# Ideas Have Genomes: Benchmarking Scientific Lineage Reasoning and Lineage-Grounded Idea Generation

arXiv: https://arxiv.org/abs/2607.08758 · HTML: https://mlsanity.com/paper/2607.08758/

## 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 42 of its 53 references that are in the map.
- First posted on arXiv 9 Jul 2026.

## Placed in

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

## Builds on (most cited first, 30 of 42)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [You Only Look Once: Unified, Real-Time Object Detection](https://mlsanity.com/paper/1506.02640/) (2015)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [YOLO9000: Better, Faster, Stronger](https://mlsanity.com/paper/1612.08242/) (2016)
- [τ-bench: A Benchmark for Tool-Agent-User Interaction in Real-World Domains](https://mlsanity.com/paper/2406.12045/) (2024)
- [Text Embeddings by Weakly-Supervised Contrastive Pre-training](https://mlsanity.com/paper/2212.03533/) (2022)
- [Chatbot Arena: An Open Platform for Evaluating LLMs by Human Preference](https://mlsanity.com/paper/2403.04132/) (2024)
- [GAIA: a benchmark for General AI Assistants](https://mlsanity.com/paper/2311.12983/) (2023)
- [Large Language Models are not Fair Evaluators](https://mlsanity.com/paper/2305.17926/) (2023)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [Length-Controlled AlpacaEval: A Simple Way to Debias Automatic Evaluators](https://mlsanity.com/paper/2404.04475/) (2024)
- [Crowdsourcing Multiple Choice Science Questions](https://mlsanity.com/paper/1707.06209/) (2017)
- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [The AI Scientist-v2: Workshop-Level Automated Scientific Discovery via Agentic Tree Search](https://mlsanity.com/paper/2504.08066/) (2025)
- [Can LLMs Generate Novel Research Ideas? A Large-Scale Human Study with 100+ NLP Researchers](https://mlsanity.com/paper/2409.04109/) (2024)
- [WildBench: Benchmarking LLMs with Challenging Tasks from Real Users in the Wild](https://mlsanity.com/paper/2406.04770/) (2024)
- [ResearchAgent: Iterative Research Idea Generation over Scientific Literature with Large Language Models](https://mlsanity.com/paper/2404.07738/) (2024)
- [SciMON: Scientific Inspiration Machines Optimized for Novelty](https://mlsanity.com/paper/2305.14259/) (2023)
- [Assisting in Writing Wikipedia-like Articles From Scratch with Large Language Models](https://mlsanity.com/paper/2402.14207/) (2024)
- [Structural Scaffolds for Citation Intent Classification in Scientific Publications](https://mlsanity.com/paper/1904.01608/) (2019)
- [SciRepEval: A Multi-Format Benchmark for Scientific Document Representations](https://mlsanity.com/paper/2211.13308/) (2022)
- [SciEval: A Multi-Level Large Language Model Evaluation Benchmark for Scientific Research](https://mlsanity.com/paper/2308.13149/) (2023)

## Abstract (arXiv)

Scientific ideas rarely start from a blank page. They inherit mechanisms, repair known limitations, and recombine pieces of earlier work, much like biological genomes. Current benchmarks still say little about whether AI systems can follow this inheritance structure. We present IdeaGene-Bench (IG-Bench), a benchmark for scientific lineage reasoning and lineage-grounded idea generation. IG-Bench is organized around the IdeaGene framework: each paper or proposal is represented as a set of minimal, typed, evidence-grounded Idea Genome objects, and a GenomeDiff aligns these objects to record inheritance, mutation, loss, external import, and novel insertion under six operational evolutionary dynamics. The benchmark contains 1,961 golden lineage traces, 1,085 curated Idea Genome objects, and 920 pairwise GenomeDiff records across 10 scientific domains. It supports two evaluations. IG-Exam (42 task types, 1,029 instances) tests closed-form lineage reasoning across Idea Genome abstraction, inheritance tracing, evolutionary reasoning, and lineage verification. IG-Arena evaluates generation with a lineage-conditioned Population-Evolution Score(PES), asking whether a proposal can be inserted as a coherent descendant of a given lineage population: it should inherit the right Idea Genome objects, vary meaningfully from nearby work, and offer selection value for future research. Experiments on 14 LLM-based scientists expose a compositional bottleneck. The strongest system reaches only 27.3% exact accuracy on lineage reasoning, and structured lineage context reshuffles system rankings rather than helping every participant uniformly.