Collaborating Authors


Machine Learning Towards Intelligent Systems: Applications, Challenges, and Opportunities Artificial Intelligence

The emergence and continued reliance on the Internet and related technologies has resulted in the generation of large amounts of data that can be made available for analyses. However, humans do not possess the cognitive capabilities to understand such large amounts of data. Machine learning (ML) provides a mechanism for humans to process large amounts of data, gain insights about the behavior of the data, and make more informed decision based on the resulting analysis. ML has applications in various fields. This review focuses on some of the fields and applications such as education, healthcare, network security, banking and finance, and social media. Within these fields, there are multiple unique challenges that exist. However, ML can provide solutions to these challenges, as well as create further research opportunities. Accordingly, this work surveys some of the challenges facing the aforementioned fields and presents some of the previous literature works that tackled them. Moreover, it suggests several research opportunities that benefit from the use of ML to address these challenges.

The MCC-F1 curve: a performance evaluation technique for binary classification Machine Learning

Many fields use the ROC curve and the PR curve as standard evaluations of binary classification methods. Analysis of ROC and PR, however, often gives misleading and inflated performance evaluations, especially with an imbalanced ground truth. Here, we demonstrate the problems with ROC and PR analysis through simulations, and propose the MCC-F1 curve to address these drawbacks. The MCC-F1 curve combines two informative single-threshold metrics, MCC and the F1 score. The MCC-F1 curve more clearly differentiates good and bad classifiers, even with imbalanced ground truths. We also introduce the MCC-F1 metric, which provides a single value that integrates many aspects of classifier performance across the whole range of classification thresholds. Finally, we provide an R package that plots MCC-F1 curves and calculates related metrics.

DCMD: Distance-based Classification Using Mixture Distributions on Microbiome Data Machine Learning

Current advances in next generation sequencing techniques have allowed researchers to conduct comprehensive research on microbiome and human diseases, with recent studies identifying associations between human microbiome and health outcomes for a number of chronic conditions. However, microbiome data structure, characterized by sparsity and skewness, presents challenges to building effective classifiers. To address this, we present an innovative approach for distance-based classification using mixture distributions (DCMD). The method aims to improve classification performance when using microbiome community data, where the predictors are composed of sparse and heterogeneous count data. This approach models the inherent uncertainty in sparse counts by estimating a mixture distribution for the sample data, and representing each observation as a distribution, conditional on observed counts and the estimated mixture, which are then used as inputs for distance-based classification. The method is implemented into a k-means and k-nearest neighbours framework and we identify two distance metrics that produce optimal results. The performance of the model is assessed using simulations and applied to a human microbiome study, with results compared against a number of existing machine learning and distance-based approaches. The proposed method is competitive when compared to the machine learning approaches and showed a clear improvement over commonly used distance-based classifiers. The range of applicability and robustness make the proposed method a viable alternative for classification using sparse microbiome count data.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search


Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations.