BioGraphletQA: Knowledge-Anchored Generation of Complex QA Datasets

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.

Retrieval of information from graph-structured knowledge bases represents a promising direction for improving the factuality of LLMs. While various solutions have been proposed, a comparison of methods is difficult due to the lack of challenging QA datasets with ground-truth targets for graph retrieval. We present SynthKGQA, an LLM-powered framework for generating high-quality Knowledge Graph Question Answering datasets from any Knowledge Graph, providing the full set of ground-truth facts in the KG to reason over questions. We show how, in addition to enabling more informative benchmarking of KG retrievers, the data produced with SynthKGQA also allows us to train better models.We apply SynthKGQA to Wikidata to generate GTSQA, a new dataset designed to test zero-shot generalization abilities of KG retrievers with respect to unseen graph structures and relation types, and benchmark popular solutions for KG-augmented LLMs on it.

While modern question answering (QA) systems excel on clean, schema-aligned corpora, real-world knowledge is rarely so neatly packaged. Answering questions over enterprise and scientific data lakes requires systems to navigate heterogeneous, weakly structured collections of tables, passages, and linked metadata. Current benchmarks abstract away this noisy discovery process, failing to evaluate end-to-end performance. To bridge this gap, we introduce LakeQuest, a human-validated benchmark of 9,846 QA pairs designed to evaluate the end-to-end retrieve-and-synthesize pipeline over realistic data lakes. LakeQuest spans three diverse domains (AI/ML metadata, retail banking, and multimodal biomedical drug information) and pairs every question with exact, modality-aware evidence pointers. By isolating source discovery from cross-modal synthesis, LakeQuest exposes critical failure modes in modern QA systems. Our baseline evaluations, including standard Retrieval-Augmented Generation (RAG) and agentic tool-use methods, reveal that high-quality retrieval does not guarantee correct reasoning. Systems consistently struggle with relation chaining in metadata graphs, policy grounding in bank ledgers, and joint tabular QA in biomedical contexts, highlighting the need for robust discovery and faithful cross-file composition mechanisms in future agentic QA systems.