HERMES: a multi-agent framework for structured knowledge extraction from ultra-long documents in geoscience

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.

Accurately extracting nuanced, contextualized data from research articles is laborious and time intensive. Here, we investigate the performance of frontier, browser-based large language models (LLMs) to extract highly contextualized information. We demonstrate four escalating workflows, 1) given an expert curated prompt and research articles, most frontier LLMs perform well at data extraction, however can struggle with interpreting scientific context and nuance, 2) given simple instructions, LLMs can author their own prompts which were almost as eNective as expert-written prompts, 3) autonomous discovery of research literature was diNicult, agents either missed or hallucinated references, and 4) LLMs can create new datasets from published guidelines that closely match human-expert judges, but still require a human-in-the-loop. Together, these findings define an auditable division of labour in which experts specify the evidence standard, models cross-check repeated extractions and researchers resolve disputed cases, providing a practical route to scaling scientific data curation without relinquishing expert oversight.

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.