Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

Resting-state functional magnetic resonance imaging (rs-fMRI) and its derived functional connectivity networks (FCNs) have become critical for understanding neurological disorders. However, collaborative analyses and the generalizability of models still face significant challenges due to privacy regulations and the non-IID (non-independent and identically distributed) property of multiple data sources. To mitigate these difficulties, we propose Domain Adversarial Federated Learning (DAFed), a novel federated deep learning framework specifically designed for non-IID fMRI data analysis in multi-site settings. DAFed addresses these challenges through feature disentanglement, decomposing the latent feature space into domain-invariant and domain-specific components, to ensure robust global learning while preserving local data specificity. Furthermore, adversarial training facilitates effective knowledge transfer between labeled and unlabeled datasets, while a contrastive learning module enhances the global representation of domain-invariant features. We evaluated DAFed on the diagnosis of autism spectrum disorder (ASD) and further validated its generalizability in the classification of Alzheimer's disease (AD), demonstrating its superior classification accuracy compared to state-of-the-art methods. Additionally, an enhanced Score-CAM module identifies key brain regions and functional connectivity significantly associated with ASD and mild cognitive impairment (MCI), respectively, uncovering shared neurobiological patterns across sites. These findings highlight the potential of DAFed to advance multi-site collaborative research in neuroimaging while protecting data confidentiality. Introduction Resting-state functional magnetic resonance imaging (rs-fMRI) has emerged as a powerful and non-invasive technique for detecting abnormal brain activity [1]. Functional connectivity networks (FCNs), derived from rs-fMRI data, quantify temporal correlations between functional interactions in different brain regions, which are extensively utilized in studies of neurological disorders and mental illnesses [2, 3]. Recently, deep learning approaches have shown remarkable potential in analyzing fMRI data and FCNs, enabling significant breakthroughs in understanding brain function [4, 5]. Despite significant advancements in deep learning models, concerns over patient privacy and legal restrictions limit data sharing across institutions. This limitation poses challenges to the reproducibility and generalizability of data-driven approaches across diverse datasets [6, 7].

Building LiDAR generative models holds promise as powerful data priors for restoration, scene manipulation, and scalable simulation in autonomous mobile robots. In recent years, approaches using diffusion models have emerged, significantly improving training stability and generation quality. Despite the success of diffusion models, generating high-quality samples requires numerous iterations of running neural networks, and the increasing computational cost can pose a barrier to robotics applications. To address this challenge, this paper presents R2Flow, a fast and high-fidelity generative model for LiDAR data. Our method is based on rectified flows that learn straight trajectories, simulating data generation with much fewer sampling steps against diffusion models. We also propose a efficient Transformer-based model architecture for processing the image representation of LiDAR range and reflectance measurements. Our experiments on the unconditional generation of the KITTI-360 dataset demonstrate the effectiveness of our approach in terms of both efficiency and quality.

Combining end-to-end speech translation (ST) and non-autoregressive (NAR) generation is promising in language and speech processing for their advantages of less error propagation and low latency. In this paper, we investigate the potential of connectionist temporal classification (CTC) for non-autoregressive speech translation (NAST). In particular, we develop a model consisting of two encoders that are guided by CTC to predict the source and target texts, respectively. Introducing CTC into NAST on both language sides has obvious challenges: 1) the conditional independent generation somewhat breaks the interdependency among tokens, and 2) the monotonic alignment assumption in standard CTC does not hold in translation tasks. In response, we develop a prediction-aware encoding approach and a cross-layer attention approach to address these issues. We also use curriculum learning to improve convergence of training. Experiments on the MuST-C ST benchmarks show that our NAST model achieves an average BLEU score of 29.5 with a speed-up of 5.67$\times$, which is comparable to the autoregressive counterpart and even outperforms the previous best result of 0.9 BLEU points.