This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a computationally efficient inference algorithm based on variational inference to approximate the posterior distribution. We demonstrate the potential of the new approach on various synthetic datasets and for predicting human health status based on microbiome profile. Our analysis incorporates data pooled from multiple microbiome studies, along with a comprehensive comparison with other benchmark methods. Results in synthetic datasets show that the proposed approach has superior support recovery property when the underlying regression coefficients share a common sparsity structure across different tasks. Our experiments on microbiome classification demonstrate the utility of the method in extracting informative taxa while providing well-calibrated predictions with uncertainty quantification and achieving competitive performance in terms of prediction metrics. Notably, despite the heterogeneity of the pooled datasets (e.g., different experimental objectives, laboratory setups, sequencing equipment, patient demographics), our method delivers robust results.

Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples. It can provide useful insights for studying the interactions between hosts and microbes, infectious disease proliferation, and novel species discovery. One important step in this analysis is the taxonomic classification of those DNA fragments. Of particular interest is the determination of the distribution of the taxa of microbes in metagenomic samples. Recent attempts using deep learning focus on architectures that classify single DNA reads independently from each other. In this work, we attempt to solve the task of directly predicting the distribution over the taxa of whole metagenomic read sets. We formulate this task as a Multiple Instance Learning (MIL) problem. We extend architectures used in single-read taxonomic classification with two different types of permutation-invariant MIL pooling layers: a) deepsets and b) attention-based pooling. We illustrate that our architecture can exploit the co-occurrence of species in metagenomic read sets and outperforms the single-read architectures in predicting the distribution over the taxa at higher taxonomic ranks.

The appeal of metric evaluation of research impact has attracted considerable interest in recent times. Although the public at large and administrative bodies are much interested in the idea, scientists and other researchers are much more cautious, insisting that metrics are but an auxiliary instrument to the qualitative peer-based judgement. The goal of this article is to propose availing of such a well positioned construct as domain taxonomy as a tool for directly assessing the scope and quality of research. We first show how taxonomies can be used to analyse the scope and perspectives of a set of research projects or papers. Then we proceed to define a research team or researcher's rank by those nodes in the hierarchy that have been created or significantly transformed by the results of the researcher. An experimental test of the approach in the data analysis domain is described. Although the concept of taxonomy seems rather simplistic to describe all the richness of a research domain, its changes and use can be made transparent and subject to open discussions.