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Background: Microbiome dysbiosis has recently been associated with different diseases and disorders. In this context, machine learning (ML) approaches can be useful either to identify new patterns or learn predictive models. However, data to be fed to ML methods can be subject to different sampling, sequencing and preprocessing techniques. Each different choice in the pipeline can lead to a different view (i.e., feature set) of the same individuals, that classical (single-view) ML approaches may fail to simultaneously consider. Moreover, some views may be incomplete, i.e., some individuals may be missing in some views, possibly due to the absence of some measurements or to the fact that some features are not available/applicable for all the individuals. Multi-view learning methods can represent a possible solution to consider multiple feature sets for the same individuals, but most existing multi-view learning methods are limited to binary classification tasks or cannot work with incomplete views., Results: We propose irBoost.SH, an extension of the multi-view boosting algorithm rBoost.SH, based on multi-armed bandits. irBoost.SH solves multi-class classification tasks and can analyze incomplete views. At each iteration, it identifies one winning view using adversarial multi-armed bandits and uses its predictions to update a shared instance weight distribution in a learning process based on boosting. In our experiments, performed on 5 multi-view microbiome datasets, the model learned by irBoost.SH always outperforms the best model learned from a single view, its closest competitor rBoost.SH, and the model learned by a multi-view approach based on feature concatenation, reaching an improvement of 11.8% of the F1-score in the prediction of the Autism Spectrum disorder and of 114% in the prediction of the Colorectal Cancer disease., Conclusions: The proposed method irBoost.SH exhibited outstanding performances in our experiments, also compared to competitor approaches. The obtained results confirm that irBoost.SH can fruitfully be adopted for the analysis of microbiome data, due to its capability to simultaneously exploit multiple feature sets obtained through different sequencing and preprocessing pipelines., (© 2024. The Author(s).)

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Marcos-Zambrano, López-Molina, Bakir-Gungor, Frohme, Karaduzovic-Hadziabdic, Klammsteiner, Ibrahimi, Lahti, Loncar Turukalo, Dhamo, Simeon, Nechyporenko, Pio, Przymus, Sampri, Trajkovik, Lacruz-Pleguezuelos, Aasmets, Araujo, Anagnostopoulos, Aydemir, Berland, Calle, Ceci, Duman, Gündoğdu, Havulinna, Kaka Bra, Kalluci, Karav, Lode, Lopes, May, Nap, Nedyalkova, Paciência, Pasic, Pujolassos, Shigdel, Susín, Thiele, Truică, Wilmes, Yilmaz, Yousef, Claesson, Truu, Carrillo de Santa Pau.)

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices., Competing Interests: CJ is employed by Biome diagnostics GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 D’Elia, Truu, Lahti, Berland, Papoutsoglou, Ceci, Zomer, Lopes, Ibrahimi, Gruca, Nechyporenko, Frohme, Klammsteiner, Pau, Marcos-Zambrano, Hron, Pio, Simeon, Suharoschi, Moreno-Indias, Temko, Nedyalkova, Apostol, Truică, Shigdel, Telalović, Bongcam-Rudloff, Przymus, Jordamović, Falquet, Tarazona, Sampri, Isola, Pérez-Serrano, Trajkovik, Klucar, Loncar-Turukalo, Havulinna, Jansen, Bertelsen and Claesson.)

The joint exploitation of data related to epidemiological, mobility, and restriction aspects of COVID-19 with machine learning algorithms can support the development of predictive models that can be used to forecast new positive cases and study the impact of more or less severe restrictions. In this work, we integrate heterogeneous data from several sources and solve a multivariate time series forecasting task, specifically targeting the Italian case at both national and regional levels, during the first three waves of the pandemic. The goal is to build a robust predictive model to predict the number of new cases over a given time horizon so that any restrictive actions can be better planned. In addition, we perform a what-if analysis based on the best-identified predictive models to evaluate the impact of specific restrictions on the trend of positive cases. Our focus on the first three waves is motivated by the fact that it represents a typical emergency scenario (when no stable cure or vaccine is available) that may occur when a new pandemic spreads. Our experimental results prove that exploiting the considered heterogeneous data leads to accurate predictive models, reaching a WAPE of 5.75% at the national level. Furthermore, in the subsequent what-if analysis, we observed that strong all-in-one initiatives, such as total lockdowns, may not be adequate, while more specific and targeted solutions should be adopted. The developed models can help policy and decision-makers better plan intervention strategies and retrospectively analyze the effects of the decisions made at different scales. Joint exploitation of data on epidemiological, mobility, and restriction aspects of COVID-19 with machine learning algorithms to learn predictive models to forecast new positive cases., (© 2023. The Author(s).)

Motivation: Gene regulation is responsible for controlling numerous physiological functions and dynamically responding to environmental fluctuations. Reconstructing the human network of gene regulatory interactions is thus paramount to understanding the cell functional organization across cell types, as well as to elucidating pathogenic processes and identifying molecular drug targets. Although significant effort has been devoted towards this direction, existing computational methods mainly rely on gene expression levels, possibly ignoring the information conveyed by mechanistic biochemical knowledge. Moreover, except for a few recent attempts, most of the existing approaches only consider the information of the organism under analysis, without exploiting the information of related model organisms., Results: We propose a novel method for the reconstruction of the human gene regulatory network, based on a transfer learning strategy that synergically exploits information from human and mouse, conveyed by gene-related metabolic features generated in silico from gene expression data. Specifically, we learn a predictive model from metabolic activity inferred via tissue-specific metabolic modelling of artificial gene knockouts. Our experiments show that the combination of our transfer learning approach with the constructed metabolic features provides a significant advantage in terms of reconstruction accuracy, as well as additional clues on the contribution of each constructed metabolic feature., Availability and Implementation: The method, the datasets and all the results obtained in this study are available at: https://doi.org/10.6084/m9.figshare.c.5237687., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 "ML4Microbiome" that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Moreno-Indias, Lahti, Nedyalkova, Elbere, Roshchupkin, Adilovic, Aydemir, Bakir-Gungor, Santa Pau, D’Elia, Desai, Falquet, Gundogdu, Hron, Klammsteiner, Lopes, Marcos-Zambrano, Marques, Mason, May, Pašić, Pio, Pongor, Promponas, Przymus, Saez-Rodriguez, Sampri, Shigdel, Stres, Suharoschi, Truu, Truică, Vilne, Vlachakis, Yilmaz, Zeller, Zomer, Gómez-Cabrero and Claesson.)

The reconstruction of Gene Regulatory Networks (GRNs) from gene expression data, supported by machine learning approaches, has received increasing attention in recent years. The task at hand is to identify regulatory links between genes in a network. However, existing methods often suffer when the number of labeled examples is low or when no negative examples are available. In this paper we propose a multi-task method that is able to simultaneously reconstruct the human and the mouse GRNs using the similarities between the two. This is done by exploiting, in a transfer learning approach, possible dependencies that may exist among them. Simultaneously, we solve the issues arising from the limited availability of examples of links by relying on a novel clustering-based approach, able to estimate the degree of certainty of unlabeled examples of links, so that they can be exploited during the training together with the labeled examples. Our experiments show that the proposed method can reconstruct both the human and the mouse GRNs more effectively compared to reconstructing each network separately. Moreover, it significantly outperforms three state-of-the-art transfer learning approaches that, analogously to our method, can exploit the knowledge coming from both organisms. Finally, a specific robustness analysis reveals that, even when the number of labeled examples is very low with respect to the number of unlabeled examples, the proposed method is almost always able to outperform its single-task counterpart.

Motivation: The reconstruction of gene regulatory networks (GRNs) from gene expression data has received increasing attention in recent years, due to its usefulness in the understanding of regulatory mechanisms involved in human diseases. Most of the existing methods reconstruct the network through machine learning approaches, by analyzing known examples of interactions. However, (i) they often produce poor results when the amount of labeled examples is limited, or when no negative example is available and (ii) they are not able to exploit information extracted from GRNs of other (better studied) related organisms, when this information is available., Results: In this paper, we propose a novel machine learning method that overcomes these limitations, by exploiting the knowledge about the GRN of a source organism for the reconstruction of the GRN of the target organism, by means of a novel transfer learning technique. Moreover, the proposed method is natively able to work in the positive-unlabeled setting, where no negative example is available, by fruitfully exploiting a (possibly large) set of unlabeled examples. In our experiments, we reconstructed the human GRN, by exploiting the knowledge of the GRN of Mus musculus. Results showed that the proposed method outperforms state-of-the-art approaches and identifies previously unknown functional relationships among the analyzed genes., Availability and Implementation: http://www.di.uniba.it/∼mignone/systems/biosfer/index.html., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: The study of functional associations between ncRNAs and human diseases is a pivotal task of modern research to develop new and more effective therapeutic approaches. Nevertheless, it is not a trivial task since it involves entities of different types, such as microRNAs, lncRNAs or target genes whose expression also depends on endogenous or exogenous factors. Such a complexity can be faced by representing the involved biological entities and their relationships as a network and by exploiting network-based computational approaches able to identify new associations. However, existing methods are limited to homogeneous networks (i.e., consisting of only one type of objects and relationships) or can exploit only a small subset of the features of biological entities, such as the presence of a particular binding domain, enzymatic properties or their involvement in specific diseases., Results: To overcome the limitations of existing approaches, we propose the system LP-HCLUS, which exploits a multi-type hierarchical clustering method to predict possibly unknown ncRNA-disease relationships. In particular, LP-HCLUS analyzes heterogeneous networks consisting of several types of objects and relationships, each possibly described by a set of features, and extracts multi-type clusters that are subsequently exploited to predict new ncRNA-disease associations. The extracted clusters are overlapping, hierarchically organized, involve entities of different types, and allow LP-HCLUS to catch multiple roles of ncRNAs in diseases at different levels of granularity. Our experimental evaluation, performed on heterogeneous attributed networks consisting of microRNAs, lncRNAs, diseases, genes and their known relationships, shows that LP-HCLUS is able to obtain better results with respect to existing approaches. The biological relevance of the obtained results was evaluated according to both quantitative (i.e., TPR@k, Areas Under the TPR@k, ROC and Precision-Recall curves) and qualitative (i.e., according to the consultation of the existing literature) criteria., Conclusions: The obtained results prove the utility of LP-HCLUS to conduct robust predictive studies on the biological role of ncRNAs in human diseases. The produced predictions can therefore be reliably considered as new, previously unknown, relationships among ncRNAs and diseases.

The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently observed, however, that no single inference method performs optimally across all datasets. It has also been shown that the integration of predictions from multiple inference methods is more robust and shows high performance across diverse datasets. Inspired by this research, in this paper, we propose a machine learning solution which learns to combine predictions from multiple inference methods. While this approach adds additional complexity to the inference process, we expect it would also carry substantial benefits. These would come from the automatic adaptation to patterns on the outputs of individual inference methods, so that it is possible to identify regulatory interactions more reliably when these patterns occur. This article demonstrates the benefits (in terms of accuracy of the reconstructed networks) of the proposed method, which exploits an iterative, semi-supervised ensemble-based algorithm. The algorithm learns to combine the interactions predicted by many different inference methods in the multi-view learning setting. The empirical evaluation of the proposed algorithm on a prokaryotic model organism (E. coli) and on a eukaryotic model organism (S. cerevisiae) clearly shows improved performance over the state of the art methods. The results indicate that gene regulatory network reconstruction for the real datasets is more difficult for S. cerevisiae than for E. coli. The software, all the datasets used in the experiments and all the results are available for download at the following link: http://figshare.com/articles/Semi_supervised_Multi_View_Learning_for_Gene_Network_Reconstruction/1604827.

Background: The understanding of mechanisms and functions of microRNAs (miRNAs) is fundamental for the study of many biological processes and for the elucidation of the pathogenesis of many human diseases. Technological advances represented by high-throughput technologies, such as microarray and next-generation sequencing, have significantly aided miRNA research in the last decade. Nevertheless, the identification of true miRNA targets and the complete elucidation of the rules governing their functional targeting remain nebulous. Computational tools have been proven to be fundamental for guiding experimental validations for the discovery of new miRNAs, for the identification of their targets and for the elucidation of their regulatory mechanisms., Description: ComiRNet (Co-clustered miRNA Regulatory Networks) is a web-based database specifically designed to provide biologists and clinicians with user-friendly and effective tools for the study of miRNA-gene target interaction data and for the discovery of miRNA functions and mechanisms. Data in ComiRNet are produced by a combined computational approach based on: 1) a semi-supervised ensemble-based classifier, which learns to combine miRNA-gene target interactions (MTIs) from several prediction algorithms, and 2) the biclustering algorithm HOCCLUS2, which exploits the large set of produced predictions, with the associated probabilities, to identify overlapping and hierarchically organized biclusters that represent miRNA-gene regulatory networks (MGRNs)., Conclusions: ComiRNet represents a valuable resource for elucidating the miRNAs' role in complex biological processes by exploiting data on their putative function in the context of MGRNs. ComiRnet currently stores about 5 million predicted MTIs between 934 human miRNAs and 30,875 mRNAs, as well as 15 bicluster hierarchies, each of which represents MGRNs at different levels of granularity. The database can be freely accessed at: http://comirnet.di.uniba.it.

Background: MicroRNAs (miRNAs) are small non-coding RNAs which play a key role in the post-transcriptional regulation of many genes. Elucidating miRNA-regulated gene networks is crucial for the understanding of mechanisms and functions of miRNAs in many biological processes, such as cell proliferation, development, differentiation and cell homeostasis, as well as in many types of human tumors. To this aim, we have recently presented the biclustering method HOCCLUS2, for the discovery of miRNA regulatory networks. Experiments on predicted interactions revealed that the statistical and biological consistency of the obtained networks is negatively affected by the poor reliability of the output of miRNA target prediction algorithms. Recently, some learning approaches have been proposed to learn to combine the outputs of distinct prediction algorithms and improve their accuracy. However, the application of classical supervised learning algorithms presents two challenges: i) the presence of only positive examples in datasets of experimentally verified interactions and ii) unbalanced number of labeled and unlabeled examples., Results: We present a learning algorithm that learns to combine the score returned by several prediction algorithms, by exploiting information conveyed by (only positively labeled/) validated and unlabeled examples of interactions. To face the two related challenges, we resort to a semi-supervised ensemble learning setting. Results obtained using miRTarBase as the set of labeled (positive) interactions and mirDIP as the set of unlabeled interactions show a significant improvement, over competitive approaches, in the quality of the predictions. This solution also improves the effectiveness of HOCCLUS2 in discovering biologically realistic miRNA:mRNA regulatory networks from large-scale prediction data. Using the miR-17-92 gene cluster family as a reference system and comparing results with previous experiments, we find a large increase in the number of significantly enriched biclusters in pathways, consistent with miR-17-92 functions., Conclusion: The proposed approach proves to be fundamental for the computational discovery of miRNA regulatory networks from large-scale predictions. This paves the way to the systematic application of HOCCLUS2 for a comprehensive reconstruction of all the possible multiple interactions established by miRNAs in regulating the expression of gene networks, which would be otherwise impossible to reconstruct by considering only experimentally validated interactions.

Background: microRNAs (miRNAs) are a class of small non-coding RNAs which have been recognized as ubiquitous post-transcriptional regulators. The analysis of interactions between different miRNAs and their target genes is necessary for the understanding of miRNAs' role in the control of cell life and death. In this paper we propose a novel data mining algorithm, called HOCCLUS2, specifically designed to bicluster miRNAs and target messenger RNAs (mRNAs) on the basis of their experimentally-verified and/or predicted interactions. Indeed, existing biclustering approaches, typically used to analyze gene expression data, fail when applied to miRNA:mRNA interactions since they usually do not extract possibly overlapping biclusters (miRNAs and their target genes may have multiple roles), extract a huge amount of biclusters (difficult to browse and rank on the basis of their importance) and work on similarities of feature values (do not limit the analysis to reliable interactions)., Results: To overcome these limitations, HOCCLUS2 i) extracts possibly overlapping biclusters, to catch multiple roles of both miRNAs and their target genes; ii) extracts hierarchically organized biclusters, to facilitate bicluster browsing and to distinguish between universe and pathway-specific miRNAs; iii) extracts highly cohesive biclusters, to consider only reliable interactions; iv) ranks biclusters according to the functional similarities, computed on the basis of Gene Ontology, to facilitate bicluster analysis., Conclusions: Our results show that HOCCLUS2 is a valid tool to support biologists in the identification of context-specific miRNAs regulatory modules and in the detection of possibly unknown miRNAs target genes. Indeed, results prove that HOCCLUS2 is able to extract cohesiveness-preserving biclusters, when compared with competitive approaches, and statistically confirm (at a confidence level of 99%) that mRNAs which belong to the same biclusters are, on average, more functionally similar than mRNAs which belong to different biclusters. Finally, the hierarchy of biclusters provides useful insights to understand the intrinsic hierarchical organization of miRNAs and their potential multiple interactions on target genes.