K. Vijay‐Shanker

Mehmet Efruz Karabulut, K. Vijay-Shanker, Yifan Peng

Identifying the relations between chemicals and proteins is an important text mining task. BioCreative VII track 1 DrugProt task aims to promote the development and evaluation of systems that can automatically detect relations between chemical compounds/drugs and genes/proteins in PubMed abstracts. In this paper, we describe our submission, which is an ensemble system, including multiple BERT-based language models. We combine the outputs of individual models using majority voting and multilayer perceptron. Our system obtained 0.7708 in precision and 0.7770 in recall, for an F1 score of 0.7739, demonstrating the effectiveness of using ensembles of BERT-based language models for automatically detecting relations between chemicals and proteins. Our code is available at https://github.com/bionlplab/drugprot_bcvii.

Peng Su, Yifan Peng, K. Vijay-Shanker

Contrastive learning has been used to learn a high-quality representation of the image in computer vision. However, contrastive learning is not widely utilized in natural language processing due to the lack of a general method of data augmentation for text data. In this work, we explore the method of employing contrastive learning to improve the text representation from the BERT model for relation extraction. The key knob of our framework is a unique contrastive pre-training step tailored for the relation extraction tasks by seamlessly integrating linguistic knowledge into the data augmentation. Furthermore, we investigate how large-scale data constructed from the external knowledge bases can enhance the generality of contrastive pre-training of BERT. The experimental results on three relation extraction benchmark datasets demonstrate that our method can improve the BERT model representation and achieve state-of-the-art performance. In addition, we explore the interpretability of models by showing that BERT with contrastive pre-training relies more on rationales for prediction. Our code and data are publicly available at: https://github.com/udel-biotm-lab/BERT-CLRE.

Peng Su, K. Vijay-Shanker

With the explosive growth of biomedical literature, designing automatic tools to extract information from the literature has great significance in biomedical research. Recently, transformer-based BERT models adapted to the biomedical domain have produced leading results. However, all the existing BERT models for relation classification only utilize partial knowledge from the last layer. In this paper, we will investigate the method of utilizing the entire layer in the fine-tuning process of BERT model. To the best of our knowledge, we are the first to explore this method. The experimental results illustrate that our method improves the BERT model performance and outperforms the state-of-the-art methods on three benchmark datasets for different relation extraction tasks. In addition, further analysis indicates that the key knowledge about the relations can be learned from the last layer of BERT model.

Peng Su, K. Vijay-Shanker

Adversarial training is a technique of improving model performance by involving adversarial examples in the training process. In this paper, we investigate adversarial training with multiple adversarial examples to benefit the relation extraction task. We also apply adversarial training technique in semi-supervised scenarios to utilize unlabeled data. The evaluation results on protein-protein interaction and protein subcellular localization task illustrate adversarial training provides improvement on the supervised model, and is also effective on involving unlabeled data in the semi-supervised training case. In addition, our method achieves state-of-the-art performance on two benchmarking datasets.

Michael Bloodgood, K. Vijay-Shanker

Actively sampled data can have very different characteristics than passively sampled data. Therefore, it's promising to investigate using different inference procedures during AL than are used during passive learning (PL). This general idea is explored in detail for the focused case of AL with cost-weighted SVMs for imbalanced data, a situation that arises for many HLT tasks. The key idea behind the proposed InitPA method for addressing imbalance is to base cost models during AL on an estimate of overall corpus imbalance computed via a small unbiased sample rather than the imbalance in the labeled training data, which is the leading method used during PL.