Novel Knowledge-Guided Generative Methods for Synthetic Transcriptomic Data

As biomedical research increasingly relies on data-intensive tools, the quality and utility of datasets are critical. Challenges such as imbalances, biases, and ethical or legal constraints often limit access to high-quality data. Synthetic data generation can help overcome these limitations. Here, we present a comparative analysis of generative models for transcriptomic data, investigating strategies to incorporate prior biological knowledge via gene graphs. This ensures that synthetic data capture real-world gene patterns, maintaining their usefulness for downstream tasks. In particular, we introduce and benchmark three variants of the Generative Adversarial Network. Among the alternatives, MK-TGAN - an innovative multi-kernel, Graph Neural Network-based model - stands out for its performance in terms of both the realism and utility of the generated data. Unlike other methods, MK-TGAN leverages prior knowledge graphs by exploiting graph neural networks. Our results show that prior knowledge integration strategies improve performance, and that MK-TGAN consistently produces synthetic samples with superior realism and biological plausibility.

QuAIL: Quality-Aware Inertial Learning for Robust Training under Data Corruption

Tabular machine learning systems are frequently trained on data affected by non-uniform corruption, including noisy measurements, missing entries, and feature-specific biases. In practice, these defects are often documented only through column-level reliability indicators rather than instance-wise quality annotations, limiting the applicability of many robustness and cleaning techniques. We present QuAIL, a quality-informed training mechanism that incorporates feature reliability priors directly into the learning process. QuAIL augments existing models with a learnable feature-modulation layer whose updates are selectively constrained by a quality-dependent proximal regularizer, thereby inducing controlled adaptation across features of varying trustworthiness. This stabilizes optimization under structured corruption without explicit data repair or sample-level reweighting. Empirical evaluation across 50 classification and regression datasets demonstrates that QuAIL consistently improves average performance over neural baselines under both random and value-dependent corruption, with especially robust behavior in low-data and systematically biased settings. These results suggest that incorporating feature reliability information directly into optimization dynamics is a practical and effective approach for resilient tabular learning.

GeMM-GAN: A Multimodal Generative Model Conditioned on Histopathology Images and Clinical Descriptions for Gene Expression Profile Generation

Biomedical research increasingly relies on integrating diverse data modalities, including gene expression profiles, medical images, and clinical metadata. While medical images and clinical metadata are routinely collected in clinical practice, gene expression data presents unique challenges for widespread research use, mainly due to stringent privacy regulations and costly laboratory experiments. To address these limitations, we present GeMM-GAN, a novel Generative Adversarial Network conditioned on histopathology tissue slides and clinical metadata, designed to synthesize realistic gene expression profiles. GeMM-GAN combines a Transformer Encoder for image patches with a final Cross Attention mechanism between patches and text tokens, producing a conditioning vector to guide a generative model in generating biologically coherent gene expression profiles. We evaluate our approach on the TCGA dataset and demonstrate that our framework outperforms standard generative models and generates more realistic and functionally meaningful gene expression profiles, improving by more than 11\% the accuracy on downstream disease type prediction compared to current state-of-the-art generative models. Code will be available at: https://github.com/francescapia/GeMM-GAN