The document discusses the use of LLM-based chatbots in life sciences, highlighting the challenges such as knowledge cutoffs and inaccuracies in generating queries. It emphasizes the role of biomedical knowledge graphs in enhancing information retrieval through nodes and relationships defined by existing ontologies. Additionally, it introduces tools for generating Cypher queries to improve the interaction with biomedical data, providing examples and access to a questions repository.

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GraphRAG for Life Science
By Tomaz Bratanic

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

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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

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● 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

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Demo time

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Questions
Repository: https://github.com/tomasonjo/clinical-agent
Slides:
Email: tomaz.bratanic@neo4j.com
LinkedIn: https://www.linkedin.com/in/tomaz-bratanic-a58891127/