The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter learning capabilities of a dynamic Bayesian network (DBN) peptide-scoring algorithm, Didea [25], by deriving emission distributions for which its conditional log-likelihood scoring function remains concave. We show that this class of emission distributions, called Convex Virtual Emissions (CVEs), naturally generalizes the log-sum-exp function while rendering both maximum likelihood estimation and conditional maximum likelihood estimation concave for a wide range of Bayesian networks. Utilizing CVEs in Didea allows efficient learning of a large number of parameters while ensuring global convergence, in stark contrast to Didea's previous parameter learning framework (which could only learn a single parameter using a costly grid search) and other trainable models [12, 13, 14] (which only ensure convergence to local optima). The newly trained scoring function substantially outperforms the state-of-the-art in both scoring function accuracy and downstream Fisher kernel analysis. Furthermore, we significantly improve Didea's runtime performance through successive optimizations to its message passing schedule and derive explicit connections between Didea's new concave score and related MS/MS scoring functions.

Potential based reward shaping is a powerful technique for accelerating convergence of reinforcement learning algorithms. Typically, such information includes an estimate of the optimal value function and is often provided by a human expert or other sources of domain knowledge. However, this information is often biased or inaccurate and can mislead many reinforcement learning algorithms. In this paper, we apply Bayesian Model Combination with multiple experts in a way that learns to trust a good combination of experts as training progresses. This approach is both computationally efficient and general, and is shown numerically to improve convergence across discrete and continuous domains and different reinforcement learning algorithms.

Symmetric determinantal point processes (DPP) are a class of probabilistic models that encode the random selection of items that have a repulsive behavior. They have attracted a lot of attention in machine learning, where returning diverse sets of items is sought for. Sampling and learning these symmetric DPP's is pretty well understood. In this work, we consider a new class of DPP's, which we call signed DPP's, where we break the symmetry and allow attractive behaviors. We set the ground for learning signed DPP's through a method of moments, by solving the so called principal assignment problem for a class of matrices $K$ that satisfy $K_{i,j}=\pm K_{j,i}$, $i\neq j$, in polynomial time.

We present the Multi-value Rule Set (MRS) for interpretable classification with feature efficient presentations. Compared to rule sets built from single-value rules, MRS adopts a more generalized form of association rules that allows multiple values in a condition. Rules of this form are more concise than classical singlevalue rules in capturing and describing patterns in data. Our formulation also pursues a higher efficiency of feature utilization, which reduces possible cost in data collection and storage. We propose a Bayesian framework for formulating an MRS model and develop an efficient inference method for learning a maximum a posteriori, incorporating theoretically grounded bounds to iteratively reduce the search space and improve the search efficiency. Experiments on synthetic and realworld data demonstrate that MRS models have significantly smaller complexity and fewer features than baseline models while being competitive in predictive accuracy. Human evaluations show that MRS is easier to understand and use compared to other rule-based models.

We study minimax convergence rates of nonparametric density estimation under a large class of loss functions called ``adversarial losses'', which, besides classical L^p losses, includes maximum mean discrepancy (MMD), Wasserstein distance, and total variation distance. These losses are closely related to the losses encoded by discriminator networks in generative adversarial networks (GANs). In a general framework, we study how the choice of loss and the assumed smoothness of the underlying density together determine the minimax rate. We also discuss implications for training GANs based on deep ReLU networks, and more general connections to learning implicit generative models in a minimax statistical sense.

Backpropagation and the chain rule of derivatives have been prominent; however, the total derivative rule has not enjoyed the same amount of attention. In this work we show how the total derivative rule leads to an intuitive visual framework for creating gradient estimators on graphical models. In particular, previous ”policy gradient theorems” are easily derived. We derive new gradient estimators based on density estimation, as well as a likelihood ratio gradient, which ”jumps” to an intermediate node, not directly to the objective function. We evaluate our methods on model-based policy gradient algorithms, achieve good performance, and present evidence towards demystifying the success of the popular PILCO algorithm.

Archived data from the US network of weather radars hold detailed information about bird migration over the last 25 years, including very high-resolution partial measurements of velocity. Historically, most of this spatial resolution is discarded and velocities are summarized at a very small number of locations due to modeling and algorithmic limitations. This paper presents a Gaussian process (GP) model to reconstruct high-resolution full velocity fields across the entire US. The GP faithfully models all aspects of the problem in a single joint framework, including spatially random velocities, partial velocity measurements, station-specific geometries, measurement noise, and an ambiguity known as aliasing. We develop fast inference algorithms based on the FFT; to do so, we employ a creative use of Laplace's method to sidestep the fact that the kernel of the joint process is non-stationary.

We present a novel extension of multi-output Gaussian processes for handling heterogeneous outputs. We assume that each output has its own likelihood function and use a vector-valued Gaussian process prior to jointly model the parameters in all likelihoods as latent functions. Our multi-output Gaussian process uses a covariance function with a linear model of coregionalisation form. Assuming conditional independence across the underlying latent functions together with an inducing variable framework, we are able to obtain tractable variational bounds amenable to stochastic variational inference. We illustrate the performance of the model on synthetic data and two real datasets: a human behavioral study and a demographic high-dimensional dataset.

Deep latent variable models (DLVMs) combine the approximation abilities of deep neural networks and the statistical foundations of generative models. Variational methods are commonly used for inference; however, the exact likelihood of these models has been largely overlooked. The purpose of this work is to study the general properties of this quantity and to show how they can be leveraged in practice. We focus on important inferential problems that rely on the likelihood: estimation and missing data imputation. First, we investigate maximum likelihood estimation for DLVMs: in particular, we show that most unconstrained models used for continuous data have an unbounded likelihood function. This problematic behaviour is demonstrated to be a source of mode collapse. We also show how to ensure the existence of maximum likelihood estimates, and draw useful connections with nonparametric mixture models. Finally, we describe an algorithm for missing data imputation using the exact conditional likelihood of a DLVM. On several data sets, our algorithm consistently and significantly outperforms the usual imputation scheme used for DLVMs.

Gaussian Processes (GPs) are a generic modelling tool for supervised learning. While they have been successfully applied on large datasets, their use in safety-critical applications is hindered by the lack of good performance guarantees. To this end, we propose a method to learn GPs and their sparse approximations by directly optimizing a PAC-Bayesian bound on their generalization performance, instead of maximizing the marginal likelihood. Besides its theoretical appeal, we find in our evaluation that our learning method is robust and yields significantly better generalization guarantees than other common GP approaches on several regression benchmark datasets.