confidence-estimation

name	confidence-estimation
description	Add, run, or debug uncertainty and confidence estimation in the agent_qwen workflow. Use when integrating structure_recongnition/confidence_estimation.py, generating per-atom/lattice confidence reports, or adding confidence artifacts to agent_qwen harness outputs.

Confidence Estimation

Use confidence_estimation_tool for uncertainty quantification in the agent_qwen workflow.

Runtime Surface

• Wrapper: agent_qwen/runtime_skills.py::_run_confidence
• Source implementation: structure_recongnition/confidence_estimation.py
• Harness insertion point: after stem2cif_tool in classic workflow, after direct_reconstruct_tool in direct workflow

Inputs

• image_path: denoised STEM image, usually recon_png
• elements: element symbols from user or template matching
• pixel_size: default 0.10
• output: JSON report path

Outputs

Return and preserve:

• confidence_report
• global_confidence
• summary

Treat this as an analysis artifact, not as a model checkpoint.