EpistasisLab / EpistasisLab/EcoXAI

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

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#6 4 comments 0 reactions 1 assignee Claimed by @HyunjunA View on GitHub
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Description

## 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
- [x] **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.
- [x] **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.

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