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, 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 (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.

Recent advances in recording technologies have allowed neuroscientists to record simultaneous spiking activity from hundreds to thousands of neurons in multiple brain regions. Such large-scale recordings pose a major challenge to existing statistical methods for neural data analysis. Here we develop highly scalable approximate inference methods for Poisson generalized linear models (GLMs) that require only a single pass over the data. Our approach relies on a recently proposed method for obtaining approximate sufficient statistics for GLMs using polynomial approximations [Huggins et al., 2017], which we adapt to the Poisson GLM setting. We focus on inference using quadratic approximations to nonlinear terms in the Poisson GLM log-likelihood with Gaussian priors, for which we derive closed-form solutions to the approximate maximum likelihood and MAP estimates, posterior distribution, and marginal likelihood.

Variational Auto-Encoders (VAE) have become very popular techniques to perform inference and learning in latent variable models as they allow us to leverage the rich representational power of neural networks to obtain flexible approximations of the posterior of latent variables as well as tight evidence lower bounds (ELBO). Com- bined with stochastic variational inference, this provides a methodology scaling to large datasets. However, for this methodology to be practically efficient, it is neces- sary to obtain low-variance unbiased estimators of the ELBO and its gradients with respect to the parameters of interest. While the use of Markov chain Monte Carlo (MCMC) techniques such as Hamiltonian Monte Carlo (HMC) has been previously suggested to achieve this [23, 26], the proposed methods require specifying reverse kernels which have a large impact on performance. Additionally, the resulting unbiased estimator of the ELBO for most MCMC kernels is typically not amenable to the reparameterization trick.

I like the fact that the method is very simple to understand and implement (see my summary), and does not require any major changes to the base SG-MCMC algorithm. Also, this seems very general and applies to a large class of SG-MCMC algorithms, and is therefore potentially very impactful to the Stochastic Gradient MCMC community. Novelty: Although Richardson-Romberg extrapolation is well known in numerical analysis, it is not widely known in the machine learning / stochastic gradient MCMC community. Clarity: The paper is well written and the presentation is clear. Comments/questions: - Can this technique be directly applied to all SG-MCMC methods?

Summary This paper proposes a control variate (CV) for the discrete distribution's REINFORCE gradient estimator (RGE). The CV is based on the Concrete distribution (CD), a continuous relaxation of the discrete distribution that admits only biased Monte Carlo (MC) estimates of the discrete distribution's gradient. Yet, using the CD as a CV results in an *unbiased* estimator for a discrete random variable's (rv) path gradient as well as lower variance than the RGE (as expected). REBAR is derived by exploiting the REINFORCE estimator for the CD and by observing that given a discrete draw, the CD's continuous parameter (z, here) can be marginalized out. REBAR has some nice connections to other estimators for discrete rv gradients, including MuProp.

The authors present a variational inference algorithm for continuous time Markov jump processes. Following previous work, they use "uniformization" to produce a discrete time skeleton at which they infer the latent states. Unlike previous work, however, the authors propose to learn this skeleton (a point estimate, via random search) and to integrate out, or collapse, the transition matrix during latent state inference. They compare their algorithm to existing MCMC schemes, which also use uniformization, but which do not collapse out the transition matrix. While this work is well motivated, I found it difficult to tease out which elements of the inference algorithm led to the observed improvement.

Title: Differentially private Bayesian learning on distributed data Comments: - This paper develops a method for differential privacy (DP) Bayesian learning in a distributed setting, where data is split up over multiple clients. This differs from the traditional DP Bayesian learning setting, in which a single party has access to the full dataset. The main issue here is that performing DP methods separately on each client would yield too much noise; the goal is then to find a way to add an appropriate amount of noise, without compromising privacy, in this setting. To solve this, the authors introduce a method that combines existing DP Bayesian learning methods with a secure multi-party communication method called the DCA algorithm. Theoretically, this paper shows that the method satisfies differential privacy.

This paper presents a sampling method that combines Hamiltonian Monte Carlo (HMC), mini-batches, tempering, and thermostats, to more efficiently explore multimodal target distributions. It is demonstrated on a number of substantial neural network problems using real data sets. This is an interesting method, and the empirical results are quite substantial. Figure 2 does a nice job of demonstrating how the omission of any of the ingredients (e.g. the tempering, or the thermostat) is detrimental to the overall result, which is a nice illustration of how the combination works together well. This is followed by some substantial image classification examples.

This submission proposes a new prior on the topic-word distribution in latent topic models. This model defines a multi-layer feedforward graph, where each layer contains a set of valid multinomial distributions over the vocabulary, and weighted combinations of each layer's "topics" are used as the Dirichlet prior for the "topics" of the next layer. The key purported benefits are sharing of statistical strengh, inference of a hierarchy of interpretable "abstract" topics, and modularity that allows composition with other topic model variants that modify the document-topic distributions. The authors present an efficient fully collapsed Gibbs sampler inference scheme - I did not thoroughly check the derivation but it seems plausible. Although: what is the computational complexity (and relative "wall clock" cost) of the given inference scheme?

The paper presents a policy gradient algorithm for a multiagent cooperative problem, modeled in a formalism (CDEC-POMDP) whose dynamics, like congestion games, depend on groups of agents rather than individuals. This paper follows the theme of several similar advances in theis field of complex multiagent planning, using factored models to propose practical/tractable approximations. The novelty here is the use of parameterized policies and training algorithms inspired by reinforcement learning (policy gradients). The work is well-motivated, relevant, and particularly well-presented. The theoretical results are new and important.