We propose a new problem formulation which is similar to, but more informative than, the binary multiple-instance learning problem. In this setting, we are given groups of instances (described by feature vectors) along with estimates of the fraction of positively-labeled instances per group. The task is to learn an instance level classifier from this information. That is, we are trying to estimate the unknown binary labels of individuals from knowledge of group statistics. We propose a principled probabilistic model to solve this problem that accounts for uncertainty in the parameters and in the unknown individual labels. This model is trained with an efficient MCMC algorithm. Its performance is demonstrated on both synthetic and real-world data arising in general object recognition.

We present a method for learning the parameters of a Bayesian network with prior knowledge about the signs of influences between variables. Our method accommodates not just the standard signs, but provides for context-specific signs as well. We show how the various signs translate into order constraints on the network parameters and how isotonic regression can be used to compute order-constrained estimates from the available data. Our experimental results show that taking prior knowledge about the signs of influences into account leads to an improved fit of the true distribution, especially when only a small sample of data is available. Moreover, the computed estimates are guaranteed to be consistent with the specified signs, thereby resulting in a network that is more likely to be accepted by experts in its domain of application.

We consider the problem of learning Bayesian network classifiers that maximize the margin over a set of classification variables. We find that this problem is harder for Bayesian networks than for undirected graphical models like maximum margin Markov networks. The main difficulty is that the parameters in a Bayesian network must satisfy additional normalization constraints that an undirected graphical model need not respect. These additional constraints complicate the optimization task. Nevertheless, we derive an effective training algorithm that solves the maximum margin training problem for a range of Bayesian network topologies, and converges to an approximate solution for arbitrary network topologies. Experimental results show that the method can demonstrate improved generalization performance over Markov networks when the directed graphical structure encodes relevant knowledge. In practice, the training technique allows one to combine prior knowledge expressed as a directed (causal) model with state of the art discriminative learning methods.

A software library for constructing and learning probabilistic models is presented. The library offers a set of building blocks from which a large variety of static and dynamic models can be built. These include hierarchical models for variances of other variables and many nonlinear models. The underlying variational Bayesian machinery, providing for fast and robust estimation but being mathematically rather involved, is almost completely hidden from the user thus making it very easy to use the library. The building blocks include Gaussian, rectified Gaussian and mixture-of-Gaussians variables and computational nodes which can be combined rather freely.

We study computational and sample complexity of parameter and structure learning in graphical models. Our main result shows that the class of factor graphs with bounded factor size and bounded connectivity can be learned in polynomial time and polynomial number of samples, assuming that the data is generated by a network in this class. This result covers both parameter estimation for a known network structure and structure learning. It implies as a corollary that we can learn factor graphs for both Bayesian networks and Markov networks of bounded degree, in polynomial time and sample complexity. Unlike maximum likelihood estimation, our method does not require inference in the underlying network, and so applies to networks where inference is intractable. We also show that the error of our learned model degrades gracefully when the generating distribution is not a member of the target class of networks.

When training data is sparse, more domain knowledge must be incorporated into the learning algorithm in order to reduce the effective size of the hypothesis space. This paper builds on previous work in which knowledge about qualitative monotonicities was formally represented and incorporated into learning algorithms (e.g., Clark & Matwin's work with the CN2 rule learning algorithm). We show how to interpret knowledge of qualitative influences, and in particular of monotonicities, as constraints on probability distributions, and to incorporate this knowledge into Bayesian network learning algorithms. We show that this yields improved accuracy, particularly with very small training sets (e.g. less than 10 examples).

This paper explores semi-qualitative probabilistic networks (SQPNs) that combine numeric and qualitative information. We first show that exact inferences with SQPNs are NPPP-Complete. We then show that existing qualitative relations in SQPNs (plus probabilistic logic and imprecise assessments) can be dealt effectively through multilinear programming. We then discuss learning: we consider a maximum likelihood method that generates point estimates given a SQPN and empirical data, and we describe a Bayesian-minded method that employs the Imprecise Dirichlet Model to generate set-valued estimates.

In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex phenomena. Simulators can be thought of as complex functions that take many inputs and provide an output. Often these simulators are themselves expensive to compute, and may be approximated by "surrogate models" such as statistical regression models. In this paper we consider a new kind of surrogate model, a Bayesian ensemble of trees (Chipman et al. 2010), with the specific goal of learning enough about the simulator that a particular feature of the simulator can be estimated. We focus on identifying the simulator's global minimum. Utilizing the Bayesian version of the Expected Improvement criterion (Jones et al. 1998), we show that this ensemble is particularly effective when the simulator is ill-behaved, exhibiting nonstationarity or abrupt changes in the response. A number of illustrations of the approach are given, including a tidal power application.

Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of the unknown data generating density. This paper contributes to the mathematical understanding of this phenomenon and helps define better justified sampling algorithms for deep learning based on auto-encoder variants. We consider an MCMC where each step samples from a Gaussian whose mean and covariance matrix depend on the previous state, defines through its asymptotic distribution a target density. First, we show that good choices (in the sense of consistency) for these mean and covariance functions are the local expected value and local covariance under that target density. Then we show that an auto-encoder with a contractive penalty captures estimators of these local moments in its reconstruction function and its Jacobian. A contribution of this work is thus a novel alternative to maximum-likelihood density estimation, which we call local moment matching. It also justifies a recently proposed sampling algorithm for the Contractive Auto-Encoder and extends it to the Denoising Auto-Encoder.

We consider unsupervised estimation of mixtures of discrete graphical models, where the class variable corresponding to the mixture components is hidden and each mixture component over the observed variables can have a potentially different Markov graph structure and parameters. We propose a novel approach for estimating the mixture components, and our output is a tree-mixture model which serves as a good approximation to the underlying graphical model mixture. Our method is efficient when the union graph, which is the union of the Markov graphs of the mixture components, has sparse vertex separators between any pair of observed variables. This includes tree mixtures and mixtures of bounded degree graphs. For such models, we prove that our method correctly recovers the union graph structure and the tree structures corresponding to maximum-likelihood tree approximations of the mixture components. The sample and computational complexities of our method scale as $\poly(p, r)$, for an $r$-component mixture of $p$-variate graphical models. We further extend our results to the case when the union graph has sparse local separators between any pair of observed variables, such as mixtures of locally tree-like graphs, and the mixture components are in the regime of correlation decay.