yuzhimanhua / Multi-BioNER

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)
https://arxiv.org/abs/1801.09851
Apache License 2.0
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Batch size & Shuffle Dataloader & Train-dev-test split & sample_num #15

Closed hantingge closed 4 years ago

hantingge commented 4 years ago

A few other questions:

  1. For the batch sizes of dataloaders, why do you use 10 for training and 50 for evaluating devel and test set?

  2. In your train_wc.py, you set shuffle=True for dataset_loader for each dataset. So when I shuffle the each dataset's dataloader, does it shuffle only at the document-level or the sentences within each document as well?

  3. Why did you merge the train and devel biomedical dataset for training? Doesn't the model overfit? I assume you have experimented training on just the train.tsv, and the F1s are lower than using merge.tsv on the test set?

  4. On line 246 and 251 in train_wc.py, what is the point of sample_num and the for loop with range(1)? (if it is always 1)

yuzhimanhua commented 4 years ago

Thanks for your interest in our work.

Q1 and Q4: Thanks for your suggestions. During parameter tuning, we wrote some code / changed some parameters and did not change them back in this final version. They will not affect the result or execution in a visible way from my perspective, but we will incorporate your suggestions in the next version.

Q2: It is a sentence-level shuffle.

Q3: This is the common practice in some previous studies. Yes, we have experimented training on just the train.tsv, and the results are lower.