Identifying chemical–disease relations (CDR) from biomedical literature could improve chemical safety and toxicity studies. This article proposes a novel syntactic and semantic information exploitation method for CDR extraction. The proposed method consists of a feature-based model, a tree kernel-based model and a neural network model. The feature-based model exploits lexical features, the tree kernel-based model captures syntactic structure features, and the neural network model generates semantic representations. The motivation of our method is to fully utilize the nice properties of the three models to explore diverse information for CDR extraction. Experiments on the BioCreative V CDR dataset show that the three models are all effective for CDR extraction, and their combination could further improve extraction performance. Database URL: http://www.biocreative.org/resources/corpora/biocreative-v-cdr-corpus/.

The sentiment classification performance relies on high-quality sentiment resources. However, these resources are imbalanced in different languages. Cross-language sentiment classification (CLSC) can leverage the rich resources in one language (source language) for sentiment classification in a resource-scarce language (target language). Bilingual embeddings could eliminate the semantic gap between two languages for CLSC, but ignore the sentiment information of text. This paper proposes an approach to learning bilingual sentiment word embeddings (BSWE) for English-Chinese CLSC. The proposed B-SWE incorporate sentiment information of text into bilingual embeddings. Furthermore, we can learn high-quality BSWE by simply employing labeled corpora and their translations, without relying on largescale parallel corpora. Experiments on NLP&CC 2013 CLSC dataset show that our approach outperforms the state-of-theart systems.

Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot make full use of the prior knowledge in knowledge bases (KB). KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in PPI extraction. This paper proposes a knowledge-aware attention network (KAN) to fuse prior knowledge about proteinprotein pairs and context information for PPI extraction. The proposed model first adopts a diagonal-disabled multi-head attention mechanism to encode context sequence along with knowledge representations learned from KB. Then a novel multi-dimensional attention mechanism is used to select the features that can best describe the encoded context. Experiment results on the BioCreative VI PPI dataset show that the proposed approach could acquire knowledge-aware dependencies between different words in a sequence and lead to a new state-of-the-art performance.

Chemical-disease relation (CDR) extraction is significantly important to various areas of biomedical research and health care. Nowadays, many large-scale biomedical knowledge bases (KBs) containing triples about entity pairs and their relations have been built. KBs are important resources for biomedical relation extraction. However, previous research pays little attention to prior knowledge. In addition, the dependency tree contains important syntactic and semantic information, which helps to improve relation extraction. So how to effectively use it is also worth studying. In this paper, we propose a novel convolutional attention network (CAN) for CDR extraction. Firstly, we extract the shortest dependency path (SDP) between chemical and disease pairs in a sentence, which includes a sequence of words, dependency directions, and dependency relation tags. Then the convolution operations are performed on the SDP to produce deep semantic dependency features. After that, an attention mechanism is employed to learn the importance/weight of each semantic dependency vector related to knowledge representations learned from KBs. Finally, in order to combine dependency information and prior knowledge, the concatenation of weighted semantic dependency representations and knowledge representations is fed to the softmax layer for classification. Experiments on the BioCreative V CDR dataset show that our method achieves comparable performance with the state-of-the-art systems, and both dependency information and prior knowledge play important roles in CDR extraction task.

Document-level Relation Extraction (RE) is particularly challenging due to complex semantic interactions among multiple entities in a document. Among exiting approaches, Graph Convolutional Networks (GCN) is one of the most effective approaches for document-level RE. However, traditional GCN simply takes word nodes and adjacency matrix to represent graphs, which is difficult to establish direct connections between distant entity pairs. In this paper, we propose Global Context-enhanced Graph Convolutional Networks (GCGCN), a novel model which is composed of entities as nodes and context of entity pairs as edges between nodes to capture rich global context information of entities in a document. Two hierarchical blocks, Context-aware Attention Guided Graph Convolution (CAGGC) for partially connected graphs and Multi-head Attention Guided Graph Convolution (MAGGC) for fully connected graphs, could take progressively more global context into account. Meantime, we leverage a large-scale distantly supervised dataset to pre-train a GCGCN model with curriculum learning, which is then fine-tuned on the human-annotated dataset for further improving document-level RE performance. The experimental results on DocRED show that our model could effectively capture rich global context information in the document, leading to a state-of-the-art result.