Nuclear magnetic resonance (NMR) spectroscopy exploits the magnetic properties of atomic nuclei to discover the structure, reaction state and chemical environment of molecules. We propose a probabilistic generative model and inference procedures for NMR spectroscopy. Specifically, we use a weighted sum of trigonometric functions undergoing exponential decay to model free induction decay (FID) signals. We discuss the challenges in estimating the components of this general model -- amplitudes, phase shifts, frequencies, decay rates, and noise variances -- and offer practical solutions. We compare with conventional Fourier transform spectroscopy for estimating the relative concentrations of chemicals in a mixture, using synthetic and experimentally acquired FID signals. We find the proposed model is particularly robust to low signal to noise ratios (SNR), and overlapping peaks in the Fourier transform of the FID, enabling accurate predictions (e.g., 1% sensitivity at low SNR) which are not possible with conventional spectroscopy (5% sensitivity).

Approximate Bayesian computation (ABC) methods are used to approximate posterior distributions using simulation rather than likelihood calculations. We introduce Gaussian process (GP) accelerated ABC, which we show can significantly reduce the number of simulations required. As computational resource is usually the main determinant of accuracy in ABC, GP-accelerated methods can thus enable more accurate inference in some models. GP models of the unknown log-likelihood function are used to exploit continuity and smoothness, reducing the required computation. We use a sequence of models that increase in accuracy, using intermediate models to rule out regions of the parameter space as implausible. The methods will not be suitable for all problems, but when they can be used, can result in significant computational savings. For the Ricker model, we are able to achieve accurate approximations to the posterior distribution using a factor of 100 fewer simulator evaluations than comparable Monte Carlo approaches, and for a population genetics model we are able to approximate the exact posterior for the first time.

We consider the high-dimensional sparse linear regression problem of accurately estimating a sparse vector using a small number of linear measurements that are contaminated by noise. It is well known that the standard cadre of computationally tractable sparse regression algorithms---such as the Lasso, Orthogonal Matching Pursuit (OMP), and their extensions---perform poorly when the measurement matrix contains highly correlated columns. To address this shortcoming, we develop a simple greedy algorithm, called SWAP, that iteratively swaps variables until convergence. SWAP is surprisingly effective in handling measurement matrices with high correlations. In fact, we prove that SWAP outputs the true support, the locations of the non-zero entries in the sparse vector, under a relatively mild condition on the measurement matrix. Furthermore, we show that SWAP can be used to boost the performance of any sparse regression algorithm. We empirically demonstrate the advantages of SWAP by comparing it with several state-of-the-art sparse regression algorithms.

We propose a novel SPARsity and Clustering (SPARC) regularizer, which is a modified version of the previous octagonal shrinkage and clustering algorithm for regression (OSCAR), where, the proposed regularizer consists of a $K$-sparse constraint and a pair-wise $\ell_{\infty}$ norm restricted on the $K$ largest components in magnitude. The proposed regularizer is able to separably enforce $K$-sparsity and encourage the non-zeros to be equal in magnitude. Moreover, it can accurately group the features without shrinking their magnitude. In fact, SPARC is closely related to OSCAR, so that the proximity operator of the former can be efficiently computed based on that of the latter, allowing using proximal splitting algorithms to solve problems with SPARC regularization. Experiments on synthetic data and with benchmark breast cancer data show that SPARC is a competitive group-sparsity inducing regularizer for regression and classification.

We study the task of retrieving relevant experiments given a query experiment. By experiment, we mean a collection of measurements from a set of `covariates' and the associated `outcomes'. While similar experiments can be retrieved by comparing available `annotations', this approach ignores the valuable information available in the measurements themselves. To incorporate this information in the retrieval task, we suggest employing a retrieval metric that utilizes probabilistic models learned from the measurements. We argue that such a metric is a sensible measure of similarity between two experiments since it permits inclusion of experiment-specific prior knowledge. However, accurate models are often not analytical, and one must resort to storing posterior samples which demands considerable resources. Therefore, we study strategies to select informative posterior samples to reduce the computational load while maintaining the retrieval performance. We demonstrate the efficacy of our approach on simulated data with simple linear regression as the models, and real world datasets.

We present a probabilistic variant of the recently introduced maxout unit. The success of deep neural networks utilizing maxout can partly be attributed to favorable performance under dropout, when compared to rectified linear units. It however also depends on the fact that each maxout unit performs a pooling operation over a group of linear transformations and is thus partially invariant to changes in its input. Starting from this observation we ask the question: Can the desirable properties of maxout units be preserved while improving their invariance properties ? We argue that our probabilistic maxout (probout) units successfully achieve this balance. We quantitatively verify this claim and report classification performance matching or exceeding the current state of the art on three challenging image classification benchmarks (CIFAR-10, CIFAR-100 and SVHN).

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 predictive covariances that, unlike a Gaussian process, explicitly depend 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.

Recent work introduced the cube-and-conquer technique to solve hard SAT instances. It partitions the search space into cubes using a lookahead solver. Each cube is tackled by a conflict-driven clause learning (CDCL) solver. Crucial for strong performance is the cutoff heuristic that decides when to switch from lookahead to CDCL. Yet, this offline heuristic is far from ideal. In this paper, we present a novel hybrid solver that applies the cube and conquer steps simultaneously. A lookahead and a CDCL solver work together on each cube, while communication is restricted to synchronization. Our concurrent cube-and-conquer solver can solve many instances faster than pure lookahead, pure CDCL and offline cube-and-conquer, and can abort early in favor of a pure CDCL search if an instance is not suitable for cube-and-conquer techniques.

We present Random Partition Kernels, a new class of kernels derived by demonstrating a natural connection between random partitions of objects and kernels between those objects. We show how the construction can be used to create kernels from methods that would not normally be viewed as random partitions, such as Random Forest. To demonstrate the potential of this method, we propose two new kernels, the Random Forest Kernel and the Fast Cluster Kernel, and show that these kernels consistently outperform standard kernels on problems involving real-world datasets. Finally, we show how the form of these kernels lend themselves to a natural approximation that is appropriate for certain big data problems, allowing $O(N)$ inference in methods such as Gaussian Processes, Support Vector Machines and Kernel PCA.

When combined properly, search techniques can reveal the full potential of sophisticated branching heuristics. We demonstrate this observation on the well-known class of random 3-SAT formulae. First, a new branching heuristic is presented, which generalizes existing work on this class. Much smaller search trees can be constructed by using this heuristic. Second, we introduce a variant of discrepancy search, called ALDS. Theoretical and practical evidence support that ALDS traverses the search tree in a near-optimal order when combined with the new heuristic. Both techniques, search and heuristic, have been implemented in the look-ahead solver march. The SAT 2009 competition results show that march is by far the strongest complete solver on random k-SAT formulae.