In many experiments, the data points collected live in high-dimensional observation spaces, yet can be assigned a set of labels or parameters. In electrophysiological recordings, for instance, the responses of populations of neurons generally depend on mixtures of experimentally controlled parameters. The heterogeneity and diversity of these parameter dependencies can make visualization and interpretation of such data extremely difficult. Standard dimensionality reduction techniques such as principal component analysis (PCA) can provide a succinct and complete description of the data, but the description is constructed independent of the relevant task variables and is often hard to interpret. Here, we start with the assumption that a particularly informative description is one that reveals the dependency of the high-dimensional data on the individual parameters. We show how to modify the loss function of PCA so that the principal components seek to capture both the maximum amount of variance about the data, while also depending on a minimum number of parameters. We call this method demixed principal component analysis (dPCA) as the principal components here segregate the parameter dependencies. We phrase the problem as a probabilistic graphical model, and present a fast Expectation-Maximization (EM) algorithm. We demonstrate the use of this algorithm for electrophysiological data and show that it serves to demix the parameter-dependence of a neural population response.

In standard Gaussian Process regression input locations are assumed to be noise free. We present a simple yet effective GP model for training on input points corrupted by i.i.d. Gaussian noise. To make computations tractable we use a local linear expansion about each input point. This allows the input noise to be recast as output noise proportional to the squared gradient of the GP posterior mean. The input noise variances are inferred from the data as extra hyperparameters. They are trained alongside other hyperparameters by the usual method of maximisation of the marginal likelihood. Training uses an iterative scheme, which alternates between optimising the hyperparameters and calculating the posterior gradient. Analytic predictive moments can then be found for Gaussian distributed test points. We compare our model to others over a range of different regression problems and show that it improves over current methods.

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Previous approaches are not high-throughput, are not generalizable or scalable, or lack sufficient data to be effective. We describe single mechanistic reactions as concerted electron movements from an electron orbital source to an electron orbital sink. We use an existing rule-based expert system to derive a dataset consisting of 2,989 productive mechanistic steps and 6.14 million non-productive mechanistic steps. We then pose identifying productive mechanistic steps as a ranking problem: rank potential orbital interactions such that the top ranked interactions yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.0% of non-productive reactions with less than a 0.1% false negative rate. Then, we train an ensemble of ranking models on pairs of interacting orbitals to learn a relative productivity function over single mechanistic reactions in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanisms at the top 89.1% of the time, rising to 99.9% of the time when top ranked lists with at most four non-productive reactions are considered. The final system allows multi-step reaction prediction. Furthermore, it is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert system does not handle.

Metric learning has become a very active research field. The most popular representative--Mahalanobis metric learning--can be seen as learning a linear transformation and then computing the Euclidean metric in the transformed space. Since a linear transformation might not always be appropriate for a given learning problem, kernelized versions of various metric learning algorithms exist. However, the problem then becomes finding the appropriate kernel function. Multiple kernel learning addresses this limitation by learning a linear combination of a number of predefined kernels; this approach can be also readily used in the context of multiple-source learning to fuse different data sources. Surprisingly, and despite the extensive work on multiple kernel learning for SVMs, there has been no work in the area of metric learning with multiple kernel learning. In this paper we fill this gap and present a general approach for metric learning with multiple kernel learning. Our approach can be instantiated with different metric learning algorithms provided that they satisfy some constraints. Experimental evidence suggests that our approach outperforms metric learning with an unweighted kernel combination and metric learning with cross-validation based kernel selection.

We introduce a new convergent variant of Q-learning, called speedy Q-learning, to address the problem of slow convergence in the standard form of the Q-learning algorithm. We prove a PAC bound on the performance of SQL, which shows that for an MDP with n state-action pairs and the discount factor \gamma only T=O\big(\log(n)/(\epsilon^{2}(1-\gamma)^{4})\big) steps are required for the SQL algorithm to converge to an \epsilon-optimal action-value function with high probability. This bound has a better dependency on 1/\epsilon and 1/(1-\gamma), and thus, is tighter than the best available result for Q-learning. Our bound is also superior to the existing results for both model-free and model-based instances of batch Q-value iteration that are considered to be more efficient than the incremental methods like Q-learning.

Multi-class Gaussian Process Classifiers (MGPCs) are often affected by over-fitting problems when labeling errors occur far from the decision boundaries. To prevent this, we investigate a robust MGPC (RMGPC) which considers labeling errors independently of their distance to the decision boundaries. Expectation propagation is used for approximate inference. Experiments with several datasets in which noise is injected in the class labels illustrate the benefits of RMGPC. This method performs better than other Gaussian process alternatives based on considering latent Gaussian noise or heavy-tailed processes. When no noise is injected in the labels, RMGPC still performs equal or better than the other methods. Finally, we show how RMGPC can be used for successfully identifying data instances which are difficult to classify accurately in practice.

We describe a novel technique for feature combination in the bag-of-words model of image classification. Our approach builds discriminative compound words from primitive cues learned independently from training images. Our main observation is that modeling joint-cue distributions independently is more statistically robust for typical classification problems than attempting to empirically estimate the dependent, joint-cue distribution directly. We use Information theoretic vocabulary compression to find discriminative combinations of cues and the resulting vocabulary of portmanteau words is compact, has the cue binding property, and supports individual weighting of cues in the final image representation. State-of-the-art results on both the Oxford Flower-102 and Caltech-UCSD Bird-200 datasets demonstrate the effectiveness of our technique compared to other, significantly more complex approaches to multi-cue image representation

Probabilistic programming languages allow modelers to specify a stochastic process using syntax that resembles modern programming languages. Because the program is in machine-readable format, a variety of techniques from compiler design and program analysis can be used to examine the structure of the distribution represented by the probabilistic program. We show how nonstandard interpretations of probabilistic programs can be used to craft efficient inference algorithms: information about the structure of a distribution (such as gradients or dependencies) is generated as a monad-like side computation while executing the program. These interpretations can be easily coded using special-purpose objects and operator overloading. We implement two examples of nonstandard interpretations in two different languages, and use them as building blocks to construct inference algorithms: automatic differentiation, which enables gradient based methods, and provenance tracking, which enables efficient construction of global proposals.

Local Coordinate Coding (LCC) [18] is a method for modeling functions of data lying on non-linear manifolds. It provides a set of anchor points which form a local coordinate system, such that each data point on the manifold can be approximated by a linear combination of its anchor points, and the linear weights become the local coordinate coding. In this paper we propose encoding data using orthogonal anchor planes, rather than anchor points. Our method needs only a few orthogonal anchor planes for coding, and it can linearize any (\alpha,\beta,p)-Lipschitz smooth nonlinear function with a fixed expected value of the upper-bound approximation error on any high dimensional data. In practice, the orthogonal coordinate system can be easily learned by minimizing this upper bound using singular value decomposition (SVD). We apply our method to model the coordinates locally in linear SVMs for classification tasks, and our experiment on MNIST shows that using only 50 anchor planes our method achieves 1.72% error rate, while LCC achieves 1.90% error rate using 4096 anchor points.

Given one feature of a novel animal, humans readily make inferences about other features of the animal. For example, winged creatures often fly, and creatures that eat fish often live in the water. We explore the knowledge that supports these inferences and compare two approaches. The first approach proposes that humans rely on abstract representations of dependency relationships between features, and is formalized here as a graphical model. The second approach proposes that humans rely on specific knowledge of previously encountered animals, and is formalized here as a family of exemplar models. We evaluate these models using a task where participants reason about chimeras, or animals with pairs of features that have not previously been observed to co-occur. The results support the hypothesis that humans rely on explicit representations of relationships between features.