Problem generating predictions

Hi, Thank for resolving the previous issues, but I’m still having some problems generating predictions despite following the exact instructions in the ReadME.

After successfully installing SciREX, I followed the 4 training instructions:

    Extract the dataset files in folder tar -xvzf scirex_dataset/release_data.tar.gz --directory scirex_dataset
    Export path to scibert export BERT_BASE_FOLDER=<path-to-scibert> . This path should contain two files atleast - vocab.txt and weights.tar.gz. Download the file here https://s3-us-west-2.amazonaws.com/ai2-s2-research/scibert/pytorch_models/scibert_scivocab_uncased.tar and untar it.
    Run CUDA_DEVICE=<cuda-device-num> bash scirex/commands/train_scirex_model.sh main to train main scirex model
    Run CUDA_DEVICE=<cuda-device-num> bash scirex/commands/train_pairwise_coreference.sh main to train secondary coreference model.

However, when I tried to follow the instructions to generate the predictions

scirex_archive=outputs/pwc_outputs/experiment_scirex_full/main \
scirex_coreference_archive=outputs/pwc_outputs/experiment_pairwise_coreference/main \
cuda_device=<cuda-device-num> \
bash scirex/commands/predict_scirex_model.sh

I got an error saying that the pwc_outputs/experiment_pairwise_coreference/main doesn’t exist. I check the directory and find that instead of experiment_pairwise_coreference, there is experiment_coreference, so I change the second line of the prediction instruction to scirex_coreference_archive=outputs/pwc_outputs/experiment_coreference/main and I get the following error:

ModuleNotFoundError: No module named 'scirex'
Predicting Salient Clustering
Traceback (most recent call last):
  File "scirex/predictors/predict_salient_clusters.py", line 25, in <module>
    predict(sys.argv[1], sys.argv[2], sys.argv[3])
  File "scirex/predictors/predict_salient_clusters.py", line 5, in predict
    clusters = [json.loads(line) for line in open(clusters_file)]
FileNotFoundError: [Errno 2] No such file or directory: 'test_outputs//cluster_predictions.jsonl'
Predicitng Salient Clusters using gold clusters as filter
Traceback (most recent call last):
  File "scirex/predictors/predict_salient_clusters_using_gold.py", line 11, in <module>
    from scirex.predictors.utils import *
ModuleNotFoundError: No module named 'scirex'
Predicting Relations End-to-End
Traceback (most recent call last):
  File "scirex/predictors/predict_n_ary_relations.py", line 16, in <module>
    from scirex.predictors.utils import merge_method_subrelations
ModuleNotFoundError: No module named 'scirex'
Predicting relations End-to-End with gold cluster filtering
Traceback (most recent call last):
  File "scirex/predictors/predict_n_ary_relations.py", line 16, in <module>
    from scirex.predictors.utils import merge_method_subrelations
ModuleNotFoundError: No module named 'scirex'
Predicting Relations on gold clusters
Traceback (most recent call last):
  File "scirex/predictors/predict_n_ary_relations.py", line 16, in <module>
    from scirex.predictors.utils import merge_method_subrelations
ModuleNotFoundError: No module named 'scirex'
Evaluating on all Predicted steps
Traceback (most recent call last):
  File "scirex/evaluation_scripts/scirex_relation_evaluate.py", line 7, in <module>
    from scirex.metrics.clustering_metrics import match_predicted_clusters_to_gold
ModuleNotFoundError: No module named 'scirex'
Evaluating on all predicted steps with filtering using gold salient clusters
Traceback (most recent call last):
  File "scirex/evaluation_scripts/scirex_relation_evaluate.py", line 7, in <module>
    from scirex.metrics.clustering_metrics import match_predicted_clusters_to_gold
ModuleNotFoundError: No module named 'scirex'

Any idea how I can fix this?

[successar]

Hi

Is this the full error message ? Is the problem occurring after the first command in this file ? https://github.com/allenai/SciREX/blob/master/scirex/commands/predict_scirex_model.sh

Can you try creating a directory called “test_outputs” before running the prediction command ?

[Yichabod]

OK I created a test_output directory and it seemed to work