Keywords: machine learning, consensus, meta-learning, bioinformatics, chemoinformatics, brainstorming, neural networks, support vector machines, decision trees, random forest, genetic algorithms, nearest neighbours, trend vectors Abstract: We present here an introduction to Brainstorming approach, that was recently proposed as a consensus meta-learning technique, and used in several practical applications in bioinformatics and chemoinformatics. In the second step all solutions are gathered and the consensus is build between them. Therefore no early solution, given even by a generally low performing algorithm, is not discarder until the late phase of prediction, when the final conclusion is drawn by comparing different machine learning models. This final phase, i.e. consensus learning, is trying to balance the generality of solution and the overall performance of trained model. 1 INTRODUCTION A novel meta-approach emerging in bioinformatics is called consensus learning. Then all solutions are gathered, and the consensus is build between them. Therefore no early solution, given even by a generally low performing algorithm, is not discarder until the late phase of prediction, when the final conclusion is drawn by comparing different machine learning models.

This paper reviews the functional aspects of statistical learning theory. The main point under consideration is the nature of the hypothesis set when no prior information is available but data. Within this framework we first discuss about the hypothesis set: it is a vectorial space, it is a set of pointwise defined functions, and the evaluation functional on this set is a continuous mapping. Based on these principles an original theory is developed generalizing the notion of reproduction kernel Hilbert space to non hilbertian sets. Then it is shown that the hypothesis set of any learning machine has to be a generalized reproducing set. Therefore, thanks to a general "representer theorem", the solution of the learning problem is still a linear combination of a kernel. Furthermore, a way to design these kernels is given. To illustrate this framework some examples of such reproducing sets and kernels are given.

Machine learning, data mining and artificial intelligence (AI) based methods have been used to determine the relations between chemical structure and biological activity, called quantitative structure activity relationships (QSARs) for the compounds. Pre-processing of the dataset, which includes the mapping from a large number of molecular descriptors in the original high dimensional space to a small number of components in the lower dimensional space while retaining the features of the original data, is the first step in this process. A common practice is to use a mapping method for a dataset without prior analysis. This pre-analysis has been stressed in our work by applying it to two important classes of QSAR prediction problems: drug design (predicting anti-HIV-1 activity) and predictive toxicology (estimating hepatocarcinogenicity of chemicals). We apply one linear and two nonlinear mapping methods on each of the datasets. Based on this analysis, we conclude the nature of the inherent relationships between the elements of each dataset, and hence, the mapping method best suited for it. We also show that proper preprocessing can help us in choosing the right feature extraction tool as well as give an insight about the type of classifier pertinent for the given problem.

The Lasso is a very well known penalized regression model, which adds an $L_{1}$ penalty with parameter $\lambda_{1}$ on the coefficients to the squared error loss function. The Fused Lasso extends this model by also putting an $L_{1}$ penalty with parameter $\lambda_{2}$ on the difference of neighboring coefficients, assuming there is a natural ordering. In this paper, we develop a fast path algorithm for solving the Fused Lasso Signal Approximator that computes the solutions for all values of $\lambda_1$ and $\lambda_2$. In the supplement, we also give an algorithm for the general Fused Lasso for the case with predictor matrix $\bX \in \mathds{R}^{n \times p}$ with $\text{rank}(\bX)=p$.

In the last few years, due to the growing ubiquity of unlabeled data, much effort has been spent by the machine learning community to develop better understanding and improve the quality of classifiers exploiting unlabeled data. Following the manifold regularization approach, Laplacian Support Vector Machines (LapSVMs) have shown the state of the art performance in semi--supervised classification. In this paper we present two strategies to solve the primal LapSVM problem, in order to overcome some issues of the original dual formulation. Whereas training a LapSVM in the dual requires two steps, using the primal form allows us to collapse training to a single step. Moreover, the computational complexity of the training algorithm is reduced from O(n^3) to O(n^2) using preconditioned conjugate gradient, where n is the combined number of labeled and unlabeled examples. We speed up training by using an early stopping strategy based on the prediction on unlabeled data or, if available, on labeled validation examples. This allows the algorithm to quickly compute approximate solutions with roughly the same classification accuracy as the optimal ones, considerably reducing the training time. Due to its simplicity, training LapSVM in the primal can be the starting point for additional enhancements of the original LapSVM formulation, such as those for dealing with large datasets. We present an extensive experimental evaluation on real world data showing the benefits of the proposed approach.

This paper proposes an original approach to cluster multi-component data sets, including an estimation of the number of clusters. From the construction of a minimal spanning tree with Prim's algorithm, and the assumption that the vertices are approximately distributed according to a Poisson distribution, the number of clusters is estimated by thresholding the Prim's trajectory. The corresponding cluster centroids are then computed in order to initialize the generalized Lloyd's algorithm, also known as $K$-means, which allows to circumvent initialization problems. Some results are derived for evaluating the false positive rate of our cluster detection algorithm, with the help of approximations relevant in Euclidean spaces. Metrics used for measuring similarity between multi-dimensional data points are based on symmetrical divergences. The use of these informational divergences together with the proposed method leads to better results, compared to other clustering methods for the problem of astrophysical data processing. Some applications of this method in the multi/hyper-spectral imagery domain to a satellite view of Paris and to an image of the Mars planet are also presented. In order to demonstrate the usefulness of divergences in our problem, the method with informational divergence as similarity measure is compared with the same method using classical metrics. In the astrophysics application, we also compare the method with the spectral clustering algorithms.

We introduce a Bernstein-type inequality which serves to uniformly control quadratic forms of gaussian variables. The latter can for example be used to derive sharp model selection criteria for linear estimation in linear regression and linear inverse problems via penalization, and we do not exclude that its scope of application can be made even broader.

Let M be a random (alpha n) x n matrix of rank r<

In the context of clustering, we consider a generative model in a Euclidean ambient space with clusters of different shapes, dimensions, sizes and densities. In an asymptotic setting where the number of points becomes large, we obtain theoretical guaranties for a few emblematic methods based on pairwise distances: a simple algorithm based on the extraction of connected components in a neighborhood graph; the spectral clustering method of Ng, Jordan and Weiss; and hierarchical clustering with single linkage. The methods are shown to enjoy some near-optimal properties in terms of separation between clusters and robustness to outliers. The local scaling method of Zelnik-Manor and Perona is shown to lead to a near-optimal choice for the scale in the first two methods. We also provide a lower bound on the spectral gap to consistently choose the correct number of clusters in the spectral method.

We investigate the issue of model selection and the use of the nonconformity (strangeness) measure in batch learning. Using the nonconformity measure we propose a new training algorithm that helps avoid the need for Cross-Validation or Leave-One-Out model selection strategies. We provide a new generalisation error bound using the notion of nonconformity to upper bound the loss of each test example and show that our proposed approach is comparable to standard model selection methods, but with theoretical guarantees of success and faster convergence. We demonstrate our novel model selection technique using the Support Vector Machine.