# Structured Extraction of Real World Medical Knowledge using LLMs for Summarization and Search

arXiv: https://arxiv.org/abs/2412.15256 · HTML: https://mlsanity.com/paper/2412.15256/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 46 references that are in the map.
- First posted on arXiv 16 Dec 2024.

## Builds on (most cited first, 16 of 16)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [On Faithfulness and Factuality in Abstractive Summarization](https://mlsanity.com/paper/2005.00661/) (2020)
- [Knowledge Graphs](https://mlsanity.com/paper/2003.02320/) (2020)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [mGTE: Generalized Long-Context Text Representation and Reranking Models for Multilingual Text Retrieval](https://mlsanity.com/paper/2407.19669/) (2024)
- [Large Language Models are Few-Shot Clinical Information Extractors](https://mlsanity.com/paper/2205.12689/) (2022)
- [HelpSteer2-Preference: Complementing Ratings with Preferences](https://mlsanity.com/paper/2410.01257/) (2024)
- [Graph-constrained Reasoning: Faithful Reasoning on Knowledge Graphs with Large Language Models](https://mlsanity.com/paper/2410.13080/) (2024)
- [Large Language Models for Biomedical Knowledge Graph Construction: Information extraction from EMR notes](https://mlsanity.com/paper/2301.12473/) (2023)
- [PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology](https://mlsanity.com/paper/2009.08478/) (2020)

## Built on by (most cited first, 3 of 3)

- [Efficient Multi-Hop Question Answering over Knowledge Graphs via LLM Planning and Embedding-Guided Search](https://mlsanity.com/paper/2511.19648/) (2025)
- [Conformal Prediction for Risk-Controlled Medical Entity Extraction Across Clinical Domains](https://mlsanity.com/paper/2603.00924/) (2026)
- [From Patient Consultations to Graphs: Leveraging LLMs for Patient Journey Knowledge Graph Construction](https://mlsanity.com/paper/2503.16533/) (2025)

## Abstract (arXiv)

Creation and curation of knowledge graphs can accelerate disease discovery and analysis in real-world data. While disease ontologies aid in biological data annotation, codified categories (SNOMED-CT, ICD10, CPT) may not capture patient condition nuances or rare diseases. Multiple disease definitions across data sources complicate ontology mapping and disease clustering. We propose creating patient knowledge graphs using large language model extraction techniques, allowing data extraction via natural language rather than rigid ontological hierarchies. Our method maps to existing ontologies (MeSH, SNOMED-CT, RxNORM, HPO) to ground extracted entities. Using a large ambulatory care EHR database with 33.6M patients, we demonstrate our method through the patient search for Dravet syndrome, which received ICD10 recognition in October 2020. We describe our construction of patient-specific knowledge graphs and symptom-based patient searches. Using confirmed Dravet syndrome ICD10 codes as ground truth, we employ LLM-based entity extraction to characterize patients in grounded ontologies. We then apply this method to identify Beta-propeller protein-associated neurodegeneration (BPAN) patients, demonstrating real-world discovery where no ground truth exists.