Addressing Noise and Estimating Uncertainty in Biomedical Data through the Exploration of Chemical Space.

Noise is a basic ingredient in data, since observed data are always contaminated by unwanted deviations, i.e., noise, which, in the case of overdetermined systems (with more data than model parameters), cause the corresponding linear system of equations to have an imperfect solution.

Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review.

Big data in health care is a fast-growing field and a new paradigm that is transforming case-based studies to large-scale, data-driven research. As big data is dependent on the advancement of new data standards, technology, and relevant research, the future development of big data applications holds foreseeable promise in the modern day health care revolution. Enormously large, rapidly growing collections of biomedical omics-data (genomics, proteomics, transcriptomics, metabolomics, glycomics, etc.

Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic.

The prediction of the dynamics of the COVID-19 outbreak and the corresponding needs of the health care system (COVID-19 patients' admissions, the number of critically ill patients, need for intensive care units, etc.) is based on the combination of a limited growth model (Verhulst model) and a short-term predictive model that allows predictions to be made for the following day. In both cases, the uncertainty analysis of the prediction is performed, i.

On the Role of Artificial Intelligence in Genomics to Enhance Precision Medicine.

The complexity of orphan diseases, which are those that do not have an effective treatment, together with the high dimensionality of the genetic data used for their analysis and the high degree of uncertainty in the understanding of the mechanisms and genetic pathways which are involved in their development, motivate the use of advanced techniques of artificial intelligence and in-depth knowledge of molecular biology, which is crucial in order to find plausible solutions in drug design, including drug repositioning. Particularly, we show that the use of robust deep sampling methodologies of the altered genetics serves to obtain meaningful results and dramatically decreases the cost of research and development in drug design, influencing very positively the use of precision medicine and the outcomes in patients. The target-centric approach and the use of strong prior hypotheses that are not matched against reality (disease genetic data) are undoubtedly the cause of the high number of drug design failures and attrition rates.

Robust pathway sampling in phenotype prediction. Application to triple negative breast cancer.

Background: Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective genetic pathways due to the high number of possible discriminatory genetic networks involved. In this research, we outline three novel sampling algorithms utilized to identify, classify and characterize the defective pathways in phenotype prediction problems, such as the Fisher's ratio sampler, the Holdout sampler and the Random sampler, and apply each one to the analysis of genetic pathways involved in tumor behavior and outcomes of triple negative breast cancers (TNBC).

Robust Sampling of Defective Pathways in Multiple Myeloma.

We present the analysis of defective pathways in multiple myeloma (MM) using two recently developed sampling algorithms of the biological pathways: The Fisher's ratio sampler, and the holdout sampler. We performed the retrospective analyses of different gene expression datasets concerning different aspects of the disease, such as the existing difference between bone marrow stromal cells in MM and healthy controls (HC), the gene expression profiling of CD34+ cells in MM and HC, the difference between hyperdiploid and non-hyperdiploid myelomas, and the prediction of the chromosome 13 deletion, to provide a deeper insight into the molecular mechanisms involved in the disease. Our analysis has shown the importance of different altered pathways related to glycosylation, infectious disease, immune system response, different aspects of metabolism, DNA repair, protein recycling and regulation of the transcription of genes involved in the differentiation of myeloid cells.

Prognostic networks for unraveling the biological mechanisms of Sarcopenia.

Sarcopenia is an age-related multifactorial process that involved several biological mechanisms, whose specific contribution and interplay is still unknown. The present study proposes prognostic networks based on machine learning approaches to unravel the interplay among those biological mechanisms mainly involved in the development of Sarcopenia. After analyzing 114 biological and clinical variables in adults older than 70 years, and using all the biological prognostic networks detected by machine learning with accuracy higher than 82%, we designed a consensus classifier based on majority vote that improve the predictive accuracy of Sarcopenia up to 91%.

MMP11 expression in intratumoral inflammatory cells in breast cancer.

Aims: It is known that matrix metalloproteinase (MMP)-11 has a role in tumour development and progression, and also that immune cells can influence cancer cells to increase their proliferative and invasive properties. The aim of the present study was to propose the evaluation of MMP11 expression by intratumoral mononuclear inflammatory cells (MICs) as a useful biological marker for breast cancer prognosis.

Methods And Results: This study comprised 246 women with invasive breast carcinoma, and a long follow-up period.

Principal component analysis in protein tertiary structure prediction.

We discuss applicability of principal component analysis (PCA) for protein tertiary structure prediction from amino acid sequence. The algorithm presented in this paper belongs to the category of protein refinement models and involves establishing a low-dimensional space where the sampling (and optimization) is carried out via particle swarm optimizer (PSO). The reduced space is found via PCA performed for a set of low-energy protein models previously found using different optimization techniques.

Particle Swarm Optimization and Uncertainty Assessment in Inverse Problems.

Most inverse problems in the industry (and particularly in geophysical exploration) are highly underdetermined because the number of model parameters too high to achieve accurate data predictions and because the sampling of the data space is scarce and incomplete; it is always affected by different kinds of noise. Additionally, the physics of the forward problem is a simplification of the reality. All these facts result in that the inverse problem solution is not unique; that is, there are different inverse solutions (called equivalent), compatible with the prior information that fits the observed data within similar error bounds.

Genomic risk prediction of aromatase inhibitor-related arthralgia in patients with breast cancer using a novel machine-learning algorithm.

Many breast cancer (BC) patients treated with aromatase inhibitors (AIs) develop aromatase inhibitor-related arthralgia (AIA). Candidate gene studies to identify AIA risk are limited in scope. We evaluated the potential of a novel analytic algorithm (NAA) to predict AIA using germline single nucleotide polymorphisms (SNP) data obtained before treatment initiation.