Abstract--The stochastic block model (SBM) is a probabilistic model for community structure in networks. Typically, only the adjacency matrix is used to perform SBM parameter inference. In this paper, we consider circumstances in which nodes have an associated vector of continuous attributes that are also used to learn the node-to-community assignments and corresponding SBM parameters. While this assumption is not realistic for every application, our model assumes that the attributes associated with the nodes in a network's community can be described by a common multivariate Gaussian model. In this augmented, attributed SBM, the objective is to simultaneously learn the SBM connectivity probabilities with the multivariate Gaussian parameters describing each community. While there are recent examples in the literature that combine connectivity and attribute information to inform community detection, our model is the first augmented stochastic block model to handle multiple continuous attributes. This provides the flexibility in biological data to, for example, augment connectivity information with continuous measurements from multiple experimental modalities. Because the lack of labeled network data often makes community detection results difficult to validate, we highlight the usefulness of our model for two network prediction tasks: link prediction and collaborative filtering. As a result of fitting this attributed stochastic block model, one can predict the attribute vector or connectivity patterns for a new node in the event of the complementary source of information (connectivity or attributes, respectively). We also highlight two biological examples where the attributed stochastic block model provides satisfactory performance in the link prediction and collaborative filtering tasks. In various applications, each node in a network is equipped with additional information (or particular attributes) that was not implicitly taken into account in the construction of the network.

For massive data, the family of subsampling algorithms is popular to downsize the data volume and reduce computational burden. Existing studies focus on approximating the ordinary least squares estimate in linear regression, where statistical leverage scores are often used to define subsampling probabilities. In this paper, we propose fast subsampling algorithms to efficiently approximate the maximum likelihood estimate in logistic regression. We first establish consistency and asymptotic normality of the estimator from a general subsampling algorithm, and then derive optimal subsampling probabilities that minimize the asymptotic mean squared error of the resultant estimator. An alternative minimization criterion is also proposed to further reduce the computational cost. The optimal subsampling probabilities depend on the full data estimate, so we develop a two-step algorithm to approximate the optimal subsampling procedure. This algorithm is computationally efficient and has a significant reduction in computing time compared to the full data approach. Consistency and asymptotic normality of the estimator from a two-step algorithm are also established. Synthetic and real data sets are used to evaluate the practical performance of the proposed method.

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.

This paper presents a comparison of six machine learning (ML) algorithms: GRU-SVM (Agarap, 2017), Linear Regression, Multilayer Perceptron (MLP), Nearest Neighbor (NN) search, Softmax Regression, and Support Vector Machine (SVM) on the Wisconsin Diagnostic Breast Cancer (WDBC) dataset (Wolberg, Street, & Mangasarian, 1992) by measuring their classification test accuracy and their sensitivity and specificity values. The said dataset consists of features which were computed from digitized images of FNA tests on a breast mass (Wolberg, Street, & Mangasarian, 1992). For the implementation of the ML algorithms, the dataset was partitioned in the following fashion: 70% for training phase, and 30% for the testing phase. The hyper-parameters used for all the classifiers were manually assigned. Results show that all the presented ML algorithms performed well (all exceeded 90% test accuracy) on the classification task. The MLP algorithm stands out among the implemented algorithms with a test accuracy of ~99.04%.

Imagine a team of researchers looking for promising drug combinations to treat a specific cancer type for which current treatments are ineffective. The team has data on the effect of certain pairs of drugs on other cancer types, but the data are very sparse--only a few drug pairs have been tested on each cancer type, and each drug pair is tested in a few cancer types, at best, or has never been tested at all. The challenge is to select the most promising drug pairs for testing with the target cancer type, so as to minimize the cost associated to unsuccessful tests. We can formalize this challenge as the following inference problem: We have a partial observation of the pairwise interactions between a set of nodes (drugs) in different "network layers" (cancer types), and we need to infer which are the unobserved interactions within each layer (drug interactions in each cancer type). This challenge is relevant for the many systems that can be represented as multilayer networks [1-4], and is also formally analogous to the challenge of predicting the existence of interactions between nodes in time-resolved networks [5-11]. For instance, we would face the same situation if we had data about the daily email or phone communications between users, and wanted to infer the existence of interactions between pairs of users on a certain unobserved day; in this case each layer would be a different day. Here, we introduce new generative models that are suitable to address the challenge above. We model all layers concurrently, so that our approach takes full advantage of the information contained in all layers to make predictions for any one of them.

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction or network inference problems. During the last decade kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify existing kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency and spectral filtering properties. Our theoretical results provide valuable insights in assessing the advantages and limitations of existing pairwise learning methods.

In large-scale distributed learning, security issues have become increasingly important. Particularly in a decentralized environment, some computing units may behave abnormally, or even exhibit Byzantine failures---arbitrary and potentially adversarial behavior. In this paper, we develop distributed learning algorithms that are provably robust against such failures, with a focus on achieving optimal statistical performance. A main result of this work is a sharp analysis of two robust distributed gradient descent algorithms based on median and trimmed mean operations, respectively. We prove statistical error rates for three kinds of population loss functions: strongly convex, non-strongly convex, and smooth non-convex. In particular, these algorithms are shown to achieve order-optimal statistical error rates for strongly convex losses. To achieve better communication efficiency, we further propose a median-based distributed algorithm that is provably robust, and uses only one communication round. For strongly convex quadratic loss, we show that this algorithm achieves the same optimal error rate as the robust distributed gradient descent algorithms.

We consider the canonical $L_0$-regularized least squares problem (aka best subsets) which is generally perceived as a `gold-standard' for many sparse learning regimes. In spite of worst-case computational intractability results, recent work has shown that advances in mixed integer optimization can be used to obtain near-optimal solutions to this problem for instances where the number of features $p \approx 10^3$. While these methods lead to estimators with excellent statistical properties, often there is a price to pay in terms of a steep increase in computation times, especially when compared to highly efficient popular algorithms for sparse learning (e.g., based on $L_1$-regularization) that scale to much larger problem sizes. Bridging this gap is a main goal of this paper. We study the computational aspects of a family of $L_0$-regularized least squares problems with additional convex penalties. We propose a hierarchy of necessary optimality conditions for these problems. We develop new algorithms, based on coordinate descent and local combinatorial optimization schemes, and study their convergence properties. We demonstrate that the choice of an algorithm determines the quality of solutions obtained; and local combinatorial optimization-based algorithms generally result in solutions of superior quality. We show empirically that our proposed framework is relatively fast for problem instances with $p\approx 10^6$ and works well, in terms of both optimization and statistical properties (e.g., prediction, estimation, and variable selection), compared to simpler heuristic algorithms. A version of our algorithm reaches up to a three-fold speedup (with $p$ up to $10^6$) when compared to state-of-the-art schemes for sparse learning such as glmnet and ncvreg.

There is no thumb rule of choosing the best kernel. The only solution is Cross-validation. Try several different Kernels, and evaluate their performance metrics such as AUC and select the one with highest AUC. If you want to compare in terms of speed, linear kernels usually compute much faster than radial or polynomial kernels.

Longitudinal patient data has the potential to improve clinical risk stratification models for disease. However, chronic diseases that progress slowly over time are often heterogeneous in their clinical presentation. Patients may progress through disease stages at varying rates. This leads to pathophysiological misalignment over time, making it difficult to consistently compare patients in a clinically meaningful way. Furthermore, patients present clinically for the first time at different stages of disease. This eliminates the possibility of simply aligning patients based on their initial presentation. Finally, patient data may be sampled at different rates due to differences in schedules or missed visits. To address these challenges, we propose a robust measure of patient similarity based on subsequence alignment. Compared to global alignment techniques that do not account for pathophysiological misalignment, focusing on the most relevant subsequences allows for an accurate measure of similarity between patients. We demonstrate the utility of our approach in settings where longitudinal data, while useful, are limited and lack a clear temporal alignment for comparison. Applied to the task of stratifying patients for risk of progression to probable Alzheimer's Disease, our approach outperforms models that use only snapshot data (AUROC of 0.839 vs. 0.812) and models that use global alignment techniques (AUROC of 0.822). Our results support the hypothesis that patients' trajectories are useful for quantifying inter-patient similarities and that using subsequence matching and can help account for heterogeneity and misalignment in longitudinal data.