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Multiple kernel clustering (MKC) algorithms optimally combine a group of pre-specified base kernels to improve clustering performance. However, existing MKC algorithms cannot efficiently address the situation where some rows and columns of base kernels are absent. This paper proposes a simple while effective algorithm to address this issue. Different from existing approaches where incomplete kernels are firstly imputed and a standard MKC algorithm is applied to the imputed kernels, our algorithm integrates imputation and clustering into a unified learning procedure. Specifically, we perform multiple kernel clustering directly with the presence of incomplete kernels, which are treated as auxiliary variables to be jointly optimized. Our algorithm does not require that there be at least one complete base kernel over all the samples. Also, it adaptively imputes incomplete kernels and combines them to best serve clustering. A three-step iterative algorithm with proved convergence is designed to solve the resultant optimization problem. Extensive experiments are conducted on four benchmark data sets to compare the proposed algorithm with existing imputation-based methods. Our algorithm consistently achieves superior performance and the improvement becomes more significant with increasing missing ratio, verifying the effectiveness and advantages of the proposed joint imputation and clustering.

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As deep learning methods form a critical part in commercially important applications such as autonomous driving and medical diagnostics, it is important to reliably detect out-of-distribution (OOD) inputs while employing these algorithms. In this work, we propose an OOD detection algorithm which comprises of an ensemble of classifiers. We train each classifier in a self-supervised manner by leaving out a random subset of training data as OOD data and the rest as in-distribution (ID) data. We propose a novel margin-based loss over the softmax output which seeks to maintain at least a margin m between the average entropy of the OOD and in-distribution samples. In conjunction with the standard cross-entropy loss, we minimize the novel loss to train an ensemble of classifiers. We also propose a novel method to combine the outputs of the ensemble of classifiers to obtain OOD detection score and class prediction. Overall, our method convincingly outperforms Hendrycks et al.[7] and the current state-of-the-art ODIN [13] on several OOD detection benchmarks.

The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for drug development, in which therapeutic/toxicological profiles of candidate drugs can be checked computationally before costly clinical trials begin.