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Directed Acyclic Graphs (DAGs) provide a powerful framework to model causal relationships among variables in multivariate settings; in addition, through the do-calculus theory, they allow for the identification and estimation of causal effects between variables also from pure observational data. In this setting, the process of inferring the DAG structure from the data is referred to as causal structure learning or causal discovery. We introduce BCDAG, an R package for Bayesian causal discovery and causal effect estimation from Gaussian observational data, implementing the Markov chain Monte Carlo (MCMC) scheme proposed by Castelletti & Mascaro (2021). Our implementation scales efficiently with the number of observations and, whenever the DAGs are sufficiently sparse, with the number of variables in the dataset. The package also provides functions for convergence diagnostics and for visualizing and summarizing posterior inference. In this paper, we present the key features of the underlying methodology along with its implementation in BCDAG. We then illustrate the main functions and algorithms on both real and simulated datasets.

Predictive models for binary data are fundamental in various fields, and the growing complexity of modern applications has motivated several flexible specifications for modeling the relationship between the observed predictors and the binary responses. A widely-implemented solution is to express the probability parameter via a probit mapping of a Gaussian process indexed by predictors. However, unlike for continuous settings, there is a lack of closed-form results for predictive distributions in binary models with Gaussian process priors. Markov chain Monte Carlo methods and approximation strategies provide common solutions to this problem, but state-of-the-art algorithms are either computationally intractable or inaccurate in moderate-to-high dimensions. In this article, we aim to cover this gap by deriving closed-form expressions for the predictive probabilities in probit Gaussian processes that rely either on cumulative distribution functions of multivariate Gaussians or on functionals of multivariate truncated normals. To evaluate these quantities we develop novel scalable solutions based on tile-low-rank Monte Carlo methods for computing multivariate Gaussian probabilities, and on mean-field variational approximations of multivariate truncated normals. Closed-form expressions for the marginal likelihood and for the posterior distribution of the Gaussian process are also discussed. As shown in simulated and real-world empirical studies, the proposed methods scale to dimensions where state-of-the-art solutions are impractical.

Fast forecasting of reservoir pressure distribution in geologic carbon storage (GCS) by assimilating monitoring data is a challenging problem. Due to high drilling cost, GCS projects usually have spatially sparse measurements from wells, leading to high uncertainties in reservoir pressure prediction. To address this challenge, we propose to use low-cost Interferometric Synthetic-Aperture Radar (InSAR) data as monitoring data to infer reservoir pressure build up. We develop a deep learning-accelerated workflow to assimilate surface displacement maps interpreted from InSAR and to forecast dynamic reservoir pressure. Employing an Ensemble Smoother Multiple Data Assimilation (ES-MDA) framework, the workflow updates three-dimensional (3D) geologic properties and predicts reservoir pressure with quantified uncertainties. We use a synthetic commercial-scale GCS model with bimodally distributed permeability and porosity to demonstrate the efficacy of the workflow. A two-step CNN-PCA approach is employed to parameterize the bimodal fields. The computational efficiency of the workflow is boosted by two residual U-Net based surrogate models for surface displacement and reservoir pressure predictions, respectively. The workflow can complete data assimilation and reservoir pressure forecasting in half an hour on a personal computer.

The $k$-center problem is to choose a subset of size $k$ from a set of $n$ points such that the maximum distance from each point to its nearest center is minimized. Let $Q=\{Q_1,\ldots,Q_n\}$ be a set of polygons or segments in the region-based uncertainty model, in which each $Q_i$ is an uncertain point, where the exact locations of the points in $Q_i$ are unknown. The geometric objects segments and polygons can be models of a point set. We define the uncertain version of the $k$-center problem as a generalization in which the objective is to find $k$ points from $Q$ to cover the remaining regions of $Q$ with minimum or maximum radius of the cluster to cover at least one or all exact instances of each $Q_i$, respectively. We modify the region-based model to allow multiple points to be chosen from a region and call the resulting model the aggregated uncertainty model. All these problems contain the point version as a special case, so they are all NP-hard with a lower bound 1.822. We give approximation algorithms for uncertain $k$-center of a set of segments and polygons. We also have implemented some of our algorithms on a data-set to show our theoretical performance guarantees can be achieved in practice.

Driven by the key challenges of cell therapy manufacturing, including high complexity, high uncertainty, and very limited process observations, we propose a hybrid model-based reinforcement learning (RL) to efficiently guide process control. We first create a probabilistic knowledge graph (KG) hybrid model characterizing the risk- and science-based understanding of biomanufacturing process mechanisms and quantifying inherent stochasticity, e.g., batch-to-batch variation. It can capture the key features, including nonlinear reactions, nonstationary dynamics, and partially observed state. This hybrid model can leverage existing mechanistic models and facilitate learning from heterogeneous process data. A computational sampling approach is used to generate posterior samples quantifying model uncertainty. Then, we introduce hybrid model-based Bayesian RL, accounting for both inherent stochasticity and model uncertainty, to guide optimal, robust, and interpretable dynamic decision making. Cell therapy manufacturing examples are used to empirically demonstrate that the proposed framework can outperform the classical deterministic mechanistic model assisted process optimization.

Imitation learning enables agents to reuse and adapt the hard-won expertise of others, offering a solution to several key challenges in learning behavior. Although it is easy to observe behavior in the real-world, the underlying actions may not be accessible. We present a new method for imitation solely from observations that achieves comparable performance to experts on challenging continuous control tasks while also exhibiting robustness in the presence of observations unrelated to the task. Our method, which we call FORM (for "Future Observation Reward Model") is derived from an inverse RL objective and imitates using a model of expert behavior learned by generative modelling of the expert's observations, without needing ground truth actions. We show that FORM performs comparably to a strong baseline IRL method (GAIL) on the DeepMind Control Suite benchmark, while outperforming GAIL in the presence of task-irrelevant features.

Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.

Despite huge success in the image domain, modern detection models such as Faster R-CNN have not been used nearly as much for video analysis. This is arguably due to the fact that detection models are designed to operate on single frames and as a result do not have a mechanism for learning motion representations directly from video. We propose a learning procedure that allows detection models such as Faster R-CNN to learn motion features directly from the RGB video data while being optimized with respect to a pose estimation task. Given a pair of video frames---Frame A and Frame B---we force our model to predict human pose in Frame A using the features from Frame B. We do so by leveraging deformable convolutions across space and time. Our network learns to spatially sample features from Frame B in order to maximize pose detection accuracy in Frame A. This naturally encourages our network to learn motion offsets encoding the spatial correspondences between the two frames. We refer to these motion offsets as DiMoFs (Discriminative Motion Features). In our experiments we show that our training scheme helps learn effective motion cues, which can be used to estimate and localize salient human motion. Furthermore, we demonstrate that as a byproduct, our model also learns features that lead to improved pose detection in still-images, and better keypoint tracking. Finally, we show how to leverage our learned model for the tasks of spatiotemporal action localization and fine-grained action recognition.

Machine Learning models become increasingly proficient in complex tasks. However, even for experts in the field, it can be difficult to understand what the model learned. This hampers trust and acceptance, and it obstructs the possibility to correct the model. There is therefore a need for transparency of machine learning models. The development of transparent classification models has received much attention, but there are few developments for achieving transparent Reinforcement Learning (RL) models. In this study we propose a method that enables a RL agent to explain its behavior in terms of the expected consequences of state transitions and outcomes. First, we define a translation of states and actions to a description that is easier to understand for human users. Second, we developed a procedure that enables the agent to obtain the consequences of a single action, as well as its entire policy. The method calculates contrasts between the consequences of a policy derived from a user query, and of the learned policy of the agent. Third, a format for generating explanations was constructed. A pilot survey study was conducted to explore preferences of users for different explanation properties. Results indicate that human users tend to favor explanations about policy rather than about single actions.

Deep reinforcement learning has recently shown many impressive successes. However, one major obstacle towards applying such methods to real-world problems is their lack of data-efficiency. To this end, we propose the Bottleneck Simulator: a model-based reinforcement learning method which combines a learned, factorized transition model of the environment with rollout simulations to learn an effective policy from few examples. The learned transition model employs an abstract, discrete (bottleneck) state, which increases sample efficiency by reducing the number of model parameters and by exploiting structural properties of the environment. We provide a mathematical analysis of the Bottleneck Simulator in terms of fixed points of the learned policy, which reveals how performance is affected by four distinct sources of error: an error related to the abstract space structure, an error related to the transition model estimation variance, an error related to the transition model estimation bias, and an error related to the transition model class bias. Finally, we evaluate the Bottleneck Simulator on two natural language processing tasks: a text adventure game and a real-world, complex dialogue response selection task. On both tasks, the Bottleneck Simulator yields excellent performance beating competing approaches.