Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful.

A method for dimension reduction with clustering, classification, or discriminant analysis is introduced. This mixture model-based approach is based on fitting generalized hyperbolic mixtures on a reduced subspace within the paradigm of model-based clustering, classification, or discriminant analysis. A reduced subspace of the data is derived by considering the extent to which group means and group covariances vary. The members of the subspace arise through linear combinations of the original data, and are ordered by importance via the associated eigenvalues. The observations can be projected onto the subspace, resulting in a set of variables that captures most of the clustering information available. The use of generalized hyperbolic mixtures gives a robust framework capable of dealing with skewed clusters. Although dimension reduction is increasingly in demand across many application areas, the authors are most familiar with biological applications and so two of the five real data examples are within that sphere. Simulated data are also used for illustration. The approach introduced herein can be considered the most general such approach available, and so we compare results to three special and limiting cases. Comparisons with several well established techniques illustrate its promising performance.

Graphs are commonly used to characterise interactions between objects of interest. Because they are based on a straightforward formalism, they are used in many scientific fields from computer science to historical sciences. In this paper, we give an introduction to some methods relying on graphs for learning. This includes both unsupervised and supervised methods. Unsupervised learning algorithms usually aim at visualising graphs in latent spaces and/or clustering the nodes. Both focus on extracting knowledge from graph topologies. While most existing techniques are only applicable to static graphs, where edges do not evolve through time, recent developments have shown that they could be extended to deal with evolving networks. In a supervised context, one generally aims at inferring labels or numerical values attached to nodes using both the graph and, when they are available, node characteristics. Balancing the two sources of information can be challenging, especially as they can disagree locally or globally. In both contexts, supervised and un-supervised, data can be relational (augmented with one or several global graphs) as described above, or graph valued. In this latter case, each object of interest is given as a full graph (possibly completed by other characteristics). In this context, natural tasks include graph clustering (as in producing clusters of graphs rather than clusters of nodes in a single graph), graph classification, etc. 1 Real networks One of the first practical studies on graphs can be dated back to the original work of Moreno [51] in the 30s. Since then, there has been a growing interest in graph analysis associated with strong developments in the modelling and the processing of these data. Graphs are now used in many scientific fields. In Biology [54, 2, 7], for instance, metabolic networks can describe pathways of biochemical reactions [41], while in social sciences networks are used to represent relation ties between actors [66, 56, 36, 34]. Other examples include powergrids [71] and the web [75]. Recently, networks have also been considered in other areas such as geography [22] and history [59, 39]. In machine learning, networks are seen as powerful tools to model problems in order to extract information from data and for prediction purposes. This is the object of this paper. For more complete surveys, we refer to [28, 62, 49, 45]. In this section, we introduce notations and highlight properties shared by most real networks. In Section 2, we then consider methods aiming at extracting information from a unique network. We will particularly focus on clustering methods where the goal is to find clusters of vertices. Finally, in Section 3, techniques that take a series of networks into account, where each network is

Energy price forecasting is a relevant yet hard task in the field of multi-step time series forecasting. In this paper we compare a well-known and established method, ARMA with exogenous variables with a relatively new technique Gradient Boosting Regression. The method was tested on data from Global Energy Forecasting Competition 2014 with a year long rolling window forecast. The results from the experiment reveal that a multi-model approach is significantly better performing in terms of error metrics. Gradient Boosting can deal with seasonality and auto-correlation out-of-the box and achieve lower rate of normalized mean absolute error on real-world data.

We give tight concentration bounds for mixtures of martingales that are simultaneously uniform over (a) mixture distributions, in a PAC-Bayes sense; and (b) all finite times. These bounds are proved in terms of the martingale variance, extending classical Bernstein inequalities, and sharpening and simplifying prior work.

We describe the neural-network training framework used in the Kaldi speech recognition toolkit, which is geared towards training DNNs with large amounts of training data using multiple GPU-equipped or multi-core machines. In order to be as hardware-agnostic as possible, we needed a way to use multiple machines without generating excessive network traffic. Our method is to average the neural network parameters periodically (typically every minute or two), and redistribute the averaged parameters to the machines for further training. Each machine sees different data. By itself, this method does not work very well. However, we have another method, an approximate and efficient implementation of Natural Gradient for Stochastic Gradient Descent (NG-SGD), which seems to allow our periodic-averaging method to work well, as well as substantially improving the convergence of SGD on a single machine.

Careful tuning of a regularization parameter is indispensable in many machine learning tasks because it has a significant impact on generalization performances. Nevertheless, current practice of regularization parameter tuning is more of an art than a science, e.g., it is hard to tell how many grid-points would be needed in cross-validation (CV) for obtaining a solution with sufficiently small CV error. In this paper we propose a novel framework for computing a lower bound of the CV errors as a function of the regularization parameter, which we call regularization path of CV error lower bounds. The proposed framework can be used for providing a theoretical approximation guarantee on a set of solutions in the sense that how far the CV error of the current best solution could be away from best possible CV error in the entire range of the regularization parameters. We demonstrate through numerical experiments that a theoretically guaranteed a choice of regularization parameter in the above sense is possible with reasonable computational costs.

Recent progress on automatic generation of image captions has shown that it is possible to describe the most salient information conveyed by images with accurate and meaningful sentences. In this paper, we propose an image caption system that exploits the parallel structures between images and sentences. In our model, the process of generating the next word, given the previously generated ones, is aligned with the visual perception experience where the attention shifting among the visual regions imposes a thread of visual ordering. This alignment characterizes the flow of "abstract meaning", encoding what is semantically shared by both the visual scene and the text description. Our system also makes another novel modeling contribution by introducing scene-specific contexts that capture higher-level semantic information encoded in an image. The contexts adapt language models for word generation to specific scene types. We benchmark our system and contrast to published results on several popular datasets. We show that using either region-based attention or scene-specific contexts improves systems without those components. Furthermore, combining these two modeling ingredients attains the state-of-the-art performance.

We study the fundamental limits on learning latent community structure in dynamic networks. Specifically, we study dynamic stochastic block models where nodes change their community membership over time, but where edges are generated independently at each time step. In this setting (which is a special case of several existing models), we are able to derive the detectability threshold exactly, as a function of the rate of change and the strength of the communities. Below this threshold, we claim that no algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this limit. The first uses belief propagation (BP), which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the BP equations. We verify our analytic and algorithmic results via numerical simulation, and close with a brief discussion of extensions and open questions.

Statistical models with constrained probability distributions are abundant in machine learning. Some examples include regression models with norm constraints (e.g., Lasso), probit, many copula models, and latent Dirichlet allocation (LDA). Bayesian inference involving probability distributions confined to constrained domains could be quite challenging for commonly used sampling algorithms. In this paper, we propose a novel augmentation technique that handles a wide range of constraints by mapping the constrained domain to a sphere in the augmented space. By moving freely on the surface of this sphere, sampling algorithms handle constraints implicitly and generate proposals that remain within boundaries when mapped back to the original space. Our proposed method, called {Spherical Augmentation}, provides a mathematically natural and computationally efficient framework for sampling from constrained probability distributions. We show the advantages of our method over state-of-the-art sampling algorithms, such as exact Hamiltonian Monte Carlo, using several examples including truncated Gaussian distributions, Bayesian Lasso, Bayesian bridge regression, reconstruction of quantized stationary Gaussian process, and LDA for topic modeling.