Clustering-Based Behavioural Analysis of Biological Objects

The article examines the problem of processing short time series for bioinformatics tasks using data mining methods in the field of pharmacology. The experiments were conducted using heart contraction (contraction and relaxation) power data that were obtained in experiments with laboratory animals with the goal of registering the power changes of heart contractions in different stages of experiment in a given period of time. The selected data were treated using data preprocessing technologies. The short time series were compared using various time-point similarity search methods using agglomerative hierarchical clustering, k- means clustering, modified k-means clustering and expectation-maximization clustering algorithms. Based on the clustering result evaluation the most suitable algorithm was chosen and the optimal number of clusters was determined for the least clustering error. The acquired clusters were used for to create cluster prototypes that aggregate the groups of similar heart contraction power objects. The article offers an examination of the errors produced by algorithms and methods as well as a discussion of the obtained clustering results using different evaluation methodologies. It also gives conclusions about the application of data mining methods in solving bioinformatics tasks and outlines further research directions

A Comparative Analysis of Short Time Series Processing Methods

This article analyzes the traditional time series processing methods that are used to perform the task of short time series analysis in demand forecasting. The main aim of this paper is to scrutinize the ability of these methods to be used when analyzing short time series. The analyzed methods include exponential smoothing, exponential smoothing with the development trend and moving average method. The paper gives the description of the structure and main operating principles. The experimental studies are conducted using real demand data. The obtained results are analyzed; and the recommendations are given about the use of these methods for short time series analysis

Gastric Cancer Risk Analysis in Unhealthy Habits Data with Classification Algorithms

Data mining methods are applied to a medical task that seeks for the information about the influence of Helicobacter Pylori on the gastric cancer risk increase by analysing the adverse factors of individual lifestyle. In the process of data pre- processing, the data are cleared of noise and other factors, reduced in dimensionality, as well as transformed for the task and cleared of non-informative attributes. Data classification using C4.5, CN2 and k-nearest neighbour algorithms is carried out to find relationships between the analysed attributes and the descriptive class attribute – Helicobacter Pylori presence that could have influence on the cancer development risk. Experimental analysis is carried out using the data of the Latvian-based project “Interdisciplinary Research Group for Early Cancer Detection and Cancer Prevention” database

Gastric Cancer Risk Analysis in Unhealthy Habits Data with Classification Algorithms

Data mining methods are applied to a medical task that seeks for the information about the influence of Helicobacter Pylori on the gastric cancer risk increase by analysing the adverse factors of individual lifestyle. In the process of data preprocessing, the data are cleared of noise and other factors, reduced in dimensionality, as well as transformed for the task and cleared of non-informative attributes. Data classification using C4.5, CN2 and k-nearest neighbour algorithms is carried out to find relationships between the analysed attributes and the descriptive class attribute – Helicobacter Pylori presence that could have influence on the cancer development risk. Experimental analysis is carried out using the data of the Latvian-based project “Interdisciplinary Research Group for Early Cancer Detection and Cancer Prevention” database

Volatile Markers for Cancer in Exhaled Breath—Could They Be the Signature of the Gut Microbiota?

It has been shown that the gut microbiota plays a central role in human health and disease. A wide range of volatile metabolites present in exhaled breath have been linked with gut microbiota and proposed as a non-invasive marker for monitoring pathological conditions. The aim of this study was to examine the possible correlation between volatile organic compounds (VOCs) in exhaled breath and the fecal microbiome by multivariate statistical analysis in gastric cancer patients (n = 16) and healthy controls (n = 33). Shotgun metagenomic sequencing was used to characterize the fecal microbiota. Breath-VOC profiles in the same participants were identified by an untargeted gas chromatography–mass spectrometry (GC–MS) technique. A multivariate statistical approach involving a canonical correlation analysis (CCA) and sparse principal component analysis identified the significant relationship between the breath VOCs and fecal microbiota. This relation was found to differ between gastric cancer patients and healthy controls. In 16 cancer cases, 14 distinct metabolites identified from the breath belonging to hydrocarbons, alcohols, aromatics, ketones, ethers, and organosulfur compounds were highly correlated with 33 fecal bacterial taxa (correlation of 0.891, p-value 0.045), whereas in 33 healthy controls, 7 volatile metabolites belonging to alcohols, aldehydes, esters, phenols, and benzamide derivatives correlated with 17 bacterial taxa (correlation of 0.871, p-value 0.0007). This study suggested that the correlation between fecal microbiota and breath VOCs was effective in identifying exhaled volatile metabolites and the functional effects of microbiome, thus helping to understand cancer-related changes and improving the survival and life expectancy in gastric cancer patients