Noname manuscript No. (will be inserted by the editor) Abstract Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wildtype conditions. Cancer and HIV are two common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, cooperation and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks ( SBCNs). SBCNs are generative probabilistic graphical models that recapitulate the potential ordering of accumulation of such DNA changes during the progression of the disease. Such models can be inferred from data by exploiting likelihood-based model-selection strategies with regularization. In this paper we discuss the theoretical foundations of our approach and we investigate in depth the influence on the model-selection task of: (i) the poset based on Suppes' theory and (ii) different regularization strategies. Furthermore, we provide an example of application of our framework to HIV genetic data high-Daniele Ramazzotti Department of Pathology, Stanford University, Stanford, CA 94305, USA Email: daniele.ramazzotti@stanford.edu Alex Graudenzi Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy Giulio Caravagna School of Informatics, University of Edinburgh, Edinburgh, UK Marco Antoniotti Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy Keywords Cumulative Phenomena· Bayesian Graphical Models· Probabilistic Causality 1 Introduction A number of diseases are characterized by the accumulation of genomic lesions in the DNA of a population of cells. Such lesions are often classified as mutations, if they involve one or few nucleotides, or chromosomal alterations, if they involve wider regions of a chromosome.

Discrimination discovery from data is an important task aiming at identifying patterns of illegal and unethical discriminatory activities against protected-by-law groups, e.g., ethnic minorities. While any legally-valid proof of discrimination requires evidence of causality, the state-of-the-art methods are essentially correlation-based, albeit, as it is well known, correlation does not imply causation. In this paper we take a principled causal approach to the data mining problem of discrimination detection in databases. Following Suppes' probabilistic causation theory, we define a method to extract, from a dataset of historical decision records, the causal structures existing among the attributes in the data. The result is a type of constrained Bayesian network, which we dub Suppes-Bayes Causal Network (SBCN). Next, we develop a toolkit of methods based on random walks on top of the SBCN, addressing different anti-discrimination legal concepts, such as direct and indirect discrimination, group and individual discrimination, genuine requirement, and favoritism. Our experiments on real-world datasets confirm the inferential power of our approach in all these different tasks.

Record linkage involves merging records in large, noisy databases to remove duplicate entities. It has become an important area because of its widespread occurrence in bibliometrics, public health, official statistics production, political science, and beyond. Traditional linkage methods directly linking records to one another are computationally infeasible as the number of records grows. As a result, it is increasingly common for researchers to treat record linkage as a clustering task, in which each latent entity is associated with one or more noisy database records. We critically assess performance bounds using the Kullback-Leibler (KL) divergence under a Bayesian record linkage framework, making connections to Kolchin partition models. We provide an upper bound using the KL divergence and a lower bound on the minimum probability of misclassifying a latent entity. We give insights for when our bounds hold using simulated data and provide practical user guidance.

A Robust Markov Decision Process (RMDP) is a sequential decision making model that accounts for uncertainty in the parameters of dynamic systems. This uncertainty introduces difficulties in learning an optimal policy, especially for environments with large state spaces. We propose two algorithms, RTD-DQN and Deep-RoK, for solving large-scale RMDPs using nonlinear approximation schemes such as deep neural networks. The RTD-DQN algorithm incorporates the robust Bellman temporal difference error into a robust loss function, yielding robust policies for the agent. The Deep-RoK algorithm is a robust Bayesian method, based on the Extended Kalman Filter (EKF), that accounts for both the uncertainty in the weights of the approximated value function and the uncertainty in the transition probabilities, improving the robustness of the agent. We provide theoretical results for our approach and test the proposed algorithms on a continuous state domain.

We discuss a Bayesian formulation to coarse-graining (CG) of PDEs where the coefficients (e.g. material parameters) exhibit random, fine scale variability. The direct solution to such problems requires grids that are small enough to resolve this fine scale variability which unavoidably requires the repeated solution of very large systems of algebraic equations. We establish a physically inspired, data-driven coarse-grained model which learns a low- dimensional set of microstructural features that are predictive of the fine-grained model (FG) response. Once learned, those features provide a sharp distribution over the coarse scale effec- tive coefficients of the PDE that are most suitable for prediction of the fine scale model output. This ultimately allows to replace the computationally expensive FG by a generative proba- bilistic model based on evaluating the much cheaper CG several times. Sparsity enforcing pri- ors further increase predictive efficiency and reveal microstructural features that are important in predicting the FG response. Moreover, the model yields probabilistic rather than single-point predictions, which enables the quantification of the unavoidable epistemic uncertainty that is present due to the information loss that occurs during the coarse-graining process.

To improve the efficiency of Monte Carlo estimation, practitioners are turning to biased Markov chain Monte Carlo procedures that trade off asymptotic exactness for computational speed. The reasoning is sound: a reduction in variance due to more rapid sampling can outweigh the bias introduced. However, the inexactness creates new challenges for sampler and parameter selection, since standard measures of sample quality like effective sample size do not account for asymptotic bias. To address these challenges, we introduce a new computable quality measure based on Stein's method that quantifies the maximum discrepancy between sample and target expectations over a large class of test functions. We use our tool to compare exact, biased, and deterministic sample sequences and illustrate applications to hyperparameter selection, convergence rate assessment, and quantifying bias-variance tradeoffs in posterior inference.

Yield curve forecasting is an important problem in finance. In this work we explore the use of Gaussian Processes in conjunction with a dynamic modeling strategy, much like the Kalman Filter, to model the yield curve. Gaussian Processes have been successfully applied to model functional data in a variety of applications. A Gaussian Process is used to model the yield curve. The hyper-parameters of the Gaussian Process model are updated as the algorithm receives yield curve data. Yield curve data is typically available as a time series with a frequency of one day. We compare existing methods to forecast the yield curve with the proposed method. The results of this study showed that while a competing method (a multivariate time series method) performed well in forecasting the yields at the short term structure region of the yield curve, Gaussian Processes perform well in the medium and long term structure regions of the yield curve. Accuracy in the long term structure region of the yield curve has important practical implications. The Gaussian Process framework yields uncertainty and probability estimates directly in contrast to other competing methods. Analysts are frequently interested in this information. In this study the proposed method has been applied to yield curve forecasting, however it can be applied to model high frequency time series data or data streams in other domains.

This paper studies a new Bayesian algorithm for the joint reconstruction and classification of reflectance confocal microscopy (RCM) images, with application to the identification of human skin lentigo. The proposed Bayesian approach takes advantage of the distribution of the multiplicative speckle noise affecting the true reflectivity of these images and of appropriate priors for the unknown model parameters. A Markov chain Monte Carlo (MCMC) algorithm is proposed to jointly estimate the model parameters and the image of true reflectivity while classifying images according to the distribution of their reflectivity. Precisely, a Metropolis-within-Gibbs sampler is investigated to sample the posterior distribution of the Bayesian model associated with RCM images and to build estimators of its parameters, including labels indicating the class of each RCM image. The resulting algorithm is applied to synthetic data and to real images from a clinical study containing healthy and lentigo patients. The lentigo is a hyperplasia that affects the skin.

We harness the power of Bayesian emulation techniques, designed to aid the analysis of complex computer models, to examine the structure of complex Bayesian analyses themselves. These techniques facilitate robust Bayesian analyses and/or sensitivity analyses of complex problems, and hence allow global exploration of the impacts of choices made in both the likelihood and prior specification. We show how previously intractable problems in robustness studies can be overcome using emulation techniques, and how these methods allow other scientists to quickly extract approximations to posterior results corresponding to their own particular subjective specification. The utility and flexibility of our method is demonstrated on a reanalysis of a real application where Bayesian methods were employed to capture beliefs about river flow. We discuss the obvious extensions and directions of future research that such an approach opens up.