HGNet: Scalable Foundation Model for Automated Knowledge Graph Generation from Scientific Literature

TL;DR

This paper introduces HGNet, a scalable framework for automated knowledge graph construction from scientific literature, combining novel entity and relation extraction methods with hierarchical consistency enforcement, achieving state-of-the-art results.

Contribution

The paper presents a two-stage framework with innovative semantic decomposition and hierarchy-aware relation extraction, formalizing hierarchical abstraction as a continuous property in Euclidean space.

Findings

Improves NER by 8.08% and RE by 5.99% on out-of-distribution tests.

Achieves 10.76% gain in NER and 26.2% in RE in zero-shot settings.

Establishes a new benchmark SPHERE for hierarchical relation extraction.

Abstract

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.