AssayFormer
Transformer encoder that reads a screen description and the genes tested so far with their hit labels and scores every candidate gene for the next batch.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. 23 linked records have results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- AssayFormer (BPMF embeddings, supervised then GRPO) (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, GenePT-PCA embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, GenePT-PCA embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, K562-PCA embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, K562-PCA embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, MF embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, MF embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, MF-Sphere embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, MF-Sphere embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, BPMF embeddings, GRPO, no screen description (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, random embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, random embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, SVD embeddings, supervised then GRPO (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayFormer, SVD embeddings, supervised only (AssayBench-Loop) Configuration · configuration of this method · 1 evaluation · 10 results
- AssayLoop: AssayLLM to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
- AssayLoop: Handoff-trained AssayLLM to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
- AssayLoop: Gemini-3.1-Pro to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
- AssayLoop: GLM-5.1 to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
- AssayLoop: GPT-5.5 to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
- AssayLoop: GPT-5.6 Sol to AssayFormer (AssayBench-Loop) Configuration · uses this model · 1 evaluation · 10 results
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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How it works, versions and access
Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this method. Consult the linked sources and evaluation records below.
Evidence
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Evidence table
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens · Original source · arXiv:2609.11877 version 1, submitted 2026-09-10; not peer reviewed
Technical metadata and extraction receipts
Stable ID: ucpheno-20261022-method-assayformer
- areas
- cells-tissues
- contexts
- research
- method types
- specialist
- reported name
- AssayFormer
- entity level
- method
- source locator
- Section 2.2; Figure 3B-C; Methods 4.4-4.5
- missing metadata
- version: reason: inapplicable; note: Family record; settings are on configurations
Related records
- subject: training (assayformer-training)
- configuration of: AssayFormer (BPMF embeddings, supervised then GRPO) (AssayBench-Loop)
- configuration of: AssayFormer, BPMF embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, BPMF embeddings, supervised only, no screen description (AssayBench-Loop)
- configuration of: AssayFormer, BPMF embeddings, GRPO with terminal-EF reward (AssayBench-Loop)
- configuration of: AssayFormer, GenePT-PCA embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, GenePT-PCA embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, K562-PCA embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, K562-PCA embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, MF embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, MF embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, MF-Sphere embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, MF-Sphere embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, BPMF embeddings, GRPO, no screen description (AssayBench-Loop)
- configuration of: AssayFormer, random embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, random embeddings, supervised only (AssayBench-Loop)
- configuration of: AssayFormer, SVD embeddings, supervised then GRPO (AssayBench-Loop)
- configuration of: AssayFormer, SVD embeddings, supervised only (AssayBench-Loop)
- uses model: AssayLoop: AssayLLM to AssayFormer (AssayBench-Loop)
- uses model: AssayLoop: Handoff-trained AssayLLM to AssayFormer (AssayBench-Loop)
- uses model: AssayLoop: Gemini-3.1-Pro to AssayFormer (AssayBench-Loop)
- uses model: AssayLoop: GLM-5.1 to AssayFormer (AssayBench-Loop)
- uses model: AssayLoop: GPT-5.5 to AssayFormer (AssayBench-Loop)
- uses model: AssayLoop: GPT-5.6 Sol to AssayFormer (AssayBench-Loop)