Can Deep Research Agents Retrieve and Organize? Evaluating the Synthesis Gap with Expert Taxonomies

arXiv:2601.12369v3 Announce Type: replace Abstract: Deep Research Agents increasingly automate survey generation, yet whether they match human experts at retrieving essential papers and organizing them into expert-like taxonomies remains unclear. Existing benchmarks emphasize writing quality or citation correctness, while standard clustering metrics ignore hierarchical structure. We introduce TaxoBench, a benchmark of 72 highly-cited LLM surveys with expert-authored taxonomy trees and 3,815 papers mapped to paper categories. TaxoBench evaluates (1) retrieval via Recall/Precision/F1, and (2) organization at a leaf level (paper-to-category assignment) and a hierarchy level via novel metrics, namely Unordered Semantic Tree Edit Distance US-TED/US-NTED and Semantic Path Similarity Sem-Path. Two modes are supported: Deep Research (topic-only, end-to-end) and Bottom-Up (expert paper set provided, organization-only). To distinguish disagreement with a single expert reference from genuine model failure, we explicitly partition findings into capability-based (reference-free) and alignment-based (reference-dependent). Evaluating 7 Deep Research Agents and 12 frontier LLMs reveals a dual bottleneck: capability-side, the best agent retrieves only 20.92% of expert-cited papers, and 1,000 model taxonomies show 75.9% sibling overlap, 51.2% MECE violations, and 83.4% structural imbalance, all detectable without any reference; alignment-side, all 12 LLMs converge to Sem-Path 28--29%, well below 47--58% achieved by three independent human-annotator groups on the same paper sets. Our benchmark is publicly available at https://github.com/KongLongGeFDU/TaxoBench