Issues

• Answer length: the prompt instructs exhaustiveness, and the document budget should be per-caller

  reactome/reactome_chatbot#172 · Filter by author adamjohnwright opened on Sep 4, 2026
  2

• Retrieval: replace SelfQueryRetriever with a plain semantic retriever?

  reactome/reactome_chatbot#171 · Filter by author adamjohnwright opened on Sep 4, 2026
  1

• Retrieval: BM25 and vector results are concatenated, not fused

  reactome/reactome_chatbot#170 · Filter by author adamjohnwright opened on Sep 4, 2026
  1

• Retrieval: golden-output harness for judging retriever changes

  reactome/reactome_chatbot#168 · Filter by author adamjohnwright opened on Sep 4, 2026

• Multiple failures with small LLM (Ollama)

  reactome/reactome_chatbot#160 · Filter by author Ehsanstp opened on Apr 26, 2026
  1

• Bug: asyncio.run() in __del__ causes RuntimeError crash in production

  reactome/reactome_chatbot#154 · Filter by author imnishantdixit opened on Mar 15, 2026

• feat: implement multi-hop pathway traversal for deeper mechanistic reasoning

  reactome/reactome_chatbot#152 · Filter by author bhavyakeerthi3 opened on Mar 15, 2026

• bug: AgentGraph hardcodes LLM and embedding models — ignores YAML configuration

  reactome/reactome_chatbot#148 · Filter by author bhavyakeerthi3 opened on Mar 15, 2026

• bug: asyncio.run() inside AgentGraph destructor triggers RuntimeError and leaks connections

  reactome/reactome_chatbot#146 · Filter by author bhavyakeerthi3 opened on Mar 14, 2026

• bug: flow_context key missing from CrossDatabaseState — topology data silently lost between nodes

  reactome/reactome_chatbot#145 · Filter by author bhavyakeerthi3 opened on Mar 14, 2026

• feat: support causal chain queries for mechanistic biological reasoning

  reactome/reactome_chatbot#143 · Filter by author bhavyakeerthi3 opened on Mar 13, 2026

• feat: route questions to RAG or MCP tools based on query intent

  reactome/reactome_chatbot#141 · Filter by author GovindhKishore opened on Mar 12, 2026

• fix(retriever): HybridRetriever passes unlimited documents to LLM with no token budget

  reactome/reactome_chatbot#138 · Filter by author GovindhKishore opened on Mar 10, 2026
  2

• feat: integrate Reactome MCP tools into LangGraph agent via LangChain tool wrappers

  reactome/reactome_chatbot#136 · Filter by author GovindhKishore opened on Mar 10, 2026

• bug: Missing automated test suite causes undetected regressions across critical modules

  reactome/reactome_chatbot#134 · Filter by author bhavyakeerthi3 opened on Mar 10, 2026

• feat: HybridRetriever passes noisy, low-relevance documents to the LLM

  reactome/reactome_chatbot#132 · Filter by author bhavyakeerthi3 opened on Mar 9, 2026

• bug: Mutable default arguments in Config methods may cause cross-session state leakage

  reactome/reactome_chatbot#130 · Filter by author AaryanCode69 opened on Mar 8, 2026

• fix: evaluator.py contains hard-coded absolute paths, making it non-portable for contributors

  reactome/reactome_chatbot#128 · Filter by author bhavyakeerthi3 opened on Mar 8, 2026
  2

• Add minimal Python MCP client for reactome-mcp integration

  reactome/reactome_chatbot#126 · Filter by author GovindhKishore opened on Mar 7, 2026

• bug: missing commas in Alliance column lists cause silent string concatenation

  reactome/reactome_chatbot#118 · Filter by author AaryanCode69 opened on Mar 4, 2026

• [Feature] Reduce Response Verbosity by Improving System Prompt Precision

  reactome/reactome_chatbot#117 · Filter by author GovindhKishore opened on Mar 4, 2026
  3

• [Feature] Improve retrieval quality by adding reranking layer to HybridRetriever

  reactome/reactome_chatbot#115 · Filter by author GovindhKishore opened on Mar 1, 2026
  1

• Application crashes with AttributeError when embeddings are missing (S3 download returns 403)

  reactome/reactome_chatbot#114 · Filter by author AaryanCode69 opened on Mar 1, 2026
  1

• Sequential Preprocessing Creates Unnecessary Latency

  reactome/reactome_chatbot#110 · Filter by author imnishantdixit opened on Feb 28, 2026

• refactor: make evaluator paths configurable via CLI arguments

  reactome/reactome_chatbot#109 · Filter by author AaryanCode69 opened on Feb 28, 2026