[BUG] The pass "eliminate_shape_gather" causes output mismatch

[BUG] The pass "eliminate_shape_gather" causes output mismatch

Issue
Running the single pass eliminate_shape_gather with onnxoptimizer 0.4.2 changes numerical outputs.

Environment

• Ubuntu 20.04
• Python 3.10
• onnx==1.19.0
• onnxruntime==1.23.2
• onnxoptimizer==0.4.2(latest)

Repro steps (run from this folder)

eliminate_shape_op_repro.tar.gz

1. Create a Python environment (Python 3.10) and install dependencies:

python3 -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -r requirements.txt

2. Optimize a case with only eliminate_shape_gather (writes model.opt.onnx next to model.onnx):

• python optimize_model.py --case ./case_03140_seed45116679

3. Differential test original and optimized models with the same oracle inputs (ORT graph optimization disabled):

• python diff_test.py --case ./case_03140_seed45116679

Expected
eliminate_shape_gather should be semantics-preserving. Applying this pass alone should not change any output values.

Differential Test Output Details

1. case_03140_seed45116679 — mismatch; output[14] max_abs=4.022e+04 max_rel=4.022e+12, output[15] max_abs=5.190e+02 max_rel=5.120e+10; overall mismatch.
2. case_05413_seed63116566 — mismatch; output[12] max_abs=4.572e+10 max_rel=1.322e+11; overall mismatch.

Case: case_03140_seed45116679 (ORT graph optimizations disabled)
  output[14]: max_abs=4.022e+04, max_rel=4.022e+12, shape=(1, 21, 24)
  output[15]: max_abs=5.190e+02, max_rel=5.120e+10, shape=(32, 21, 24)
Overall: max_abs=4.022e+04, max_rel=4.022e+12


Case: case_05413_seed63116566 (ORT graph optimizations disabled)
  output[12]: max_abs=4.572e+10, max_rel=1.322e+11, shape=(44, 1, 52, 14, 1)
Overall: max_abs=4.572e+10, max_rel=1.322e+11

Attachments

• requirements.txt
• optimize_model.py
• diff_test.py (runs original and optimized with same oracle inputs; ORT graph optimizations disabled)
• run_optimized_model.py (executes optimized model with oracle inputs)
• case_03140_seed45116679/,case_05413_seed63116566/, (original models and oracle inputs)

Start by running optimize_model.py and diff_test.py for both attached cases with ORT graph optimizations disabled, then inspect run_optimized_model.py and the supplied models and oracle inputs to isolate the eliminate_shape_gather transformation. Done means both optimized models produce the same output values as the originals in the differential tests.