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Bio-Inspired Generative Network with Knowledge Integration
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DOI：10.3390/app152412918.png)
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Abstract
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Generating realistic synthetic gene expression data that captures the complex interdependencies and biological context of cellular systems remains a significant challenge. Existing methods often struggle to reproduce intricate co-expression patterns and incorporate prior biological knowledge effectively. To address these limitations, we propose BioGen-KI, a novel bio-inspired generative network with knowledge integration. Our framework leverages a hybrid deep learning architecture that integrates embeddings learned from biological knowledge graphs (e.g., gene regulatory networks, pathway databases) with a conditional generative adversarial network (cGAN). The knowledge graph embeddings guide the generator to produce synthetic expression profiles that respect known biological relationships, while conditioning on contextual information (e.g., cell type, experimental condition) allows for targeted data synthesis. Furthermore, we introduce a biologically informed discriminator that evaluates not only the statistical realism but also the biological plausibility of the generated data, encouraging the preservation of pathway coherence and relevant gene interactions. We demonstrate the efficacy of BioGen-KI by generating synthetic gene expression datasets that exhibit improved statistical similarity to real data and, critically, better preservation of biologically meaningful relationships compared to baseline GAN models and methods relying solely on statistical characteristics. Evaluation on downstream tasks, such as clustering and differential gene expression analysis, highlights the utility of BioGen-KI-generated data for enhancing the robustness and interpretability of biological data analysis. This work presents a significant step towards generating more biologically faithful synthetic gene expression data for research and development.
Keywords:
gene expression
synthetic data generation
generative adversarial networks (GANs)
knowledge graph integration
biological networks
data augmentation
machine learning
deep learning
bioinformatics
computational biology
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