Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to existing methods on simulated data designed to mimic real microbiome data. We then illustrate results obtained for our motivating data set, a clinical study aimed at characterizing the tumor microbiome of pancreatic cancer patients

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Learning to Complete 3D Scenes from Single Depth Images

Building a complete 3D model of a scene given only a single depth image is underconstrained. To acquire a full volumetric model, one typically needs either multiple views, or a single view together with a library of unambiguous 3D models that will fit the shape of each individual object in the scene. In this thesis, we present alternative methods for inferring the hidden geometry of table-top scenes. We first introduce two depth-image datasets consisting of multiple scenes, each with a ground truth voxel occupancy grid. We then introduce three methods for predicting voxel occupancy. The first predicts the occupancy of each voxel using a novel feature vector which measures the relationship between the query voxel and surfaces in the scene observed by the depth camera. We use a Random Forest to map each voxel of unknown state to a prediction of occupancy. We observed that predicting the occupancy of each voxel independently can lead to noisy solutions. We hypothesize that objects of dissimilar semantic classes often share similar 3D shape components, enabling a limited dataset to model the shape of a wide range of objects, and hence estimate their hidden geometry. Demonstrating this hypothesis, we propose an algorithm that can make structured completions of unobserved geometry. Finally, we propose an alternative framework for understanding the 3D geometry of scenes using the observation that individual objects can appear in multiple different scenes, but in different configurations. We introduce a supervised method to find regions corresponding to the same object across different scenes. We demonstrate that it is possible to then use these groupings of partially observed objects to reconstruct missing geometry. We then perform a critical review of the approaches we have taken, including an assessment of our metrics and datasets, before proposing extensions and future work

Proceedings of the 35th International Workshop on Statistical Modelling : July 20- 24, 2020 Bilbao, Basque Country, Spain

466 p.The InternationalWorkshop on Statistical Modelling (IWSM) is a reference workshop in promoting statistical modelling, applications of Statistics for researchers, academics and industrialist in a broad sense. Unfortunately, the global COVID-19 pandemic has not allowed holding the 35th edition of the IWSM in Bilbao in July 2020. Despite the situation and following the spirit of the Workshop and the Statistical Modelling Society, we are delighted to bring you the proceedings book of extended abstracts

Deep Causal Learning for Robotic Intelligence

This invited review discusses causal learning in the context of robotic intelligence. The paper introduced the psychological findings on causal learning in human cognition, then it introduced the traditional statistical solutions on causal discovery and causal inference. The paper reviewed recent deep causal learning algorithms with a focus on their architectures and the benefits of using deep nets and discussed the gap between deep causal learning and the needs of robotic intelligence

Action recognition in depth videos using nonparametric probabilistic graphical models

Action recognition involves automatically labelling videos that contain human motion with action classes. It has applications in diverse areas such as smart surveillance, human computer interaction and content retrieval. The recent advent of depth sensing technology that produces depth image sequences has offered opportunities to solve the challenging action recognition problem. The depth images facilitate robust estimation of a human skeleton’s 3D joint positions and a high level action can be inferred from a sequence of these joint positions. A natural way to model a sequence of joint positions is to use a graphical model that describes probabilistic dependencies between the observed joint positions and some hidden state variables. A problem with these models is that the number of hidden states must be fixed a priori even though for many applications this number is not known in advance. This thesis proposes nonparametric variants of graphical models with the number of hidden states automatically inferred from data. The inference is performed in a full Bayesian setting by using the Dirichlet Process as a prior over the model’s infinite dimensional parameter space. This thesis describes three original constructions of nonparametric graphical models that are applied in the classification of actions in depth videos. Firstly, the action classes are represented by a Hidden Markov Model (HMM) with an unbounded number of hidden states. The formulation enables information sharing and discriminative learning of parameters. Secondly, a hierarchical HMM with an unbounded number of actions and poses is used to represent activities. The construction produces a simplified model for activity classification by using logistic regression to capture the relationship between action states and activity labels. Finally, the action classes are modelled by a Hidden Conditional Random Field (HCRF) with the number of intermediate hidden states learned from data. Tractable inference procedures based on Markov Chain Monte Carlo (MCMC) techniques are derived for all these constructions. Experiments with multiple benchmark datasets confirm the efficacy of the proposed approaches for action recognition

Proceedings of the 35th International Workshop on Statistical Modelling : July 20- 24, 2020 Bilbao, Basque Country, Spain

466 p.The InternationalWorkshop on Statistical Modelling (IWSM) is a reference workshop in promoting statistical modelling, applications of Statistics for researchers, academics and industrialist in a broad sense. Unfortunately, the global COVID-19 pandemic has not allowed holding the 35th edition of the IWSM in Bilbao in July 2020. Despite the situation and following the spirit of the Workshop and the Statistical Modelling Society, we are delighted to bring you the proceedings book of extended abstracts