Modern image generation (IG) models have been shown to capture rich semantics valuable for image understanding (IU) tasks. However, the potential of IU models to improve IG performance remains uncharted. We address this issue using a token-based IG framework, which relies on effective tokenizers to map images into token sequences. Currently, pixel reconstruction (e.g., VQGAN) dominates the training objective for tokenizers. In contrast, our approach adopts the feature reconstruction objective, where tokenizers are trained by distilling knowledge from pretrained IU encoders. Comprehensive comparisons indicate that tokeniz-ers with strong IU capabilities achieve superior IG performance across a variety of metrics, datasets, tasks, and proposal networks.

Our objective in this paper is to probe large vision models to determine to what extent they'understand' different physical properties of the 3D scene depicted in an image. To this end, we make the following contributions: (i) We introduce a general and lightweight protocol to evaluate whether features of an off-the-shelf large vision model encode a number of physical'properties' of the 3D scene, by training discriminative classifiers on the features for these properties. The probes are applied on datasets of real images with annotations for the property.

In this work, we present a novel direction to build an image tokenizer directly on top of a frozen vision foundation model, which is a largely underexplored area. Specifically, we employ a frozen vision foundation model as the encoder of our tokenizer. To enhance its effectiveness, we introduce two key components: (1) a region-adaptive quantization framework that reduces redundancy in the pre-trained features on regular 2D grids, and (2) a semantic reconstruction objective that aligns the tokenizer's outputs with the foundation model's representations to preserve semantic fidelity. Based on these designs, our proposed image tokenizer, VFMTok, achieves substantial improvements in image reconstruction and generation quality, while also enhancing token efficiency. It further boosts autoregressive (AR) generation -- achieving a gFID of 1.36 on ImageNet benchmarks, while accelerating model convergence by three times, and enabling high-fidelity class-conditional synthesis without the need for classifier-free guidance (CFG). The code is available at https://github.com/CVMI-Lab/VFMTok.

Modern image generation (IG) models have been shown to capture rich semantics valuable for image understanding (IU) tasks. However, the potential of IU models to improve IG performance remains uncharted. We address this issue using a token-based IG framework, which relies on effective tokenizers to map images into token sequences. Currently, pixel reconstruction (e.g., VQGAN) dominates the training objective for tokenizers. In contrast, our approach adopts the feature reconstruction objective, where tokenizers are trained by distilling knowledge from pretrained IU encoders. Comprehensive comparisons indicate that tokeniz-ers with strong IU capabilities achieve superior IG performance across a variety of metrics, datasets, tasks, and proposal networks.

We present CELL-E 2, a novel bidirectional transformer that can generate images depicting protein subcellular localization from the amino acid sequences (and vice versa). Protein localization is a challenging problem that requires integrating sequence and image information, which most existing methods ignore. CELL-E 2 extends the work of CELL-E, not only capturing the spatial complexity of protein localization and produce probability estimates of localization atop a nucleus image, but also being able to generate sequences from images, enabling de novo protein design. We train and finetune CELL-E 2 on two large-scale datasets of human proteins. We also demonstrate how to use CELL-E 2 to create hundreds of novel nuclear localization signals (NLS).

In this section, we show additional examples of generated images by our Contextual RQ-Transformer. We use 1.4B parameters of Contextual RQ-Transformer trained on ImageNet for class-conditional

While multiplex immunofluorescence (mIF) imaging provides deep, spatially-resolved molecular data, integrating this information with the morphological standard of Hematoxylin & Eosin (H&E) can be very important for obtaining complementary information about the underlying tissue. Generating a virtual H&E stain from mIF data offers a powerful solution, providing immediate morphological context. Crucially, this approach enables the application of the vast ecosystem of H&E-based computer-aided diagnosis (CAD) tools to analyze rich molecular data, bridging the gap between molecular and morphological analysis. In this work, we investigate the use of a multi-level Vector-Quantized Generative Adversarial Network (VQGAN) to create high-fidelity virtual H&E stains from mIF images. We rigorously evaluated our VQGAN against a standard conditional GAN (cGAN) baseline on two publicly available colorectal cancer datasets, assessing performance on both image similarity and functional utility for downstream analysis. Our results show that while both architectures produce visually plausible images, the virtual stains generated by our VQGAN provide a more effective substrate for computer-aided diagnosis. Specifically, downstream nuclei segmentation and semantic preservation in tissue classification tasks performed on VQGAN-generated images demonstrate superior performance and agreement with ground-truth analysis compared to those from the cGAN. This work establishes that a multi-level VQGAN is a robust and superior architecture for generating scientifically useful virtual stains, offering a viable pathway to integrate the rich molecular data of mIF into established and powerful H&E-based analytical workflows.