# From Document Silos to Process Intelligence: A Multi-Layer Knowledge Graph for CMC Process Development

arXiv: https://arxiv.org/abs/2609.11493 · HTML: https://mlsanity.com/paper/2609.11493/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 11 of its 38 references that are in the map.
- First posted on arXiv 10 Sep 2026.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 11 of 11)

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [Retrieval-Augmented Generation with Knowledge Graphs for Customer Service Question Answering](https://mlsanity.com/paper/2404.17723/) (2024)
- [Docling: An Efficient Open-Source Toolkit for AI-driven Document Conversion](https://mlsanity.com/paper/2501.17887/) (2025)
- [A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective](https://mlsanity.com/paper/2102.10062/) (2021)
- [Docling Technical Report](https://mlsanity.com/paper/2408.09869/) (2024)
- [Accelerating Scientific Discovery with Generative Knowledge Extraction, Graph-Based Representation, and Multimodal Intelligent Graph Reasoning](https://mlsanity.com/paper/2403.11996/) (2024)
- [Benchmarking Retrieval-Augmented Generation for Chemistry](https://mlsanity.com/paper/2505.07671/) (2025)
- [ODKE+: Ontology-Guided Open-Domain Knowledge Extraction with LLMs](https://mlsanity.com/paper/2509.04696/) (2025)

## Abstract (arXiv)

Chemistry, Manufacturing and Controls (CMC) process development generates an enormous body of technical information across a multi-stage, knowledge-intensive continuum from drug discovery to commercial manufacturing. This knowledge is traditionally fragmented across functions and heterogeneous formats, causing traceability gaps and significant knowledge-management costs during technology transfer and regulatory filing. We present a modular agentic-AI platform that converts a heterogeneous corpus of process-development documents into a queryable, dual-layer knowledge graph. A base knowledge layer builds a lexical graph with a Document-Section-Chunk hierarchy through lossless ingestion of digital, scanned, handwritten, and multilingual documents, while an intelligence layer extracts ontology-aligned entities and bridges cross-document concepts through a provenance-anchored domain graph. LLM agents operate across both layers, selecting the retrieval path best suited to each question. We evaluate the lexical layer with a novel three-tier protocol measuring the deployment-fidelity of a retrieval-augmented generation (RAG) system on proprietary data, demonstrated on 505 questions curated from 38 development reports of a Sanofi small-molecule program. Tier-1 multiple-choice accuracy of 95% signals strong platform reliability; the stricter Tier-2 LLM-judge pass rate of 85%, which degrades on comparative and corpus-wide questions, reveals a failure taxonomy that Tier-1 accuracy alone fails to capture. A router agent selects between layers according to question type. We anticipate this protocol will enable future designers of agentic platforms to assess their systems against nonpublic databases, and that graph-based architectures will see broader adoption in pharma as a means of transforming fragmented document repositories into structured process intelligence.