We introduce Fisher consistency in the sense of unbiasedness as a desirable property for estimators of class prior probabilities. Lack of Fisher consistency could be used as a criterion to dismiss estimators that are unlikely to deliver precise estimates in test datasets under prior probability and more general dataset shift. The usefulness of this unbiasedness concept is demonstrated with three examples of classifiers used for quantification: Adjusted Classify & Count, EM-algorithm and CDE-Iterate. We find that Adjusted Classify & Count and EM-algorithm are Fisher consistent. A counter-example shows that CDE-Iterate is not Fisher consistent and, therefore, cannot be trusted to deliver reliable estimates of class probabilities.

The multivariate linear regression model with shuffled data and additive Gaussian noise arises in various correspondence estimation and matching problems. Focusing on the denoising aspect of this problem, we provide a characterization the minimax error rate that is sharp up to logarithmic factors. We also analyze the performance of two versions of a computationally efficient estimator, and establish their consistency for a large range of input parameters. Finally, we provide an exact algorithm for the noiseless problem and demonstrate its performance on an image point-cloud matching task. Our analysis also extends to datasets with outliers.

Using predictive models to identify patterns that can act as biomarkers for different neuropathoglogical conditions is becoming highly prevalent. In this paper, we consider the problem of Autism Spectrum Disorder (ASD) classification. While non-invasive imaging measurements, such as the rest state fMRI, are typically used in this problem, it can be beneficial to incorporate a wide variety of non-imaging features, including personal and socio-cultural traits, into predictive modeling. We propose to employ a graph-based approach for combining both types of feature, where a contextual graph encodes the traits of a larger population while the brain activity patterns are defined as a multivariate function at the nodes of the graph. Since the underlying graph dictates the performance of the resulting predictive models, we explore the use of different graph construction strategies. Furthermore, we develop a bootstrapped version of graph convolutional neural networks (G-CNNs) that utilizes an ensemble of weakly trained G-CNNs to avoid overfitting and also reduce the sensitivity of the models on the choice of graph construction. We demonstrate its effectiveness on the Autism Brain Imaging Data Exchange (ABIDE) dataset and show that the proposed approach outperforms state-of-the-art approaches for this problem.

Current statistical inference problems in areas like astronomy, genomics, and marketing routinely involve the simultaneous testing of thousands -- even millions -- of null hypotheses. For high-dimensional multivariate distributions, these hypotheses may concern a wide range of parameters, with complex and unknown dependence structures among variables. In analyzing such hypothesis testing procedures, gains in efficiency and power can be achieved by performing variable reduction on the set of hypotheses prior to testing. We present in this paper an approach using data-adaptive multiple testing that serves exactly this purpose. This approach applies data mining techniques to screen the full set of covariates on equally sized partitions of the whole sample via cross-validation. This generalized screening procedure is used to create average ranks for covariates, which are then used to generate a reduced (sub)set of hypotheses, from which we compute test statistics that are subsequently subjected to standard multiple testing corrections. The principal advantage of this methodology lies in its providing valid statistical inference without the \textit{a priori} specifying which hypotheses will be tested. Here, we present the theoretical details of this approach, confirm its validity via a simulation study, and exemplify its use by applying it to the analysis of data on microRNA differential expression.

In this work we perform outlier detection using ensembles of neural networks obtained by variational approximation of the posterior in a Bayesian neural network setting. The variational parameters are obtained by sampling from the true posterior by gradient descent. We show our outlier detection results are comparable to those obtained using other efficient ensembling methods.

For effective treatment of Alzheimer disease (AD), it is important to identify subjects who are most likely to exhibit rapid cognitive decline. Herein, we developed a novel framework based on a deep convolutional neural network which can predict future cognitive decline in mild cognitive impairment (MCI) patients using flurodeoxyglucose and florbetapir positron emission tomography (PET). The architecture of the network only relies on baseline PET studies of AD and normal subjects as the training dataset. Feature extraction and complicated image preprocessing including nonlinear warping are unnecessary for our approach. Accuracy of prediction (84.2%) for conversion to AD in MCI patients outperformed conventional feature-based quantification approaches. ROC analyses revealed that performance of CNN-based approach was significantly higher than that of the conventional quantification methods (p < 0.05). Output scores of the network were strongly correlated with the longitudinal change in cognitive measurements. These results show the feasibility of deep learning as a tool for predicting disease outcome using brain images.

In applications of graphical models, we typically have more information than just the samples themselves. A prime example is the estimation of brain connectivity networks based on fMRI data, where in addition to the samples themselves, the spatial positions of the measurements are readily available. With particular regard for this application, we are thus interested in ways to incorporate additional knowledge most effectively into graph estimation. Our approach to this is to make neighborhood selection receptive to additional knowledge by strengthening the role of the tuning parameters. We demonstrate that this concept (i) can improve reproducibility, (ii) is computationally convenient and efficient, and (iii) carries a lucid Bayesian interpretation. We specifically show that the approach provides effective estimations of brain connectivity graphs from fMRI data. However, providing a general scheme for the inclusion of additional knowledge, our concept is expected to have applications in a wide range of domains.

This article was posted by Manish Saraswat on Analytics Vidhya. Manish who works in marketing and Data Science at Analytics Vidhya believes that education can change this world. R, Data Science and Machine Learning keep him busy. Machine learning and data science are being looked as the drivers of the next industrial revolution happening in the world today. This also means that there are numerous exciting startups looking for data scientists.

A growing number of threats to Android phones creates challenges for malware detection. Manually labeling the samples into benign or different malicious families requires tremendous human efforts, while it is comparably easy and cheap to obtain a large amount of unlabeled APKs from various sources. Moreover, the fast-paced evolution of Android malware continuously generates derivative malware families. These families often contain new signatures, which can escape detection when using static analysis. These practical challenges can also cause traditional supervised machine learning algorithms to degrade in performance. In this paper, we propose a framework that uses model-based semi-supervised (MBSS) classification scheme on the dynamic Android API call logs. The semi-supervised approach efficiently uses the labeled and unlabeled APKs to estimate a finite mixture model of Gaussian distributions via conditional expectation-maximization and efficiently detects malwares during out-of-sample testing. We compare MBSS with the popular malware detection classifiers such as support vector machine (SVM), $k$-nearest neighbor (kNN) and linear discriminant analysis (LDA). Under the ideal classification setting, MBSS has competitive performance with 98\% accuracy and very low false positive rate for in-sample classification. For out-of-sample testing, the out-of-sample test data exhibit similar behavior of retrieving phone information and sending to the network, compared with in-sample training set. When this similarity is strong, MBSS and SVM with linear kernel maintain 90\% detection rate while $k$NN and LDA suffer great performance degradation. When this similarity is slightly weaker, all classifiers degrade in performance, but MBSS still performs significantly better than other classifiers.

Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble method that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper adaptation of the algorithms used to deal with this challenging classification task. Results: The ensemble method we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. During the BioASQ 2014 challenge we obtained the first place during the first batch and the third in the two following batches. Our success in the BioASQ challenge proved that a fully automated machine-learning approach, which does not implement any heuristics and rule-based approaches, can be highly competitive and outperform other approaches in similar challenging contexts.