Ontology-Guided Knowledge Graph Construction from Structured Metadata and Climate Science Publications

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat cites edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce Agents-K1, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce Scholar-KG, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

Automated knowledge graph (KG) construction is essential for navigating the rapidly expanding body of scientific literature. However, existing approaches struggle to recognize long multi-word entities, often fail to generalize across domains, and typically overlook the hierarchical nature of scientific knowledge. While general-purpose large language models (LLMs) offer adaptability, they are computationally expensive and yield inconsistent accuracy on specialized tasks. As a result, current KGs are shallow and inconsistent, limiting their utility for exploration and synthesis. We propose a two-stage framework for scalable, zero-shot scientific KG construction. The first stage, Z-NERD, introduces (i) Orthogonal Semantic Decomposition (OSD), which promotes domain-agnostic entity recognition by isolating semantic "turns" in text, and (ii) a Multi-Scale TCQK attention mechanism that captures coherent multi-word entities through n-gram-aware attention heads. The second stage, HGNet, performs relation extraction with hierarchy-aware message passing, explicitly modeling parent, child, and peer relations. To enforce global consistency, we introduce two complementary objectives: a Differentiable Hierarchy Loss to discourage cycles and shortcut edges, and a Continuum Abstraction Field (CAF) Loss that embeds abstraction levels along a learnable axis in Euclidean space. This is the first approach to formalize hierarchical abstraction as a continuous property within standard Euclidean embeddings, offering a simpler alternative to hyperbolic methods. We release SPHERE (https://github.com/basiralab/SPHERE), a multi-domain benchmark for hierarchical relation extraction. Our framework establishes a new state of the art on SciERC, SciER, and SPHERE, improving NER by 8.08% and RE by 5.99% on out-of-distribution tests. In zero-shot settings, gains reach 10.76% for NER and 26.2% for RE.

We present EXYGEN (EXplore Your Graphs ENgine), a framework for knowledge graph (KG) understanding that enables conversational access to KGs at scale. We address two questions in sequence. First, how effectively can LLMs perform text-to-SPARQL generation given only automatically derived structured metadata and small graph samples, rather than task-specific fine-tuning? We integrate VoID descriptions and ShEx schemas into a retrieval-augmented generation (RAG) pipeline and ablate KG-derived context on the SciQA benchmark. Our best configuration -- combining ShEx schemas, retrieved triples, and example question-query pairs -- reaches an exact match of 0.419 on execution results without any LLM fine-tuning. We further find that lexical metrics such as F1 poorly predict query correctness, and that larger general-purpose LLMs can outperform smaller code-specialized ones once given sufficient context. Second, we ask how to generate the structured metadata that this method relies on from very large KGs, where KG metadata generation becomes computationally intractable. We introduce a predicate-coverage-aware parallel graph sampling strategy that preserves structural diversity while remaining computationally tractable. On OpenCitations Meta and GESIS, it retains high predicate coverage with minimal triple loss and reduces runtime by over 80x; on ORKG, sampling is not just faster but the only tractable path to obtain complete metadata. Together, these results show that structured schema context and lightweight prompting can substantially reduce reliance on fine-tuning for scalable conversational access to KGs, though closing the remaining gap to fully fine-tuned approaches will likely require reducing dependence on curated question-query exemplars -- whether through synthetic generation or an execution-feedback-driven approach -- and validating these findings beyond a single benchmark.