While machine learning is traditionally a resource intensive task, embedded systems, autonomous navigation, and the vision of the Internet of Things fuel the interest in resource-efficient approaches. These approaches aim for a carefully chosen trade-off between performance and resource consumption in terms of computation and energy. The development of such approaches is among the major challenges in current machine learning research and key to ensure a smooth transition of machine learning technology from a scientific environment with virtually unlimited computing resources into everyday's applications. In this article, we provide an overview of the current state of the art of machine learning techniques facilitating these real-world requirements. In particular, we focus on resource-efficient inference based on deep neural networks (DNNs), the predominant machine learning models of the past decade. We give a comprehensive overview of the vast literature that can be mainly split into three non-mutually exclusive categories: (i) quantized neural networks, (ii) network pruning, and (iii) structural efficiency. These techniques can be applied during training or as post-processing, and they are widely used to reduce the computational demands in terms of memory footprint, inference speed, and energy efficiency. We also briefly discuss different concepts of embedded hardware for DNNs and their compatibility with machine learning techniques as well as potential for energy and latency reduction. We substantiate our discussion with experiments on well-known benchmark data sets using compression techniques (quantization, pruning) for a set of resource-constrained embedded systems, such as CPUs, GPUs and FPGAs. The obtained results highlight the difficulty of finding good trade-offs between resource efficiency and prediction quality.

Bayesian optimization (BO) has become a popular strategy for global optimization of expensive real-world functions. Contrary to a common expectation that BO is suited to optimizing black-box functions, it actually requires domain knowledge about those functions to deploy BO successfully. Such domain knowledge often manifests in Gaussian process (GP) priors that specify initial beliefs on functions. However, even with expert knowledge, it is non-trivial to quantitatively define a prior. This is especially true for hyperparameter tuning problems on complex machine learning models, where landscapes of tuning objectives are often difficult to comprehend. We seek an alternative practice for setting these functional priors. In particular, we consider the scenario where we have data from similar functions that allow us to pre-train a tighter distribution a priori. We detail what pre-training entails for GPs using a KL divergence based loss function, and propose a new pre-training based BO framework named HyperBO. Theoretically, we show bounded posterior predictions and near-zero regrets for HyperBO without assuming the "ground truth" GP prior is known. To verify our approach in realistic setups, we collect a large multi-task hyperparameter tuning dataset by training tens of thousands of configurations of near-state-of-the-art deep learning models on popular image and text datasets, as well as a protein sequence dataset. Our results show that on average, HyperBO is able to locate good hyperparameters at least 3 times more efficiently than the best competing methods on both our new tuning dataset and existing multi-task BO benchmarks.

Neural network approaches for meta-learning distributions over functions have desirable properties such as increased flexibility and a reduced complexity of inference. Building on the successes of denoising diffusion models for generative modelling, we propose Neural Diffusion Processes (NDPs), a novel approach that learns to sample from a rich distribution over functions through its finite marginals. By introducing a custom attention block we are able to incorporate properties of stochastic processes, such as exchangeability, directly into the NDP's architecture. We empirically show that NDPs can capture functional distributions close to the true Bayesian posterior, demonstrating that they can successfully emulate the behaviour of Gaussian processes and surpass the performance of neural processes. NDPs enable a variety of downstream tasks, including regression, implicit hyperparameter marginalisation, non-Gaussian posterior prediction and global optimisation.

Neural networks and Gaussian processes are complementary in their strengths and weaknesses. Having a better understanding of their relationship comes with the promise to make each method benefit from the strengths of the other. In this work, we establish an equivalence between the forward passes of neural networks and (deep) sparse Gaussian process models. The theory we develop is based on interpreting activation functions as interdomain inducing features through a rigorous analysis of the interplay between activation functions and kernels. This results in models that can either be seen as neural networks with improved uncertainty prediction or deep Gaussian processes with increased prediction accuracy. These claims are supported by experimental results on regression and classification datasets.

Probabilistic circuits (PCs) are a promising avenue for probabilistic modeling, as they permit a wide range of exact and efficient inference routines. Recent “deep-learning-style” implementations of PCs strive for a better scalability, but are still difficult to train on real-world data, due to their sparsely connected computational graphs. In this paper, we propose Einsum Networks (EiNets), a novel implementation design for PCs, improving prior art in several regards. At their core, EiNets combine a large number of arithmetic operations in a single monolithic einsum-operation, leading to speedups and memory savings of up to two orders of magnitude, in comparison to previous implementations. As an algorithmic contribution, we show that the implementation of Expectation-Maximization (EM) can be simplified for PCs, by leveraging automatic differentiation. Furthermore, we demonstrate that EiNets scale well to datasets which were previously out of reach, such as SVHN and CelebA, and that they can be used as faithful generative image models.

Latent variable models allow capturing the hidden structure underlying the data. In particular, feature allocation models represent each observation by a linear combination of latent variables. These models are often used to make predictions either for new observations or for missing information in the original data, as well as to perform exploratory data analysis. Although there is an extensive literature on latent feature allocation models for homogeneous datasets, where all the attributes that describe each object are of the same (continuous or discrete) type, there is no general framework for practical latent feature modeling for heterogeneous datasets. In this paper, we introduce a general Bayesian nonparametric latent feature allocation model suitable for heterogeneous datasets, where the attributes describing each object can be arbitrary combinations of real-valued, positive real-valued, categorical, ordinal and count variables. The proposed model presents several important properties. First, it is suitable for heterogeneous data while keeping the properties of conjugate models, which enables us to develop an inference algorithm that presents linear complexity with respect to the number of objects and attributes per MCMC iteration. Second, the Bayesian nonparametric component allows us to place a prior distribution on the number of features required to capture the latent structure in the data. Third, the latent features in the model are binary-valued, which facilitates the interpretability of the obtained latent features in exploratory data analysis. Finally, a software package, called GLFM toolbox, is made publicly available for other researchers to use and extend. It is available at https://ivaleram.github.io/GLFM/. We show the flexibility of the proposed model by solving both prediction and data analysis tasks on several real-world datasets.

There is currently a great expansion of the impact of machine learning algorithms on our lives, prompting the need for objectives other than pure performance, including fairness. Fairness here means that the outcome of an automated decisionmaking system should not discriminate between subgroups characterized by sensitive attributes such as gender or race. Given any existing differentiable classifier, we make only slight adjustments to the architecture including adding a new hidden layer, in order to enable the concurrent adversarial optimization for fairness and accuracy. Our framework provides one way to quantify the tradeoff between fairness and accuracy, while also leading to strong empirical performance.

Making sense of a dataset in an automatic and unsupervised fashion is a challenging problem in statistics and AI. Classical approaches for exploratory data analysis are usually not flexible enough to deal with the uncertainty inherent to real-world data: they are often restricted to fixed latent interaction models and homogeneous likelihoods; they are sensitive to missing, corrupt and anomalous data; moreover, their expressiveness generally comes at the price of intractable inference. As a result, supervision from statisticians is usually needed to find the right model for the data. However, since domain experts are not necessarily also experts in statistics, we propose Automatic Bayesian Density Analysis (ABDA) to make exploratory data analysis accessible at large. Specifically, ABDA allows for automatic and efficient missing value estimation, statistical data type and likelihood discovery, anomaly detection and dependency structure mining, on top of providing accurate density estimation. Extensive empirical evidence shows that ABDA is a suitable tool for automatic exploratory analysis of mixed continuous and discrete tabular data.

Sum-product networks (SPNs) are flexible density estimators and have received significant attention due to their attractive inference properties. While parameter learning in SPNs is well developed, structure learning leaves something to be desired: Even though there is a plethora of SPN structure learners, most of them are somewhat ad-hoc and based on intuition rather than a clear learning principle. In this paper, we introduce a well-principled Bayesian framework for SPN structure learning. First, we decompose the problem into i) laying out a computational graph, and ii) learning the so-called scope function over the graph. The first is rather unproblematic and akin to neural network architecture validation. The second represents the effective structure of the SPN and needs to respect the usual structural constraints in SPN, i.e. completeness and decomposability. While representing and learning the scope function is somewhat involved in general, in this paper, we propose a natural parametrisation for an important and widely used special case of SPNs. These structural parameters are incorporated into a Bayesian model, such that simultaneous structure and parameter learning is cast into monolithic Bayesian posterior inference. In various experiments, our Bayesian SPNs often improve test likelihoods over greedy SPN learners. Further, since the Bayesian framework protects against overfitting, we can evaluate hyper-parameters directly on the Bayesian model score, waiving the need for a separate validation set, which is especially beneficial in low data regimes. Bayesian SPNs can be applied to heterogeneous domains and can easily be extended to nonparametric formulations. Moreover, our Bayesian approach is the first, which consistently and robustly learns SPN structures under missing data.

Interpretability of representations in both deep generative and discriminative models is highly desirable. Current methods jointly optimize an objective combining accuracy and interpretability. However, this may reduce accuracy, and is not applicable to already trained models. We propose two interpretability frameworks. First, we provide an interpretable lens for an existing model. We use a generative model which takes as input the representation in an existing (generative or discriminative) model, weakly supervised by limited side information. Applying a flexible and invertible transformation to the input leads to an interpretable representation with no loss in accuracy. We extend the approach using an active learning strategy to choose the most useful side information to obtain, allowing a human to guide what "interpretable" means. Our second framework relies on joint optimization for a representation which is both maximally informative about the side information and maximally compressive about the non-interpretable data factors. This leads to a novel perspective on the relationship between compression and regularization. We also propose a new interpretability evaluation metric based on our framework. Empirically, we achieve state-of-the-art results on three datasets using the two proposed algorithms.

Dropout, a stochastic regularisation technique for training of neural networks, has recently been reinterpreted as a specific type of approximate inference algorithm for Bayesian neural networks. The main contribution of the reinterpretation is in providing a theoretical framework useful for analysing and extending the algorithm. We show that the proposed framework suffers from several issues; from undefined or pathological behaviour of the true posterior related to use of improper priors, to an ill-defined variational objective due to singularity of the approximating distribution relative to the true posterior. Our analysis of the improper log uniform prior used in variational Gaussian dropout suggests the pathologies are generally irredeemable, and that the algorithm still works only because the variational formulation annuls some of the pathologies. To address the singularity issue, we proffer Quasi-KL (QKL) divergence, a new approximate inference objective for approximation of high-dimensional distributions. We show that motivations for variational Bernoulli dropout based on discretisation and noise have QKL as a limit. Properties of QKL are studied both theoretically and on a simple practical example which shows that the QKL-optimal approximation of a full rank Gaussian with a degenerate one naturally leads to the Principal Component Analysis solution.

Policy gradient methods are a widely used class of model-free reinforcement learning algorithms where a state-dependent baseline is used to reduce gradient estimator variance. Several recent papers extend the baseline to depend on both the state and action and suggest that this significantly reduces variance and improves sample efficiency without introducing bias into the gradient estimates. To better understand this development, we decompose the variance of the policy gradient estimator and numerically show that learned state-action-dependent baselines do not in fact reduce variance over a state-dependent baseline in commonly tested benchmark domains. We confirm this unexpected result by reviewing the open-source code accompanying these prior papers, and show that subtle implementation decisions cause deviations from the methods presented in the papers and explain the source of the previously observed empirical gains. Furthermore, the variance decomposition highlights areas for improvement, which we demonstrate by illustrating a simple change to the typical value function parameterization that can significantly improve performance.

In this paper, we propose a conceptually simple and general framework called MetaGAN for few-shot learning problems. Most state-of-the-art few-shot classification models can be integrated with MetaGAN in a principled and straightforward way. By introducing an adversarial generator conditioned on tasks, we augment vanilla few-shot classification models with the ability to discriminate between real and fake data. We argue that this GAN-based approach can help few-shot classifiers to learn sharper decision boundary, which could generalize better. We show that with our MetaGAN framework, we can extend supervised few-shot learning models to naturally cope with unsupervised data. Different from previous work in semi-supervised few-shot learning, our algorithms can deal with semi-supervision at both sample-level and task-level. We give theoretical justifications of the strength of MetaGAN, and validate the effectiveness of MetaGAN on challenging few-shot image classification benchmarks.

Motivation: A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may undergo further branching; the contrary is true during recombination, where two or more statistical processes converge. A key objective is to identify the time of this bifurcation (branch or recombination time) from time series measurements, e.g. by comparing a control time series with perturbed time series. Gaussian processes (GPs) represent an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here, we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs). Results: We first benchmark the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns of Arabidopsis thaliana gene expression following inoculation with the hemibotrophic bacteria, Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and show that genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors. Availability and implementation: https://github.com/cap76/BranchingGPs. Supplementary information: Supplementary data are available at Bioinformatics online.

We present an architectural design of a library for Bayesian modelling and inference in modern functional programming languages. The novel aspect of our approach are modular implementations of existing state-of-the-art inference algorithms. Our design relies on three inherently functional features: higher-order functions, inductive data-types, and support for either type-classes or an expressive module system. We provide a performant Haskell implementation of this architecture, demonstrating that high-level and modular probabilistic programming can be added as a library in sufficiently expressive languages. We review the core abstractions in this architecture: inference representations, inference transformations, and inference representation transformers. We then implement concrete instances of these abstractions, counterparts to particle filters and Metropolis-Hastings samplers, which form the basic building blocks of our library. By composing these building blocks we obtain state-of-the-art inference algorithms: Resample-Move Sequential Monte Carlo, Particle Marginal Metropolis-Hastings, and Sequential Monte Carlo Squared. We evaluate our implementation against existing probabilistic programming systems and find it is already competitively performant, although we conjecture that existing functional programming optimisation techniques could reduce the overhead associated with the abstractions we use. We show that our modular design enables deterministic testing of inherently stochastic Monte Carlo algorithms. Finally, we demonstrate using OCaml that an expressive module system can also implement our design.

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

The Gumbel trick is a method to sample from a discrete probability distribution, or to estimate its normalizing partition function. The method relies on repeatedly applying a random perturbation to the distribution in a particular way, each time solving for the most likely configuration. We derive an entire family of related methods, of which the Gumbel trick is one member, and show that the new methods have superior properties in several settings with minimal additional computational cost. In particular, for the Gumbel trick to yield computational benefits for discrete graphical models, Gumbel perturbations on all configurations are typically replaced with so-called low-rank perturbations. We show how a subfamily of our new methods adapts to this setting, proving new upper and lower bounds on the log partition function and deriving a family of sequential samplers for the Gibbs distribution. Finally, we balance the discussion by showing how the simpler analytical form of the Gumbel trick enables additional theoretical results.

Even though active learning forms an important pillar of machine learning, deep learning tools are not prevalent within it. Deep learning poses several difficulties when used in an active learning setting. First, active learning (AL) methods generally rely on being able to learn and update models from small amounts of data. Recent advances in deep learning, on the other hand, are notorious for their dependence on large amounts of data. Second, many AL acquisition functions rely on model uncertainty, yet deep learning methods rarely represent such model uncertainty. In this paper we combine recent advances in Bayesian deep learning into the active learning framework in a practical way. We develop an active learning framework for high dimensional data, a task which has been extremely challenging so far, with very sparse existing literature. Taking advantage of specialised models such as Bayesian convolutional neural networks, we demonstrate our active learning techniques with image data, obtaining a significant improvement on existing active learning approaches. We demonstrate this on both the MNIST dataset, as well as for skin cancer diagnosis from lesion images (ISIC2016 task).

We present a model for random simple graphs with power law (i.e., heavy-tailed) degree distributions. To attain this behavior, the edge probabilities in the graph are constructed from Bertoin–Fujita–Roynette–Yor (BFRY) random variables, which have been recently utilized in Bayesian statistics for the construction of power law models in several applications. Our construction readily extends to capture the structure of latent factors, similarly to stochastic block-models, while maintaining its power law degree distribution. The BFRY random variables are well approximated by gamma random variables in a variational Bayesian inference routine, which we apply to several network datasets for which power law degree distributions are a natural assumption. By learning the parameters of the BFRY distribution via probabilistic inference, we are able to automatically select the appropriate power law behavior from the data. In order to further scale our inference procedure, we adopt stochastic gradient ascent routines where the gradients are computed on minibatches (i.e., subsets) of the edges in the graph.

We propose a Bayesian nonparametric prior over feature allocations for sequential data, the birth-death feature allocation process (BDFP). The BDFP models the evolution of the feature allocation of a set of N objects across a covariate (e.g.~time) by creating and deleting features. A BDFP is exchangeable, projective, stationary and reversible, and its equilibrium distribution is given by the Indian buffet process (IBP). We show that the Beta process on an extended space is the de Finetti mixing distribution underlying the BDFP. Finally, we present the finite approximation of the BDFP, the Beta Event Process (BEP), that permits simplified inference. The utility of the BDFP as a prior is demonstrated on real world dynamic genomics and social network data.

Hamiltonian Monte Carlo (HMC) exploits Hamiltonian dynamics to construct efficient proposals for Markov chain Monte Carlo (MCMC). In this paper, we present a generalization of HMC which exploits non-canonical Hamiltonian dynamics. We refer to this algorithm as magnetic HMC, since in 3 dimensions a subset of the dynamics map onto the mechanics of a charged particle coupled to a magnetic field. We establish a theoretical basis for the use of non-canonical Hamiltonian dynamics in MCMC, and construct a symplectic, leapfrog-like integrator allowing for the implementation of magnetic HMC. Finally, we exhibit several examples where these non-canonical dynamics can lead to improved mixing of magnetic HMC relative to ordinary HMC.

A common practice in statistics and machine learning is to assume that the statistical data types (e.g., ordinal, categorical or real-valued) of variables, and usually also the likelihood model, is known. However, as the availability of real-world data increases, this assumption becomes too restrictive. Data are often heterogeneous, complex, and improperly or incompletely documented. Surprisingly, despite their practical importance, there is still a lack of tools to automatically discover the statistical types of, as well as appropriate likelihood (noise) models for, the variables in a dataset. In this paper, we fill this gap by proposing a Bayesian method, which accurately discovers the statistical data types in both synthetic and real data.

Off-policy model-free deep reinforcement learning methods using previously collected data can improve sample efficiency over on-policy policy gradient techniques. On the other hand, on-policy algorithms are often more stable and easier to use. This paper examines, both theoretically and empirically, approaches to merging on- and off-policy updates for deep reinforcement learning. Theoretical results show that off-policy updates with a value function estimator can be interpolated with on-policy policy gradient updates whilst still satisfying performance bounds. Our analysis uses control variate methods to produce a family of policy gradient algorithms, with several recently proposed algorithms being special cases of this family. We then provide an empirical comparison of these techniques with the remaining algorithmic details fixed, and show how different mixing of off-policy gradient estimates with on-policy samples contribute to improvements in empirical performance. The final algorithm provides a generalization and unification of existing deep policy gradient techniques, has theoretical guarantees on the bias introduced by off-policy updates, and improves on the state-of-the-art model-free deep RL methods on a number of OpenAI Gym continuous control benchmarks.

GPflow is a Gaussian process library that uses TensorFlow for its core computations and Python for its front end. The distinguishing features of GPflow are that it uses variational inference as the primary approximation method, provides concise code through the use of automatic differentiation, has been engineered with a particular emphasis on software testing and is able to exploit GPU hardware.

Bayesian generalised ensemble (BayesGE) is a new method that addresses two major drawbacks of standard Markov chain Monte Carlo algorithms for inference in high-dimensional probability models: inapplicability to estimate the partition function and poor mixing properties. BayesGE uses a Bayesian approach to iteratively update the belief about the density of states (distribution of the log likelihood under the prior) for the model, with the dual purpose of enhancing the sampling efficiency and making the estimation of the partition function tractable. We benchmark BayesGE on Ising and Potts systems and show that it compares favourably to existing state-of-the-art methods.

The variational framework for learning inducing variables (Titsias, 2009) has had a large impact on the Gaussian process literature. The framework may be interpreted as minimizing a rigorously defined Kullback-Leibler divergence between the approximating and posterior processes. To our knowledge this connection has thus far gone unremarked in the literature. In this paper we give a substantial generalization of the literature on this topic. We give a new proof of the result for infinite index sets which allows inducing points that are not data points and likelihoods that depend on all function values. We then discuss augmented index sets and show that, contrary to previous works, marginal consistency of augmentation is not enough to guarantee consistency of variational inference with the original model. We then characterize an extra condition where such a guarantee is obtainable. Finally we show how our framework sheds light on interdomain sparse approximations and sparse approximations for Cox processes.

Drawing a sample from a discrete distribution is one of the building components for Monte Carlo methods. Like other sampling algorithms, discrete sampling suffers from the high computational burden in large-scale inference problems. We study the problem of sampling a discrete random variable with a high degree of dependency that is typical in large-scale Bayesian inference and graphical models, and propose an efficient approximate solution with a subsampling approach. We make a novel connection between the discrete sampling and Multi-Armed Bandits problems with a finite reward population and provide three algorithms with theoretical guarantees. Empirical evaluations show the robustness and efficiency of the approximate algorithms in both synthetic and real-world large-scale problems.

Deep learning tools have gained tremendous attention in applied machine learning. However such tools for regression and classification do not capture model uncertainty. In comparison, Bayesian models offer a mathematically grounded framework to reason about model uncertainty, but usually come with a prohibitive computational cost. In this paper we develop a new theoretical framework casting dropout training in deep neural networks (NNs) as approximate Bayesian inference in deep Gaussian processes. A direct result of this theory gives us tools to model uncertainty with dropout NNs – extracting information from existing models that has been thrown away so far. This mitigates the problem of representing uncertainty in deep learning without sacrificing either computational complexity or test accuracy. We perform an extensive study of the properties of dropout’s uncertainty. Various network architectures and non-linearities are assessed on tasks of regression and classification, using MNIST as an example. We show a considerable improvement in predictive log-likelihood and RMSE compared to existing state-of-the-art methods, and finish by using dropout’s uncertainty in deep reinforcement learning.

There has been a surge of research interest in developing tools and analysis for Bayesian optimization, the task of finding the global maximizer of an unknown, expensive function through sequential evaluation using Bayesian decision theory. However, many interesting problems involve optimizing multiple, expensive to evaluate objectives simultaneously, and relatively little research has addressed this setting from a Bayesian theoretic standpoint. A prevailing choice when tackling this problem, is to model the multiple objectives as being independent, typically for ease of computation. In practice, objectives are correlated to some extent. In this work, we incorporate the modelling of inter-task correlations, developing an approximation to overcome intractable integrals. We illustrate the power of modelling dependencies between objectives on a range of synthetic and real world multi-objective optimization problems.

Recurrent neural networks (RNNs) stand at the forefront of many recent developments in deep learning. Yet a major difficulty with these models is their tendency to overfit, with dropout shown to fail when applied to recurrent layers. Recent results at the intersection of Bayesian modelling and deep learning offer a Bayesian interpretation of common deep learning techniques such as dropout. This grounding of dropout in approximate Bayesian inference suggests an extension of the theoretical results, offering insights into the use of dropout with RNN models. We apply this new variational inference based dropout technique in LSTM and GRU models, assessing it on language modelling and sentiment analysis tasks. The new approach outperforms existing techniques, and to the best of our knowledge improves on the single model state-of-the-art in language modelling with the Penn Treebank (73.4 test perplexity). This extends our arsenal of variational tools in deep learning.

Tensor factorization is a powerful tool to analyse multi-way data. Recently proposed nonlinear factorization methods, although capable of capturing complex relationships, are computationally quite expensive and may suffer a severe learning bias in case of extreme data sparsity. Therefore, we propose a distributed, flexible nonlinear tensor factorization model, which avoids the expensive computations and structural restrictions of the Kronecker-product in the existing TGP formulations, allowing an arbitrary subset of tensor entries to be selected for training. Meanwhile, we derive a tractable and tight variational evidence lower bound (ELBO) that enables highly decoupled, parallel computations and high-quality inference. Based on the new bound, we develop a distributed, key-value-free inference algorithm in the MapReduce framework, which can fully exploit the memory cache mechanism in fast MapReduce systems such as Spark. Experiments demonstrate the advantages of our method over several state-of-the-art approaches, in terms of both predictive performance and computational efficiency.

We present an information-theoretic framework for solving global black-box optimization problems that also have black-box constraints. Of particular interest to us is to efficiently solve problems with decoupled constraints, in which subsets of the objective and constraint functions may be evaluated independently. For example, when the objective is evaluated on a CPU and the constraints are evaluated independently on a GPU. These problems require an acquisition function that can be separated into the contributions of the individual function evaluations. We develop one such acquisition function and call it Predictive Entropy Search with Constraints (PESC). PESC is an approximation to the expected information gain criterion and it compares favorably to alternative approaches based on improvement in several synthetic and real- world problems. In addition to this, we consider problems with a mix of functions that are fast and slow to evaluate. These problems require balancing the amount of time spent in the meta- computation of PESC and in the actual evaluation of the target objective. We take a bounded rationality approach and develop a partial update for PESC which trades off accuracy against speed. We then propose a method for adaptively switching between the partial and full updates for PESC. This allows us to interpolate between versions of PESC that are efficient in terms of function evaluations and those that are efficient in terms of wall-clock time. Overall, we demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.

We propose a method for unsupervised many-to-many object matching from multiple networks, which is the task of finding correspondences between groups of nodes in different networks. For example, the proposed method can discover shared word groups from multi-lingual document-word networks without cross-language alignment information. We assume that multiple networks share groups, and each group has its own interaction pattern with other groups. Using infinite relational models with this assumption, objects in different networks are clustered into common groups depending on their interaction patterns, discovering a matching. The effectiveness of the proposed method is experimentally demonstrated by using synthetic and real relational data sets, which include applications to cross-domain recommendation without shared user/item identifiers and multi-lingual word clustering.

We consider the problem of daily human activity recognition (HAR) using multiple wireless inertial sensors, and specifically, HAR systems with a very low number of sensors, each one providing an estimation of the performed activities. We propose new Bayesian models to combine the output of the sensors. The models are based on a soft outputs combination of individual classifiers to deal with the small number of sensors. We also incorporate the dynamic nature of human activities as a first-order homogeneous Markov chain. We develop both inductive and transductive inference methods for each model to be employed in supervised and semisupervised situations, respectively. Using different real HAR databases, we compare our classifiers combination models against a single classifier that employs all the signals from the sensors. Our models exhibit consistently a reduction of the error rate and an increase of robustness against sensor failures. Our models also outperform other classifiers combination models that do not consider soft outputs and an Markovian structure of the human activities.

Gaussian process classification is a popular method with a number of appealing properties. We show how to scale the model within a variational inducing point framework, out-performing the state of the art on benchmark datasets. Importantly, the variational formulation an be exploited to allow classification in problems with millions of data points, as we demonstrate in experiments.

This article makes several improvements to the classic PPM algorithm, resulting in a new algorithm with superior compression effectiveness on human text. The key differences of our algorithm to classic PPM are that (A) rather than the original escape mechanism, we use a generalised blending method with explicit hyper-parameters that control the way symbol counts are combined to form predictions, (B) different hyper-parameters are used for classes of different contexts, and (C) these hyper-parameters are updated dynamically using gradient information. The resulting algorithm (PPM-DP) compresses human text better than all currently published variants of PPM, CTW, DMC, LZ, CSE and BWT, with runtime only slightly slower than classic PPM.

The machine learning community has recently shown a lot of interest in practical probabilistic programming systems that target the problem of Bayesian inference. Such systems come in different forms, but they all express probabilistic models as computational processes using syntax resembling programming languages. In the functional programming community monads are known to offer a convenient and elegant abstraction for programming with probability distributions, but their use is often limited to very simple inference problems. We show that it is possible to use the monad abstraction to construct probabilistic models for machine learning, while still offering good performance of inference in challenging models. We use a GADT as an underlying representation of a probability distribution and apply Sequential Monte Carlo-based methods to achieve efficient inference. We define a formal semantics via measure theory. We demonstrate a clean and elegant implementation that achieves performance comparable with Anglican, a state-of-the-art probabilistic programming system.

Multivariate categorical data occur in many applications of machine learning. One of the main difficulties with these vectors of categorical variables is sparsity. The number of possible observations grows exponentially with vector length, but dataset diversity might be poor in comparison. Recent models have gained significant improvement in supervised tasks with this data. These models embed observations in a continuous space to capture similarities between them. Building on these ideas we propose a Bayesian model for the unsupervised task of distribution estimation of multivariate categorical data. We model vectors of categorical variables as generated from a non-linear transformation of a continuous latent space. Non-linearity captures multi-modality in the distribution. The continuous representation addresses sparsity. Our model ties together many existing models, linking the linear categorical latent Gaussian model, the Gaussian process latent variable model, and Gaussian process classification. We derive inference for our model based on recent developments in sampling based variational inference. We show empirically that the model outperforms its linear and discrete counterparts in imputation tasks of sparse data.

Bayesian nonparametric mixture models based on the Dirichlet process (DP) have been widely used for solving problems like clustering, density estimation and topic modelling. These models make weak assumptions about the underlying process that generated the observed data. Thus, when more data are collected, the complexity of these models can change accordingly. These theoretical properties often lead to superior predictive performance when compared to traditional finite mixture models. However, despite the increasing amount of data available, the application of Bayesian nonparametric mixture models is so far limited to relatively small data sets. In this paper, we propose an efficient distributed inference algorithm for the DP and the HDP mixture model. The proposed method is based on a variant of the slice sampler for DPs. Since this sampler does not involve a pre-determined truncation, the stationary distribution of the sampling algorithm is unbiased. We provide both local thread-level and distributed machine-level parallel implementations and study the performance of this sampler through an extensive set of experiments on image and text data. When compared to existing inference algorithms, the proposed method exhibits state-of-the-art accuracy and strong scalability with up to 512 cores.

Multi-task feature selection methods often make the hypothesis that learning tasks share relevant and irrelevant features. However, this hypothesis may be too restrictive in practice. For example, there may be a few tasks with specific relevant and irrelevant features (outlier tasks). Similarly, a few of the features may be relevant for only some of the tasks (outlier features). To account for this, we propose a model for multi-task feature selection based on a robust prior distribution that introduces a set of binary latent variables to identify outlier tasks and outlier features. Expectation propagation can be used for efficient approximate inference under the proposed prior. Several experiments show that a model based on the new robust prior provides better predictive performance than other benchmark methods.

Unknown constraints arise in many types of expensive black-box optimization problems. Several methods have been proposed recently for performing Bayesian optimization with constraints, based on the expected improvement (EI) heuristic. However, EI can lead to pathologies when used with constraints. For example, in the case of decoupled constraints—i.e., when one can independently evaluate the objective or the constraints—EI can encounter a pathology that prevents exploration. Additionally, computing EI requires a current best solution, which may not exist if none of the data collected so far satisfy the constraints. By contrast, information-based approaches do not suffer from these failure modes. In this paper, we present a new information-based method called Predictive Entropy Search with Constraints (PESC). We analyze the performance of PESC and show that it compares favorably to EI-based approaches on synthetic and benchmark problems, as well as several real-world examples. We demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.

Stochastic variational inference (SVI) is emerging as the most promising candidate for scaling inference in Bayesian probabilistic models to large datasets. However, the performance of these methods has been assessed primarily in the context of Bayesian topic models, particularly latent Dirichlet allocation (LDA). Deriving several new algorithms, and using synthetic, image and genomic datasets, we investigate whether the understanding gleaned from LDA applies in the setting of sparse latent factor models, specifically beta process factor analysis (BPFA). We demonstrate that the big picture is consistent: using Gibbs sampling within SVI to maintain certain posterior dependencies is extremely effective. However, we also show that different posterior dependencies are important in BPFA relative to LDA.

Sequential Monte Carlo (SMC), or particle filtering, is a popular class of methods for sampling from an intractable target distribution using a sequence of simpler intermediate distributions. Like other importance sampling-based methods, performance is critically dependent on the proposal distribution: a bad proposal can lead to arbitrarily inaccurate estimates of the target distribution. This paper presents a new method for automatically adapting the proposal using an approximation of the Kullback-Leibler divergence between the true posterior and the proposal distribution. The method is very flexible, applicable to any parameterized proposal distribution and it supports online and batch variants. We use the new framework to adapt powerful proposal distributions with rich parameterizations based upon neural networks leading to Neural Adaptive Sequential Monte Carlo (NASMC). Experiments indicate that NASMC significantly improves inference in a non-linear state space model outperforming adaptive proposal methods including the Extended Kalman and Unscented Particle Filters. Experiments also indicate that improved inference translates into improved parameter learning when NASMC is used as a subroutine of Particle Marginal Metropolis Hastings. Finally we show that NASMC is able to train a latent variable recurrent neural network (LV-RNN) achieving results that compete with the state-of-the-art for polymorphic music modelling. NASMC can be seen as bridging the gap between adaptive SMC methods and the recent work in scalable, black-box variational inference.

Gaussian process (GP) models form a core part of probabilistic machine learning. Considerable research effort has been made into attacking three issues with GP models: how to compute efficiently when the number of data is large; how to approximate the posterior when the likelihood is not Gaussian and how to estimate covariance function parameter posteriors. This paper simultaneously addresses these, using a variational approximation to the posterior which is sparse in sup- port of the function but otherwise free-form. The result is a Hybrid Monte-Carlo sampling scheme which allows for a non-Gaussian approximation over the function values and covariance parameters simultaneously, with efficient computations based on inducing-point sparse GPs.

We propose an exploratory approach to statistical model criticism using maximum mean discrepancy (MMD) two sample tests. Typical approaches to model criticism require a practitioner to select a statistic by which to measure discrepancies between data and a statistical model. MMD two sample tests are instead constructed as an analytic maximisation over a large space of possible statistics and therefore automatically select the statistic which most shows any discrepancy. We demonstrate on synthetic data that the selected statistic, called the witness function, can be used to identify where a statistical model most misrepresents the data it was trained on. We then apply the procedure to real data where the models being assessed are restricted Boltzmann machines, deep belief networks and Gaussian process regression and demonstrate the ways in which these models fail to capture the properties of the data they are trained on.

We develop \textit{parallel predictive entropy search} (PPES), a novel algorithm for Bayesian optimization of expensive black-box objective functions. At each iteration, PPES aims to select a \textit{batch} of points which will maximize the information gain about the global maximizer of the objective. Well known strategies exist for suggesting a single evaluation point based on previous observations, while far fewer are known for selecting batches of points to evaluate in parallel. The few batch selection schemes that have been studied all resort to greedy methods to compute an optimal batch. To the best of our knowledge, PPES is the first non-greedy batch Bayesian optimization strategy. We demonstrate the benefit of this approach in optimization performance on both synthetic and real world applications, including problems in machine learning, rocket science and robotics.

Infinite Hidden Markov Models (iHMM's) are an attractive, nonparametric generalization of the classical Hidden Markov Model which can automatically infer the number of hidden states in the system. However, due to the infinite-dimensional nature of the transition dynamics, performing inference in the iHMM is difficult. In this paper, we present an infinite-state Particle Gibbs (PG) algorithm to resample state trajectories for the iHMM. The proposed algorithm uses an efficient proposal optimized for iHMMs, and leverages ancestor sampling to improve the mixing of the standard PG algorithm. Our algorithm demonstrates significant convergence improvements on synthetic and real world data sets.

Hidden conditional random fields (HCRFs) are discriminative latent variable models which have been shown to successfully learn the hidden structure of a given classification problem. An Infinite hidden conditional random field is a hidden conditional random field with a countably infinite number of hidden states, which rids us not only of the necessity to specify a priori a fixed number of hidden states available but also of the problem of overfitting. Markov chain Monte Carlo (MCMC) sampling algorithms are often employed for inference in such models. However, convergence of such algorithms is rather difficult to verify, and as the complexity of the task at hand increases the computational cost of such algorithms often becomes prohibitive. These limitations can be overcome by variational techniques. In this paper, we present a generalized framework for infinite HCRF models, and a novel variational inference approach on a model based on coupled Dirichlet Process Mixtures, the HCRF-DPM. We show that the variational HCRF-DPM is able to converge to a correct number of represented hidden states, and performs as well as the best parametric HCRFs-chosen via cross-validation-for the difficult tasks of recognizing instances of agreement, disagreement, and pain in audiovisual sequences.

We introduce a conceptually novel structured prediction model, GPstruct, which is kernelized, non-parametric and Bayesian, by design. We motivate the model with respect to existing approaches, among others, conditional random fields (CRFs), maximum margin Markov networks (M3N), and structured support vector machines (SVMstruct), which embody only a subset of its properties. We present an inference procedure based on Markov Chain Monte Carlo. The framework can be instantiated for a wide range of structured objects such as linear chains, trees, grids, and other general graphs. As a proof of concept, the model is benchmarked on several natural language processing tasks and a video gesture segmentation task involving a linear chain structure. We show prediction accuracies for GPstruct which are comparable to or exceeding those of CRFs and SVMstruct.

In this paper we introduce the Pitman Yor Diffusion Tree (PYDT), a Bayesian non-parametric prior over tree structures which generalises the Dirichlet Diffusion Tree [30] and removes the restriction to binary branching structure. The generative process is described and shown to result in an exchangeable distribution over data points. We prove some theoretical properties of the model including showing its construction as the continuum limit of a nested Chinese restaurant process model. We then present two alternative MCMC samplers which allow us to model uncertainty over tree structures, and a computationally efficient greedy Bayesian EM search algorithm. Both algorithms use message passing on the tree structure. The utility of the model and algorithms is demonstrated on synthetic and real world data, both continuous and binary.

Latent variable models for network data extract a summary of the relational structure underlying an observed network. The simplest possible models subdivide nodes of the network into clusters; the probability of a link between any two nodes then depends only on their cluster assignment. Currently available models can be classified by whether clusters are disjoint or are allowed to overlap. These models can explain a "flat" clustering structure. Hierarchical Bayesian models provide a natural approach to capture more complex dependencies. We propose a model in which objects are characterised by a latent feature vector. Each feature is itself partitioned into disjoint groups (subclusters), corresponding to a second layer of hierarchy. In experimental comparisons, the model achieves significantly improved predictive performance on social and biological link prediction tasks. The results indicate that models with a single layer hierarchy over-simplify real networks.

Random forests works by averaging several predictions of de-correlated trees. We show a conceptually radical approach to generate a random forest: random sampling of many trees from a prior distribution, and subsequently performing a weighted ensemble of predictive probabilities. Our approach uses priors that allow sampling of decision trees even before looking at the data, and a power likelihood that explores the space spanned by combination of decision trees. While each tree performs Bayesian inference to compute its predictions, our aggregation procedure uses the power likelihood rather than the likelihood and is therefore strictly speaking not Bayesian. Nonetheless, we refer to it as a Bayesian random forest but with a built-in safety. The safeness comes as it has good predictive performance even if the underlying probabilistic model is wrong. We demonstrate empirically that our Safe-Bayesian random forest outperforms MCMC or SMC based Bayesian decision trees in term of speed and accuracy, and achieves competitive performance to entropy or Gini optimised random forest, yet is very simple to construct.

This paper presents the beginnings of an automatic statistician, focusing on regression problems. Our system explores an open-ended space of statistical models to discover a good explanation of a data set, and then produces a detailed report with figures and natural-language text. Our approach treats unknown regression functions nonparametrically using Gaussian processes, which has two important consequences. First, Gaussian processes can model functions in terms of high-level properties (e.g. smoothness, trends, periodicity, changepoints). Taken together with the compositional structure of our language of models this allows us to automatically describe functions in simple terms. Second, the use of flexible nonparametric models and a rich language for composing them in an open-ended manner also results in state-of-the-art extrapolation performance evaluated over 13 real time series data sets from various domains.

In this paper, we propose a non-parametric conditional factor regression (NCFR) model for domains with multi-dimensional input and response. NCFR enhances linear regression in two ways: a) introducing low-dimensional latent factors leading to dimensionality reduction and b) integrating the Indian Buffet Process as prior for the latent layer to dynamically derive an optimal number of sparse factors. Thanks to IBP’s enhancements to the latent factors, NCFR can significantly avoid over-fitting even in the case of a very small sample size compared to the dimensionality. Experimental results on three diverse datasets comparing NCRF to a few baseline alternatives give evidence of its robust learning, remarkable predictive performance, good mixing and computational efficiency.

Choosing appropriate architectures and regularization strategies of deep networks is crucial to good predictive performance. To shed light on this problem, we analyze the analogous problem of constructing useful priors on compositions of functions. Specifically, we study the deep Gaussian process, a type of infinitely-wide, deep neural network. We show that in standard architectures, the representational capacity of the network tends to capture fewer degrees of freedom as the number of layers increases, retaining only a single degree of freedom in the limit. We propose an alternate network architecture which does not suffer from this pathology. We also examine deep covariance functions, obtained by composing infinitely many feature transforms. Lastly, we characterize the class of models obtained by performing dropout on Gaussian processes.

We investigate the Student-t process as an alternative to the Gaussian process as a nonparametric prior over functions. We derive closed form expressions for the marginal likelihood and predictive distribution of a Student-t process, by integrating away an inverse Wishart process prior over the covariance kernel of a Gaussian process model. We show surprising equivalences between different hierarchical Gaussian process models leading to Student-t processes, and derive a new sampling scheme for the inverse Wishart process, which helps elucidate these equivalences. Overall, we show that a Student-t process can retain the attractive properties of a Gaussian process – a nonparametric representation, analytic marginal and predictive distributions, and easy model selection through covariance kernels – but has enhanced flexibility, and a predictive covariance that, unlike a Gaussian process, explicitly depends on the values of training observations. We verify empirically that a Student-t process is especially useful in situations where there are changes in covariance structure, or in applications like Bayesian optimization, where accurate predictive covariances are critical for good performance. These advantages come at no additional computational cost over Gaussian processes.

Structured prediction is an important and well studied problem with many applications across machine learning. GPstruct is a recently proposed structured prediction model that offers appealing properties such as being kernelised, non-parametric, and supporting Bayesian inference (Bratières et al. 2013). The model places a Gaussian process prior over energy functions which describe relationships between input variables and structured output variables. However, the memory demand of GPstruct is quadratic in the number of latent variables and training runtime scales cubically. This prevents GPstruct from being applied to problems involving grid factor graphs, which are prevalent in computer vision and spatial statistics applications. Here we explore a scalable approach to learning GPstruct models based on ensemble learning, with weak learners (predictors) trained on subsets of the latent variables and bootstrap data, which can easily be distributed. We show experiments with 4M latent variables on image segmentation. Our method outperforms widely-used conditional random field models trained with pseudo-likelihood. Moreover, in image segmentation problems it improves over recent state-of-the-art marginal optimisation methods in terms of predictive performance and uncertainty calibration. Finally, it generalises well on all training set sizes.

Recent work done by Lovell, Adams, and Mansingka (2012) and Williamson, Dubey, and Xing (2013) has suggested an alternative parametrisation for the Dirichlet process in order to derive non-approximate parallel MCMC inference for it - work which has been picked-up and implemented in several different fields. In this paper we show that the approach suggested is impractical due to an extremely unbalanced distribution of the data. We characterise the requirements of efficient parallel inference for the Dirichlet process and show that the proposed inference fails most of these requirements (while approximate approaches often satisfy most of them). We present both theoretical and experimental evidence, analysing the load balance for the inference and showing that it is independent of the size of the dataset and the number of nodes available in the parallel implementation. We end with suggestions of alternative paths of research for efficient non-approximate parallel inference for the Dirichlet process.

We define the beta diffusion tree, a random tree structure with a set of leaves that defines a collection of overlapping subsets of objects, known as a feature allocation. The generative process for the tree is defined in terms of particles (representing the objects) diffusing in some continuous space, analogously to the Dirichlet and Pitman-Yor diffusion trees (Neal, 2003b; Knowles & Ghahramani, 2011), both of which define tree structures over clusters of the particles. With the beta diffusion tree, however, multiple copies of a particle may exist and diffuse to multiple locations in the continuous space, resulting in (a random number of) possibly overlapping clusters of the objects. We demonstrate how to build a hierarchically-clustered factor analysis model with the beta diffusion tree and how to perform inference over the random tree structures with a Markov chain Monte Carlo algorithm. We conclude with several numerical experiments on missing data problems with data sets of gene expression arrays, international development statistics, and intranational socioeconomic measurements.

Fully observed large binary matrices appear in a wide variety of contexts. To model them, probabilistic matrix factorization (PMF) methods are an attractive solution. However, current batch algorithms for PMF can be inefficient because they need to analyze the entire data matrix before producing any parameter updates. We derive an efficient stochastic inference algorithm for PMF models of fully observed binary matrices. Our method exhibits faster convergence rates than more expensive batch approaches and has better predictive performance than scalable alternatives. The proposed method includes new data subsampling strategies which produce large gains over standard uniform subsampling. We also address the task of automatically selecting the size of the minibatches of data used by our method. For this, we derive an algorithm that adjusts this hyper-parameter online.

We propose a probabilistic matrix factorization model for collaborative filtering that learns from data that is missing not at random(MNAR). Matrix factorization models exhibit state-of-the-art predictive performance in collaborative filtering. However, these models usually assume that the data is missing at random (MAR), and this is rarely the case. For example, the data is not MAR if users rate items they like more than ones they dislike. When the MAR assumption is incorrect, inferences are biased and predictive performance can suffer. Therefore, we model both the generative process for the data and the missing data mechanism. By learning these two models jointly we obtain improved performance over state-of-the-art methods when predicting the ratings and when modeling the data observation process. We present the first viable MF model for MNAR data. Our results are promising and we expect that further research on NMAR models will yield large gains in collaborative filtering.

We present a new matrix factorization model for rating data and a corresponding active learning strategy to address the cold-start problem. Cold-start is one of the most challenging tasks for recommender systems: what to recommend with new users or items for which one has little or no data. An approach is to use active learning to collect the most useful initial ratings. However, the performance of active learning depends strongly upon having accurate estimates of i) the uncertainty in model parameters and ii) the intrinsic noisiness of the data. To achieve these estimates we propose a heteroskedastic Bayesian model for ordinal matrix factorization. We also present a computationally efficient framework for Bayesian active learning with this type of complex probabilistic model. This algorithm successfully distinguishes between informative and noisy data points. Our model yields state-of-the-art predictive performance and, coupled with our active learning strategy, enables us to gain useful information in the cold-start setting from the very first active sample.

We present a nonparametric prior over reversible Markov chains. We use completely random measures, specifically gamma processes, to construct a countably infinite graph with weighted edges. By enforcing symmetry to make the edges undirected we define a prior over random walks on graphs that results in a reversible Markov chain. The resulting prior over infinite transition matrices is closely related to the hierarchical Dirichlet process but enforces reversibility. A reinforcement scheme has recently been proposed with similar properties, but the de Finetti measure is not well characterised. We take the alternative approach of explicitly constructing the mixing measure, which allows more straightforward and efficient inference at the cost of no longer having a closed form predictive distribution. We use our process to construct a reversible infinite HMM which we apply to two real datasets, one from epigenomics and one ion channel recording.

Classical methods such as Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA) are ubiquitous in statistics. However, these techniques are only able to reveal linear relationships in data. Although nonlinear variants of PCA and CCA have been proposed, these are computationally prohibitive in the large scale. In a separate strand of recent research, randomized methods have been proposed to construct features that help reveal nonlinear patterns in data. For basic tasks such as regression or classification, random features exhibit little or no loss in performance, while achieving drastic savings in computational requirements. In this paper we leverage randomness to design scalable new variants of nonlinear PCA and CCA; our ideas extend to key multivariate analysis tools such as spectral clustering or LDA. We demonstrate our algorithms through experiments on real-world data, on which we compare against the state-of-the-art. A simple R implementation of the presented algorithms is provided.

Many automatic visualization methods have been proposed. However, a visualization that is automatically generated might be different to how a user wants to arrange the objects in visualization space. By allowing users to re-locate objects in the embedding space of the visualization, they can adjust the visualization to their preference. We propose an active learning framework for interactive visualization which selects objects for the user to re-locate so that they can obtain their desired visualization by re-locating as few as possible. The framework is based on an information theoretic criterion, which favors objects that reduce the uncertainty of the visualization. We present a concrete application of the proposed framework to the Laplacian eigenmap visualization method. We demonstrate experimentally that the proposed framework yields the desired visualization with fewer user interactions than existing methods.

Despite its importance, choosing the structural form of the kernel in nonparametric regression remains a black art. We define a space of kernel structures which are built compositionally by adding and multiplying a small number of base kernels. We present a method for searching over this space of structures which mirrors the scientific discovery process. The learned structures can often decompose functions into interpretable components and enable long-range extrapolation on time-series datasets. Our structure search method outperforms many widely used kernels and kernel combination methods on a variety of prediction tasks.

Current Bayesian models for dynamic social network data have focused on modelling the influence of evolving unobserved structure on observed social interactions. However, an understanding of how observed social relationships from the past affect future unobserved structure in the network has been neglected. In this paper, we introduce a new probabilistic model for capturing this phenomenon, which we call latent feature propagation, in social networks. We demonstrate our model’s capability for inferring such latent structure in varying types of social network datasets, and experimental studies show this structure achieves higher predictive performance on link prediction and forecasting tasks.

Copulas allow to learn marginal distributions separately from the multivariate dependence structure (copula) that links them together into a density function. Vine factorizations ease the learning of high-dimensional copulas by constructing a hierarchy of conditional bivariate copulas. However, to simplify inference, it is common to assume that each of these conditional bivariate copulas is independent from its conditioning variables. In this paper, we relax this assumption by discovering the latent functions that specify the shape of a conditional copula given its conditioning variables. We learn these functions by following a Bayesian approach based on sparse Gaussian processes with expectation propagation for scalable, approximate inference. Experiments on real-world datasets show that, when modeling all conditional dependencies, we obtain better estimates of the underlying copula of the data.

Inference for latent feature models is inherently difficult as the inference space grows exponentially with the size of the input data and number of latent features. In this work, we use Kurihara & Wellings (2008)’s maximization-expectation framework to perform approximate MAP inference for linear-Gaussian latent feature models with an Indian Buffet Process (IBP) prior. This formulation yields a submodular function of the features that corresponds to a lower bound on the model evidence. By adding a constant to this function, we obtain a nonnegative submodular function that can be maximized via a greedy algorithm that obtains at least a 1/3-approximation to the optimal solution. Our inference method scales linearly with the size of the input data, and we show the efficacy of our method on the largest datasets currently analyzed using an IBP model.

The accurate prediction of time-changing covariances is an important problem in the modeling of multivariate financial data. However, some of the most popular models suffer from a) overfitting problems and multiple local optima, b) failure to capture shifts in market conditions and c) large computational costs. To address these problems we introduce a novel dynamic model for time-changing covariances. Over-fitting and local optima are avoided by following a Bayesian approach instead of computing point estimates. Changes in market conditions are captured by assuming a diffusion process in parameter values, and finally computationally efficient and scalable inference is performed using particle filters. Experiments with financial data show excellent performance of the proposed method with respect to current standard models.

Many people share their activities with others through online communities. These shared activities have an impact on other users' activities. For example, users are likely to become interested in items that are adopted (e.g. liked, bought and shared) by their friends. In this paper, we propose a probabilistic model for discovering latent influence from sequences of item adoption events. An inhomogeneous Poisson process is used for modeling a sequence, in which adoption by a user triggers the subsequent adoption of the same item by other users. For modeling adoption of multiple items, we employ multiple inhomogeneous Poisson processes, which share parameters, such as influence for each user and relations between users. The proposed model can be used for finding influential users, discovering relations between users and predicting item popularity in the future. We present an efficient Bayesian inference procedure of the proposed model based on the stochastic EM algorithm. The effectiveness of the proposed model is demonstrated by using real data sets in a social bookmark sharing service.

The Internet has enabled the creation of a growing number of large-scale knowledge bases in a variety of domains containing complementary information. Tools for automatically aligning these knowledge bases would make it possible to unify many sources of structured knowledge and answer complex queries. However, the efficient alignment of large-scale knowledge bases still poses a considerable challenge. Here, we present Simple Greedy Matching (SiGMa), a simple algorithm for aligning knowledge bases with millions of entities and facts. SiGMa is an iterative propagation algorithm that leverages both the structural information from the relationship graph and flexible similarity measures between entity properties in a greedy local search, which makes it scalable. Despite its greedy nature, our experiments indicate that SiGMa can efficiently match some of the world's largest knowledge bases with high accuracy. We provide additional experiments on benchmark datasets which demonstrate that SiGMa can outperform state-of-the-art approaches both in accuracy and efficiency.

We offer a solution to the problem of efficiently translating algorithms between different types of discrete statistical model. We investigate the expressive power of three classes of model-those with binary variables, with pairwise factors, and with planar topology-as well as their four intersections. We formalize a notion of "simple reduction" for the problem of inferring marginal probabilities and consider whether it is possible to "simply reduce" marginal inference from general discrete factor graphs to factor graphs in each of these seven subclasses. We characterize the reducibility of each class, showing in particular that the class of binary pairwise factor graphs is able to simply reduce only positive models. We also exhibit a continuous "spectral reduction" based on polynomial interpolation, which overcomes this limitation. Experiments assess the performance of standard approximate inference algorithms on the outputs of our reductions.

We present a new model based on Gaussian processes (GPs) for learning pairwise preferences expressed by multiple users. Inference is simplified by using a \emph{preference kernel} for GPs which allows us to combine supervised GP learning of user preferences with unsupervised dimensionality reduction for multi-user systems. The model not only exploits collaborative information from the shared structure in user behavior, but may also incorporate user features if they are available. Approximate inference is implemented using a combination of expectation propagation and variational Bayes. Finally, we present an efficient active learning strategy for querying preferences. The proposed technique performs favorably on real-world data against state-of-the-art multi-user preference learning algorithms.

Factor analysis models effectively summarise the covariance structure of high dimensional data, but the solutions are typically hard to interpret. This motivates attempting to find a disjoint partition, i.e. a clustering, of observed variables so that variables in a cluster are highly correlated. We introduce a Bayesian non-parametric approach to this problem, and demonstrate advantages over heuristic methods proposed to date.

A fundamental problem in the analysis of structured relational data like graphs, networks, databases, and matrices is to extract a summary of the common struc- ture underlying relations between individual entities. Relational data are typically encoded in the form of arrays; invariance to the ordering of rows and columns corresponds to exchangeable arrays. Results in probability theory due to Aldous, Hoover and Kallenberg show that exchangeable arrays can be represented in terms of a random measurable function which constitutes the natural model parameter in a Bayesian model. We obtain a flexible yet simple Bayesian nonparametric model by placing a Gaussian process prior on the parameter function. Efficient inference utilises elliptical slice sampling combined with a random sparse approximation to the Gaussian process. We demonstrate applications of the model to network data and clarify its relation to models in the literature, several of which emerge as special cases.

Numerical integration is an key component of many problems in scientific computing, statistical modelling, and machine learning. Bayesian Quadrature is a model-based method for numerical integration which, relative to standard Monte Carlo methods, offers increased sample efficiency and a more robust estimate of the uncertainty in the estimated integral. We propose a novel Bayesian Quadrature approach for numerical integration when the integrand is non-negative, such as the case of computing the marginal likelihood, predictive distribution, or normalising constant of a probabilistic model. Our approach approximately marginalises the quadrature model's hyperparameters in closed form, and introduces an active learning scheme to optimally select function evaluations, as opposed to using Monte Carlo samples. We demonstrate our method on both a number of synthetic benchmarks and a real scientific problem from astronomy.

Continuous relaxations play an important role in discrete optimization, but have not seen much use in approximate probabilistic inference. Here we show that a general form of the Gaussian Integral Trick makes it possible to transform a wide class of discrete variable undirected models into fully continuous systems. The continuous representation allows the use of gradient-based Hamiltonian Monte Carlo for inference, results in new ways of estimating normalization constants (partition functions), and in general opens up a number of new avenues for inference in difficult discrete systems. We demonstrate some of these continuous relaxation inference algorithms on a number of illustrative problems.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

How do people determine which elements of a set are most representative of that set? We extend an existing Bayesian measure of representativeness, which indicates the representativeness of a sample from a distribution, to define a measure of the representativeness of an item to a set. We show that this measure is formally related to a machine learning method known as Bayesian Sets. Building on this connection, we derive an analytic expression for the representativeness of objects described by a sparse vector of binary features. We then apply this measure to a large database of images, using it to determine which images are the most representative members of different sets. Comparing the resulting predictions to human judgments of representativeness provides a test of this measure with naturalistic stimuli, and illustrates how databases that are more commonly used in computer vision and machine learning can be used to evaluate psychological theories.

Traffic classification using machine learning continues to be an active research area. The majority of work in this area uses off-the-shelf machine learning tools and treats them as black-box classifiers. This approach turns all the modelling complexity into a feature selection problem. In this paper, we build a problem-specific solution to the traffic classification problem by designing a custom probabilistic graphical model. Graphical models are a modular framework to design classifiers which incorporate domain-specific knowledge. More specifically, our solution introduces semi-supervised learning which means we learn from both labelled and unlabelled traffic flows. We show that our solution performs competitively compared to previous approaches while using less data and simpler features. Copyright © 2010 ACM.

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.

We define a copula process which describes the dependencies between arbitrarily many random variables independently of their marginal distributions. As an example, we develop a stochastic volatility model, Gaussian Copula Process Volatility (GCPV), to predict the latent standard deviations of a sequence of random variables. To make predictions we use Bayesian inference, with the Laplace approximation, and with Markov chain Monte Carlo as an alternative. We find our model can outperform GARCH on simulated and financial data. And unlike GARCH, GCPV can easily handle missing data, incorporate covariates other than time, and model a rich class of covariance structures.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

MOTIVATION: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets. RESULTS: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs. AVAILABILITY: If interested in the code for the work presented in this article, please contact the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Semi-supervised learning (SSL), is classification where additional unlabeled data can be used to improve accuracy. Generative approaches are appealing in this situation, as a model of the data's probability density can assist in identifying clusters. Nonparametric Bayesian methods, while ideal in theory due to their principled motivations, have been difficult to apply to SSL in practice. We present a nonparametric Bayesian method that uses Gaussian processes for the generative model, avoiding many of the problems associated with Dirichlet process mixture models. Our model is fully generative and we take advantage of recent advances in Markov chain Monte Carlo algorithms to provide a practical inference method. Our method compares favorably to competing approaches on synthetic and real-world multi-class data.

We often seek to identify co-occurring hidden features in a set of observations. The Indian Buffet Process (IBP) provides a non-parametric prior on the features present in each observation, but current inference techniques for the IBP often scale poorly. The collapsed Gibbs sampler for the IBP has a running time cubic in the number of observations, and the uncollapsed Gibbs sampler, while linear, is often slow to mix. We present a new linear-time collapsed Gibbs sampler for conjugate likelihood models and demonstrate its efficacy on large real-world datasets.

Nonparametric Bayesian models provide a framework for flexible probabilistic modelling of complex datasets. Unfortunately, Bayesian inference methods often require high-dimensional averages and can be slow to compute, especially with the potentially unbounded representations associated with nonparametric models. We address the challenge of scaling nonparametric Bayesian inference to the increasingly large datasets found in real-world applications, focusing on the case of parallelising inference in the Indian Buffet Process (IBP). Our approach divides a large data set between multiple processors. The processors use message passing to compute likelihoods in an asynchronous, distributed fashion and to propagate statistics about the global Bayesian posterior. This novel MCMC sampler is the first parallel inference scheme for IBP-based models, scaling to datasets orders of magnitude larger than had previously been possible.

BACKGROUND: Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained. RESULTS: We present an R/Bioconductor port of a fast novel algorithm for Bayesian agglomerative hierarchical clustering and demonstrate its use in clustering gene expression microarray data. The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. CONCLUSION: Biologically plausible results are presented from a well studied data set: expression profiles of A. thaliana subjected to a variety of biotic and abiotic stresses. Our method avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric.

Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture (DPM) models provide a nonparametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most previously published applications of Bayesian model-based clustering methods have been to short time series data. In this paper, we present a case study of the application of nonparametric Bayesian clustering methods to the clustering of high-dimensional nontime series gene expression data using full Gaussian covariances. We use the probability that two genes belong to the same cluster in a DPM model as a measure of the similarity of these gene expression profiles. Conversely, this probability can be used to define a dissimilarity measure, which, for the purposes of visualization, can be input to one of the standard linkage algorithms used for hierarchical clustering. Biologically plausible results are obtained from the Rosetta compendium of expression profiles which extend previously published cluster analyses of this data.

Bayesian methods provide a framework for representing and manipulating uncertainty, for learning from noisy data, and for making decisions that maximize expected utility----components which are important to both AI and Machine Learning. However, although Bayesian methods have become more popular in recent years, there remains a good degree of skepticism with respect to taking a fully Bayesian approach. This talk will introduce fundamental topics in Bayesian statistics as they apply to machine learning and AI, and address some misconceptions about Bayesian approaches. I will then discuss some current work on non-parametric Bayesian machine learning, particularly in the area of unsupervised learning.

While data mining in chemoinformatics studied graph data with dozens of nodes, systems biology and the Internet are now generating graph data with thousands and millions of nodes. Hence data mining faces the algorithmic challenge of coping with this significant increase in graph size: Classic algorithms for data analysis are often too expensive and too slow on large graphs. While one strategy to overcome this problem is to design novel efficient algorithms, the other is to 'reduce' the size of the large graph by sampling. This is the scope of this paper: We will present novel Metropolis algorithms for sampling a 'representative' small subgraph from the original large graph, with 'representative' describing the requirement that the sample shall preserve crucial graph properties of the original graph. In our experiments, we improve over the pioneering work of Leskovec and Faloutsos (KDD 2006), by producing representative subgraph samples that are both smaller and of higher quality than those produced by other methods from the literature.

The infinite hidden Markov model is a non-parametric extension of the widely used hidden Markov model. Our paper introduces a new inference algorithm for the infinite Hidden Markov model called beam sampling. Beam sampling combines slice sampling, which limits the number of states considered at each time step to a finite number, with dynamic programming, which samples whole state trajectories efficiently. Our algorithm typically outperforms the Gibbs sampler and is more robust. We present applications of iHMM inference using the beam sampler on changepoint detection and text prediction problems.

We present a principled Bayesian framework for modeling partial memberships of data points to clusters. Unlike a standard mixture model which assumes that each data point belongs to one and only one mixture component, or cluster, a partial membership model allows data points to have fractional membership in multiple clusters. Algorithms which assign data points partial memberships to clusters can be useful for tasks such as clustering genes based on microarray data (Gasch & Eisen, 2002). Our Bayesian Partial Membership Model (BPM) uses exponential family distributions to model each cluster, and a product of these distibtutions, with weighted parameters, to model each datapoint. Here the weights correspond to the degree to which the datapoint belongs to each cluster. All parameters in the BPM are continuous, so we can use Hybrid Monte Carlo to perform inference and learning. We discuss relationships between the BPM and Latent Dirichlet Allocation, Mixed Membership models, Exponential Family PCA, and fuzzy clustering. Lastly, we show some experimental results and discuss nonparametric extensions to our model. 1.

We introduces a new probability distribution over a potentially infinite number of binary Markov chains which we call the Markov Indian buffet process. This process extends the IBP to allow temporal dependencies in the hidden variables. We use this stochastic process to build a nonparametric extension of the factorial hidden Markov model. After working out an inference scheme which combines slice sampling and dynamic programming we demonstrate how the infinite factorial hidden Markov model can be used for blind source separation.

Principal Components Analysis (PCA) has become established as one of the key tools for dimensionality reduction when dealing with real valued data. Approaches such as exponential family PCA and non-negative matrix factorisation have successfully extended PCA to non-Gaussian data types, but these techniques fail to take advantage of Bayesian inference and can suffer from problems of overfitting and poor generalisation. This paper presents a fully probabilistic approach to PCA, which is generalised to the exponential family, based on Hybrid Monte Carlo sampling. We describe the model which is based on a factorisation of the observed data matrix, and show performance of the model on both synthetic and real data.

Variational Bayesian Expectation-Maximization (VBEM), an approximate inference method for probabilistic models based on factorizing over latent variables and model parameters, has been a standard technique for practical Bayesian inference. In this paper, we introduce a more general approximate inference framework for conjugate-exponential family models, which we call Latent-Space Variational Bayes (LSVB). In this approach, we integrate out model parameters in an exact way, leaving only the latent variables. It can be shown that the LSVB approach gives better estimates of the model evidence as well as the distribution over latent variables than the VBEM approach, but in practice, the distribution over latent variables has to be approximated. As a practical implementation, we present a First-order LSVB (FoLSVB) algorithm to approximate this distribution over latent variables. From this approximate distribution, one can estimate the model evidence and the posterior over model parameters. The FoLSVB algorithm is directly comparable to the VBEM algorithm and has the same computational complexity. We discuss how LSVB generalizes the recently proposed collapsed variational methods [20] to general conjugate-exponential families. Examples based on mixtures of Gaussians and mixtures of Bernoullis with synthetic and real-world data sets are used to illustrate some advantages of our method over VBEM.

In this letter, we consider a variational approximate Bayesian inference framework,latent-spacevariationalBayes(LSVB), in the general context ofconjugate-exponentialfamily models with latent variables. In the LSVB approach, we integrate out model parameters in an exact way and then perform the variational inference over only the latent variables. It can be shown that LSVB can achieve better estimates of the model evidence as well as the distribution over the latent variables than the popular variational Bayesian expectation-maximization (VBEM). However, the distribution over the latent variables in LSVB has to be approximated in practice. As an approximate implementation of LSVB, we propose asecond-orderLSVB(SoLSVB)method. In particular, VBEM can be derived as a special case of a first-order approximation in LSVB (Sung). SoLSVB can capture higher order statistics neglected in VBEM and can therefore achieve a better approximation. Examples of Gaussian mixture models are used to illustrate the comparison between our method and VBEM, demonstrating the improvement.

When predicting class labels for objects within a relational database, it is often helpful to consider a model for relationships: this allows for information between class labels to be shared and to improve prediction performance. However, there are different ways by which objects can be related within a relational database. One traditional way corresponds to a Markov network structure: each existing relation is represented by an undirected edge. This encodes that, conditioned on input features, each object label is independent of other object labels given its neighbors in the graph. However, there is no reason why Markov networks should be the only representation of choice for symmetric dependence structures. Here we discuss the case when relationships are postulated to exist due to hidden com- mon causes. We discuss how the resulting graphical model differs from Markov networks, and how it describes different types of real-world relational processes. A Bayesian nonparametric classification model is built upon this graphical repre- sentation and evaluated with several empirical studies.

Spectral clustering is a simple yet powerful method for finding structure in data using spectral properties of an associated pairwise similarity matrix. This paper provides new insights into how the method works and uses these to derive new algorithms which given the data alone automatically learn different plausible data partitionings. The main theoretical contribution is a generalization of a key result in the field, the multicut lemma [7]. We use this generalization to derive two algorithms. The first uses the eigenvalues of a given affinity matrix to infer the number of clusters in data, and the second combines learning the affinity matrix with inferring the number of clusters. A hierarchical implementation of the algorithms is also derived. The algorithms are theoretically motivated and demonstrated on nontrivial data sets.

We present a Bayesian framework for content-based image retrieval which models the distribution of color and texture features within sets of related images. Given a userspecified text query (e.g. "penguins") the system first extracts a set of images, from a labelled corpus, corresponding to that query. The distribution over features of these images is used to compute a Bayesian score for each image in a large unlabelled corpus. Unlabelled images are then ranked using this score and the top images are returned. Although the Bayesian score is based on computing marginal likelihoods, which integrate over model parameters, in the case of sparse binary data the score reduces to a single matrix-vector multiplication and is therefore extremely efficient to compute. We show that our method works surprisingly well despite its simplicity and the fact that no relevance feedback is used. We compare different choices of features, and evaluate our results using human subjects.

In this paper, we propose separable lattice hidden Markov models, in which multiple hidden state sequences interact to model the observation on a lattice. The proposed model can be efficiently applied for modeling images, image sequences, 3-D object models and higher dimensional applications, due to the composite structure of Markov chains which reduces the complexity while retaining good properties for multi-dimensional data. In case of 2-D lattices, the proposed model performs an elastic matching in both horizontal and vertical directions; this makes it possible to model not only invariances to the size and location of an object but also nonlinear warping in each dimension. We present a training algorithm for separable lattice HMMs based on a variational approximation. Moreover, the deterministic annealing EM (DAEM) algorithm was applied to the variational algorithm for separable lattice HMMs. Face recognition experiments on the XM2VTS database show that the proposed model has good properties for face image modeling.

We consider the problem of clustering in its most basic form where only a local metric on the data space is given. No parametric statistical model is assumed, and the number of clusters is learned from the data. We introduce, analyze and demonstrate a novel approach to clustering where data points are viewed as nodes of a graph, and pairwise similarities are used to derive a transition probability matrix P for a Markov random walk between them. The algorithm automatically reveals structure at increasing scales by varying the number of steps taken by this random walk. Points are represented as rows of Pt, which are the t-step distributions of the walk starting at that point; these distributions are then clustered using a KL-minimizing iterative algorithm. Both the number of clusters, and the number of steps that 'best reveal' it, are found by optimizing spectral properties of P.

We consider the gender classification task of discriminating between images of faces of men and women from face images. In appearance-based approaches, the initial images are preprocessed (e.g. normalized) and input into classifiers. Recently, SVMs which are popular kernel classifiers have been applied to gender classification and have shown excellent performance. We propose to use one of Bayesian kernel methods which is Gaussian Process Classifiers (GPCs) for gender classification. The main advantage of Bayesian kernel methods such as GPCs over SVMs is that they determine the hyperparameters of the kernel based on Bayesian model selection criterion. Our results show that GPCs outperformed SVMs with cross validation.

Correlation between instances is often modelled via a kernel function using in- put attributes of the instances. Relational knowledge can further reveal additional pairwise correlations between variables of interest. In this paper, we develop a class of models which incorporates both reciprocal relational information and in- put attributes using Gaussian process techniques. This approach provides a novel non-parametric Bayesian framework with a data-dependent covariance function for supervised learning tasks. We also apply this framework to semi-supervised learning. Experimental results on several real world data sets verify the usefulness of this algorithm.

We introduce binary matrix factorization, a novel model for unsupervised ma- trix decomposition. The decomposition is learned by fitting a non-parametric Bayesian probabilistic model with binary latent variables to a matrix of dyadic data. Unlike bi-clustering models, which assign each row or column to a single cluster based on a categorical hidden feature, our binary feature model reflects the prior belief that items and attributes can be associated with more than one latent cluster at a time. We provide simple learning and inference rules for this new model and show how to extend it to an infinite model in which the number of features is not a priori fixed but is allowed to grow with the size of the data. 1 Distributed representations for dyadic data One of the major goals of probabilistic unsupervised learning is to discover underlying or hidden structure in a dataset by using latent variables to describe a complex data generation process. In this paper we focus on dyadic data: our domains have two finite sets of objects/entities and observa- tions are made on dyads (pairs with one element from each set). Examples include sparse matrices of movie-viewer ratings, word-document counts or product-customer purchases. A simple way to capture structure in this kind of data is to do “bi-clustering” (possibly using mixture models) by grouping the rows and (independently or simultaneously) the columns[6, 13, 9]. The modelling as- sumption in such a case is that movies come in types and viewers in types and that knowing componential structure: each item (row) has associated with it an unobserved vector of binary features; similarly each attribute (column) has a hidden vector of binary features. Knowing the matrixX into (a distribution defined by) the productUWV> , whereU andV are binary feature matrices, andW is a real-valued weight matrix. Below, we develop this binary matrix factorization the type of movie and type of viewer is sufficient to predict the response. Clustering or mixture models are quite restrictive – their major disadvantage is that they do not admit a componential or distributed representation because items cannot simultaneously belong to several classes. (A movie, for example, might be explained as coming from a cluster of “dramas” or “comedies”; a viewer as a “single male” or as a “young mother”.) We might instead prefer a model (e.g. [10, 5]) in which objects can be assigned to multiple latent clusters: a movie might be a drama and have won an Os- car and have subtitles; a viewer might be single and female and a university graduate. Inference in such models falls under the broad area of factorial learning (e.g. [7, 1, 3, 12]), in which multiple interacting latent causes explain each observed datum. features of the item and the features of the attribute are sufficient to generate (before noise) the response at that location in the matrix. In effect, we are factorizing a real-valued data (response) In this paper, we assume that both data items (rows) and attributes (columns) have this kind of

Gaussian process classifiers (GPCs) are Bayesian probabilistic kernel classifiers. In GPCs, the probability of belonging to a certain class at an input location is monotonically related to the value of some latent function at that location. Starting from a Gaussian process prior over this latent function, data are used to infer both the posterior over the latent function and the values of hyperparameters to determine various aspects of the function. Recently, the expectation propagation (EP) approach has been proposed to infer the posterior over the latent function. Based on this work, we present an approximate EM algorithm, the EM-EP algorithm, to learn both the latent function and the hyperparameters. This algorithm is found to converge in practice and provides an efficient Bayesian framework for learning hyperparameters of the kernel. A multiclass extension of the EM-EP algorithm for GPCs is also derived. In the experimental results, the EM-EP algorithms are as good or better than other methods for GPCs or Support Vector Machines (SVMs) with cross-validation.

In this paper, we develop a segmental semi-Markov model (SSMM) for protein secondary structure prediction which incorporates multiple sequence alignment profiles with the purpose of improving the predictive performance. The segmental model is a generalization of the hidden Markov model where a hidden state generates segments of various length and secondary structure type. A novel parameterized model is proposed for the likelihood function that explicitly represents multiple sequence alignment profiles to capture the segmental conformation. Numerical results on benchmark data sets show that incorporating the profiles results in substantial improvements and the generalization performance is promising. By incorporating the information from long range interactions in beta-sheets, this model is also capable of carrying out inference on contact maps. This is an important advantage of probabilistic generative models over the traditional discriminative approach to protein secondary structure prediction. The Web server of our algorithm and supplementary materials are available at http://public.kgi.edu/-wild/bsm.html.

In this paper, we propose a probabilistic kernel approach to preference learning based on Gaussian processes. A new likelihood function is proposed to capture the preference relations in the Bayesian framework. The generalized formulation is also applicable to tackle many multiclass problems. The overall approach has the advantages of Bayesian methods for model selection and probabilistic prediction. Experimental results compared against the constraint classification approach on several benchmark datasets verify the usefulness of this algorithm.

We present a novel algorithm for agglomerative hierarchical clustering based on evaluating marginal likelihoods of a probabilistic model. This algorithm has several advantages over traditional distance-based agglomerative clustering algorithms. (1) It defines a probabilistic model of the data which can be used to compute the predictive distribution of a test point and the probability of it belonging to any of the existing clusters in the tree. (2) It uses a model-based criterion to decide on merging clusters rather than an ad-hoc distance metric. (3) Bayesian hypothesis testing is used to decide which merges are advantageous and to output the recommended depth of the tree. (4) The algorithm can be interpreted as a novel fast bottom-up approximate inference method for a Dirichlet process (i.e. countably infinite) mixture model (DPM). It provides a new lower bound on the marginal likelihood of a DPM by summing over exponentially many clusterings of the data in polynomial time. We describe procedures for learning the model hyperpa-rameters, computing the predictive distribution, and extensions to the algorithm. Experimental results on synthetic and real-world data sets demonstrate useful properties of the algorithm.

We provide a general framework for learning precise, compact, and fast representations of the Bayesian predictive distribution for a model. This framework is based on minimizing the KL divergence between the true predictive density and a suitable compact approximation. We consider various methods for doing this, both sampling based approximations, and deterministic approximations such as expectation propagation. These methods are tested on a mixture of Gaussians model for density estimation and on binary linear classification, with both synthetic data sets for visualization and several real data sets. Our results show significant reductions in prediction time and memory footprint.

Inspired by “Google™ Sets”, we consider the problem of retrieving items from a concept or cluster, given a query consisting of a few items from that cluster. We formulate this as a Bayesian inference problem and de- scribe a very simple algorithm for solving it. Our algorithm uses a model- based concept of a cluster and ranks items using a score which evaluates the marginal probability that each item belongs to a cluster containing the query items. For exponential family models with conjugate priors this marginal probability is a simple function of sufficient statistics. We focus on sparse binary data and show that our score can be evaluated ex- actly using a single sparse matrix multiplication, making it possible to apply our algorithm to very large datasets. We evaluate our algorithm on three datasets: retrieving movies from EachMovie, finding completions of author sets from the NIPS dataset, and finding completions of sets of words appearing in the Grolier encyclopedia. We compare to Google™ Sets and show that Bayesian Sets gives very reasonable set completions.

We define a probability distribution over equivalence classes of binary matrices with a finite number of rows and an unbounded number of columns. This distribution is suitable for use as a prior in probabilistic models that represent objects using a potentially infinite array of features. We identify a simple generative process that results in the same distribution over equivalence classes, which we call the Indian buffet process. We illustrate the use of this distribution as a prior in an infinite latent feature model, deriving a Markov chain Monte Carlo algorithm for inference in this model and applying the algorithm to an image dataset.

Nested sampling is a new Monte Carlo method by Skilling [1] intended for general Bayesian computation. Nested sampling provides a robust alternative to annealing-based methods for computing normalizing constants. It can also generate estimates of other quantities such as posterior expectations. The key technical requirement is an ability to draw samples uniformly from the prior sub ject to a constraint on the likelihood. We provide a demonstration with the Potts model, an undirected graphical model.

We present a new Gaussian process (GP) regression model whose covariance is parameterized by the the locations of M pseudo-input points, which we learn by a gradient based optimization. We take M N, where N is the number of real data points, and hence obtain a sparse regression method which has O(M 2 N ) training cost and O(M 2 ) prediction cost per test case. We also find hyperparameters of the covariance function in the same joint optimization. The method can be viewed as a Bayesian regression model with particular input dependent noise. The method turns out to be closely related to several other sparse GP approaches, and we discuss the relation in detail. We finally demonstrate its performance on some large data sets, and make a direct comparison to other sparse GP methods. We show that our method can match full GP performance with small M , i.e. very sparse solutions, and it significantly outperforms other approaches in this regime.

We propose a probabilistic model based on Independent Component Analysis for learning multiple related tasks. In our model the task parameters are assumed to be generated from independent sources which account for the relatedness of the tasks. We use Laplace distributions to model hidden sources which makes it possible to identify the hidden, independent components instead of just modeling correlations. Furthermore, our model enjoys a sparsity property which makes it both parsimonious and robust. We also propose efficient algorithms for both empirical Bayes method and point estimation. Our experimental results on two multi-label text classification data sets show that the proposed approach is promising.

MOTIVATION: We have used state-space models (SSMs) to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T cell activation. SSMs are a class of dynamic Bayesian networks in which the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be directly measured in a gene expression profiling experiment, for example: genes that have not been included in the microarray, levels of regulatory proteins, the effects of mRNA and protein degradation, etc. RESULTS: We have approached the problem of inferring the model structure of these state-space models using both classical and Bayesian methods. In our previous work, a bootstrap procedure was used to derive classical confidence intervals for parameters representing 'gene-gene' interactions over time. In this article, variational approximations are used to perform the analogous model selection task in the Bayesian context. Certain interactions are present in both the classical and the Bayesian analyses of these regulatory networks. The resulting models place JunB and JunD at the centre of the mechanisms that control apoptosis and proliferation. These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available at http://www.cse.ebuffalo.edu/faculty/mbeal/software.html.

MOTIVATION: In clinical practice, pathological phenotypes are often labelled with ordinal scales rather than binary, e.g. the Gleason grading system for tumour cell differentiation. However, in the literature of microarray analysis, these ordinal labels have been rarely treated in a principled way. This paper describes a gene selection algorithm based on Gaussian processes to discover consistent gene expression patterns associated with ordinal clinical phenotypes. The technique of automatic relevance determination is applied to represent the significance level of the genes in a Bayesian inference framework. RESULTS: The usefulness of the proposed algorithm for ordinal labels is demonstrated by the gene expression signature associated with the Gleason score for prostate cancer data. Our results demonstrate how multi-gene markers that may be initially developed with a diagnostic or prognostic application in mind are also useful as an investigative tool to reveal associations between specific molecular and cellular events and features of tumour physiology. Our algorithm can also be applied to microarray data with binary labels with results comparable to other methods in the literature.

We present a probabilistic kernel approach to ordinal regression based on Gaussian processes. A threshold model that generalizes the probit function is used as the likelihood function for ordinal variables. Two inference techniques, based on the Laplace approximation and the expectation propagation algorithm respectively, are derived for hyperparameter learning and model selection. We compare these two Gaussian process approaches with a previous ordinal regression method based on support vector machines on some benchmark and real-world data sets, including applications of ordinal regression to collaborative filtering and gene expression analysis. Experimental results on these data sets verify the usefulness of our approach.

In this paper, we present a graphical model for protein secondary structure prediction. This model extends segmental semi-Markov models (SSMM) to exploit multiple sequence alignment profiles which contain information from evolutionarily related sequences. A novel parameterized model is proposed as the likelihood function for the SSMM to capture the segmental conformation. By incorporating the information from long range interactions in ß-sheets, this model is capable of carrying out inference on contact maps. The numerical results on benchmark data sets show that incorporating the profiles results in substantial improvements and the generalization performance is promising.

In many real-world classification problems the input contains a large number of potentially ir-relevant features. This paper proposes a new Bayesian framework for determining the rele-vance of input features. This approach extends one of the most successful Bayesian methods for feature selection and sparse learning, known as Automatic Relevance Determination (ARD). ARD finds the relevance of features by optimiz-ing the model marginal likelihood, also known as the evidence. We show that this can lead to over-fitting. To address this problem, we propose Pre-dictive ARD based on estimating the predictive performance of the classifier. While the actual leave-one-out predictive performance is generally very costly to compute, the expectation propaga-tion (EP) algorithm proposed by Minka provides an estimate of this predictive performance as a side-effect of its iterations. We exploit this in our algorithm to do feature selection, and to select data points in a sparse Bayesian kernel classifier. Moreover, we provide two other improvements to previous algorithms, by replacing Laplace’s approximation with the generally more accurate EP, and by incorporating the fast optimization algorithm proposed by Faul and Tipping. Our experiments show that our method based on the EP estimate of predictive performance is more accurate on test data than relevance determina-tion by optimizing the evidence.

In this paper we propose a probabilistic model for online document clus- tering. We use non-parametric Dirichlet process prior to model the grow- ing number of clusters, and use a prior of general English language model as the base distribution to handle the generation of novel clusters. Furthermore, cluster uncertainty is modeled with a Bayesian Dirichlet- multinomial distribution. We use empirical Bayes method to estimate hyperparameters based on a historical dataset. Our probabilistic model is applied to the novelty detection task in Topic Detection and Tracking (TDT) and compared with existing approaches in the literature.

We present an algorithm based on convex optimization for constructing kernels for semi-supervised learning. The kernel matrices are derived from the spectral decomposition of graph Laplacians, and combine la- beled and unlabeled data in a systematic fashion. Unlike previous work using diffusion kernels and Gaussian random field kernels, a nonpara- metric kernel approach is presented that incorporates order constraints during optimization. This results in flexible kernels and avoids the need to choose among different parametric forms. Our approach relies on a quadratically constrained quadratic program (QCQP), and is compu- tationally feasible for large datasets. We evaluate the kernels on real datasets using support vector machines, with encouraging results.

MOTIVATION: We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. RESULTS: Bootstrap confidence intervals are developed for parameters representing 'gene-gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. AVAILABILITY: Supplementary data and Matlab computer source code will be made available on the web at the URL given below. SUPPLEMENTARY INFORMATION: http://public.kgi.edu/~wild/LDS/index.htm

We generalise the Gaussian process (GP) framework for regression by learning a nonlinear transformation of the GP outputs. This allows for non-Gaussian processes and non-Gaussian noise. The learning algo- rithm chooses a nonlinear transformation such that transformed data is well-modelled by a GP. This can be seen as including a preprocessing transformation as an integral part of the probabilistic modelling problem, rather than as an ad-hoc step. We demonstrate on several real regression problems that learning the transformation can lead to significantly better performance than using a regular GP, or a GP with a fixed transformation.

In this paper, we study a special kind of learning problem in which each training instance is given a set of (or distribution over) candidate class labels and only one of the candidate labels is the correct one. Such a problem can occur, e.g., in an information retrieval setting where a set of words is associated with an image, or if classes labels are organized hierarchically. We propose a novel discriminative approach for handling the ambiguity of class labels in the training examples. The experiments with the proposed approach over five different UCI datasets show that our approach is able to find the correct label among the set of candidate labels and actually achieve performance close to the case when each training instance is given a single correct label. In contrast, naIve methods degrade rapidly as more ambiguity is introduced into the labels.

We investigate Bayesian alternatives to classical Monte Carlo methods for evaluating integrals. Bayesian Monte Carlo (BMC) allows the in- corporation of prior knowledge, such as smoothness of the integrand, into the estimation. In a simple problem we show that this outperforms any classical importance sampling method. We also attempt more chal- lenging multidimensional integrals involved in computing marginal like- lihoods of statistical models (a.k.a. partition functions and model evi- dences). We find that Bayesian Monte Carlo outperformed Annealed Importance Sampling, although for very high dimensional problems or problems with massive multimodality BMC may be less adequate. One advantage of the Bayesian approach to Monte Carlo is that samples can be drawn from any distribution. This allows for the possibility of active design of sample points so as to maximise information gain.

MOTIVATION: The Bayesian network approach is a framework which combines graphical representation and probability theory, which includes, as a special case, hidden Markov models. Hidden Markov models trained on amino acid sequence or secondary structure data alone have been shown to have potential for addressing the problem of protein fold and superfamily classification. RESULTS: This paper describes a novel implementation of a Bayesian network which simultaneously learns amino acid sequence, secondary structure and residue accessibility for proteins of known three-dimensional structure. An awareness of the errors inherent in predicted secondary structure may be incorporated into the model by means of a confusion matrix. Training and validation data have been derived for a number of protein superfamilies from the Structural Classification of Proteins (SCOP) database. Cross validation results using posterior probability classification demonstrate that the Bayesian network performs better in classifying proteins of known structural superfamily than a hidden Markov model trained on amino acid sequences alone.

We show that it is possible to extend hidden Markov models to have a countably infinite number of hidden states. By using the theory of Dirichlet processes we can implicitly integrate out the infinitely many transition parameters, leaving only three hyperparameters which can be learned from data. These three hyperparameters define a hierarchical Dirichlet process capable of capturing a rich set of transition dynamics. The three hyperparameters control the time scale of the dynamics, the sparsity of the underlying state-transition matrix, and the expected num- ber of distinct hidden states in a finite sequence. In this framework it is also natural to allow the alphabet of emitted symbols to be infinite— consider, for example, symbols being possible words appearing in En- glish text.

We present an extension to the Mixture of Experts (ME) model, where the individual experts are Gaussian Process (GP) regression models. Us- ing an input-dependent adaptation of the Dirichlet Process, we imple- ment a gating network for an infinite number of Experts. Inference in this model may be done efficiently using a Markov Chain relying on Gibbs sampling. The model allows the effective covariance function to vary with the inputs, and may handle large datasets – thus potentially over- coming two of the biggest hurdles with GP models. Simulations show the viability of this approach.

We provide a tutorial on learning and inference in hidden Markov models in the context of the recent literature on Bayesian networks. This perspective makes it possible to consider novel generalizations of hidden Markov models with multiple hidden state variables, multiscale representations, and mixed discrete and continuous variables. Although exact inference in these generalizations is usually intractable, one can use approximate inference algorithms such as Markov chain sampling and variational methods. We describe how such methods are applied to these generalized hidden Markov models. We conclude this review with a discussion of Bayesian methods for model selection in generalized HMMs.

Tree structured belief networks are attractive for image segmentation tasks. However, networks with fixed architectures are not very suitable as they lead to blocky artefacts, and led to the introduction of dynamic trees (DTs). The Dynamic trees architecture provide a prior distribution over tree structures, and simulated annealing (SA) was used to search for structures with high posterior probability. In this paper we introduce a mean field approach to inference in DTs. We find that the mean field method captures the posterior better than just using the maximum a posteriori solution found by SA.

Variational approximations are becoming a widespread tool for Bayesian learning of graphical models. We provide some theoret(cid:173) ical results for the variational updates in a very general family of conjugate-exponential graphical models. We show how the belief propagation and the junction tree algorithms can be used in the inference step of variational Bayesian learning. Applying these re(cid:173) sults to the Bayesian analysis of linear-Gaussian state-space models we obtain a learning procedure that exploits the Kalman smooth(cid:173) ing propagation, while integrating over all model parameters. We demonstrate how this can be used to infer the hidden state dimen(cid:173) sionality of the state-space model in a variety of synthetic problems and one real high-dimensional data set.

The Bayesian paradigm apparently only sometimes gives rise to Occam's Razor; at other times very large models perform well. We give simple examples of both kinds of behaviour. The two views are reconciled when measuring complexity of functions, rather than of the machinery used to implement them. We analyze the complexity of functions for some linear in the parameter models that are equivalent to Gaussian Processes, and always find Occam's Razor at work.

We introduce a new statistical model for time series that iteratively segments data into regimes with approximately linear dynamics and learnsthe parameters of each of these linear regimes. This model combines and generalizes two of the most widely used stochastic time-series models -- hidden Markov models and linear dynamical systems -- and is closely related to models that are widely used in the control and econometrics literatures. It can also be derived by extending the mixture of experts neural network (Jacobs, Jordan, Nowlan, & Hinton, 1991) to its fully dynamical version, in which both expert and gating networks are recurrent. Inferring the posterior probabilities of the hidden states of this model is computationally intractable, and therefore the exact expectation maximization (EM) algorithm cannot be applied. However, we present a variational approximation that maximizes a lower bound on the log-likelihood and makes use of both the forward and backward recursions for hidden Markov models and the Kalman filter recursions for linear dynamical systems. We tested the algorithm on artificial data sets and a natural data set of respiration force from a patient with sleep apnea. The results suggest that variational approximations are a viable method for inference and learning in switching state-space models.

We present a split-and-merge expectation-maximization (SMEM) algorithm to overcome the local maxima problem in parameter estimation of finite mixture models. In the case of mixture models, local maxima often involve having too many components of a mixture model in one part of the space and too few in another, widely separated part of the space. To escape from such configurations, we repeatedly perform simultaneous split-and-merge operations using a new criterion for efficiently selecting the split-and-merge candidates. We apply the proposed algorithm to the training of gaussian mixtures and mixtures of factor analyzers using synthetic and real data and show the effectiveness of using the split-and-merge operations to improve the likelihood of both the training data and of held-out test data. We also show the practical usefulness of the proposed algorithm by applying it to image compression and pattern recognition problems.

Factor analysis, principal component analysis, mixtures of gaussian clusters, vector quantization, Kalman filter models, and hidden Markov models can all be unified as variations of unsupervised learning under a single basic generative model. This is achieved by collecting together disparate observations and derivations made by many previous authors and introducing a new way of linking discrete and continuous state models using a simple nonlinearity. Through the use of other nonlinearities, we show how independent component analysis is also a variation of the same basic generative model. We show that factor analysis and mixtures of gaussians can be implemented in autoencoder neural networks and learned using squared error plus the same regularization term. We introduce a new model for static data, known as sensible principal component analysis, as well as a novel concept of spatially adaptive observation noise. We also review some of the literature involving global and local mixtures of the basic models and provide pseudocode for inference and learning for all the basic models.

For many types of machine learning algorithms, one can compute the statistically `optimal' way to select training data. In this paper, we review how optimal data selection techniques have been used with feedforward neural networks. We then show how the same principles may be used to select data for two alternative, statistically-based learning architectures: mixtures of Gaussians and locally weighted regression. While the techniques for neural networks are computationally expensive and approximate, the techniques for mixtures of Gaussians and locally weighted regression are both efficient and accurate. Empirically, we observe that the optimality criterion sharply decreases the number of training examples the learner needs in order to achieve good performance.

For many types of learners one can compute the statistically "op(cid:173) timal" way to select data. We review how these techniques have been used with feedforward neural networks [MacKay, 1992; Cohn, 1994] . We then show how the same principles may be used to select data for two alternative, statistically-based learning architectures: mixtures of Gaussians and locally weighted regression. While the techniques for neural networks are expensive and approximate, the techniques for mixtures of Gaussians and locally weighted regres(cid:173) sion are both efficient and accurate. 1 ACTIVE LEARNING - BACKGROUND An active learning problem is one where the learner has the ability or need to influence or select its own training data. Many problems of great practical interest allow active learning, and many even require it. We consider the problem of actively learning a mapping X - Y based on a set of training examples {(Xi,Yi)}~l' where Xi E X and Yi E Y. The learner is allowed to iteratively select new inputs x (possibly from a constrained set), observe the resulting output y, and incorporate the new examples (x, y) into its training set. The primary question of active learning is how to choose which x to try next. There are many heuristics for choosing x based on intuition, including choosing places where we don't have data, where we perform poorly [Linden and Weber, 1993], where we have low confidence [Thrun and Moller, 1992], where we expect it 706 David Cohn, Zoubin Ghahramani, Michael I. Jordon to change our model [Cohn et aI, 1990], and where we previously found data that resulted in learning [Schmidhuber and Storck, 1993]. In this paper we consider how one may select x "optimally" from a statistical viewpoint. We first review how the statistical approach can be applied to neural networks, as described in MacKay [1992] and Cohn [1994]. We then consider two alternative, statistically-based learning architectures: mixtures of Gaussians and locally weighted regression. While optimal data selection for a neural network is computationally expensive and approximate, we find that optimal data selection for the two statistical models is efficient and accurate. 2 ACTIVE LEARNING - A STATISTICAL APPROACH We denote the learner's output given input x as y(x). The mean squared error of this output can be expressed as the sum of the learner's bias and variance. The variance 0'3 (x) indicates the learner's uncertainty in its estimate at x. 1 Our goal will be to select a new example x such that when the resulting example (x, y) is added to the training set, the integrated variance IV is minimized: IV = J 0'3 P (x)dx. (1) Here, P(x) is the (known) distribution over X. In practice, we will compute a Monte Carlo approximation of this integral, evaluating 0'3 at a number of random points drawn according to P(x). Selecting x so as to minimize IV requires computing 0-3, the new variance at x given (x, y). Until we actually commit to an x, we do not know what corresponding y we will see, so the minimization cannot be performed deterministically.2 Many learning architectures, however, provide an estimate of PWlx) based on current data, so we can use this estimate to compute the expectation of 0-3. Selecting x to minimize the expected integrated variance provides a solid statistical basis for choosing new examples. 2.1 EXAMPLE: ACTIVE LEARNING WITH A NEURAL

Many real world learning problems are best characterized by an interaction of multiple independent causes or factors. Discover(cid:173) ing such causal structure from the data is the focus of this paper. Based on Zemel and Hinton's cooperative vector quantizer (CVQ) architecture, an unsupervised learning algorithm is derived from the Expectation-Maximization (EM) framework. Due to the com(cid:173) binatorial nature of the data generation process, the exact E-step is computationally intractable. Two alternative methods for com(cid:173) puting the E-step are proposed: Gibbs sampling and mean-field approximation, and some promising empirical results are presented.

One of the fundamental properties that both neural networks and the central nervous system share is the ability to learn and gener(cid:173) alize from examples. While this property has been studied exten(cid:173) sively in the neural network literature it has not been thoroughly explored in human perceptual and motor learning. We have chosen a coordinate transformation system-the visuomotor map which transforms visual coordinates into motor coordinates-to study the generalization effects of learning new input-output pairs. Using a paradigm of computer controlled altered visual feedback, we have studied the generalization of the visuomotor map subsequent to both local and context-dependent remappings. A local remapping of one or two input-output pairs induced a significant global, yet decaying, change in the visuomotor map, suggesting a representa(cid:173) tion for the map composed of units with large functional receptive fields. Our study of context-dependent remappings indicated that a single point in visual space can be mapped to two different fin(cid:173) ger locations depending on a context variable-the starting point of the movement. Furthermore, as the context is varied there is a gradual shift between the two remappings, consistent with two visuomotor modules being learned and gated smoothly with the context.

Based on computational principles, with as yet no direct experi(cid:173) mental validation, it has been proposed that the central nervous system (CNS) uses an internal model to simulate the dynamic be(cid:173) havior of the motor system in planning, control and learning (Sut(cid:173) ton and Barto, 1981; Ito, 1984; Kawato et aI., 1987; Jordan and Rumelhart, 1992; Miall et aI., 1993). We present experimental re(cid:173) sults and simulations based on a novel approach that investigates the temporal propagation of errors in the sensorimotor integration process. Our results provide direct support for the existence of an internal model.