Key error in predict_salient_mentions.py

[viswavi]

I trained the baseline SciREX model, and then tried to make predictions for it, but ran into a problem in the step to predict salient mentions. When I tried running:

python scirex/predictors/predict_salient_mentions.py $scirex_archive $test_output_folder/ner_predictions.jsonl $test_output_folder/salient_mentions_predictions.jsonl $cuda_device

I got the error:

  span_ix = span_mask.view(-1).nonzero().squeeze(1).long()
36it [00:02, 15.88it/s]
Traceback (most recent call last):
  File "scirex/predictors/predict_salient_mentions.py", line 92, in <module>
    main()
  File "scirex/predictors/predict_salient_mentions.py", line 88, in main
    predict(archive_folder, test_file, output_file, cuda_device)
  File "scirex/predictors/predict_salient_mentions.py", line 57, in predict
    metadata = output_res['metadata']
KeyError: 'metadata'

It seems that one in every so often, the output of the salient mention prediction decoder is missing the metadata field.

As a stopgap solution, I'm just skipping batches with this issue, but am concerned that I'll accidentally bias my evaluation somehow by doing this.

[successar]

Did you reduce the batch size to train the model?

[viswavi]

I did. Reduced batch size to 2 (but training 19 epochs still completed after 3 days without complaint)

[successar]

This is fine. The reason that output doesn't contain any metadata is because the input doesn't actually have any predicted spans, so you can safely ignore them.

[Laxmaan]

I'm getting the same error later on in predict_n_ary_relations.py. I used a batch size of 4 for training.
I implemented the fix for the salient mentions as shown above but I run into an error at this stage as well.

Traceback (most recent call last): File "scirex/predictors/predict_n_ary_relations.py", line 109, in <module> predict(argv[1], argv[2], argv[3], argv[4], int(argv[5])) File "scirex/predictors/predict_n_ary_relations.py", line 77, in predict output_res = model.decode_relations(batch) File "/storage/home/lpb5347/scratch/scirex/SciREX/scirex/models/scirex_model.py", line 385, in decode_relations res["n_ary_relation"] = self._cluster_n_ary_relation.decode(output_n_ary_relation) File "/storage/home/lpb5347/scratch/scirex/SciREX/scirex/models/relations/entity_relation.py", line 211, in decode "metadata" : output_dict['metadata']

[jeremyadamsfisher]

Is there a resolution to this? I'm struggling with this issue in predict_n_ary_relations.py with a batch size of 1

[viswavi]

@jeremyadamsfisher a stopgap resolution is to just skip these documents here (here's how I did it in my branch)

However, even with this fix, this gives quite different results on the relation prediction metrics for "End-to-End (gold salient clustering)", which may be an issue if you care about this metric. I think the code does not currently match their paper for this particular evaluation.

With this fix, here's the results that I was able to reproduce vs the originally reported results:

[viswavi]

On an unrelated note, I added a few metrics (particularly for relation extraction) as well as significance testing scripts in my branch here: https://github.com/viswavi/SciREX, if you find it useful.

[jeremyadamsfisher]

Thanks @viswavi!