ASPER: Answer Set Programming Enhanced Neural Network Models for Joint Entity-Relation Extraction

A plethora of approaches have been proposed for joint entity-relation (ER) extraction. Most of these methods largely depend on a large amount of manually annotated training data. However, manual data annotation is time consuming, labor intensive, and error prone. Human beings learn using both data (through induction) and knowledge (through deduction). Answer Set Programming (ASP) has been a widely utilized approach for knowledge representation and reasoning that is elaboration tolerant and adept at reasoning with incomplete information. This paper proposes a new approach, ASP-enhanced Entity-Relation extraction (ASPER), to jointly recognize entities and relations by learning from both data and domain knowledge. In particular, ASPER takes advantage of the factual knowledge (represented as facts in ASP) and derived knowledge (represented as rules in ASP) in the learning process of neural network models. We have conducted experiments on two real datasets and compare our method with three baselines. The results show that our ASPER model consistently outperforms the baselines.

Attention-based Multi-Input Deep Learning Architecture for Biological Activity Prediction: An Application in EGFR Inhibitors

Machine learning and deep learning have gained popularity and achieved immense success in Drug discovery in recent decades. Historically, machine learning and deep learning models were trained on either structural data or chemical properties by separated model. In this study, we proposed an architecture training simultaneously both type of data in order to improve the overall performance. Given the molecular structure in the form of SMILES notation and their label, we generated the SMILES-based feature matrix and molecular descriptors. These data was trained on an deep learning model which was also integrated with the Attention mechanism to facilitate training and interpreting. Experiments showed that our model could raise the performance of model. With the maximum MCC 0.56 and AUC 91% by cross-validation on EGFR inhibitors dataset, our architecture was outperforming the referring model. We also successfully integrated Attention mechanism into our model, which helped to interpret the contribution of chemical structures on bioactivity.