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Traditionally, in supervised machine learning, (a significant) part of the available data (usually 50% to 80%) is used for training and the rest for validation. In many problems, however, the data is highly imbalanced in regard to different…
Nested sampling is a promising tool for Bayesian statistical analysis because it simultaneously performs parameter estimation and facilitates model comparison. MultiNest is one of the most popular nested sampling implementations, and has…
The elicitation of an ordinal judgment on multiple alternatives is often required in many psychological and behavioral experiments to investigate preference/choice orientation of a specific population. The Plackett-Luce model is one of the…
With medical tests becoming increasingly available, concerns about over-testing and over-treatment dramatically increase. Hence, it is important to understand the influence of testing on treatment selection in general practice. Most…
Many statistical studies are concerned with the analysis of observations organized in a matrix form whose elements are count data. When these observations are assumed to follow a Poisson or a multinomial distribution, it is of interest to…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
In Cowell et al. (2007), a Bayesian network for analysis of mixed traces of DNA was presented using gamma distributions for modelling peak sizes in the electropherogram. It was demonstrated that the analysis was sensitive to the choice of a…
Matrix completion has been well studied under the uniform sampling model and the trace-norm regularized methods perform well both theoretically and numerically in such a setting. However, the uniform sampling model is unrealistic for a…
Scientific studies in the last two decades have established the central role of the microbiome in disease and health. Differential abundance analysis seeks to identify microbial taxa associated with sample groups defined by a factor such as…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
High-throughput sequencing has transformed microbiome research, but it also produces inherently compositional data that challenge standard statistical and machine learning methods. In this work, we propose a multinomial classification…
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome…
The era of big data is coming, and evidence-based medicine is attracting increasing attention to improve decision making in medical practice via integrating evidence from well designed and conducted clinical research. Meta-analysis is a…
Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. For communities of up to medium diversity,…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…