Elizaveta Nosova | Searcharxiv

arXiv2026

Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies

Biomedical knowledge exists in two complementary but distinct forms: unstructured scientific literature and structured knowledge graphs (KGs). Aligning them is essential for knowledge grounding, evidence retrieval, and KG completion, yet existing methods do not explicitly align free-text evidence with KG triples. We present a unified framework for systematically studying design choices for aligning biomedical text and KGs. With a text encoder and a KG embedding model both frozen, we learn only a lightweight projection between their spaces via a contrastive objective. This enables a fair comparison across six design dimensions: text encoder, KG embedding model, projection head, triple composition, training direction, and hard-negatives sampling. We construct CTD-Align, a corpus of over 22K one-to-one tripledocument pairs linking chemical-gene interactions from the Comparative Toxicogenomics Database to supporting PubMed passages. We evaluate alignment on it in two retrieval settings: document-to-triple and triple-to-document. We find that the triple composition and the training direction (i.e., shared retrieval space) have the greatest impact, whereas the text encoder and hard-negatives sampling matter little. Overall, simple choices win: projecting text into the KG space with a linear head over concatenated subject, predicate, and object embeddings performs best. These findings establish lightweight contrastive alignment as an effective, practical foundation for bridging biomedical text and KGs.

cs.CL↗

arXiv2026

MultiGlobeQA: A Multilingual and Globally Diverse Benchmark for Geospatial Reasoning

Geospatial reasoning, i.e., computing distances, containment, and other spatial relations over real-world entities, is central to navigation and logistics, yet large language models (LLMs) struggle with the required geometric and topological computation despite storing considerable geographic knowledge. Existing benchmarks localize these failures only partially: they are synthetic or smallscale, largely monolingual, and offer limited control over geographic coverage. We introduce MultiGlobeQA, a multilingual benchmark of 46,060 question-answer pairs spanning 14 spatial-function families and 15 answer formats, with execution-based ground truth over three knowledge graphs. It covers 201 countries and territories via income- and density-stratified sampling, with parallel questions in English and 16 additional high- and low-resource languages. Across parametric, reasoning, and agentic settings, LLMs collapse on tasks requiring grid indexing and shape computation, while topological relations and directions fare best. Retrieval and tool use yield considerable gains, yet performance plateaus below two thirds even when gold facts are supplied, indicating that computation, not access to knowledge, is the bottleneck. Models also underperform on low-income regions, a gap that gold facts widen rather than close.

cs.CL↗