Adverse drug-drug interactions (DDIs) remain a leading cause of morbidity and mortality around the world. Identifying potential DDIs during the drug design process is critical in guiding targeted clinical drug safety testing. Although detection of adverse DDIs is conducted during Phase IV clinical trials, there are still a large number of new DDIs founded by accidents after the drugs were put on market. With the arrival of big data era, more and more pharmaceutical research and development data are becoming available, which provides an invaluable resource for digging insights that can potentially be leveraged in early prediction of DDIs. Many computational approaches have been proposed in recent years for DDI prediction. However, most of them focused on binary prediction (with or without DDI), despite the fact that each DDI is associated with a different type. Predicting the actual DDI type will help us better understand the DDI mechanism and identify proper ways to prevent it. In this paper, we formulate the DDI type prediction problem as a multitask dyadic regression problem, where the prediction of each specific DDI type is treated as a task. Compared with conventional matrix completion approaches which can only impute the missing entries in the DDI matrix, our approach can directly regress those dyadic relationships (DDIs) and thus can be extend to new drugs more easily. We developed an effective proximal gradient method to solve the problem. Evaluation on real world datasets is presented to demonstrate the effectiveness of the proposed approach.

One fundamental problem in causal inference is the treatment effect estimation in observational studies when variables are confounded. Control for confounding effect is generally handled by propensity score. But it treats all observed variables as confounders and ignores the adjustment variables, which have no influence on treatment but are predictive of the outcome. Recently, it has been demonstrated that the adjustment variables are effective in reducing the variance of the estimated treatment effect. However, how to automatically separate the confounders and adjustment variables in observational studies is still an open problem, especially in the scenarios of high dimensional variables, which are common in big data era. In this paper, we propose a Data-Driven Variable Decomposition (D$^2$VD) algorithm, which can 1) automatically separate confounders and adjustment variables with a data driven approach, and 2) simultaneously estimate treatment effect in observational studies with high dimensional variables. Under standard assumptions, we show experimentally that the proposed D$^2$VD algorithm can automatically separate the variables precisely, and estimate treatment effect more accurately and with tighter confidence intervals than the state-of-the-art methods on both synthetic data and real online advertising dataset.

For quite some time, the analysis of leukocyte images has drawn significant attention from the fields of medicine and computer vision alike where various techniques have been used to automate the manual analysis and classification of such images. Analysing such samples manually for detecting leukocytes is time-consuming and prone to error as the cells have different morphological features. Therefore, in order to automate and optimize the process, the nature-inspired Plant Growth Simulation Algorithm (PGSA) has been applied in this paper. An automated detection technique of white blood cells embedded in obscured, stained and smeared images of blood samples has been presented in this paper which is based on a random bionic algorithm and makes use of a fitness function that measures the similarity of the generated candidate solution to an actual leukocyte. As the proposed algorithm proceeds the set of candidate solutions evolves, guaranteeing their fit with the actual leukocytes outlined in the edge map of the image. The experimental results of the stained images and the empirical results reported validate the higher precision and sensitivity of the proposed method than the existing methods. Further, the proposed method reduces the feasible sets of candidate points in each iteration, thereby decreasing the required run time of load flow, objective function evaluation, thus reaching the goal state in minimum time and within the desired constraints.

In many reinforcement learning applications, it is desirable to determine confidence interval lower bounds on the performance of any given policy without executing said policy. In this context, we propose two bootstrapping off-policy evaluation methods which use learned MDP transition models in order to estimate lower confidence bounds on policy performance with limited data. We empirically evaluate the proposed methods in a standard policy evaluation tasks.

Species distribution models relate the geographic occurrence pattern of a species to environmental features and are used for a variety of scientific and management purposes. One source of data for building species distribution models is citizen science, in which volunteers report locations where they observed (or did not observe) sets of species. Since volunteers have variable levels of expertise, citizen science data may contain both false positives and false negatives in the location labels (present vs. absent) they provide, but many common modeling approaches for this task do not address these sources of noise explicitly. In this paper, we propose to formulate the species distribution modeling task as a classification problem with class-conditional noise. Our approach builds on other applications of class-conditional noise models to crowdsourced data, but we focus on leveraging features of the noise processes that are distinct from the class features. We describe the conditions under which the parameters of our proposed model are identifiable and apply it to simulated data and data from the eBird citizen science project.

Partial label learning aims to induce a multi-class classifier from training examples where each of them is associated with a set of candidate labels, among which only one label is valid. The common discriminative solution to learn from partial label examples assumes one parametric model for each class label, whose predictions are aggregated to optimize specific objectives such as likelihood or margin over the training examples. Nonetheless, existing discriminative approaches treat the predictions from all parametric models in an equal manner, where the confidence of each candidate label being the ground-truth label is not differentiated. In this paper, a boosting-style partial label learning approach is proposed to enabling confidence-rated discriminative modeling. Specifically, the ground-truth confidence of each candidate label is maintained in each boosting round and utilized to train the base classifier. Extensive experiments on artificial as well as real-world partial label data sets validate the effectiveness of the confidence-rated discriminative modeling.

We propose a framework to improve the performance of distantly-supervised relation extraction, by jointly learning to solve two related tasks: concept-instance extraction and relation extraction. We further extend this framework to make a novel use of document structure: in some small, well-structured corpora, sections can be identified that correspond to relation arguments, and distantly-labeled examples from such sections tend to have good precision. Using these as seeds we extract additional relation examples by applying label propagation on a graph composed of noisy examples extracted from a large unstructured testing corpus. Combined with the soft constraint that concept examples should have the same type as the second argument of the relation, we get significant improvements over several state-of-the-art approaches to distantly-supervised relation extraction, and reasonable extraction performance even with very small set of distant labels.

Adverse drug reaction (ADR) is a major burden for patients and healthcare industry. It usually causes preventable hospitalizations and deaths, while associated with a huge amount of cost. Traditional preclinical in vitro safety profiling and clinical safety trials are restricted in terms of small scale, long duration, huge financial costs and limited statistical signifi- cance. The availability of large amounts of drug and ADR data potentially allows ADR predictions during the drugs’ early preclinical stage with data analytics methods to inform more targeted clinical safety tests. Despite their initial success, existing methods have trade-offs among interpretability, predictive power and efficiency. This urges us to explore methods that could have all these strengths and provide practical solutions for real world ADR predictions. We cast the ADR-drug relation structure into a three-layer hierarchical Bayesian model. We interpret each ADR as a symbolic word and apply latent Dirichlet allocation (LDA) to learn topics that may represent certain biochemical mechanism that relates ADRs with drug structures. Based on LDA, we designed an equivalent regularization term to incorporate the hierarchical ADR domain knowledge. Finally, we developed a mixed input model leveraging a fast collapsed Gibbs sampling method that the complexity of each iteration of Gibbs sampling proportional only to the number of positive ADRs. Experiments on real world data show our models achieved higher prediction accuracy and shorter running time than the state-of-the-art alternatives.

Multimodality has been recently exploited to overcome the challenges of emotion recognition. In this paper, we present a study of fusion of electroencephalogram (EEG) features and musical features extracted from musical stimuli at decision level in recognizing the time-varying binary classes of arousal and valence. Our empirical results demonstrate that EEG modality was suffered from the non-stability of EEG signals, yet fusing with music modality could alleviate the issue and enhance the performance of emotion recognition.

The k-fold cross-validation is commonly used to evaluate the effectiveness of SVMs with the selected hyper-parameters. It is known that the SVM k-fold cross-validation is expensive, since it requires training k SVMs. However, little work has explored reusing the h-th SVM for training the (h+1)-th SVM for improving the efficiency of k-fold cross-validation. In this paper, we propose three algorithms that reuse the h-th SVM for improving the efficiency of training the (h+1)-th SVM. Our key idea is to efficiently identify the support vectors and to accurately estimate their associated weights (also called alpha values) of the next SVM by using the previous SVM. Our experimental results show that our algorithms are several times faster than the k-fold cross-validation which does not make use of the previously trained SVM. Moreover, our algorithms produce the same results (hence same accuracy) as the k-fold cross-validation which does not make use of the previously trained SVM.