BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool

Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics research by effectively capturing biologically relevant relationships among molecular entities. While these methods are powerful for representing molecular interactions, there remains a need for tools specifically designed to effectively utilize these network representations across diverse downstream analyses. To fulfill this need, we introduce BioNeuralNet, a flexible and modular Python framework tailored for end-to-end network-based multi-omics data analysis. BioNeuralNet leverages Graph Neural Networks (GNNs) to learn biologically meaningful low-dimensional representations from multi-omics networks, converting these complex molecular networks into versatile embeddings. BioNeuralNet supports all major stages of multi-omics network analysis, including several network construction techniques, generation of low-dimensional representations, and a broad range of downstream analytical tasks. Its extensive utilities, including diverse GNN architectures, and compatibility with established Python packages (e.g., scikit-learn, PyTorch, NetworkX), enhance usability and facilitate quick adoption. BioNeuralNet is an open-source, user-friendly, and extensively documented framework designed to support flexible and reproducible multi-omics network analysis in precision medicine.

RWKV-UNet: Improving UNet with Long-Range Cooperation for Effective Medical Image Segmentation

In recent years, there have been significant advancements in deep learning for medical image analysis, especially with convolutional neural networks (CNNs) and transformer models. However, CNNs face limitations in capturing long-range dependencies while transformers suffer high computational complexities. To address this, we propose RWKV-UNet, a novel model that integrates the RWKV (Receptance Weighted Key Value) structure into the U-Net architecture. This integration enhances the model's ability to capture long-range dependencies and improve contextual understanding, which is crucial for accurate medical image segmentation. We build a strong encoder with developed inverted residual RWKV (IR-RWKV) blocks combining CNNs and RWKVs. We also propose a Cross-Channel Mix (CCM) module to improve skip connections with multi-scale feature fusion, achieving global channel information integration. Experiments on benchmark datasets, including Synapse, ACDC, BUSI, CVC-ClinicDB, CVC-ColonDB, Kvasir-SEG, ISIC 2017 and GLAS show that RWKV-UNet achieves state-of-the-art performance on various types of medical image segmentation. Additionally, smaller variants, RWKV-UNet-S and RWKV-UNet-T, balance accuracy and computational efficiency, making them suitable for broader clinical applications.

How Initial Connectivity Shapes Biologically Plausible Learning in Recurrent Neural Networks

The impact of initial connectivity on learning has been extensively studied in the context of backpropagation-based gradient descent, but it remains largely underexplored in biologically plausible learning settings. Focusing on recurrent neural networks (RNNs), we found that the initial weight magnitude significantly influences the learning performance of biologically plausible learning rules in a similar manner to its previously observed effect on training via backpropagation through time (BPTT). By examining the maximum Lyapunov exponent before and after training, we uncovered the greater demands that certain initialization schemes place on training to achieve desired information propagation properties. Consequently, we extended the recently proposed gradient flossing method, which regularizes the Lyapunov exponents, to biologically plausible learning and observed an improvement in learning performance. To our knowledge, we are the first to examine the impact of initialization on biologically plausible learning rules for RNNs and to subsequently propose a biologically plausible remedy. Such an investigation could lead to predictions about the influence of initial connectivity on learning dynamics and performance, as well as guide neuromorphic design.