Yifan Shang | Searcharxiv

arXiv2026

scMIR: a vision-language foundation model for single-cell light microscopy image representation

Single-cell light microscopy images have become an important data source for characterizing cell phenotypes, but their complexity and heterogeneity pose challenges to high-throughput automated analysis. Existing representation learning methods mostly rely on task-oriented modeling, which is limited by specific datasets and predefined tasks, making them difficult to generalize across different cell types and microscopy modalities, and experimental conditions. Although general-purpose methods have improved the generalization ability of image representation in recent years, their limited utilization of experimental background and biological context information still poses challenges in complex phenotypic analysis. Here, we propose scMIR, a vision-language foundation model for single-cell light microscopy image representation. By synergistically combining self-supervised image reconstruction with text-guided cross-modal alignment, scMIR can simultaneously encode morphological and biological semantic information in a unified representation space. scMIR is pre-trained on 207,957 image-text pairs, covering various cell types, microscopy modalities, and perturbation conditions. scMIR outperforms existing general models and task-oriented methods as systematically evaluated on various complex tasks using 16 benchmark datasets, including cell classification, clustering, phenotype inference, and batch effect correction tasks. Furthermore, scMIR shows a strong generalization ability across various tasks without requiring task-specific fine-tuning. With its unique advantages, we envision scMIR may promote the standardization and automation of high-throughput phenotyping workflows through supporting various downstream analysis tasks.

cs.CV↗

arXiv2026

Towards Understanding Continual Factual Knowledge Acquisition of Language Models: From Theory to Algorithm

Continual Pre-Training (CPT) is essential for enabling Language Models (LMs) to integrate new knowledge without erasing old. While classical CPT techniques like data replay have become the standard paradigm, the mechanisms underlying how LMs acquire and retain facts over time, termed as continual Factual Knowledge Acquisition (cFKA), remain unclear. In this work, we present a theoretical framework that characterizes the training dynamics of cFKA using a single-layer Transformer, offering a unified explanation for the behavior of representative CPT methods. Our analysis reveals that regularization-based methods merely adjust the convergence rate of parameters without altering the inherent forgetting tendency, whereas data replay methods succeed in shifting convergence dynamics and stabilizing pretrained knowledge. Building on these insights, we propose a novel generative data replay approach, called \textbf{S}electing \textbf{T}okens via attenti\textbf{O}n \textbf{C}ontribution~(STOC), which identifies influential factual snippets to guide replay data generation. Extensive experiments on both synthetic and real-world datasets validate our findings and demonstrate that STOC effectively enhances cFKA by mitigating catastrophic forgetting.

cs.CL↗