Sayeem Been Zaman | Searcharxiv

arXiv2026

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances

Generative artificial intelligence (GenAI) is transforming bioinformatics by advancing genomics, proteomics, transcriptomics, structural biology, and drug discovery. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework, this review addresses six research questions to evaluate influential GenAI strategies in terms of methodological innovation, predictive performance, specialization, limitations, and data use. RQ1 shows that GenAI supports sequence analysis, molecular design, and integrative data modelling, often outperforming traditional methods through improved pattern recognition and generation. RQ2 finds that specialized architectures generally outperform general-purpose models because of domain-specific pretraining and context-aware design. RQ3 identifies benefits in molecular analysis and biological data integration, including improved accuracy and reduced analytical error. RQ4 reports advances in structural modelling, functional prediction, and synthetic data generation, supported by established benchmarks. RQ5 highlights key limitations, including poor scalability, data bias, and restricted generalizability, and recommends stronger evaluation and biologically grounded modelling. RQ6 shows that molecular datasets, including UniProtKB and ProteinNet12, cellular datasets, including CELLxGENE and GTEx, and textual resources, including PubMedQA and OMIM, support model training and generalization. Overall, this review demonstrates the growing potential of GenAI to advance computational biology through more accurate, specialized, and integrative bioinformatics analysis.

cs.CL↗

arXiv2025

DeepAgent: A Dual Stream Multi Agent Fusion for Robust Multimodal Deepfake Detection

The increasing use of synthetic media, particularly deepfakes, is an emerging challenge for digital content verification. Although recent studies use both audio and visual information, most integrate these cues within a single model, which remains vulnerable to modality mismatches, noise, and manipulation. To address this gap, we propose DeepAgent, an advanced multi-agent collaboration framework that simultaneously incorporates both visual and audio modalities for the effective detection of deepfakes. DeepAgent consists of two complementary agents. Agent-1 examines each video with a streamlined AlexNet-based CNN to identify the symbols of deepfake manipulation, while Agent-2 detects audio-visual inconsistencies by combining acoustic features, audio transcriptions from Whisper, and frame-reading sequences of images through EasyOCR. Their decisions are fused through a Random Forest meta-classifier that improves final performance by taking advantage of the different decision boundaries learned by each agent. This study evaluates the proposed framework using three benchmark datasets to demonstrate both component-level and fused performance. Agent-1 achieves a test accuracy of 94.35% on the combined Celeb-DF and FakeAVCeleb datasets. On the FakeAVCeleb dataset, Agent-2 and the final meta-classifier attain accuracies of 93.69% and 81.56%, respectively. In addition, cross-dataset validation on DeepFakeTIMIT confirms the robustness of the meta-classifier, which achieves a final accuracy of 97.49%, and indicates a strong capability across diverse datasets. These findings confirm that hierarchy-based fusion enhances robustness by mitigating the weaknesses of individual modalities and demonstrate the effectiveness of a multi-agent approach in addressing diverse types of manipulations in deepfakes.

cs.CV↗