Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

BACKGROUND: Investigating and understanding drug-drug interactions (DDIs) is important in improving the effectiveness of clinical care. DDIs can occur when two or more drugs are administered together. Experimentally based DDI detection methods require a large cost and time. Hence, there is a great interest in developing efficient and useful computational methods for inferring potential DDIs. Standard binary classifiers require both positives and negatives for training. In a DDI context, drug pairs that are known to interact can serve as positives for predictive methods. But, the negatives or drug pairs that have been confirmed to have no interaction are scarce. To address this lack of negatives, we introduce a Positive-Unlabeled Learning method for inferring potential DDIs. RESULTS: The proposed method consists of three steps: i) application of Growing Self Organizing Maps to infer negatives from the unlabeled dataset; ii) using a pairwise similarity function to quantify the overlap between individual features of drugs and iii) using support vector machine classifier for inferring DDIs. We obtained 6036 DDIs from DrugBank database. Using the proposed approach, we inferred 589 drug pairs that are likely to not interact with each other; these drug pairs are used as representative data for the negative class in binary classification for DDI prediction. Moreover, we classify the predicted DDIs as Cytochrome P450 (CYP) enzyme-Dependent and CYP-Independent interactions invoking their locations on the Growing Self Organizing Map, due to the particular importance of these enzymes in clinically significant interaction effects. Further, we provide a case study on three predicted CYP-Dependent DDIs to evaluate the clinical relevance of this study. CONCLUSION: Our proposed approach showed an absolute improvement in F1-score of 14 and 38% in comparison to the method that randomly selects unlabeled data points as likely negatives, depending on the choice of similarity function. We inferred 5300 possible CYP-Dependent DDIs and 592 CYP-Independent DDIs with the highest posterior probabilities. Our discoveries can be used to improve clinical care as well as the research outcomes of drug development

Viewpoint Discovery and Understanding in Social Networks

The Web has evolved to a dominant platform where everyone has the opportunity to express their opinions, to interact with other users, and to debate on emerging events happening around the world. On the one hand, this has enabled the presence of different viewpoints and opinions about a - usually controversial - topic (like Brexit), but at the same time, it has led to phenomena like media bias, echo chambers and filter bubbles, where users are exposed to only one point of view on the same topic. Therefore, there is the need for methods that are able to detect and explain the different viewpoints. In this paper, we propose a graph partitioning method that exploits social interactions to enable the discovery of different communities (representing different viewpoints) discussing about a controversial topic in a social network like Twitter. To explain the discovered viewpoints, we describe a method, called Iterative Rank Difference (IRD), which allows detecting descriptive terms that characterize the different viewpoints as well as understanding how a specific term is related to a viewpoint (by detecting other related descriptive terms). The results of an experimental evaluation showed that our approach outperforms state-of-the-art methods on viewpoint discovery, while a qualitative analysis of the proposed IRD method on three different controversial topics showed that IRD provides comprehensive and deep representations of the different viewpoints

Automatic text filtering using limited supervision learning for epidemic intelligence

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Multi-Instance Multi-Label Learning

In this paper, we propose the MIML (Multi-Instance Multi-Label learning) framework where an example is described by multiple instances and associated with multiple class labels. Compared to traditional learning frameworks, the MIML framework is more convenient and natural for representing complicated objects which have multiple semantic meanings. To learn from MIML examples, we propose the MimlBoost and MimlSvm algorithms based on a simple degeneration strategy, and experiments show that solving problems involving complicated objects with multiple semantic meanings in the MIML framework can lead to good performance. Considering that the degeneration process may lose information, we propose the D-MimlSvm algorithm which tackles MIML problems directly in a regularization framework. Moreover, we show that even when we do not have access to the real objects and thus cannot capture more information from real objects by using the MIML representation, MIML is still useful. We propose the InsDif and SubCod algorithms. InsDif works by transforming single-instances into the MIML representation for learning, while SubCod works by transforming single-label examples into the MIML representation for learning. Experiments show that in some tasks they are able to achieve better performance than learning the single-instances or single-label examples directly.Comment: 64 pages, 10 figures; Artificial Intelligence, 201