Spectral estimation (SE) aims to identify how the energy of a signal (e.g., a time series) is distributed across different frequencies. This can become particularly challenging when only partial and noisy observations of the signal are available, where current methods fail to handle uncertainty appropriately. In this context, we propose a joint probabilistic model for signals, observations and spectra, where SE is addressed as an inference problem. Assuming a Gaussian process prior over the signal, we apply Bayes' rule to find the analytic posterior distribution of the spectrum given a set of observations. Besides its expressiveness and natural account of spectral uncertainty, the proposed model also provides a functional-form representation of the power spectral density, which can be optimised efficiently. Comparison with previous approaches is addressed theoretically, showing that the proposed method is an infinite-dimensional variant of the Lomb-Scargle approach, and also empirically through three experiments.

Model-free reinforcement learning (RL) algorithms directly parameterize and update value functions or policies, bypassing the modeling of the environment. They are typically simpler, more flexible to use, and thus more prevalent in modern deep RL than model-based approaches. However, empirical work has suggested that they require large numbers of samples to learn. The theoretical question of whether not model-free algorithms are in fact \emph{sample efficient} is one of the most fundamental questions in RL. The problem is unsolved even in the basic scenario with finitely many states and actions. We prove that, in an episodic MDP setting, Q-learning with UCB exploration achieves regret $\tlO(\sqrt{H^3 SAT})$ where $S$ and $A$ are the numbers of states and actions, $H$ is the number of steps per episode, and $T$ is the total number of steps. Our regret matches the optimal regret up to a single $\sqrt{H}$ factor. Thus we establish the sample efficiency of a classical model-free approach. Moreover, to the best of our knowledge, this is the first model-free analysis to establish $\sqrt{T}$ regret \emph{without} requiring access to a ``simulator.''

It is commonly believed that an agent making decisions on behalf of two or more principals who have different utility functions should adopt a Pareto optimal policy, i.e. a policy that cannot be improved upon for one principal without making sacrifices for another. Harsanyi's theorem shows that when the principals have a common prior on the outcome distributions of all policies, a Pareto optimal policy for the agent is one that maximizes a fixed, weighted linear combination of the principals' utilities. In this paper, we derive a more precise generalization for the sequential decision setting in the case of principals with different priors on the dynamics of the environment. We refer to this generalization as the Negotiable Reinforcement Learning (NRL) framework. In this more general case, the relative weight given to each principal's utility should evolve over time according to how well the agent's observations conform with that principal's prior. To gain insight into the dynamics of this new framework, we implement a simple NRL agent and empirically examine its behavior in a simple environment.

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.

We propose a Bayesian decision making framework for control of Markov Decision Processes (MDPs) with unknown dynamics and large, possibly continuous, state, action, and parameter spaces in data-poor environments. Most of the existing adaptive controllers for MDPs with unknown dynamics are based on the reinforcement learning framework and rely on large data sets acquired by sustained direct interaction with the system or via a simulator. This is not feasible in many applications, due to ethical, economic, and physical constraints. The proposed framework addresses the data poverty issue by decomposing the problem into an offline planning stage that does not rely on sustained direct interaction with the system or simulator and an online execution stage. In the offline process, parallel Gaussian process temporal difference (GPTD) learning techniques are employed for near-optimal Bayesian approximation of the expected discounted reward over a sample drawn from the prior distribution of unknown parameters. In the online stage, the action with the maximum expected return with respect to the posterior distribution of the parameters is selected. This is achieved by an approximation of the posterior distribution using a Markov Chain Monte Carlo (MCMC) algorithm, followed by constructing multiple Gaussian processes over the parameter space for efficient prediction of the means of the expected return at the MCMC sample. The effectiveness of the proposed framework is demonstrated using a simple dynamical system model with continuous state and action spaces, as well as a more complex model for a metastatic melanoma gene regulatory network observed through noisy synthetic gene expression data.

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.

Natural scenes contain many layers of part-subpart structure, and distributions over them are thus naturally represented by stochastic image grammars, with one production per decomposition of a part. Unfortunately, in contrast to language grammars, where the number of possible split points for a production $A \rightarrow BC$ is linear in the length of $A$, in an image there are an exponential number of ways to split a region into subregions. This makes parsing intractable and requires image grammars to be severely restricted in practice, for example by allowing only rectangular regions. In this paper, we address this problem by associating with each production a submodular Markov random field whose labels are the subparts and whose labeling segments the current object into these subparts. We call the result a submodular field grammar (SFG). Finding the MAP split of a region into subregions is now tractable, and by exploiting this we develop an efficient approximate algorithm for MAP parsing of images with SFGs. Empirically, we present promising improvements in accuracy when using SFGs for scene understanding, and show exponential improvements in inference time compared to traditional methods, while returning comparable minima.

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.