Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies.

Neural Information Processing Systems http://nips.cc/

Federated learning has attracted increasing attention due to the promise of balancing privacy and large-scale learning; numerous approaches have been proposed. However, most existing approaches focus on problems with balanced data, and prediction performance is far from satisfactory for many real-world applications where the number of samples in different classes is highly imbalanced. To address this challenging problem, we developed a novel federated learning method for imbalanced data by directly optimizing the area under curve (AUC) score. In particular, we formulate the AUC maximization problem as a federated compositional minimax optimization problem, develop a local stochastic compositional gradient descent ascent with momentum algorithm, and provide bounds on the computational and communication complexities of our algorithm. To the best of our knowledge, this is the first work to achieve such favorable theoretical results. Finally, extensive experimental results confirm the efficacy of our method.

Neural Information Processing Systems http://nips.cc/