A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories

A lot of scientific literature is unstructured, which makes extracting information for biomedical databases difficult. Hong and colleagues show that a distant supervision approach, using latent tree learning and recurrent units, can extract drug-target interactions from literature that were previously unknown. Knowledge about the relations between biomedical entities (such as drugs and targets) is widely distributed in more than 30 million research articles and consistently plays an important role in the development of biomedical science. In this work, we propose a novel machine learning framework, named BERE, for automatically extracting biomedical relations from large-scale literature repositories. BERE uses a hybrid encoding network to better represent each sentence from both semantic and syntactic aspects, and employs a feature aggregation network to make predictions after considering all relevant statements. More importantly, BERE can also be trained without any human annotation via a distant supervision technique. Through extensive tests, BERE has demonstrated promising performance in extracting biomedical relations, and can also find meaningful relations that were not reported in existing databases, thus providing useful hints to guide wet-lab experiments and advance the biological knowledge discovery process.