A functional gene module identification algorithm in gene expression data based on genetic algorithm and gene ontology.

Since genes do not function individually, the gene module is considered an important tool for interpreting gene expression profiles. In order to consider both functional similarity and expression similarity in module identification, GMIGAGO, a functional Gene Module Identification algorithm based on Genetic Algorithm and Gene Ontology, was proposed in this work. GMIGAGO is an overlapping gene module identification algorithm, which mainly includes two stages: In the first stage (initial identification of gene modules), Improved Partitioning Around Medoids Based on Genetic Algorithm (PAM-GA) is used for the initial clustering on gene expression profiling, and traditional gene co-expression modules can be obtained. Only similarity of expression levels is considered at this stage. In the second stage (optimization of functional similarity within gene modules), Genetic Algorithm for Functional Similarity Optimization (FSO-GA) is used to optimize gene modules based on gene ontology, and functional similarity within gene modules can be improved. Without loss of generality, we compared GMIGAGO with state-of-the-art gene module identification methods on six gene expression datasets, and GMIGAGO identified the gene modules with the highest functional similarity (much higher than state-of-the-art algorithms). GMIGAGO was applied in BRCA, THCA, HNSC, COVID-19, Stem, and Radiation datasets, and it identified some interesting modules which performed important biological functions. The hub genes in these modules could be used as potential targets for diseases or radiation protection. In summary, GMIGAGO has excellent performance in mining molecular mechanisms, and it can also identify potential biomarkers for individual precision therapy.

Spatial robust fuzzy clustering of COVID 19 time series based on B-splines.

The aim of the work is to identify a clustering structure for the 20 Italian regions according to the main variables related to COVID-19 pandemic. Data are observed over time, spanning from the last week of February 2020 to the first week of February 2021. Dealing with geographical units observed at several time occasions, the proposed fuzzy clustering model embedded both space and time information. Properly, an Exponential distance-based Fuzzy Partitioning Around Medoids algorithm with spatial penalty term has been proposed to classify the spline representation of the time trajectories. The results show that the heterogeneity among regions along with the spatial contiguity is essential to understand the spread of the pandemic and to design effective policies to mitigate the effects.