Fang‐Xiang Wu

Minghan Fu, Fang-Xiang Wu

The learning rate is a critical hyperparameter for deep learning tasks since it determines the extent to which the model parameters are updated during the learning course. However, the choice of learning rates typically depends on empirical judgment, which may not result in satisfactory outcomes without intensive try-and-error experiments. In this study, we propose a novel learning rate adaptation scheme called QLABGrad. Without any user-specified hyperparameter, QLABGrad automatically determines the learning rate by optimizing the Quadratic Loss Approximation-Based (QLAB) function for a given gradient descent direction, where only one extra forward propagation is required. We theoretically prove the convergence of QLABGrad with a smooth Lipschitz condition on the loss function. Experiment results on multiple architectures, including MLP, CNN, and ResNet, on MNIST, CIFAR10, and ImageNet datasets, demonstrate that QLABGrad outperforms various competing schemes for deep learning.

Xiangru Tang, Zhuoyun Yu, Jiapeng Chen et al.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Ludi Li, Junbin Mao, Hanhe Lin et al.

Multi-pulse magnetic resonance imaging (MRI) is widely utilized for clinical practice such as Alzheimer's disease diagnosis. To train a robust model for multi-pulse MRI classification, it requires large and diverse data from various medical institutions while protecting privacy by preventing raw data sharing across institutions. Although federated learning (FL) is a feasible solution to address this issue, it poses challenges of model convergence due to the effect of data heterogeneity and substantial communication overhead due to large numbers of parameters transmitted within the model. To address these challenges, we propose CEPerFed, a communication-efficient personalized FL method. It mitigates the effect of data heterogeneity by incorporating client-side historical risk gradients and historical mean gradients to coordinate local and global optimization. The former is used to weight the contributions from other clients, enhancing the reliability of local updates, while the latter enforces consistency between local updates and the global optimization direction to ensure stable convergence across heterogeneous data distributions. To address the high communication overhead, we propose a hierarchical SVD (HSVD) strategy that transmits only the most critical information required for model updates. Experiments on five classification tasks demonstrate the effectiveness of the CEPerFed method. The code will be released upon acceptance at https://github.com/LD0416/CEPerFed.