Inference with Finetuned BERT Model outputting odd results
## Environment info
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     Don't forget to fill out the missing fields in that output! -->

- `transformers` version: 3.5.1
- Platform: Linux-4.14.203-116.332.amzn1.x86_64-x86_64-with-glibc2.10
- Python version: 3.7.6
- PyTorch version (GPU?): 1.7.0 (True)
- Tensorflow version (GPU?): 2.3.1 (True)
- Using GPU in script?: No
- Using distributed or parallel set-up in script?: No

### Who can help
<!-- Your issue will be replied to more quickly if you can figure out the right person to tag with @
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@LysandreJik @patrickvonplaten 

Models:

- albert, bert, xlm: @LysandreJik
- blenderbot, bart, marian, pegasus, encoderdecoder,  t5: @patrickvonplaten, @patil-suraj
- longformer, reformer, transfoxl, xlnet: @patrickvonplaten
- fsmt: @stas00
- funnel: @sgugger
- gpt2: @patrickvonplaten, @LysandreJik
- rag: @patrickvonplaten, @lhoestq
- tensorflow: @jplu

Library:

- benchmarks: @patrickvonplaten
- deepspeed: @stas00
- ray/raytune: @richardliaw, @amogkam
- text generation: @patrickvonplaten
- tokenizers: @n1t0, @LysandreJik
- trainer: @sgugger
- pipelines: @LysandreJik

Documentation: @sgugger

HF projects:

- nlp datasets: [different repo](https://github.com/huggingface/nlp)
- rust tokenizers: [different repo](https://github.com/huggingface/tokenizers)

Examples:

- maintained examples (not research project or legacy): @sgugger, @patil-suraj
- research_projects/bert-loses-patience: @JetRunner
- research_projects/distillation: @VictorSanh

 -->

## Information

Model I am using (Bert, XLNet ...): Bert

The problem arises when using:
* [ ] the official example scripts: (give details below)
* [x] my own modified scripts: (give details below)

The tasks I am working on is:
* [ ] an official GLUE/SQUaD task: (give the name)
* [x] my own task or dataset: (give details below)

## To reproduce

Steps to reproduce the behavior:

1. Trained HuggingFace Transformers model BertForSequenceClassification on custom dataset with PyTorch backend.
2. Used provided convert_graph_to_onnx.py script to convert model (from saved checkpoint) to ONNX format.
3. Loaded the model with ONNXRuntime
4. Instantiated BertTokenizer.from_pretrained('bert-based-uncased') and fed in various input text to encode_plus method.
5. Fed outputs of this to the ONNXRuntime session.

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## Expected behavior

<!-- A clear and concise description of what you would expect to happen. -->

The expected behavior is that the output of sess.run on the aforementioned inputs should output an array of dimension (1, 100) (corresponding to 100 classes) with each value between 0 and 1, with all entries summing to 1. We get the correct dimension, however, we get values between about -3.04 and 7.14 (unsure what these values refer to).

Hi,

is it possible to ask this question on the [forum](https://discuss.huggingface.co/) rather than here? Since this question is a perfect use case for that.

Thank you. <|||||>This issue has been automatically marked as stale because it has not had recent activity. If you think this still needs to be addressed please comment on this thread.

Please note that issues that do not follow the [contributing guidelines](https://github.com/huggingface/transformers/blob/master/CONTRIBUTING.md) are likely to be ignored.