Teaching Stats for Data Science

“Data science” is a useful catchword for methods and concepts original to the field of statistics, but typically being applied to large, multivariate, observational records. Such datasets call for techniques not often part of an introduction to statistics: modeling, consideration of covariates, sophisticated visualization, and causal reasoning. This article re-imagines introductory statistics as an introduction to data science and proposes a sequence of 10 blocks that together compose a suitable course for extracting information from contemporary data. Recent extensions to the mosaic packages for R together with tools from the “tidyverse” provide a concise and readable notation for wrangling, visualization, model-building, and model interpretation: the fundamental computational tasks of data science

Probabilistic Graphical Model Representation in Phylogenetics

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution

Learning to Associate Words and Images Using a Large-scale Graph

We develop an approach for unsupervised learning of associations between co-occurring perceptual events using a large graph. We applied this approach to successfully solve the image captcha of China's railroad system. The approach is based on the principle of suspicious coincidence. In this particular problem, a user is presented with a deformed picture of a Chinese phrase and eight low-resolution images. They must quickly select the relevant images in order to purchase their train tickets. This problem presents several challenges: (1) the teaching labels for both the Chinese phrases and the images were not available for supervised learning, (2) no pre-trained deep convolutional neural networks are available for recognizing these Chinese phrases or the presented images, and (3) each captcha must be solved within a few seconds. We collected 2.6 million captchas, with 2.6 million deformed Chinese phrases and over 21 million images. From these data, we constructed an association graph, composed of over 6 million vertices, and linked these vertices based on co-occurrence information and feature similarity between pairs of images. We then trained a deep convolutional neural network to learn a projection of the Chinese phrases onto a 230-dimensional latent space. Using label propagation, we computed the likelihood of each of the eight images conditioned on the latent space projection of the deformed phrase for each captcha. The resulting system solved captchas with 77% accuracy in 2 seconds on average. Our work, in answering this practical challenge, illustrates the power of this class of unsupervised association learning techniques, which may be related to the brain's general strategy for associating language stimuli with visual objects on the principle of suspicious coincidence.Comment: 8 pages, 7 figures, 14th Conference on Computer and Robot Vision 201