Artificial Intelligence for Microbiology and Microbiome Research

Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning and deep learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between machine learning and deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation & prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention & therapeutics. Finally, we discuss challenges unique to this field, including the balance between interpretability and complexity, the "small n, large p" problem, and the critical need for standardized benchmarking datasets to validate and compare models. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.

Graph Convolutional Network-based Feature Selection for High-dimensional and Low-sample Size Data

Feature selection is a powerful dimension reduction technique which selects a subset of relevant features for model construction. Numerous feature selection methods have been proposed, but most of them fail under the high-dimensional and low-sample size (HDLSS) setting due to the challenge of overfitting. In this paper, we present a deep learning-based method - GRAph Convolutional nEtwork feature Selector (GRACES) - to select important features for HDLSS data. We demonstrate empirical evidence that GRACES outperforms other feature selection methods on both synthetic and real-world datasets.

A Survey on Hyperlink Prediction

As a natural extension of link prediction on graphs, hyperlink prediction aims for the inference of missing hyperlinks in hypergraphs, where a hyperlink can connect more than two nodes. Hyperlink prediction has applications in a wide range of systems, from chemical reaction networks, social communication networks, to protein-protein interaction networks. In this paper, we provide a systematic and comprehensive survey on hyperlink prediction. We propose a new taxonomy to classify existing hyperlink prediction methods into four categories: similarity-based, probability-based, matrix optimization-based, and deep learning-based methods. To compare the performance of methods from different categories, we perform a benchmark study on various hypergraph applications using representative methods from each category. Notably, deep learning-based methods prevail over other methods in hyperlink prediction.

Tailoring Artificial Neural Networks for Optimal Learning

As one of the most important paradigms of recurrent neural networks, the echo state network (ESN) has been applied to a wide range of fields, from robotics to medicine to finance, and language processing. A key feature of the ESN paradigm is its reservoir ---a directed and weighted network--- that represents the connections between neurons and projects the input signals into a high dimensional space. Despite extensive studies, the impact of the reservoir network on the ESN performance remains unclear. Here we systematically address this fundamental question. Through spectral analysis of the reservoir network we reveal a key factor that largely determines the ESN memory capacity and hence affects its performance. Moreover, we find that adding short loops to the reservoir network can tailor ESN for specific tasks and optimal learning. We validate our findings by applying ESN to forecast both synthetic and real benchmark time series. Our results provide a new way to design task-specific recurrent neural networks, as well as new insights in understanding complex networked systems.