Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. In this paper, we formulate GRN inference as a sparse regression problem and investigate the performance of a popular feature selection method, least angle regression (LARS) combined with stability selection. We introduce a novel, robust and accurate scoring technique for stability selection, which improves the performance of feature selection with LARS. The resulting method, which we call TIGRESS (Trustful Inference of Gene REgulation using Stability Selection), was ranked among the top methods in the DREAM5 gene network reconstruction challenge. We investigate in depth the influence of the various parameters of the method and show that a fine parameter tuning can lead to significant improvements and state-of-the-art performance for GRN inference. TIGRESS reaches state-of-the-art performance on benchmark data. This study confirms the potential of feature selection techniques for GRN inference. Code and data are available on http://cbio.ensmp.fr/~ahaury. Running TIGRESS online is possible on GenePattern: http://www.broadinstitute.org/cancer/software/genepattern/.

Both humans and artificial systems frequently use trial and error methods to problem solving. In order to be effective, this type of strategy implies having high quality control knowledge to guide the quest for the optimal solution. Unfortunately, this control knowledge is rarely perfect. Moreover, in artificial systems-as in humans-self-evaluation of one's own knowledge is often difficult. Yet, this self-evaluation can be very useful to manage knowledge and to determine when to revise it. The objective of our work is to propose an automated approach to evaluate the quality of control knowledge in artificial systems based on a specific trial and error strategy, namely the informed tree search strategy. Our revision approach consists in analysing the system's execution logs, and in using the belief theory to evaluate the global quality of the knowledge. We present a real-world industrial application in the form of an experiment using this approach in the domain of cartographic generalisation. Thus far, the results of using our approach have been encouraging.

Objectives: Electronic health records (EHRs) are only a first step in capturing and utilizing health-related data - the challenge is turning that data into useful information. Furthermore, EHRs are increasingly likely to include data relating to patient outcomes, functionality such as clinical decision support, and genetic information as well, and, as such, can be seen as repositories of increasingly valuable information about patients' health conditions and responses to treatment over time. Methods: We describe a case study of 423 patients treated by Centerstone within Tennessee and Indiana in which we utilized electronic health record data to generate predictive algorithms of individual patient treatment response. Multiple models were constructed using predictor variables derived from clinical, financial and geographic data. Results: For the 423 patients, 101 deteriorated, 223 improved and in 99 there was no change in clinical condition. Based on modeling of various clinical indicators at baseline, the highest accuracy in predicting individual patient response ranged from 70-72% within the models tested. In terms of individual predictors, the Centerstone Assessment of Recovery Level - Adult (CARLA) baseline score was most significant in predicting outcome over time (odds ratio 4.1 + 2.27). Other variables with consistently significant impact on outcome included payer, diagnostic category, location and provision of case management services. Conclusions: This approach represents a promising avenue toward reducing the current gap between research and practice across healthcare, developing data-driven clinical decision support based on real-world populations, and serving as a component of embedded clinical artificial intelligences that "learn" over time.

High-dimensional data common in genomics, proteomics, and chemometrics often contains complicated correlation structures. Recently, partial least squares (PLS) and Sparse PLS methods have gained attention in these areas as dimension reduction techniques in the context of supervised data analysis. We introduce a framework for Regularized PLS by solving a relaxation of the SIMPLS optimization problem with penalties on the PLS loadings vectors. Our approach enjoys many advantages including flexibility, general penalties, easy interpretation of results, and fast computation in high-dimensional settings. We also outline extensions of our methods leading to novel methods for Non-negative PLS and Generalized PLS, an adaption of PLS for structured data. We demonstrate the utility of our methods through simulations and a case study on proton Nuclear Magnetic Resonance (NMR) spectroscopy data.

Given a collection of objects and an associated similarity measure, the all-pairs similarity search problem asks us to find all pairs of objects with similarity greater than a certain user-specified threshold. Locality-sensitive hashing (LSH) based methods have become a very popular approach for this problem. However, most such methods only use LSH for the first phase of similarity search - i.e. efficient indexing for candidate generation. In this paper, we present BayesLSH, a principled Bayesian algorithm for the subsequent phase of similarity search - performing candidate pruning and similarity estimation using LSH. A simpler variant, BayesLSH-Lite, which calculates similarities exactly, is also presented. BayesLSH is able to quickly prune away a large majority of the false positive candidate pairs, leading to significant speedups over baseline approaches. For BayesLSH, we also provide probabilistic guarantees on the quality of the output, both in terms of accuracy and recall. Finally, the quality of BayesLSH's output can be easily tuned and does not require any manual setting of the number of hashes to use for similarity estimation, unlike standard approaches. For two state-of-the-art candidate generation algorithms, AllPairs and LSH, BayesLSH enables significant speedups, typically in the range 2x-20x for a wide variety of datasets.

Supporting the efficient discovery and use of Web APIs is increasingly important as their use and popularity grows. Yet, a simple task like finding potentially interesting APIs and their related documentation turns out to be hard and time consuming even when using the best resources currently available on the Web. In this paper we describe our research towards an automated Web API documentation crawler and search engine. This paper presents two main contributions. First, we have devised and exploited crowdsourcing techniques to generate a curated dataset of Web APIs documentation. Second, thanks to this dataset, we have devised an engine able to automatically detect documentation pages. Our preliminary experiments have shown that we obtain an accuracy of 80% and a precision increase of 15 points over a keyword-based heuristic we have used as baseline.

Learning algorithms normally assume that there is at most one annotation or label per data point. However, in some scenarios, such as medical diagnosis and on-line collaboration,multiple annotations may be available. In either case, obtaining labels for data points can be expensive and time-consuming (in some circumstances ground-truth may not exist). Semi-supervised learning approaches have shown that utilizing the unlabeled data is often beneficial in these cases. This paper presents a probabilistic semi-supervised model and algorithm that allows for learning from both unlabeled and labeled data in the presence of multiple annotators. We assume that it is known what annotator labeled which data points. The proposed approach produces annotator models that allow us to provide (1) estimates of the true label and (2) annotator variable expertise for both labeled and unlabeled data. We provide numerical comparisons under various scenarios and with respect to standard semi-supervised learning. Experiments showed that the presented approach provides clear advantages over multi-annotator methods that do not use the unlabeled data and over methods that do not use multi-labeler information.

Gaussian processes (GPs) provide a probabilistic nonparametric representation of functions in regression, classification, and other problems. Unfortunately, exact learning with GPs is intractable for large datasets. A variety of approximate GP methods have been proposed that essentially map the large dataset into a small set of basis points. Among them, two state-of-the-art methods are sparse pseudo-input Gaussian process (SPGP) (Snelson and Ghahramani, 2006) and variablesigma GP (VSGP) Walder et al. (2008), which generalizes SPGP and allows each basis point to have its own length scale. However, VSGP was only derived for regression. In this paper, we propose a new sparse GP framework that uses expectation propagation to directly approximate general GP likelihoods using a sparse and smooth basis. It includes both SPGP and VSGP for regression as special cases. Plus as an EP algorithm, it inherits the ability to process data online. As a particular choice of approximating family, we blur each basis point with a Gaussian distribution that has a full covariance matrix representing the data distribution around that basis point; as a result, we can summarize local data manifold information with a small set of basis points. Our experiments demonstrate that this framework outperforms previous GP classification methods on benchmark datasets in terms of minimizing divergence to the non-sparse GP solution as well as lower misclassification rate.

Imitation learning in robots, also called programing by demonstration, has made important advances in recent years, allowing humans to teach context dependant motor skills/tasks to robots. We propose to extend the usual contexts investigated to also include acoustic linguistic expressions that might denote a given motor skill, and thus we target joint learning of the motor skills and their potential acoustic linguistic name. In addition to this, a modification of a class of existing algorithms within the imitation learning framework is made so that they can handle the unlabeled demonstration of several tasks/motor primitives without having to inform the imitator of what task is being demonstrated or what the number of tasks are, which is a necessity for language learning, i.e; if one wants to teach naturally an open number of new motor skills together with their acoustic names. Finally, a mechanism for detecting whether or not linguistic input is relevant to the task is also proposed, and our architecture also allows the robot to find the right framing for a given identified motor primitive. With these additions it becomes possible to build an imitator that bridges the gap between imitation learning and language learning by being able to learn linguistic expressions using methods from the imitation learning community. In this sense the imitator can learn a word by guessing whether a certain speech pattern present in the context means that a specific task is to be executed. The imitator is however not assumed to know that speech is relevant and has to figure this out on its own by looking at the demonstrations: indeed, the architecture allows the robot to transparently also learn tasks which should not be triggered by an acoustic word, but for example by the color or position of an object or a gesture made by someone in the environment. To demonstrate this ability to find the ...

This paper presents a new approach to disambiguate company names in the Twitter social network. We have focused on making lighter the processing of comparing company profiles with tweets in order to obtain a competitive real-time system. With this aim, we only use the home page of each company as information source to create a unique profile. On the other hand, we compute the similarity of a tweet in connection to a profile by comparing the content of the tweet with the profile. Both steps do not use any other external information source and all the process is developed in an unsupervised way. We have tested our application with the test WePS-3 CLEF ORM corpus obtaining encouraging results.