Helicase: Uncertainty-Guided Supply Chain Knowledge Graph Construction with Autonomous Multi-Agent LLMs
Authors: Yunbo Long, Haolang Zhao, Ge Zheng, Alexandra Brintrup
Abstract
LLM-based multi-agent systems have been widely adopted for knowledge retrieval and report generation, synthesizing known information through web search and textual reasoning. However, many critical information tasks in supply chains are not simple one-shot queries: they are structural inference problems requiring multi-hop reasoning across complex, fragmented web resources. Questions such as \textit{``Which Tesla components use lithium from Australian mines?''} have no answer in any single document; answers must be computationally synthesized through the autonomous construction and analysis of dynamic knowledge graphs assembled from fragmented, heterogeneous sources. Moreover, such discovery processes must be uncertainty-aware: decisions depend not only on answers but on calibrated confidence in their reliability, traceable to source quality and reasoning consistency. To address this capability gap, we propose \textit{Helicase}, an autonomous multi-agent LLM system for uncertainty-guided supply chain knowledge graph construction. \textit{Helicase} decomposes high-level supply-chain queries into executable investigation plans, coordinates specialized web-search, reasoning, and coding agents through iterative verification loops, and incrementally constructs query-specific supply chain knowledge graphs with per-fact uncertainty annotations. Its three-layer uncertainty framework tracks uncertainty at the action, trajectory, and memory layers, enabling both structural inference and calibrated confidence assessment. To evaluate autonomous reasoning across the full complexity spectrum, we introduce SCQA (Supply Chain Query Assessment), a benchmark of 80 supply chain queries organized into four quadrants spanning single-hop to multi-hop inference under both high and low data visibility.
AI agents in supply chains face a fundamental epistemic gap: large language models (LLMs) interpret policies but lack physical grounding, while reinforcement learning (RL) optimizes flows but is semantically blind to unstructured constraints. We introduce REFLECTICHAIN, bridging this gap through a Generative Supply Chain World Model (SC-WM) - encoding heterogeneous supply networks into a 6-dim graph-latent space with physical conservation - and Double-Loop Learning that separates epistemic uncertainty (KL-trust-region-bounded policy adaptation) from aleatoric uncertainty (stochastic latent rollouts). On Semi-Sim, a 10-node semiconductor benchmark with SIR risk propagation, 6 perturbation types, and 10 policy constraint templates, REFLECTICHAIN improves Rationale Consistency Score by 33.0% (p < 0.0001, d = 2.78), maintains 82.3% operability under adversarial shocks, and exhibits anti-fragile behavior (+40.2% gain under moderate pressure). We identify three operational epistemic mechanisms - uncertainty separation, knowledge-boundary detection, and empirical Bayesian policy updating - and discuss five limitation categories.
Retrieval-Augmented Generation (RAG) fails systematically on queries requiring structural reasoning over interconnected entities. We compare eight retrieval architectures for aerospace supply chain intelligence, progressing from text retrieval through graph traversal to graph computation. Using a 46-node knowledge graph with 64 typed edges, we evaluate 23 queries across 10 intent categories and demonstrate that five query classes are structurally unreachable for vector retrieval. Our central finding is the operator vocabulary thesis: the barrier to LLM-based graph reasoning is not model intelligence but the computational operators available as tools. An LLM Query Planner with 9 typed traversal primitives outperforms bespoke handlers (F1 = 0.632 vs. 0.472) while generalizing to unseen queries. Adding 6 graph computation tools, the LLM selectively adopts them for exactly the query categories where traversal fails. We also identify a measurement gap: entity-level F1 systematically underscores structural queries where comprehensive answers are correct.
Existing LLM-driven knowledge graph (KG) construction methods predominantly employ stateless batch processing pipelines, exhibiting structural deficiencies in cross-chunk semantic relation capture, entity disambiguation, and construction process interpretability. These limitations undermine KG quality, retrieval precision, and deployment trust in high-stakes domains. We propose RAGA (Reading And Graph-building Agent), an LLM-based autonomous KG construction and retrieval fusion framework. RAGA provides an atomic toolset supporting full KG lifecycle CRUD operations and embeds a Read-Search-Verify-Construct cognitive constraint into a ReAct tool loop. A KG-vector synchronization mechanism enables hybrid symbolic-vector retrieval, while evidence-anchored verification links every knowledge entry to its source text for auditable provenance. Preliminary experiments on a subset of the QASPER scientific QA dataset indicate that RAGA's fusion retrieval outperforms zero-shot baselines, with KG integration providing measurable gains in both answer and evidence quality. The framework design and experimental baseline serve as a reference for agent-driven autonomous KG construction.