Critic agent for hypothesis generation: exclude 1-hop GWAS genes + dedup hypotheses

[HyunjunA]

Goal

Add a critic step to hypothesis generation that (1) prevents the model from leaning on already-known GWAS genes, and (2) guarantees no duplicate hypotheses are produced.

Tasks

• Exclude 1-hop GWAS hit genes from the model. Genes that are direct (1-hop) GWAS hits for the target disease must NOT be used as model features, so the pipeline does not just rediscover known associations and is pushed toward novel candidates.
• Critic check for duplicate hypotheses — remove duplicates. Implemented as a standalone public:hypothesis-dedup skill: exact match on normalized text + cosine similarity (GET /api/hypotheses/similar, threshold 0.85) against both already-stored and in-batch hypotheses; duplicates are dropped before storage. Wired into the hypothesize stage.

Notes

• Dedup currently runs as an agent self-check inside the hypothesize stage; it could be promoted to a dedicated critic stage later.

[mikeherv]

Push the logic (For the Critique agent, currently hard-coded - allow the user to have options to use the critique agent). Make it optional, default if OFF.

[mikeherv]

These should be in a PostEvaluation agent - (after Test and Validate -> Veredict (Critique agent) - then execute the 2 items below:
Currently hard-coded in the orchestrator (as the Analysis agent) :

• Assess the verdict_results.json and run api calls to the backend to update the hypothesis table database. (Currently hardcoded in the Orchestrator).
• Update the profile.md and insights.md with whatever important nuance was observed in the report.md from the job