Information Extraction from Biomedical Texts

Recently, there has been much effort in making biomedical knowledge, typically stored in scientific articles, more accessible and interoperable. As a matter of fact, the unstructured nature of such texts makes it difficult to apply knowledge discovery and inference techniques. Annotating information units with semantic information in these texts is the first step to make the knowledge machine-analyzable. In this work, we first study methods for automatic information extraction from natural language text. Then we discuss the main benefits and disadvantages of the state-of-art information extraction systems and, as a result of this, we adopt a machine learning approach to automatically learn extraction patterns in our experiments. Unfortunately, machine learning techniques often require a huge amount of training data, which can be sometimes laborious to gather. In order to face up to this tedious problem, we investigate the concept of weakly supervised or bootstrapping techniques. Finally, we show in our experiments that our machine learning methods performed reasonably well and significantly better than the baseline. Moreover, in the weakly supervised learning task we were able to substantially bring down the amount of labeled data needed for training of the extraction system