Accurate and detailed models of the progression of neurodegenerative diseases such as Alzheimer's (AD) are crucially important for reliable early diagnosis and the determination and deployment of effective treatments. In this paper, we introduce the ALPACA (Alzheimer's disease Probabilistic Cascades) model, a generative model linking latent Alzheimer's progression dynamics to observable biomarker data. In contrast with previous works which model disease progression as a fixed ordering of events, we explicitly model the variability over such orderings among patients which is more realistic, particularly for highly detailed disease progression models. We describe efficient learning algorithms for ALPACA and discuss promising experimental results on a real cohort of Alzheimer's patients from the Alzheimer's Disease Neuroimaging Initiative.

In this paper, we consider Bayesian reinforcement learning (BRL) where actions incur costs in addition to rewards, and thus exploration has to be constrained in terms of the expected total cost while learning to maximize the expected long-term total reward. In order to formalize cost-sensitive exploration, we use the constrained Markov decision process (CMDP) as the model of the environment, in which we can naturally encode exploration requirements using the cost function. We extend BEETLE, a model-based BRL method, for learning in the environment with cost constraints. We demonstrate the cost-sensitive exploration behaviour in a number of simulated problems.

We present a Bayesian nonparametric model for genetic sequence data in which a set of genetic sequences is modelled using a Markov model of partitions. The partitions at consecutive locations in the genome are related by their clusters first splitting and then merging. Our model can be thought of as a discrete time analogue of continuous time fragmentation-coagulation processes [Teh et al 2011], preserving the important properties of projectivity, exchangeability and reversibility, while being more scalable. We apply this model to the problem of genotype imputation, showing improved computational efficiency while maintaining the same accuracies as in [Teh et al 2011].

Parametric policy search algorithms are one of the methods of choice for the optimisation of Markov Decision Processes, with Expectation Maximisation and natural gradient ascent being considered the current state of the art in the field. In this article we provide a unifying perspective of these two algorithms by showing that their step-directions in the parameter space are closely related to the search direction of an approximate Newton method. This analysis leads naturally to the consideration of this approximate Newton method as an alternative gradient-based method for Markov Decision Processes. We are able show that the algorithm has numerous desirable properties, absent in the naive application of Newton's method, that make it a viable alternative to either Expectation Maximisation or natural gradient ascent. Empirical results suggest that the algorithm has excellent convergence and robustness properties, performing strongly in comparison to both Expectation Maximisation and natural gradient ascent.

We propose a Deep Boltzmann Machine for learning a generative model of multimodal data. We show how to use the model to extract a meaningful representation of multimodal data. We find that the learned representation is useful for classification and information retreival tasks, and hence conforms to some notion of semantic similarity. The model defines a probability density over the space of multimodal inputs. By sampling from the conditional distributions over each data modality, it possible to create the representation even when some data modalities are missing. Our experimental results on bi-modal data consisting of images and text show that the Multimodal DBM can learn a good generative model of the joint space of image and text inputs that is useful for information retrieval from both unimodal and multimodal queries. We further demonstrate that our model can significantly outperform SVMs and LDA on discriminative tasks. Finally, we compare our model to other deep learning methods, including autoencoders and deep belief networks, and show that it achieves significant gains.

We present a new graph-based approach for incorporating domain knowledge in reinforcement learning applications. The domain knowledge is given as a weighted graph, or a kernel matrix, that loosely indicates which states should have similar optimal actions. We first introduce a bias into the policy search process by deriving a distribution on policies such that policies that disagree with the provided graph have low probabilities. This distribution corresponds to a Markov Random Field. We then present a reinforcement and an apprenticeship learning algorithms for finding such policy distributions. We also illustrate the advantage of the proposed approach on three problems: swing-up cart-balancing with nonuniform and smooth frictions, gridworlds, and teaching a robot to grasp new objects.

Markov logic is a widely used tool in statistical relational learning, which uses a weighted first-order logic knowledge base to specify a Markov random field (MRF) or a conditional random field (CRF). In many applications, a Markov logic network (MLN) is trained in one domain, but used in a different one. This paper focuses on dynamic Markov logic networks, where the domain of time points typically varies between training and testing. It has been previously pointed out that the marginal probabilities of truth assignments to ground atoms can change if one extends or reduces the domains of predicates in an MLN. We show that in addition to this problem, the standard way of unrolling a Markov logic theory into a MRF may result in time-inhomogeneity of the underlying Markov chain. Furthermore, even if these representational problems are not significant for a given domain, we show that the more practical problem of generating samples in a sequential conditional random field for the next slice relying on the samples from the previous slice has high computational cost in the general case, due to the need to estimate a normalization factor for each sample. We propose a new discriminative model, slice normalized dynamic Markov logic networks (SN-DMLN), that suffers from none of these issues. It supports efficient online inference, and can directly model influences between variables within a time slice that do not have a causal direction, in contrast with fully directed models (e.g., DBNs). Experimental results show an improvement in accuracy over previous approaches to online inference in dynamic Markov logic networks.

A key function of brains is undoubtedly the abstraction and maintenance of information from the environment for later use. Neurons in association cortex play an important role in this process: during learning these neurons become tuned to relevant features and represent the information that is required later as a persistent elevation of their activity. It is however not well known how these neurons acquire their task-relevant tuning. Here we introduce a biologically plausible learning scheme that explains how neurons become selective for relevant information when animals learn by trial and error. We propose that the action selection stage feeds back attentional signals to earlier processing levels. These feedback signals interact with feedforward signals to form synaptic tags at those connections that are responsible for the stimulus-response mapping. A globally released neuromodulatory signal interacts with these tagged synapses to determine the sign and strength of plasticity. The learning scheme is generic because it can train networks in different tasks, simply by varying inputs and rewards. It explains how neurons in association cortex learn to (1) temporarily store task-relevant information in non-linear stimulus-response mapping tasks and (2) learn to optimally integrate probabilistic evidence for perceptual decision making.

The National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) database contains a large amount of information, regarding the way of life, medical conditions, depression, etc., of a representative sample of the U.S. population. In the present paper, we are interested in seeking the hidden causes behind the suicide attempts, for which we propose to model the subjects using a nonparametric latent model based on the Indian Buffet Process (IBP). Due to the nature of the data, we need to adapt the observation model for discrete random variables. We propose a generative model in which the observations are drawn from a multinomial-logit distribution given the IBP matrix. The implementation of an efficient Gibbs sampler is accomplished using the Laplace approximation, which allows us to integrate out the weighting factors of the multinomial-logit likelihood model. Finally, the experiments over the NESARC database show that our model properly captures some of the hidden causes that model suicide attempts.

We consider infinite-horizon stationary $\gamma$-discounted Markov Decision Processes, for which it is known that there exists a stationary optimal policy. Using Value and Policy Iteration with some error $\epsilon$ at each iteration, it is well-known that one can compute stationary policies that are $\frac{2\gamma{(1-\gamma)^2}\epsilon$-optimal. After arguing that this guarantee is tight, we develop variations of Value and Policy Iteration for computing non-stationary policies that can be up to $\frac{2\gamma}{1-\gamma}\epsilon$-optimal, which constitutes a significant improvement in the usual situation when $\gamma$ is close to $1$. Surprisingly, this shows that the problem of ``computing near-optimal non-stationary policies'' is much simpler than that of ``computing near-optimal stationary policies''.