ResViT: A Framework for Deepfake Videos Detection

Deepfake makes it quite easy to synthesize videos or images using deep learning techniques, which leads to substantial danger and worry for most of the world\u27s renowned people. Spreading false news or synthesizing one\u27s video or image can harm people and their lack of trust on social and electronic media. To efficiently identify deepfake images, we propose ResViT, which uses the ResNet model for feature extraction, while the vision transformer is used for classification. The ResViT architecture uses the feature extractor to extract features from the images of the videos, which are used to classify the input as fake or real. Moreover, the ResViT architectures focus equally on data pre-processing, as it improves performance. We conducted extensive experiments on the five mostly used datasets our results with the baseline model on the following datasets of Celeb-DF, Celeb-DFv2, FaceForensics++, FF-Deepfake Detection, and DFDC2. Our analysis revealed that ResViT performed better than the baseline and achieved the prediction accuracy of 80.48%, 87.23%, 75.62%, 78.45%, and 84.55% on Celeb-DF, Celeb-DFv2, FaceForensics++, FF-Deepfake Detection, and DFDC2 datasets, respectively

Genome-wide imputed differential expression enrichment analysis identifies trait-relevant tissues

The identification of pathogenically-relevant genes and tissues for complex traits can be a difficult task. We developed an approach named genome-wide imputed differential expression enrichment (GIDEE), to prioritise trait-relevant tissues by combining genome-wide association study (GWAS) summary statistic data with tissue-specific expression quantitative trait loci (eQTL) data from 49 GTEx tissues. Our GIDEE approach analyses robustly imputed gene expression and tests for enrichment of differentially expressed genes in each tissue. Two tests (mean squared z-score and empirical Brown’s method) utilise the full distribution of differential expression p-values across all genes, while two binomial tests assess the proportion of genes with tissue-wide significant differential expression. GIDEE was applied to nine training datasets with known trait-relevant tissues and ranked 49 GTEx tissues using the individual and combined enrichment tests. The best-performing enrichment test produced an average rank of 1.55 out of 49 for the known trait-relevant tissue across the nine training datasets—ranking the correct tissue first five times, second three times, and third once. Subsequent application of the GIDEE approach to 20 test datasets—whose pathogenic tissues or cell types are uncertain or unknown—provided important prioritisation of tissues relevant to the trait’s regulatory architecture. GIDEE prioritisation may thus help identify both pathogenic tissues and suitable proxy tissue/cell models (e.g., using enriched tissues/cells that are more easily accessible). The application of our GIDEE approach to GWAS datasets will facilitate follow-up in silico and in vitro research to determine the functional consequence(s) of their risk loci

Identifying and understanding the molecular mechanisms of migraine via functional interpretation of genome-wide association study (GWAS) data

Migraine is the most common brain disorder, affecting almost 14% of the adult population, yet its molecular mechanisms and pathogenic tissue(s) remain unclear. In this thesis, I have developed a novel approach that uses genome-wide association study (GWAS) summary statistics and expression quantitative trait loci (eQTL) data to impute genetically regulated tissue-specific gene expression and prioritise disease-relevant pathogenic tissues. In subsequent studies, I compared three transcriptome imputation models to characterise genome-wide significant migraine GWAS risk loci and identified 14 novel migraine risk loci that were confirmed to be true risk loci in a recent larger migraine GWAS

Genome-wide imputed differential expression enrichment analysis identifies trait-relevant tissues

The identification of pathogenically-relevant genes and tissues for complex traits can be a difficult task. We developed an approach named genome-wide imputed differential expression enrichment (GIDEE), to prioritise trait-relevant tissues by combining genome-wide association study (GWAS) summary statistic data with tissue-specific expression quantitative trait loci (eQTL) data from 49 GTEx tissues. Our GIDEE approach analyses robustly imputed gene expression and tests for enrichment of differentially expressed genes in each tissue. Two tests (mean squared z-score and empirical Brown's method) utilise the full distribution of differential expression p-values across all genes, while two binomial tests assess the proportion of genes with tissue-wide significant differential expression. GIDEE was applied to nine training datasets with known trait-relevant tissues and ranked 49 GTEx tissues using the individual and combined enrichment tests. The best-performing enrichment test produced an average rank of 1.55 out of 49 for the known trait-relevant tissue across the nine training datasets-ranking the correct tissue first five times, second three times, and third once. Subsequent application of the GIDEE approach to 20 test datasets-whose pathogenic tissues or cell types are uncertain or unknown-provided important prioritisation of tissues relevant to the trait's regulatory architecture. GIDEE prioritisation may thus help identify both pathogenic tissues and suitable proxy tissue/cell models (e.g., using enriched tissues/cells that are more easily accessible). The application of our GIDEE approach to GWAS datasets will facilitate follow-up in silico and in vitro research to determine the functional consequence(s) of their risk loci. </p

Integrating eQTL and GWAS data characterises established and identifies novel migraine risk loci

Migraine-a painful, throbbing headache disorder-is the most common complex brain disorder, yet its molecular mechanisms remain unclear. Genome-wide association studies (GWAS) have proven successful in identifying migraine risk loci; however, much work remains to identify the causal variants and genes. In this paper, we compared three transcriptome-wide association study (TWAS) imputation models-MASHR, elastic net, and SMultiXcan-to characterise established genome-wide significant (GWS) migraine GWAS risk loci, and to identify putative novel migraine risk gene loci. We compared the standard TWAS approach of analysing 49 GTEx tissues with Bonferroni correction for testing all genes present across all tissues (Bonferroni), to TWAS in five tissues estimated to be relevant to migraine, and TWAS with Bonferroni correction that took into account the correlation between eQTLs within each tissue (Bonferroni-matSpD). Elastic net models performed in all 49 GTEx tissues using Bonferroni-matSpD characterised the highest number of established migraine GWAS risk loci (n = 20) with GWS TWAS genes having colocalisation (PP4 > 0.5) with an eQTL. SMultiXcan in all 49 GTEx tissues identified the highest number of putative novel migraine risk genes (n = 28) with GWS differential expression at 20 non-GWS GWAS loci. Nine of these putative novel migraine risk genes were later found to be at and in linkage disequilibrium with true (GWS) migraine risk loci in a recent, more powerful migraine GWAS. Across all TWAS approaches, a total of 62 putative novel migraine risk genes were identified at 32 independent genomic loci. Of these 32 loci, 21 were true risk loci in the recent, more powerful migraine GWAS. Our results provide important guidance on the selection, use, and utility of imputation-based TWAS approaches to characterise established GWAS risk loci and identify novel risk gene loci.</p