Scuba:Scalable kernel-based gene prioritization

Abstract Background The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can help to cope with these problems. In particular, kernel-based methods are a powerful resource for the integration of heterogeneous biological knowledge, however, their practical implementation is often precluded by their limited scalability. Results We propose Scuba, a scalable kernel-based method for gene prioritization. It implements a novel multiple kernel learning approach, based on a semi-supervised perspective and on the optimization of the margin distribution. Scuba is optimized to cope with strongly unbalanced settings where known disease genes are few and large scale predictions are required. Importantly, it is able to efficiently deal both with a large amount of candidate genes and with an arbitrary number of data sources. As a direct consequence of scalability, Scuba integrates also a new efficient strategy to select optimal kernel parameters for each data source. We performed cross-validation experiments and simulated a realistic usage setting, showing that Scuba outperforms a wide range of state-of-the-art methods. Conclusions Scuba achieves state-of-the-art performance and has enhanced scalability compared to existing kernel-based approaches for genomic data. This method can be useful to prioritize candidate genes, particularly when their number is large or when input data is highly heterogeneous. The code is freely available at https://github.com/gzampieri/Scuba

e-Distance Weighted Support Vector Regression

We propose a novel support vector regression approach called e-Distance Weighted Support Vector Regression (e-DWSVR).e-DWSVR specifically addresses two challenging issues in support vector regression: first, the process of noisy data; second, how to deal with the situation when the distribution of boundary data is different from that of the overall data. The proposed e-DWSVR optimizes the minimum margin and the mean of functional margin simultaneously to tackle these two issues. In addition, we use both dual coordinate descent (CD) and averaged stochastic gradient descent (ASGD) strategies to make e-DWSVR scalable to large scale problems. We report promising results obtained by e-DWSVR in comparison with existing methods on several benchmark datasets

Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data

Due to its causal semantics, Bayesian networks (BN) have been widely employed to discover the underlying data relationship in exploratory studies, such as brain research. Despite its success in modeling the probability distribution of variables, BN is naturally a generative model, which is not necessarily discriminative. This may cause the ignorance of subtle but critical network changes that are of investigation values across populations. In this paper, we propose to improve the discriminative power of BN models for continuous variables from two different perspectives. This brings two general discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the first framework, we employ Fisher kernel to bridge the generative models of GBN and the discriminative classifiers of SVMs, and convert the GBN parameter learning to Fisher kernel learning via minimizing a generalization error bound of SVMs. In the second framework, we employ the max-margin criterion and build it directly upon GBN models to explicitly optimize the classification performance of the GBNs. The advantages and disadvantages of the two frameworks are discussed and experimentally compared. Both of them demonstrate strong power in learning discriminative parameters of GBNs for neuroimaging based brain network analysis, as well as maintaining reasonable representation capacity. The contributions of this paper also include a new Directed Acyclic Graph (DAG) constraint with theoretical guarantee to ensure the graph validity of GBN.Comment: 16 pages and 5 figures for the article (excluding appendix

Distribution matching for transduction

Many transductive inference algorithms assume that distributions over training and test estimates should be related, e.g. by providing a large margin of separation on both sets. We use this idea to design a transduction algorithm which can be used without modification for classification, regression, and structured estimation. At its heart we exploit the fact that for a good learner the distributions over the outputs on training and test sets should match. This is a classical two-sample problem which can be solved efficiently in its most general form by using distance measures in Hilbert Space. It turns out that a number of existing heuristics can be viewed as special cases of our approach.

Kernel Ellipsoidal Trimming

Ellipsoid estimation is an issue of primary importance in many practical areas such as control, system identification, visual/audio tracking, experimental design, data mining, robust statistics and novelty/outlier detection. This paper presents a new method of kernel information matrix ellipsoid estimation (KIMEE) that finds an ellipsoid in a kernel defined feature space based on a centered information matrix. Although the method is very general and can be applied to many of the aforementioned problems, the main focus in this paper is the problem of novelty or outlier detection associated with fault detection. A simple iterative algorithm based on Titterington's minimum volume ellipsoid method is proposed for practical implementation. The KIMEE method demonstrates very good performance on a set of real-life and simulated datasets compared with support vector machine methods

Exploiting sparsity to build efficient kernel based collaborative filtering for top-N item recommendation

The increasing availability of implicit feedback datasets has raised the interest in developing effective collaborative filtering techniques able to deal asymmetrically with unambiguous positive feedback and ambiguous negative feedback. In this paper, we propose a principled kernel-based collaborative filtering method for top-N item recommendation with implicit feedback. We present an efficient implementation using the linear kernel, and we show how to generalize it to kernels of the dot product family preserving the efficiency. We also investigate on the elements which influence the sparsity of a standard cosine kernel. This analysis shows that the sparsity of the kernel strongly depends on the properties of the dataset, in particular on the long tail distribution. We compare our method with state-of-the-art algorithms achieving good results both in terms of efficiency and effectiveness