To interpret the genetic profile present in a patient sample, it is necessary to know which mutations have important roles in the development of the corresponding cancer type. Named entity recognition is a core step in the text mining pipeline which facilitates mining valuable cancer information from the scientific literature. However, due to the scarcity of related datasets, previous NER attempts in this domain either suffer from low performance when deep learning based models are deployed, or they apply feature based machine learning models or rule based models to tackle this problem, which requires intensive efforts from domain experts, and limit the model generalization capability. In this paper, we propose EPICURE, an ensemble pre trained model equipped with a conditional random field pattern layer and a span prediction pattern layer to extract cancer mutations from text. We also adopt a data augmentation strategy to expand our training set from multiple datasets. Experimental results on three benchmark datasets show competitive results compared to the baseline models.

Pre-training models such as BERT have achieved great success in many natural language processing tasks. However, how to obtain better sentence representation through these pre-training models is still worthy to exploit. Previous work has shown that the anisotropy problem is an critical bottleneck for BERT-based sentence representation which hinders the model to fully utilize the underlying semantic features. Therefore, some attempts of boosting the isotropy of sentence distribution, such as flow-based model, have been applied to sentence representations and achieved some improvement. In this paper, we find that the whitening operation in traditional machine learning can similarly enhance the isotropy of sentence representations and achieve competitive results. Furthermore, the whitening technique is also capable of reducing the dimensionality of the sentence representation. Our experimental results show that it can not only achieve promising performance but also significantly reduce the storage cost and accelerate the model retrieval speed.