Machine learning research is often conducted in vitro, divorced from motivating practical applications. A researcher might develop a new method for the general task of classification, then assess its utility by comparing its performance (such as accuracy or AUC) to that of existing classification models on publicly available datasets. In terms of advancing machine learning as an academic discipline, this approach has thus far proven quite fruitful. However, it is our view that the most interesting open problems in machine learning are those that arise during its application to real-world problems. We illustrate this point by reviewing two of our interdisciplinary collaborations, both of which have posed unique machine learning problems, providing fertile ground for novel research.

Item recommendation is the task of predicting a personalized ranking on a set of items (e.g. websites, movies, products). In this paper, we investigate the most common scenario with implicit feedback (e.g. clicks, purchases). There are many methods for item recommendation from implicit feedback like matrix factorization (MF) or adaptive knearest-neighbor (kNN). Even though these methods are designed for the item prediction task of personalized ranking, none of them is directly optimized for ranking. In this paper we present a generic optimization criterion BPR-Opt for personalized ranking that is the maximum posterior estimator derived from a Bayesian analysis of the problem. We also provide a generic learning algorithm for optimizing models with respect to BPR-Opt. The learning method is based on stochastic gradient descent with bootstrap sampling. We show how to apply our method to two state-of-the-art recommender models: matrix factorization and adaptive kNN. Our experiments indicate that for the task of personalized ranking our optimization method outperforms the standard learning techniques for MF and kNN. The results show the importance of optimizing models for the right criterion.

The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to automatically assign gene function using a controlled vocabularies like Gene Ontology. However, most existing approaches for predicting gene functions solve independent classification problems to predict genes that are involved in a given function category, independently of the rest. Here, we propose two simple methods for incorporating information about the hierarchical nature of the categorization scheme. In the first method, we use information about a gene's previous annotation to set an initial prior on its label. In a second approach, we extend a graph-based semi-supervised learning algorithm for predicting gene function in a hierarchy. We show that we can efficiently solve this problem by solving a linear system of equations. We compare these approaches with a previous label reconciliation-based approach. Results show that using the hierarchy information directly, compared to using reconciliation methods, improves gene function prediction.

A novel multi-resolution cluster detection (MCD) method is proposed to identify irregularly shaped clusters in space. Multi-scale test statistic on a single cell is derived based on likelihood ratio statistic for Bernoulli sequence, Poisson sequence and Normal sequence. A neighborhood variability measure is defined to select the optimal test threshold. The MCD method is compared with single scale testing methods controlling for false discovery rate and the spatial scan statistics using simulation and f-MRI data. The MCD method is shown to be more effective for discovering irregularly shaped clusters, and the implementation of this method does not require heavy computation, making it suitable for cluster detection for large spatial data.

Supervised linear feature extraction can be achieved by fitting a reduced rank multivariate model. This paper studies rank penalized and rank constrained vector generalized linear models. From the perspective of thresholding rules, we build a framework for fitting singular value penalized models and use it for feature extraction. Through solving the rank constraint form of the problem, we propose progressive feature space reduction for fast computation in high dimensions with little performance loss. A novel projective cross-validation is proposed for parameter tuning in such nonconvex setups. Real data applications are given to show the power of the methodology in supervised dimension reduction and feature extraction.

The choice of the kernel is critical to the success of many learning algorithms but it is typically left to the user. Instead, the training data can be used to learn the kernel by selecting it out of a given family, such as that of non-negative linear combinations of p base kernels, constrained by a trace or L1 regularization. This paper studies the problem of learning kernels with the same family of kernels but with an L2 regularization instead, and for regression problems. We analyze the problem of learning kernels with ridge regression. We derive the form of the solution of the optimization problem and give an efficient iterative algorithm for computing that solution. We present a novel theoretical analysis of the problem based on stability and give learning bounds for orthogonal kernels that contain only an additive term O(pp/m) when compared to the standard kernel ridge regression stability bound. We also report the results of experiments indicating that L1 regularization can lead to modest improvements for a small number of kernels, but to performance degradations in larger-scale cases. In contrast, L2 regularization never degrades performance and in fact achieves significant improvements with a large number of kernels.

In a typical online learning scenario, a learner is required to process a large data stream using a small memory buffer. Such a requirement is usually in conflict with a learner's primary pursuit of prediction accuracy. To address this dilemma, we introduce a novel Bayesian online classi cation algorithm, called the Virtual Vector Machine. The virtual vector machine allows you to smoothly trade-off prediction accuracy with memory size. The virtual vector machine summarizes the information contained in the preceding data stream by a Gaussian distribution over the classi cation weights plus a constant number of virtual data points. The virtual data points are designed to add extra non-Gaussian information about the classi cation weights. To maintain the constant number of virtual points, the virtual vector machine adds the current real data point into the virtual point set, merges two most similar virtual points into a new virtual point or deletes a virtual point that is far from the decision boundary. The information lost in this process is absorbed into the Gaussian distribution. The extra information provided by the virtual points leads to improved predictive accuracy over previous online classification algorithms.

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.