Bayesian learning of joint distributions of objects

There is increasing interest in broad application areas in defining flexible joint models for data having a variety of measurement scales, while also allowing data of complex types, such as functions, images and documents. We consider a general framework for nonparametric Bayes joint modeling through mixture models that incorporate dependence across data types through a joint mixing measure. The mixing measure is assigned a novel infinite tensor factorization (ITF) prior that allows flexible dependence in cluster allocation across data types. The ITF prior is formulated as a tensor product of stick-breaking processes. Focusing on a convenient special case corresponding to a Parafac factorization, we provide basic theory justifying the flexibility of the proposed prior and resulting asymptotic properties. Focusing on ITF mixtures of product kernels, we develop a new Gibbs sampling algorithm for routine implementation relying on slice sampling. The methods are compared with alternative joint mixture models based on Dirichlet processes and related approaches through simulations and real data applications.Comment: Appearing in Proceedings of the 16th International Conference on Artificial Intelligence and Statistics (AISTATS) 2013, Scottsdale, AZ, US

Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

Neurofibromatosis type 1 (NF1) is a monogenic syndrome that gives rise to numerous symptoms including cognitive impairment, skeletal abnormalities, and growth of benign nerve sheath tumors. Nearly all NF1 patients develop cutaneous neurofibromas (cNFs), which occur on the skin surface, whereas 40-60% of patients develop plexiform neurofibromas (pNFs), which are deeply embedded in the peripheral nerves. Patients with pNFs have a ~10% lifetime chance of these tumors becoming malignant peripheral nerve sheath tumors (MPNSTs). These tumors have a severe prognosis and few treatment options other than surgery. Given the lack of therapeutic options available to patients with these tumors, identification of druggable pathways or other key molecular features could aid ongoing therapeutic discovery studies. In this work, we used statistical and machine learning methods to analyze 77 NF1 tumors with genomic data to characterize key signaling pathways that distinguish these tumors and identify candidates for drug development. We identified subsets of latent gene expression variables that may be important in the identification and etiology of cNFs, pNFs, other neurofibromas, and MPNSTs. Furthermore, we characterized the association between these latent variables and genetic variants, immune deconvolution predictions, and protein activity predictions

The Machine Learning Landscape of Top Taggers

Based on the established task of identifying boosted, hadronically decaying top quarks, we compare a wide range of modern machine learning approaches. Unlike most established methods they rely on low-level input, for instance calorimeter output. While their network architectures are vastly different, their performance is comparatively similar. In general, we find that these new approaches are extremely powerful and great fun.Comment: Yet another tagger included