Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases (ICD) as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the ICD, which is currently under active development by the WHO contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding how these stakeholders collaborate will enable us to improve editing environments that support such collaborations. We uncover how large ontology-engineering projects, such as the ICD in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users subsequently change) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain.

While considerable advances have been made in estimating high-dimensional structured models from independent data using Lasso-type models, limited progress has been made for settings when the samples are dependent. We consider estimating structured VAR (vector auto-regressive models), where the structure can be captured by any suitable norm, e.g., Lasso, group Lasso, order weighted Lasso, sparse group Lasso, etc. In VAR setting with correlated noise, although there is strong dependence over time and covariates, we establish bounds on the non-asymptotic estimation error of structured VAR parameters. Surprisingly, the estimation error is of the same order as that of the corresponding Lasso-type estimator with independent samples, and the analysis holds for any norm. Our analysis relies on results in generic chaining, sub-exponential martingales, and spectral representation of VAR models. Experimental results on synthetic data with a variety of structures as well as real aviation data are presented, validating theoretical results.

In this work we consider the problem of anomaly detection in heterogeneous, multivariate, variable-length time series datasets. Our focus is on the aviation safety domain, where data objects are flights and time series are sensor readings and pilot switches. In this context the goal is to detect anomalous flight segments, due to mechanical, environmental, or human factors in order to identifying operationally significant events and provide insights into the flight operations and highlight otherwise unavailable potential safety risks and precursors to accidents. For this purpose, we propose a framework which represents each flight using a semi-Markov switching vector autoregressive (SMS-VAR) model. Detection of anomalies is then based on measuring dissimilarities between the model's prediction and data observation. The framework is scalable, due to the inherent parallel nature of most computations, and can be used to perform online anomaly detection. Extensive experimental results on simulated and real datasets illustrate that the framework can detect various types of anomalies along with the key parameters involved.

Training deep networks is a time-consuming process, with networks for object recognition often requiring multiple days to train. For this reason, leveraging the resources of a cluster to speed up training is an important area of work. However, widely-popular batch-processing computational frameworks like MapReduce and Spark were not designed to support the asynchronous and communication-intensive workloads of existing distributed deep learning systems. We introduce SparkNet, a framework for training deep networks in Spark. Our implementation includes a convenient interface for reading data from Spark RDDs, a Scala interface to the Caffe deep learning framework, and a lightweight multi-dimensional tensor library. Using a simple parallelization scheme for stochastic gradient descent, SparkNet scales well with the cluster size and tolerates very high-latency communication. Furthermore, it is easy to deploy and use with no parameter tuning, and it is compatible with existing Caffe models. We quantify the dependence of the speedup obtained by SparkNet on the number of machines, the communication frequency, and the cluster's communication overhead, and we benchmark our system's performance on the ImageNet dataset.

In a multi-class classification problem, it is standard to model the output of a neural network as a categorical distribution conditioned on the inputs. The output must therefore be positive and sum to one, which is traditionally enforced by a softmax. This probabilistic mapping allows to use the maximum likelihood principle, which leads to the well-known log-softmax loss. However the choice of the softmax function seems somehow arbitrary as there are many other possible normalizing functions. It is thus unclear why the log-softmax loss would perform better than other loss alternatives. In particular Vincent et al. (2015) recently introduced a class of loss functions, called the spherical family, for which there exists an efficient algorithm to compute the updates of the output weights irrespective of the output size. In this paper, we explore several loss functions from this family as possible alternatives to the traditional log-softmax. In particular, we focus our investigation on spherical bounds of the log-softmax loss and on two spherical log-likelihood losses, namely the log-Spherical Softmax suggested by Vincent et al. (2015) and the log-Taylor Softmax that we introduce. Although these alternatives do not yield as good results as the log-softmax loss on two language modeling tasks, they surprisingly outperform it in our experiments on MNIST and CIFAR-10, suggesting that they might be relevant in a broad range of applications.

Hidden semi-Markov models (HSMMs) are latent variable models which allow latent state persistence and can be viewed as a generalization of the popular hidden Markov models (HMMs). In this paper, we introduce a novel spectral algorithm to perform inference in HSMMs. Unlike expectation maximization (EM), our approach correctly estimates the probability of given observation sequence based on a set of training sequences. Our approach is based on estimating moments from the sample, whose number of dimensions depends only logarithmically on the maximum length of the hidden state persistence. Moreover, the algorithm requires only a few matrix inversions and is therefore computationally efficient. Empirical evaluations on synthetic and real data demonstrate the advantage of the algorithm over EM in terms of speed and accuracy, especially for large datasets.

The plausibility of uncommon events and miracles based on testimony of such an event has been much discussed. When analyzing the probabilities involved, it has mostly been assumed that the common events can be taken as data in the calculations. However, we usually have only testimonies for the common events. While this difference does not have a significant effect on the inductive part of the inference, it has a large influence on how one should view the reliability of testimonies. In this work, a full Bayesian solution is given for the more realistic case, where one has a large number of testimonies for a common event and one testimony for an uncommon event. It is seen that, in order for there to be a large amount of testimonies for a common event, the testimonies will probably be quite reliable. For this reason, because the testimonies are quite reliable based on the testimonies for the common events, the probability for the uncommon event, given a testimony for it, is also higher. Hence, one should be more open-minded when considering the plausibility of uncommon events.

Hyper-parameters play a major role in the learning and inference process of latent Dirichlet allocation (LDA). In order to begin the LDA latent variables learning process, these hyper-parameters values need to be pre-determined. We propose an extension for LDA that we call 'Latent Dirichlet allocation Gibbs Newton' (LDA-GN), which places non-informative priors over these hyper-parameters and uses Gibbs sampling to learn appropriate values for them. At the heart of LDA-GN is our proposed 'Gibbs-Newton' algorithm, which is a new technique for learning the parameters of multivariate Polya distributions. We report Gibbs-Newton performance results compared with two prominent existing approaches to the latter task: Minka's fixed-point iteration method and the Moments method. We then evaluate LDA-GN in two ways: (i) by comparing it with standard LDA in terms of the ability of the resulting topic models to generalize to unseen documents; (ii) by comparing it with standard LDA in its performance on a binary classification task.

Human language is used to express logical and mathematical computations whose cognitive bases still remain unexplained. We ask ourselves if language acquisition involves a kind of implicit logical and mathematical programming that could explain such performances. Examples of these performances are some logical propositions, transferred by natural language, valid for different languages and for large populations of humans sharing similar cultural traditions. In the present work we choose -as a largely accepted logical statement-one of the most cited expressions that Arthur Conan Doyle attributed to Sherlock Holmes, the "old maxim" mentioned by the character in the story "The Adventure of the Beryl Coronet". For an allusion to this maxim in a scientific context see Cairns-Smith (1990).

A machine capable of performing complex tasks without requiring laborious programming would be tremendously useful in almost any human endeavor, from performing menial jobs for us to helping the advancement of basic and applied research. Given the current availability of powerful hardware and large amounts of machine-readable data, as well as the widespread interest in sophisticated machine learning methods, the times should be ripe for the development of intelligent machines. Still, since "solving AI" seems too complex a task to be pursued all at once, in the last decades the computational community has preferred to focus on solving relatively narrow empirical problems that are important for specific applications, but do not address the overarching goal of developing general-purpose intelligent machines. In this article, we propose an alternative approach: we first define the general characteristics we think intelligent machines should possess, and then we present a concrete roadmap to develop them in realistic, small steps, that are however incrementally structured in such a way that, jointly, they should lead us close to the ultimate goal of implementing a powerful AI. The article is organized as follows.