Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries. Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.Comment: Pacific Symposium on Biocomputing, 201

Latent Space Model for Multi-Modal Social Data

With the emergence of social networking services, researchers enjoy the increasing availability of large-scale heterogenous datasets capturing online user interactions and behaviors. Traditional analysis of techno-social systems data has focused mainly on describing either the dynamics of social interactions, or the attributes and behaviors of the users. However, overwhelming empirical evidence suggests that the two dimensions affect one another, and therefore they should be jointly modeled and analyzed in a multi-modal framework. The benefits of such an approach include the ability to build better predictive models, leveraging social network information as well as user behavioral signals. To this purpose, here we propose the Constrained Latent Space Model (CLSM), a generalized framework that combines Mixed Membership Stochastic Blockmodels (MMSB) and Latent Dirichlet Allocation (LDA) incorporating a constraint that forces the latent space to concurrently describe the multiple data modalities. We derive an efficient inference algorithm based on Variational Expectation Maximization that has a computational cost linear in the size of the network, thus making it feasible to analyze massive social datasets. We validate the proposed framework on two problems: prediction of social interactions from user attributes and behaviors, and behavior prediction exploiting network information. We perform experiments with a variety of multi-modal social systems, spanning location-based social networks (Gowalla), social media services (Instagram, Orkut), e-commerce and review sites (Amazon, Ciao), and finally citation networks (Cora). The results indicate significant improvement in prediction accuracy over state of the art methods, and demonstrate the flexibility of the proposed approach for addressing a variety of different learning problems commonly occurring with multi-modal social data.Comment: 12 pages, 7 figures, 2 table

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Because of the intrinsic complexity of natural language, automatically extracting accurate information from text remains a challenge. We have applied rich featurevectors derived from dependency graphs to predict protein-protein interactions using machine learning techniques. We present the first extensive analysis of applyingfeature selection in this domain, and show that it can produce more cost-effective models. For the first time, our technique was also evaluated on several large-scalecross-dataset experiments, which offers a more realistic view on model performance. During benchmarking, we encountered several fundamental problems hindering comparability with other methods. We present a set of practical guidelines to set up ameaningful evaluation. Finally, we have analysed the feature sets from our experiments before and after feature selection, and evaluated the contribution of both lexical and syntacticinformation to our method. The gained insight will be useful to develop better performing methods in this domain

Interaction Embeddings for Prediction and Explanation in Knowledge Graphs

Knowledge graph embedding aims to learn distributed representations for entities and relations, and is proven to be effective in many applications. Crossover interactions --- bi-directional effects between entities and relations --- help select related information when predicting a new triple, but haven't been formally discussed before. In this paper, we propose CrossE, a novel knowledge graph embedding which explicitly simulates crossover interactions. It not only learns one general embedding for each entity and relation as most previous methods do, but also generates multiple triple specific embeddings for both of them, named interaction embeddings. We evaluate embeddings on typical link prediction tasks and find that CrossE achieves state-of-the-art results on complex and more challenging datasets. Furthermore, we evaluate embeddings from a new perspective --- giving explanations for predicted triples, which is important for real applications. In this work, an explanation for a triple is regarded as a reliable closed-path between the head and the tail entity. Compared to other baselines, we show experimentally that CrossE, benefiting from interaction embeddings, is more capable of generating reliable explanations to support its predictions.Comment: This paper is accepted by WSDM201

Fitting Prediction Rule Ensembles with R Package pre

Prediction rule ensembles (PREs) are sparse collections of rules, offering highly interpretable regression and classification models. This paper presents the R package pre, which derives PREs through the methodology of Friedman and Popescu (2008). The implementation and functionality of package pre is described and illustrated through application on a dataset on the prediction of depression. Furthermore, accuracy and sparsity of PREs is compared with that of single trees, random forest and lasso regression in four benchmark datasets. Results indicate that pre derives ensembles with predictive accuracy comparable to that of random forests, while using a smaller number of variables for prediction