Parameterizing the approximate posterior of a generative model with neural networks has become a common theme in recent machine learning research. While providing appealing flexibility, this approach makes it difficult to impose or assess structural constraints such as conditional independence. We propose a framework for learning representations that relies on Auto-Encoding Variational Bayes and whose search space is constrained via kernel-based measures of independence. In particular, our method employs the $d$-variable Hilbert-Schmidt Independence Criterion (dHSIC) to enforce independence between the latent representations and arbitrary nuisance factors. We show how to apply this method to a range of problems, including the problems of learning invariant representations and the learning of interpretable representations. We also present a full-fledged application to single-cell RNA sequencing (scRNA-seq). In this setting the biological signal in mixed in complex ways with sequencing errors and sampling effects. We show that our method out-performs the state-of-the-art in this domain.

Autoregressive feedback is considered a necessity for successful unconditional text generation using stochastic sequence models. However, such feedback is known to introduce systematic biases into the training process and it obscures a principle of generation: committing to global information and forgetting local nuances. We show that a non-autoregressive deep state space model with a clear separation of global and local uncertainty can be built from only two ingredients: An independent noise source and a deterministic transition function. Recent advances on flow-based variational inference can be used to train an evidence lower-bound without resorting to annealing, auxiliary losses or similar measures. The result is a highly interpretable generative model on par with comparable auto-regressive models on the task of word generation.

Causal discovery from empirical data is a fundamental problem in many scientific domains. Observational data allows for identifiability only up to Markov equivalence class. In this paper we first propose a polynomial time algorithm for learning the exact correctly-oriented structure of the transitive reduction of any causal Bayesian network with high probability, by using interventional path queries. Each path query takes as input an origin node and a target node, and answers whether there is a directed path from the origin to the target. This is done by intervening on the origin node and observing samples from the target node. We theoretically show the logarithmic sample complexity for the size of interventional data per path query, for continuous and discrete networks. We then show how to learn the transitive edges using also logarithmic sample complexity (albeit in time exponential in the maximum number of parents for discrete networks), which allows us to learn the full network. We further extend our work by reducing the number of interventional path queries for learning rooted trees. We also provide an analysis of imperfect interventions.

Social goods, such as healthcare, smart city, and information networks, often produce ordered event data in continuous time. The generative processes of these event data can be very complex, requiring flexible models to capture their dynamics. Temporal point processes offer an elegant framework for modeling event data without discretizing the time. However, the existing maximum-likelihood-estimation (MLE) learning paradigm requires hand-crafting the intensity function beforehand and cannot directly monitor the goodness-of-fit of the estimated model in the process of training. To alleviate the risk of model-misspecification in MLE, we propose to generate samples from the generative model and monitor the quality of the samples in the process of training until the samples and the real data are indistinguishable. We take inspiration from reinforcement learning (RL) and treat the generation of each event as the action taken by a stochastic policy. We parameterize the policy as a flexible recurrent neural network and gradually improve the policy to mimic the observed event distribution. Since the reward function is unknown in this setting, we uncover an analytic and nonparametric form of the reward function using an inverse reinforcement learning formulation. This new RL framework allows us to derive an efficient policy gradient algorithm for learning flexible point process models, and we show that it performs well in both synthetic and real data.

For many classic structured prediction problems, probability distributions over the dependent variables can be efficiently computed using widely-known algorithms and data structures (such as forward-backward, and its corresponding trellis for exact probability distributions in Markov models). However, we know of no previous work studying efficient representations of exact distributions over clusterings. This paper presents definitions and proofs for a dynamic-programming inference procedure that computes the partition function, the marginal probability of a cluster, and the MAP clustering---all exactly. Rather than the Nth Bell number, these exact solutions take time and space proportional to the substantially smaller powerset of N. Indeed, we improve upon the time complexity of the algorithm introduced by Kohonen and Corander (2016) for this problem by a factor of N. While still large, this previously unknown result is intellectually interesting in its own right, makes feasible exact inference for important real-world small data applications (such as medicine), and provides a natural stepping stone towards sparse-trellis approximations that enable further scalability (which we also explore). In experiments, we demonstrate the superiority of our approach over approximate methods in analyzing real-world gene expression data used in cancer treatment.

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.