SciNER: A Novel Scientific Named Entity Recognizing Framework

There is an increasing number of scientific publications produced by the booming science community. It is very important for automatic scientific analysis to extract entities such as tasks and methods from unstructured scientific publications. At present, the span-based methods are the best way for scientific NER tasks, which usually generate a few entities by searching hundreds of candidate spans in a sentence. However, these existing methods have a few drawbacks. Firstly, the span extractor obtains more negative samples than positive samples, and thus it makes the input extremely imbalance. Secondly, the pruner has no predictive ability at the beginning of the joint training process in an end-to-end model. To tackle the above problem, in this paper, we propose a novel scientific named entity recognizing pipeline framework, called SciNER. Specifically, in the first stage, there is a pruner to filter out most illegal entities. The span extractor in the pruner performs under-sampling to balance the positive and negative samples. In the second stage, the entity recognizer is trained by the pruned spans. Extensive experiments demonstrate that SciNER outperforms state-of-the-art baselines on several datasets in both computer science and biomedical domains (Code is available at: https://github.com/ethan-yt/sciner).