GraphRAG for LifeSciences Hands-On with the Clinical Knowledge Graph

Tomaz Bratanic
Graph ML and GenAI Expert - Neo4j

1. © 2022 Neo4j, Inc. All rights reserved. 1
GraphRAG for Life Science


By Tomaz Bratanic

2. 2
LLM-based chatbots
Using the retrieval-augmented generation

3. © 2022 Neo4j, Inc. All rights reserved. 3
LLMs are great, but:
•Knowledge
cutoff date
•Hallucinations
•Lack of
information
source
•Lack of
domain-specific
or private
information

4. Retrieval-augmented generation (in-context passing) flow

5. Chat with your PDF - Vector similarity search

7. © 2022 Neo4j, Inc. All rights reserved. 7
●Consists of nodes
and relationships
●Nodes are used to
represent entities,
concepts, and more
●Relationships
describe the context
and how it is
connected to other
nodes

Biomedical knowledge graph

8. Constructing a biomedical knowledge graph
Using existing biomedical ontologies combined with NLP extraction

9. Graph RAG
MATCH(g:Gene)
WHERE g.id = $gene
MATCH (g)-[r:VARIANT_FOUND_IN_GENE ]-(v:Known_variant)
WHERE NOT v.clinical_relevance = '-' AND NOT v.disease = '-'
RETURN g.id as gene, v.disease AS disease,
v.pvariant_id AS variant_id, v.clinical_relevance as relevance
LIMIT 20

10. Generating Cypher with LLM lack accuracy and robustness

11. Solution: Agentic tools with predefined Cypher templates

12. Providing agent with tools

13. Agent tool definition
MATCH (p:Protein)-[r:ASSOCIATED_WITH]-(d:Disease)
WHERE d.name CONTAINS $disease
OPTIONAL MATCH
(p)-[r2:ASSOCIATED_WITH]->(t:Tissue)
RETURN d.name as disease, p.name as drug_target,
t.name as expressed_tissue
LIMIT 10
class DiseaseTissueInput(BaseModel):
disease: str = Field(description= "disease mentioned in
the question")


class DiseaseTissueTool(BaseTool):
name = "DiseaseTissue"
description = "useful for when you need to find tissues
where proteins with a specific disease are expressed"
Parameterized Cypher
statement


Parameter description
Tool description

14. 14
Demo time
● What are associated foods with cancer?
● What are known clinically relevant gene variants for gene CLN3?
● In which tissues are expressed proteins associated with prostate carcinoma?

15. 15
Questions
Repository: https://github.com/tomasonjo/clinical-agent
Slides:
https://www.slideshare.net/slideshow/graphrag-for-life-science-to-increase-llm-acc
uracy/269616483
Email: [email protected]
LinkedIn: https://www.linkedin.com/in/tomaz-bratanic-a58891127/