Yucheng Liao

Yucheng Liao, Jiajun Liang, Kaiqian Cui et al.

Instruction-based image editing through natural language has emerged as a powerful paradigm for intuitive visual manipulation. While recent models achieve impressive results on single edits, they suffer from severe quality degradation under multi-turn editing. Through systematic analysis, we identify progressive loss of high-frequency information as the primary cause of this quality degradation. We present FreqEdit, a training-free framework that enables stable editing across 10+ consecutive iterations. Our approach comprises three synergistic components: (1) high-frequency feature injection from reference velocity fields to preserve fine-grained details, (2) an adaptive injection strategy that spatially modulates injection strength for precise region-specific control, and (3) a path compensation mechanism that periodically recalibrates the editing trajectory to prevent over-constraint. Extensive experiments demonstrate that FreqEdit achieves superior performance in both identity preservation and instruction following compared to seven state-of-the-art baselines.

Yucheng Liao, Han Wen, Weinan E et al.

Data-independent acquisition mass spectrometry (DIA-MS) has established itself as a cornerstone of proteomic profiling and large-scale systems biology, offering unparalleled depth and reproducibility. Current DIA analysis frameworks, however, require semi-supervised training within each run for peptide-spectrum match (PSM) re-scoring. This approach is prone to overfitting and lacks generalizability across diverse species and experimental conditions. Here, we present DIA-CLIP, a pre-trained model shifting the DIA analysis paradigm from semi-supervised training to universal cross-modal representation learning. By integrating dual-encoder contrastive learning framework with encoder-decoder architecture, DIA-CLIP establishes a unified cross-modal representation for peptides and corresponding spectral features, achieving high-precision, zero-shot PSM inference. Extensive evaluations across diverse benchmarks demonstrate that DIA-CLIP consistently outperforms state-of-the-art tools, yielding up to a 45% increase in protein identification while achieving a 12% reduction in entrapment identifications. Moreover, DIA-CLIP holds immense potential for diverse practical applications, such as single-cell and spatial proteomics, where its enhanced identification depth facilitates the discovery of novel biomarkers and the elucidates of intricate cellular mechanisms.

Jiale Zhao, Pengzhi Mao, Kaifei Wang et al.

Deep learning has advanced mass spectrometry data interpretation, yet most models remain feature extractors rather than unified scoring frameworks. We present pUniFind, the first large-scale multimodal pre-trained model in proteomics that integrates end-to-end peptide-spectrum scoring with open, zero-shot de novo sequencing. Trained on over 100 million open search-derived spectra, pUniFind aligns spectral and peptide modalities via cross modality prediction and outperforms traditional engines across diverse datasets, particularly achieving a 42.6 percent increase in the number of identified peptides in immunopeptidomics. Supporting over 1,300 modifications, pUniFind identifies 60 percent more PSMs than existing de novo methods despite a 300-fold larger search space. A deep learning based quality control module further recovers 38.5 percent additional peptides including 1,891 mapped to the genome but absent from reference proteomes while preserving full fragment ion coverage. These results establish a unified, scalable deep learning framework for proteomic analysis, offering improved sensitivity, modification coverage, and interpretability.

Yucheng Liao, Yuanyu Wan, Chang Yao et al.

We investigate the problem of online learning with monotone and continuous DR-submodular reward functions, which has received great attention recently. To efficiently handle this problem, especially in the case with complicated decision sets, previous studies have proposed an efficient projection-free algorithm called Mono-Frank-Wolfe (Mono-FW) using $O(T)$ gradient evaluations and linear optimization steps in total. However, it only attains a $(1-1/e)$-regret bound of $O(T^{4/5})$. In this paper, we propose an improved projection-free algorithm, namely POBGA, which reduces the regret bound to $O(T^{3/4})$ while keeping the same computational complexity as Mono-FW. Instead of modifying Mono-FW, our key idea is to make a novel combination of a projection-based algorithm called online boosting gradient ascent, an infeasible projection technique, and a blocking technique. Furthermore, we consider the decentralized setting and develop a variant of POBGA, which not only reduces the current best regret bound of efficient projection-free algorithms for this setting from $O(T^{4/5})$ to $O(T^{3/4})$, but also reduces the total communication complexity from $O(T)$ to $O(\sqrt{T})$.