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Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of…
Oceans are the essential lifeblood of the Earth: they provide over 70% of the oxygen and over 97% of the water. Plankton and corals are two of the most fundamental components of ocean ecosystems, the former due to their function at many…
The main purpose of data mining and analytics is to find novel, potentially useful patterns that can be utilized in real-world applications to derive beneficial knowledge. For identifying and evaluating the usefulness of different kinds of…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
Ultrametric matrices have a rich structure that is not apparent from their definition. Notably, the subclass of strictly ultrametric matrices are covariance matrices of certain weighted rooted binary trees. In applications, these matrices…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
Identification of antimicrobial peptides is an important and necessary issue in today's era. Antimicrobial peptides are essential as an alternative to antibiotics for biomedical applications and many other practical applications. These…
Background: Understanding the relationship between the Omics and the phenotype is a central problem in precision medicine. The high dimensionality of metabolomics data challenges learning algorithms in terms of scalability and…
Insects play such a crucial role in ecosystems that a shift in demography of just a few species can have devastating consequences at environmental, social and economic levels. Despite this, evaluation of insect demography is strongly…
Global biodiversity is declining at an unprecedented rate, yet little information is known about most species and how their populations are changing. Indeed, some 90% of Earth's species are estimated to be completely unknown. Machine…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Maximum entropy principle (MEP) offers an effective and unbiased approach to inferring unknown probability distributions when faced with incomplete information, while neural networks provide the flexibility to learn complex distributions…
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…
Ultrasound imaging is widely used in clinical practice due to its cost-effectiveness, mobility, and safety. However, current AI research often treats disease prediction and tissue segmentation as two separate tasks and their model requires…
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…
Massive Multi-Omics Microbiome Database (M3DB) is a data warehousing and analytics solution designed to handle diverse, complex, and unprecedented volumes of sequence and taxonomic classification data obtained in a typical microbiome…
Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
Signal peptide (SP) is a short peptide located in the N-terminus of proteins. It is essential to target and transfer transmembrane and secreted proteins to correct positions. Compared with traditional experimental methods to identify signal…