GASVeM: A New Machine Learning Methodology for Multi-SNP Analysis of GWAS Data Based on Genetic Algorithms and Support Vector Machines

PsiOvi Staging Model for Schizophrenia (PsiOvi SMS): A New Internet Tool for Staging Patients with Schizophrenia

BACKGROUND

One of the challenges of psychiatry is the staging of patients, especially those with severe mental disorders. Therefore, we aim to develop an empirical staging model for schizophrenia.

METHODS

Data were obtained from 212 stable outpatients with schizophrenia: demographic, clinical, psychometric (PANSS, CAINS, CDSS, OSQ, CGI-S, PSP, MATRICS), inflammatory peripheral blood markers (C-reactive protein, interleukins-1RA and 6, and platelet/lymphocyte [PLR], neutrophil/lymphocyte [NLR], and monocyte/lymphocyte [MLR] ratios). We used machine learning techniques to develop the model (genetic algorithms, support vector machines) and applied a fitness function to measure the model's accuracy (% agreement between patient classification of our model and the CGI-S).

RESULTS

Our model includes 12 variables from 5 dimensions: 1) psychopathology: positive, negative, depressive, general psychopathology symptoms; 2) clinical features: number of hospitalizations; 3) cognition: processing speed, visual learning, social cognition; 4) biomarkers: PLR, NLR, MLR; and 5) functioning: PSP total score. Accuracy was 62% (SD = 5.3), and sensitivity values were appropriate for mild, moderate, and marked severity (from 0.62106 to 0.6728).

DISCUSSION

We present a multidimensional, accessible, and easy-to-apply model that goes beyond simply categorizing patients according to CGI-S score. It provides clinicians with a multifaceted patient profile that facilitates the design of personalized intervention plans.

Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes

One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (F_ST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.

Feature Fusion and Detection in Alzheimer’s Disease Using a Novel Genetic Multi-Kernel SVM Based on MRI Imaging and Gene Data

Voxel-based morphometry provides an opportunity to study Alzheimer’s disease (AD) at a subtle level. Therefore, identifying the important brain voxels that can classify AD, early mild cognitive impairment (EMCI) and healthy control (HC) and studying the role of these voxels in AD will be crucial to improve our understanding of the neurobiological mechanism of AD. Combining magnetic resonance imaging (MRI) imaging and gene information, we proposed a novel feature construction method and a novel genetic multi-kernel support vector machine (SVM) method to mine important features for AD detection. Specifically, to amplify the differences among AD, EMCI and HC groups, we used the eigenvalues of the top 24 Single Nucleotide Polymorphisms (SNPs) in a p-value matrix of 24 genes associated with AD for feature construction. Furthermore, a genetic multi-kernel SVM was established with the resulting features. The genetic algorithm was used to detect the optimal weights of 3 kernels and the multi-kernel SVM was used after training to explore the significant features. By analyzing the significance of the features, we identified some brain regions affected by AD, such as the right superior frontal gyrus, right inferior temporal gyrus and right superior temporal gyrus. The findings proved the good performance and generalization of the proposed model. Particularly, significant susceptibility genes associated with AD were identified, such as CSMD1, RBFOX1, PTPRD, CDH13 and WWOX. Some significant pathways were further explored, such as the calcium signaling pathway (corrected p-value = 1.35 × 10⁻⁶) and cell adhesion molecules (corrected p-value = 5.44 × 10⁻⁴). The findings offer new candidate abnormal brain features and demonstrate the contribution of these features to AD.

A New Algorithm for Multivariate Genome Wide Association Studies Based on Differential Evolution and Extreme Learning Machines

Genome-wide association studies (GWAS) are observational studies of a large set of genetic variants, whose aim is to find those that are linked to a certain trait or illness. Due to the multivariate nature of these kinds of studies, machine learning methodologies have been already applied in them, showing good performance. This work presents a new methodology for GWAS that makes use of extreme learning machines and differential evolution. The proposed methodology was tested with the help of the genetic information (370,750 single-nucleotide polymorphisms) of 2049 individuals, 1076 of whom suffer from colorectal cancer. The possible relationship of 10 different pathways with this illness was tested. The results achieved showed that the proposed methodology is suitable for detecting relevant pathways for the trait under analysis with a lower computational cost than other machine learning methodologies previously proposed.

Research on Pathogenic Hippocampal Voxel Detection in Alzheimer's Disease Using Clustering Genetic Random Forest

Alzheimer's disease (AD) is an age-related neurological disease, which is closely associated with hippocampus, and subdividing the hippocampus into voxels can capture subtle signals that are easily missed by region of interest (ROI) methods. Therefore, studying interpretable associations between voxels can better understand the effect of voxel set on the hippocampus and AD. In this study, by analyzing the hippocampal voxel data, we propose a novel method based on clustering genetic random forest to identify the important voxels. Specifically, we divide the left and right hippocampus into voxels to constitute the initial feature set. Moreover, the random forest is constructed using the randomly selected samples and features. The genetic evolution is used to amplify the difference in decision trees and the clustering evolution is applied to generate offspring in genetic evolution. The important voxels are the features that reach the peak classification. The results demonstrate that our method has good classification and stability. Particularly, through biological analysis of the obtained voxel set, we find that they play an important role in AD by affecting the function of the hippocampus. These discoveries demonstrate the contribution of the voxel set to AD.

A Knowledge-Based Hybrid Approach on Particle Swarm Optimization Using Hidden Markov Models

Bio-inspired computing is an engaging area of artificial intelligence which studies how natural phenomena provide a rich source of inspiration in the design of smart procedures able to become powerful algorithms. Many of these procedures have been successfully used in classification, prediction, and optimization problems. Swarm intelligence methods are a kind of bio-inspired algorithm that have been shown to be impressive optimization solvers for a long time. However, for these algorithms to reach their maximum performance, the proper setting of the initial parameters by an expert user is required. This task is extremely comprehensive and it must be done in a previous phase of the search process. Different online methods have been developed to support swarm intelligence techniques, however, this issue remains an open challenge. In this paper, we propose a hybrid approach that allows adjusting the parameters based on a state deducted by the swarm intelligence algorithm. The state deduction is determined by the classification of a chain of observations using the hidden Markov model. The results show that our proposal exhibits good performance compared to the original version.