Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal biological knowledge graph, and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. We demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm, and performing counterfactual inference to estimate the causal effect of medical countermeasures for severely ill patients.

In application areas where data generation is expensive, Gaussian processes are a preferred supervised learning model due to their high data-efficiency. Particularly in model-based control, Gaussian processes allow the derivation of performance guarantees using probabilistic model error bounds. To make these approaches applicable in practice, two open challenges must be solved i) Existing error bounds rely on prior knowledge, which might not be available for many real-world tasks. (ii) The relationship between training data and the posterior variance, which mainly drives the error bound, is not well understood and prevents the asymptotic analysis. This article addresses these issues by presenting a novel uniform error bound using Lipschitz continuity and an analysis of the posterior variance function for a large class of kernels. Additionally, we show how these results can be used to guarantee safe control of an unknown dynamical system and provide numerical illustration examples.

The density estimation is one of the core problems in statistics. Despite this, existing techniques like maximum likelihood estimation are computationally inefficient due to the intractability of the normalizing constant. For this reason an interest to score matching has increased being independent on the normalizing constant. However, such estimator is consistent only for distributions with the full space support. One of the approaches to make it consistent is to add noise to the input data which is called Denoising Score Matching. In this work we derive analytical expression for the Denoising Score matching using the Kernel Exponential Family as a model distribution. The usage of the kernel exponential family is motivated by the richness of this class of densities. To tackle the computational complexity we use Random Fourier Features based approximation of the kernel function. The analytical expression allows to drop additional regularization terms based on the higher-order derivatives as they are already implicitly included. Moreover, the obtained expression explicitly depends on the noise variance, so the validation loss can be straightforwardly used to tune the noise level. Along with benchmark experiments, the model was tested on various synthetic distributions to study the behaviour of the model in different cases. The empirical study shows comparable quality to the competing approaches, while the proposed method being computationally faster. The latter one enables scaling up to complex high-dimensional data.

Trip destination prediction is an area of increasing importance in many applications such as trip planning, autonomous driving and electric vehicles. Even though this problem could be naturally addressed in an online learning paradigm where data is arriving in a sequential fashion, the majority of research has rather considered the offline setting. In this paper, we present a unified framework for trip destination prediction in an online setting, which is suitable for both online training and online prediction. For this purpose, we develop two clustering algorithms and integrate them within two online prediction models for this problem. We investigate the different configurations of clustering algorithms and prediction models on a real-world dataset. By using traditional clustering metrics and accuracy, we demonstrate that both the clustering and the entire framework yield consistent results compared to the offline setting. Finally, we propose a novel regret metric for evaluating the entire online framework in comparison to its offline counterpart. This metric makes it possible to relate the source of erroneous predictions to either the clustering or the prediction model. Using this metric, we show that the proposed methods converge to a probability distribution resembling the true underlying distribution and enjoy a lower regret than all of the baselines.

Traditional communication systems design is dominated by methods that are based on statistical models. These statistical-model-based algorithms, which we refer to henceforth as model-based methods, rely on mathematical models that describe the transmission process, signal propagation, receiver noise, interference, and many other components of the system that affect the end-to-end signal transmission and reception. Such mathematical models use parameters that vary over time as the channel conditions, the environment, network traffic, or network topology change. Therefore, for optimal operation, many of the algorithms used in communication systems rely on the underlying mathematical models as well as the estimation of the model parameters. However, there are cases where this approach fails, in particular when the mathematical models for one or more of the system components are highly complex, hard to estimate, poorly understood, do not well-capture the underlying physics of the system, or do not lend themselves to computationally-efficient algorithms.

Recent advances in probabilistic modelling have led to a large number of simulation-based inference algorithms which do not require numerical evaluation of likelihoods. However, a public benchmark with appropriate performance metrics for such 'likelihood-free' algorithms has been lacking. This has made it difficult to compare algorithms and identify their strengths and weaknesses. We set out to fill this gap: We provide a benchmark with inference tasks and suitable performance metrics, with an initial selection of algorithms including recent approaches employing neural networks and classical Approximate Bayesian Computation methods. We found that the choice of performance metric is critical, that even state-of-the-art algorithms have substantial room for improvement, and that sequential estimation improves sample efficiency. Neural network-based approaches generally exhibit better performance, but there is no uniformly best algorithm. We provide practical advice and highlight the potential of the benchmark to diagnose problems and improve algorithms. The results can be explored interactively on a companion website. All code is open source, making it possible to contribute further benchmark tasks and inference algorithms.

The analysis is borrowed from the regression setting and aims to decompose the prediction error of a given classifier into the terms of B&V to evaluate their effects on the performance. Therefore, it can help answer questions such as "How can we compare the accuracy of two different types of classifiers?", "What is it that makes stronger classifiers perform well? Is it the reduction in the bias they bring about, or in variance, or both?". Other than being theoretically interesting, the answers to these questions are also meant to provide better classifier design strategies which bring about improved prediction performance. After the initial decomposition of the prediction error into the standard B&V terms in the regression setting by [1], different studies have attempted to carry over this analysis into the classification setting while preserving the meanings of the terms and the additive property of the decomposition.

Due to the importance of uncertainty quantification (UQ), Bayesian approach to inverse problems has recently gained popularity in applied mathematics, physics, and engineering. However, traditional Bayesian inference methods based on Markov Chain Monte Carlo (MCMC) tend to be computationally intensive and inefficient for such high dimensional problems. To address this issue, several methods based on surrogate models have been proposed to speed up the inference process. More specifically, the calibration-emulation-sampling (CES) scheme has been proven to be successful in large dimensional UQ problems. In this work, we propose a novel CES approach for Bayesian inference based on deep neural network (DNN) models for the emulation phase. The resulting algorithm is not only computationally more efficient, but also less sensitive to the training set. Further, by using an Autoencoder (AE) for dimension reduction, we have been able to speed up our Bayesian inference method up to three orders of magnitude. Overall, our method, henceforth called \emph{Dimension-Reduced Emulative Autoencoder Monte Carlo (DREAM)} algorithm, is able to scale Bayesian UQ up to thousands of dimensions in physics-constrained inverse problems. Using two low-dimensional (linear and nonlinear) inverse problems we illustrate the validity this approach. Next, we apply our method to two high-dimensional numerical examples (elliptic and advection-diffussion) to demonstrate its computational advantage over existing algorithms.

The development and deployment of machine learning (ML) systems can be executed easily with modern tools, but the process is typically rushed and means-to-an-end. The lack of diligence can lead to technical debt, scope creep and misaligned objectives, model misuse and failures, and expensive consequences. Engineering systems, on the other hand, follow well-defined processes and testing standards to streamline development for high-quality, reliable results. The extreme is spacecraft systems, where mission critical measures and robustness are ingrained in the development process. Drawing on experience in both spacecraft engineering and ML (from research through product across domain areas), we have developed a proven systems engineering approach for machine learning development and deployment. Our "Machine Learning Technology Readiness Levels" (MLTRL) framework defines a principled process to ensure robust, reliable, and responsible systems while being streamlined for ML workflows, including key distinctions from traditional software engineering. Even more, MLTRL defines a lingua franca for people across teams and organizations to work collaboratively on artificial intelligence and machine learning technologies. Here we describe the framework and elucidate it with several real world use-cases of developing ML methods from basic research through productization and deployment, in areas such as medical diagnostics, consumer computer vision, satellite imagery, and particle physics.

In the biopharmaceutical manufacturing, fermentation process plays a critical role impacting on productivity and profit. Since biotherapeutics are manufactured in living cells whose biological mechanisms are complex and have highly variable outputs, in this paper, we introduce a model-based reinforcement learning framework accounting for model risk to support bioprocess online learning and guide the optimal and robust customized stopping policy for fermentation process. Specifically, built on the dynamic mechanisms of protein and impurity generation, we first construct a probabilistic model characterizing the impact of underlying bioprocess stochastic uncertainty on impurity and protein growth rates. Since biopharmaceutical manufacturing often has very limited data during the development and early stage of production, we derive the posterior distribution quantifying the process model risk, and further develop the Bayesian rule based knowledge update to support the online learning on underlying stochastic process. With the prediction risk accounting for both bioprocess stochastic uncertainty and model risk, the proposed reinforcement learning framework can proactively hedge all sources of uncertainties and support the optimal and robust customized decision making. We conduct the structural analysis of optimal policy and study the impact of model risk on the policy selection. We can show that it asymptotically converges to the optimal policy obtained under perfect information of underlying stochastic process. Our case studies demonstrate that the proposed framework can greatly improve the biomanufacturing industrial practice.