This paper describes a probabilistic framework for studying associations between multiple genotypes, biomarkers, and phenotypic traits in the presence of noise and unobserved confounders for large genetic studies. The framework builds on sparse linear methods developed for regression and modified here for inferring causal structures of richer networks with latent variables. The method is motivated by the use of genotypes as ``instruments'' to infer causal associations between phenotypic biomarkers and outcomes, without making the common restrictive assumptions of instrumental variable methods. The method may be used for an effective screening of potentially interesting genotype phenotype and biomarker-phenotype associations in genome-wide studies, which may have important implications for validating biomarkers as possible proxy endpoints for early stage clinical trials. Where the biomarkers are gene transcripts, the method can be used for fine mapping of quantitative trait loci (QTLs) detected in genetic linkage studies. The method is applied for examining effects of gene transcript levels in the liver on plasma HDL cholesterol levels for a sample of sequenced mice from a heterogeneous stock, with $\sim 10^5$ genetic instruments and $\sim 47 \times 10^3$ gene transcripts.

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

In the interpretation of experimental data, one is actually looking for plausible explanations. We look for a measure of plausibility, with which we can compare different possible explanations, and which can be combined when there are different sets of data. This is contrasted to the conventional measure for probabilities as well as to the proposed measure of possibilities. We define what characteristics this measure of plausibility should have. In getting to the conception of this measure, we explore the relation of plausibility to abductive reasoning, and to Bayesian probabilities. We also compare with the Dempster-Schaefer theory of evidence, which also has its own definition for plausibility. Abduction can be associated with biconditionality in inference rules, and this provides a platform to relate to the Collins-Michalski theory of plausibility. Finally, using a formalism for wiring logic onto Hopfield neural networks, we ask if this is relevant in obtaining this measure.

This paper introduces a principled approach for the design of a scalable general reinforcement learning agent. Our approach is based on a direct approximation of AIXI, a Bayesian optimality notion for general reinforcement learning agents. Previously, it has been unclear whether the theory of AIXI could motivate the design of practical algorithms. We answer this hitherto open question in the affirmative, by providing the first computationally feasible approximation to the AIXI agent. To develop our approximation, we introduce a new Monte-Carlo Tree Search algorithm along with an agent-specific extension to the Context Tree Weighting algorithm. Empirically, we present a set of encouraging results on a variety of stochastic and partially observable domains. We conclude by proposing a number of directions for future research.

Intrusion detection systems (IDSs) fall into two high-level categories: network-based systems (NIDS) that monitor network behaviors, and host-based systems (HIDS) that monitor system calls. In this work, we present a general technique for both systems. We use anomaly detection, which identifies patterns not conforming to a historic norm. In both types of systems, the rates of change vary dramatically over time (due to burstiness) and over components (due to service difference). To efficiently model such systems, we use continuous time Bayesian networks (CTBNs) and avoid specifying a fixed update interval common to discrete-time models. We build generative models from the normal training data, and abnormal behaviors are flagged based on their likelihood under this norm. For NIDS, we construct a hierarchical CTBN model for the network packet traces and use Rao-Blackwellized particle filtering to learn the parameters. We illustrate the power of our method through experiments on detecting real worms and identifying hosts on two publicly available network traces, the MAWI dataset and the LBNL dataset. For HIDS, we develop a novel learning method to deal with the finite resolution of system log file time stamps, without losing the benefits of our continuous time model. We demonstrate the method by detecting intrusions in the DARPA 1998 BSM dataset.

Abstract: We consider the problem of estimating the inverse covariance matrix by maximizing the likelihood function with a penalty added to encourage the sparsity of the resulting matrix. We propose a new approach based on the split Bregman method to solve the regularized maximum likelihood estimation problem. We show that our method is significantly faster than the widely used graphical lasso method, which is based on blockwise coordinate descent, on both artificial and real-world data.

A learning algorithm based on primary school teaching and learning is presented. The methodology is to continuously evaluate a student and to give them training on the examples for which they repeatedly fail, until, they can correctly answer all types of questions. This incremental learning procedure produces better learning curves by demanding the student to optimally dedicate their learning time on the failed examples. When used in machine learning, the algorithm is found to train a machine on a data with maximum variance in the feature space so that the generalization ability of the network improves. The algorithm has interesting applications in data mining, model evaluations and rare objects discovery.

Statistical models of natural stimuli provide an important tool for researchers in the fields of machine learning and computational neuroscience. A canonical way to quantitatively assess and compare the performance of statistical models is given by the likelihood. One class of statistical models which has recently gained increasing popularity and has been applied to a variety of complex data are deep belief networks. Analyses of these models, however, have been typically limited to qualitative analyses based on samples due to the computationally intractable nature of the model likelihood. Motivated by these circumstances, the present article provides a consistent estimator for the likelihood that is both computationally tractable and simple to apply in practice. Using this estimator, a deep belief network which has been suggested for the modeling of natural image patches is quantitatively investigated and compared to other models of natural image patches. Contrary to earlier claims based on qualitative results, the results presented in this article provide evidence that the model under investigation is not a particularly good model for natural images

The Monty Hall problem is the TV game scenario where you, the contestant, are presented with three doors, with a car hidden behind one and goats hidden behind the other two. After you select a door, the host (Monty Hall) opens a second door to reveal a goat. You are then invited to stay with your original choice of door, or to switch to the remaining unopened door, and claim whatever you find behind it. Assuming your objective is to win the car, is your best strategy to stay or switch, or does it not matter? Jason Rosenhouse has provided the definitive analysis of this game, along with several intriguing variations, and discusses some of its psychological and philosophical implications. This extended review examines several themes from the book in some detail from a Bayesian perspective, and points out one apparently inadvertent error.

The problem of maximum-likelihood (ML) estimation of discrete tree-structured distributions is considered. Chow and Liu established that ML-estimation reduces to the construction of a maximum-weight spanning tree using the empirical mutual information quantities as the edge weights. Using the theory of large-deviations, we analyze the exponent associated with the error probability of the event that the ML-estimate of the Markov tree structure differs from the true tree structure, given a set of independently drawn samples. By exploiting the fact that the output of ML-estimation is a tree, we establish that the error exponent is equal to the exponential rate of decay of a single dominant crossover event. We prove that in this dominant crossover event, a non-neighbor node pair replaces a true edge of the distribution that is along the path of edges in the true tree graph connecting the nodes in the non-neighbor pair. Using ideas from Euclidean information theory, we then analyze the scenario of ML-estimation in the very noisy learning regime and show that the error exponent can be approximated as a ratio, which is interpreted as the signal-to-noise ratio (SNR) for learning tree distributions. We show via numerical experiments that in this regime, our SNR approximation is accurate.