BackgroundAs more and more researchers are turning to big data for new opportunities of biomedical discoveries, machine learning models, as the backbone of big data analysis, are mentioned more often in biomedical journals. However, owing to the inherent complexity of machine learning methods, they are prone to misuse. Because of the flexibility in specifying machine learning models, the results are often insufficiently reported in research articles, hindering reliable assessment of model validity and consistent interpretation of model outputs.ObjectiveTo attain a set of guidelines on the use of machine learning predictive models within clinical settings to make sure the models are correctly applied and sufficiently reported so that true discoveries can be distinguished from random coincidence.MethodsA multidisciplinary panel of machine learning experts, clinicians, and traditional statisticians were interviewed, using an iterative process in accordance with the Delphi method.ResultsThe process produced a set of guidelines that consists of (1) a list of reporting items to be included in a research article and (2) a set of practical sequential steps for developing predictive models.ConclusionsA set of guidelines was generated to enable correct application of machine learning models and consistent reporting of model specifications and results in biomedical research. We believe that such guidelines will accelerate the adoption of big data analysis, particularly with machine learning methods, in the biomedical research community.

Wireless Sensor Networks (WSNs) are a new technology foreseen to be used increasingly in the near future due to their data acquisition and data processing abilities. Security for WSNs is an area that needs to be considered in order to protect the functionality of these networks, the data they convey and the location of their members. The security models and protocols used in wired and other networks are not suited to WSNs because of their severe resource constraints, especially concerning energy. In this article, we propose a centralized intrusion detection scheme based on Support Vector Machines (SVMs) and sliding windows. We find that our system can detect black hole attacks and selective forwarding attacks with high accuracy without depleting the nodes of their energy.

We propose a new algorithm for the incremental training of support vector machines (SVMs) that is suitable for problems of sequentially arriving data and fast constraint parameter variation. Our method involves using a "warm-start" algorithm for the training of SVMs, which allows us to take advantage of the natural incremental properties of the standard active set approach to linearly constrained optimization problems. Incremental training involves quickly retraining a support vector machine after adding a small number of additional training vectors to the training set of an existing (trained) support vector machine. Similarly, the problem of fast constraint parameter variation involves quickly retraining an existing support vector machine using the same training set but different constraint parameters. In both cases, we demonstrate the computational superiority of incremental training over the usual batch retraining method.

Scaling Bayesian optimization to high dimensions is challenging task as the global optimization of high-dimensional acquisition function can be expensive and often infeasible. Existing methods depend either on limited "active" variables or the additive form of the objective function. We propose a new method for high-dimensional Bayesian optimization, that uses a dropout strategy to optimize only a subset of variables at each iteration. We derive theoretical bounds for the regret and show how it can inform the derivation of our algorithm. We demonstrate the efficacy of our algorithms for optimization on two benchmark functions and two realworld applications -training cascade classifiers and optimizing alloy composition.

Many real-world functions are defined over both categorical and category-specific continuous variables and thus cannot be optimized by traditional Bayesian optimization (BO) methods. To optimize such functions, we propose a new method that formulates the problem as a multi-armed bandit problem, wherein each category corresponds to an arm with its reward distribution centered around the optimum of the objective function in continuous variables. Our goal is to identify the best arm and the maximizer of the corresponding continuous function simultaneously. Our algorithm uses a Thompson sampling scheme that helps connecting both multi-arm bandit and BO in a unified framework. We extend our method to batch BO to allow parallel optimization when multiple resources are available. We theoretically analyze our method for convergence and prove sub-linear regret bounds. We perform a variety of experiments: optimization of several benchmark functions, hyper-parameter tuning of a neural network, and automatic selection of the best machine learning model along with its optimal hyper-parameters (a.k.a automated machine learning). Comparisons with other methods demonstrate the effectiveness of our proposed method.