Tao Chen

Xinzhe Zheng, Hao Du, Fanding Xu et al.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

Yongqi Huang, Peng Ye, Chenyu Huang et al.

Upcycled Mixture-of-Experts (MoE) models have shown great potential in various tasks by converting the original Feed-Forward Network (FFN) layers in pre-trained dense models into MoE layers. However, these models still suffer from significant parameter inefficiency due to the introduction of multiple experts. In this work, we propose a novel DeRS (Decompose, Replace, and Synthesis) paradigm to overcome this shortcoming, which is motivated by our observations about the unique redundancy mechanisms of upcycled MoE experts. Specifically, DeRS decomposes the experts into one expert-shared base weight and multiple expert-specific delta weights, and subsequently represents these delta weights in lightweight forms. Our proposed DeRS paradigm can be applied to enhance parameter efficiency in two different scenarios, including: 1) DeRS Compression for inference stage, using sparsification or quantization to compress vanilla upcycled MoE models; and 2) DeRS Upcycling for training stage, employing lightweight sparse or low-rank matrixes to efficiently upcycle dense models into MoE models. Extensive experiments across three different tasks show that the proposed methods can achieve extreme parameter efficiency while maintaining the performance for both training and compression of upcycled MoE models.

Zongheng Guo, Tao Chen, Manuela Ferrario

Photoplethysmogram (PPG) and electrocardiogram (ECG) are commonly recorded in intesive care unit (ICU) and operating room (OR). However, the high incidence of poor, incomplete, and inconsistent signal quality, can lead to false alarms or diagnostic inaccuracies. The methods explored so far suffer from limited generalizability, reliance on extensive labeled data, and poor cross-task transferability. To overcome these challenges, we introduce QualityFM, a novel multimodal foundation model for these physiological signals, designed to acquire a general-purpose understanding of signal quality. Our model is pre-trained on an large-scale dataset comprising over 21 million 30-second waveforms and 179,757 hours of data. Our approach involves a dual-track architecture that processes paired physiological signals of differing quality, leveraging a self-distillation strategy where an encoder for high-quality signals is used to guide the training of an encoder for low-quality signals. To efficiently handle long sequential signals and capture essential local quasi-periodic patterns, we integrate a windowed sparse attention mechanism within our Transformer-based model. Furthermore, a composite loss function, which combines direct distillation loss on encoder outputs with indirect reconstruction loss based on power and phase spectra, ensures the preservation of frequency-domain characteristics of the signals. We pre-train three models with varying parameter counts (9.6 M to 319 M) and demonstrate their efficacy and practical value through transfer learning on three distinct clinical tasks: false alarm of ventricular tachycardia detection, the identification of atrial fibrillation and the estimation of arterial blood pressure (ABP) from PPG and ECG signals.

Ke Wang, Gang Li, Junlan Chen et al.

China is the world's largest automotive market and is ambitious for autonomous vehicles (AVs) development. As one of the key goals of AVs, pedestrian safety is an important issue in China. Despite the rapid development of driverless technologies in recent years, there is a lack of researches on the adaptability of AVs to pedestrians. To fill the gap, this study would discuss the adaptability of current driverless technologies to China urban pedestrians by reviewing the latest researches. The paper firstly analyzed typical Chinese pedestrian behaviors and summarized the safety demands of pedestrians for AVs through articles and open database data, which are worked as the evaluation criteria. Then, corresponding driverless technologies are carefully reviewed. Finally, the adaptability would be given combining the above analyses. Our review found that autonomous vehicles have trouble in the occluded pedestrian environment and Chinese pedestrians do not accept AVs well. And more explorations should be conducted on standard human-machine interaction, interaction information overload avoidance, occluded pedestrians detection and nation-based receptivity research. The conclusions are very useful for motor corporations and driverless car researchers to place more attention on the complexity of the Chinese pedestrian environment, for transportation experts to protect pedestrian safety in the context of AVs, and for governors to think about making new pedestrians policies to welcome the upcoming driverless cars.