feat: implement multi-hop pathway traversal for deeper mechanistic reasoning#153
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bhavyakeerthi3 wants to merge 7 commits intoreactome:mainfrom
Open
feat: implement multi-hop pathway traversal for deeper mechanistic reasoning#153bhavyakeerthi3 wants to merge 7 commits intoreactome:mainfrom
bhavyakeerthi3 wants to merge 7 commits intoreactome:mainfrom
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…y data between nodes Without this field, LangGraph silently drops the topology data returned by identify_flow() before verify_mechanism() can read it, making the entire topological flow reasoning feature a no-op in production. Also adds a regression test (test_flow_context_in_state) to ensure the field is never accidentally removed.
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Fixes #152
Description
This PR implements recursive traversal in
ReactomeTopologyTool. Previously the tool fetched only immediate local context direct inputs, outputs, and one level of preceding events. This enhancement allows the agent to follow both causal and hierarchical links recursively, providing significantly deeper mechanistic context.Changes
get_flow_contextto follow multi-step hops through the Reactome graphhasEvent(Pathway → Sub-segment) andprecedingEvent(Reaction → Upstream trigger)max_depth=2default with per-level breadth cap of 3 events — balances context richness against LLM window limitsImpact
The agent can now answer complex process-oriented queries like "What triggers this cascade?" by tracing causal flow across multiple hops in the Reactome pathway network — rather than seeing only the immediate reaction context.
Verification
R-HSA-109581) correctly expanded into sub-pathwaysR-HSA-111452Files Affected
src/tools/reactome_topology.pytests/test_flow_reasoning.py