an effective training signal whose benefits are at least partially domain-general.