Daily Papers

Tables are pervasive in diverse documents, making table recognition (TR) a fundamental task in document analysis. Existing modular TR pipelines separately model table structure and content, leading to suboptimal integration and complex workflows. End-to-end approaches rely heavily on large-scale TR data and struggle in data-constrained scenarios. To address these issues, we propose TDATR (Table Detail-Aware Table Recognition) improves end-to-end TR through table detail-aware learning and cell-level visual alignment. TDATR adopts a ``perceive-then-fuse'' strategy. The model first performs table detail-aware learning to jointly perceive table structure and content through multiple structure understanding and content recognition tasks designed under a language modeling paradigm. These tasks can naturally leverage document data from diverse scenarios to enhance model robustness. The model then integrates implicit table details to generate structured HTML outputs, enabling more efficient TR modeling when trained with limited data. Furthermore, we design a structure-guided cell localization module integrated into the end-to-end TR framework, which efficiently locates cell and strengthens vision-language alignment. It enhances the interpretability and accuracy of TR. We achieve state-of-the-art or highly competitive performance on seven benchmarks without dataset-specific fine-tuning.

Aligning visual features with language embeddings is a key challenge in vision-language models (VLMs). The performance of such models hinges on having a good connector that maps visual features generated by a vision encoder to a shared embedding space with the LLM while preserving semantic similarity. Existing connectors, such as multilayer perceptrons (MLPs), often produce out-of-distribution or noisy inputs, leading to misalignment between the modalities. In this work, we propose a novel vision-text alignment method, AlignVLM, that maps visual features to a weighted average of LLM text embeddings. Our approach leverages the linguistic priors encoded by the LLM to ensure that visual features are mapped to regions of the space that the LLM can effectively interpret. AlignVLM is particularly effective for document understanding tasks, where scanned document images must be accurately mapped to their textual content. Our extensive experiments show that AlignVLM achieves state-of-the-art performance compared to prior alignment methods. We provide further analysis demonstrating improved vision-text feature alignment and robustness to noise.

We study the intriguing connection between visual data, deep networks, and the brain. Our method creates a universal channel alignment by using brain voxel fMRI response prediction as the training objective. We discover that deep networks, trained with different objectives, share common feature channels across various models. These channels can be clustered into recurring sets, corresponding to distinct brain regions, indicating the formation of visual concepts. Tracing the clusters of channel responses onto the images, we see semantically meaningful object segments emerge, even without any supervised decoder. Furthermore, the universal feature alignment and the clustering of channels produce a picture and quantification of how visual information is processed through the different network layers, which produces precise comparisons between the networks.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

Multimodal large language models (MLLMs) trained with visual instruction tuning have achieved strong performance across diverse tasks, yet they remain limited in vision-centric tasks such as object counting or spatial reasoning. We attribute this gap to the prevailing text-only supervision paradigm, which provides only indirect guidance for the visual pathway and often leads MLLMs to discard fine-grained visual details during training. In this paper, we present VIsual Representation ALignment (VIRAL), a simple yet effective regularization strategy that aligns the internal visual representations of MLLMs with those of pre-trained vision foundation models (VFMs). By explicitly enforcing this alignment, VIRAL enables the model not only to retain critical visual details from the input vision encoder but also to complement additional visual knowledge from VFMs, thereby enhancing its ability to reason over complex visual inputs. Our experiments demonstrate consistent improvements across all tasks on widely adopted multimodal benchmarks. Furthermore, we conduct comprehensive ablation studies to validate the key design choices underlying our framework. We believe this simple finding opens up an important direction for the effective integration of visual information in training MLLMs.

Cats and humans differ in ocular anatomy. Most notably, Felis Catus (domestic cats) have vertically elongated pupils linked to ambush predation; yet, how such specializations manifest in downstream visual representations remains incompletely understood. We present a unified, frozen-encoder benchmark that quantifies feline-human cross-species representational alignment in the wild, across convolutional networks, supervised Vision Transformers, windowed transformers, and self-supervised ViTs (DINO), using layer-wise Centered Kernel Alignment (linear and RBF) and Representational Similarity Analysis, with additional distributional and stability tests reported in the paper. Across models, DINO ViT-B/16 attains the most substantial alignment (mean CKA-RBF approx0.814, mean CKA-linear approx0.745, mean RSA approx0.698), peaking at early blocks, indicating that token-level self-supervision induces early-stage features that bridge species-specific statistics. Supervised ViTs are competitive on CKA yet show weaker geometric correspondence than DINO (e.g., ViT-B/16 RSA approx0.53 at block8; ViT-L/16 approx0.47 at block14), revealing depth-dependent divergences between similarity and representational geometry. CNNs remain strong baselines but below plain ViTs on alignment, and windowed transformers underperform plain ViTs, implicating architectural inductive biases in cross-species alignment. Results indicate that self-supervision coupled with ViT inductive biases yields representational geometries that more closely align feline and human visual systems than widely used CNNs and windowed Transformers, providing testable neuroscientific hypotheses about where and how cross-species visual computations converge. We release our code and dataset for reference and reproducibility.

Recent advancements in text-to-image models, particularly diffusion models, have shown significant promise. However, compositional text-to-image models frequently encounter difficulties in generating high-quality images that accurately align with input texts describing multiple objects, variable attributes, and intricate spatial relationships. To address this limitation, we employ large vision-language models (LVLMs) for multi-dimensional assessment of the alignment between generated images and their corresponding input texts. Utilizing this assessment, we fine-tune the diffusion model to enhance its alignment capabilities. During the inference phase, an initial image is produced using the fine-tuned diffusion model. The LVLM is then employed to pinpoint areas of misalignment in the initial image, which are subsequently corrected using the image editing algorithm until no further misalignments are detected by the LVLM. The resultant image is consequently more closely aligned with the input text. Our experimental results validate that the proposed methodology significantly improves text-image alignment in compositional image generation, particularly with respect to object number, attribute binding, spatial relationships, and aesthetic quality.

Existing methods for reconstructing animatable 3D animals from videos typically rely on sparse semantic keypoints to fit parametric models. However, obtaining such keypoints is labor-intensive, and keypoint detectors trained on limited animal data are often unreliable. To address this, we propose 4D-Animal, a novel framework that reconstructs animatable 3D animals from videos without requiring sparse keypoint annotations. Our approach introduces a dense feature network that maps 2D representations to SMAL parameters, enhancing both the efficiency and stability of the fitting process. Furthermore, we develop a hierarchical alignment strategy that integrates silhouette, part-level, pixel-level, and temporal cues from pre-trained 2D visual models to produce accurate and temporally coherent reconstructions across frames. Extensive experiments demonstrate that 4D-Animal outperforms both model-based and model-free baselines. Moreover, the high-quality 3D assets generated by our method can benefit other 3D tasks, underscoring its potential for large-scale applications. The code is released at https://github.com/zhongshsh/4D-Animal.

It has recently been discovered that using a pre-trained vision-language model (VLM), e.g., CLIP, to align a whole query image with several finer text descriptions generated by a large language model can significantly enhance zero-shot performance. However, in this paper, we empirically find that the finer descriptions tend to align more effectively with local areas of the query image rather than the whole image, and then we theoretically validate this finding. Thus, we present a method called weighted visual-text cross alignment (WCA). This method begins with a localized visual prompting technique, designed to identify local visual areas within the query image. The local visual areas are then cross-aligned with the finer descriptions by creating a similarity matrix using the pre-trained VLM. To determine how well a query image aligns with each category, we develop a score function based on the weighted similarities in this matrix. Extensive experiments demonstrate that our method significantly improves zero-shot performance across various datasets, achieving results that are even comparable to few-shot learning methods.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

A high-performing, general-purpose visual understanding model should map visual inputs to a taxonomic tree of labels, identify novel categories beyond the training set for which few or no publicly available images exist. Large Multimodal Models (LMMs) have achieved remarkable progress in fine-grained visual recognition (FGVR) for known categories. However, they remain limited in hierarchical visual recognition (HVR) that aims at predicting consistent label paths from coarse to fine categories, especially for novel categories. To tackle these challenges, we propose Taxonomy-Aware Representation Alignment (TARA), a simple yet effective strategy to inject taxonomic knowledge into LMMs. TARA leverages representations from biology foundation models (BFMs) that encode rich biological relationships through hierarchical contrastive learning. By aligning the intermediate representations of visual features with those of BFMs, LMMs are encouraged to extract discriminative visual cues well structured in the taxonomy tree. Additionally, we align the representations of the first answer token with the ground-truth label, flexibly bridging the gap between contextualized visual features and categories of varying granularity according to user intent. Experiments demonstrate that TARA consistently enhances LMMs' hierarchical consistency and leaf node accuracy, enabling reliable recognition of both known and novel categories within complex biological taxonomies. Code is available at https://github.com/PKU-ICST-MIPL/TARA_CVPR2026.

Accurate segmentation of regions of interest in biomedical images holds substantial value in image analysis. Although several foundation models for biomedical segmentation have currently achieved excellent performance on certain datasets, they typically demonstrate sub-optimal performance on unseen domain data. We owe the deficiency to lack of vision-language knowledge before segmentation. Multimodal Large Language Models (MLLMs) bring outstanding understanding and reasoning capabilities to multimodal tasks, which inspires us to leverage MLLMs to inject Vision-Language Knowledge (VLK), thereby enabling vision models to demonstrate superior generalization capabilities on cross-domain datasets. In this paper, we propose using MLLMs to guide SAM in learning microscopy crose-domain data, unifying Segment Anything in Microscopy, named uLLSAM. Specifically, we propose the Vision-Language Semantic Alignment (VLSA) module, which injects VLK into Segment Anything Model (SAM). We find that after SAM receives global VLK prompts, its performance improves significantly, but there are deficiencies in boundary contour perception. Therefore, we further propose Semantic Boundary Regularization (SBR) to prompt SAM. Our method achieves performance improvements of 7.71% in Dice and 12.10% in SA across 9 in-domain microscopy datasets, achieving state-of-the-art performance. Our method also demonstrates improvements of 6.79% in Dice and 10.08% in SA across 10 out-ofdomain datasets, exhibiting strong generalization capabilities. Code is available at https://github.com/ieellee/uLLSAM.

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

Existing image-text modality alignment in Vision Language Models (VLMs) treats each text token equally in an autoregressive manner. Despite being simple and effective, this method results in sub-optimal cross-modal alignment by over-emphasizing the text tokens that are less correlated with or even contradictory with the input images. In this paper, we advocate for assigning distinct contributions for each text token based on its visual correlation. Specifically, we present by contrasting image inputs, the difference in prediction logits on each text token provides strong guidance of visual correlation. We therefore introduce Contrastive ALignment (CAL), a simple yet effective re-weighting strategy that prioritizes training visually correlated tokens. Our experimental results demonstrate that CAL consistently improves different types of VLMs across different resolutions and model sizes on various benchmark datasets. Importantly, our method incurs minimal additional computational overhead, rendering it highly efficient compared to alternative data scaling strategies. Codes are available at https://github.com/foundation-multimodal-models/CAL.

Vision-language models like CLIP have shown impressive capabilities in aligning images and text, but they often struggle with lengthy and detailed text descriptions because of their training focus on short and concise captions. We present GOAL (Global-local Object Alignment Learning), a novel fine-tuning method that enhances CLIP's ability to handle lengthy text by leveraging both global and local semantic alignments between image and lengthy text. Our approach consists of two key components: Local Image-Sentence Matching (LISM), which identifies corresponding pairs between image segments and descriptive sentences, and Token Similarity-based Learning (TSL), which efficiently propagates local element attention through these matched pairs. Evaluating GOAL on three new benchmarks for image-lengthy text retrieval, we demonstrate significant improvements over baseline CLIP fine-tuning, establishing a simple yet effective approach for adapting CLIP to detailed textual descriptions. Through extensive experiments, we show that our method's focus on local semantic alignment alongside global context leads to more nuanced and representative embeddings, particularly beneficial for tasks requiring fine-grained understanding of lengthy text descriptions.

Visual preference alignment involves training Large Vision-Language Models (LVLMs) to predict human preferences between visual inputs. This is typically achieved by using labeled datasets of chosen/rejected pairs and employing optimization algorithms like direct preference optimization (DPO). Existing visual alignment methods, primarily designed for single-image scenarios, struggle to effectively handle the complexity of multi-image tasks due to the scarcity of diverse training data and the high cost of annotating chosen/rejected pairs. We present Multi-Image Augmented Direct Preference Optimization (MIA-DPO), a visual preference alignment approach that effectively handles multi-image inputs. MIA-DPO mitigates the scarcity of diverse multi-image training data by extending single-image data with unrelated images arranged in grid collages or pic-in-pic formats, significantly reducing the costs associated with multi-image data annotations. Our observation reveals that attention values of LVLMs vary considerably across different images. We use attention values to identify and filter out rejected responses the model may have mistakenly focused on. Our attention-aware selection for constructing the chosen/rejected pairs without relying on (i) human annotation, (ii) extra data, and (iii) external models or APIs. MIA-DPO is compatible with various architectures and outperforms existing methods on five multi-image benchmarks, achieving an average performance boost of 3.0% on LLaVA-v1.5 and 4.3% on the recent InternLM-XC2.5. Moreover, MIA-DPO has a minimal effect on the model's ability to understand single images.

Positional embeddings (PE) play a crucial role in Vision Transformers (ViTs) by providing spatial information otherwise lost due to the permutation invariant nature of self attention. While absolute positional embeddings (APE) have shown theoretical advantages over relative positional embeddings (RPE), particularly due to the ability of sinusoidal functions to preserve spatial inductive biases like monotonicity and shift invariance, a fundamental challenge arises when mapping a 2D grid to a 1D sequence. Existing methods have mostly overlooked or never explored the impact of patch ordering in positional embeddings. To address this, we propose LOOPE, a learnable patch-ordering method that optimizes spatial representation for a given set of frequencies, providing a principled approach to patch order optimization. Empirical results show that our PE significantly improves classification accuracy across various ViT architectures. To rigorously evaluate the effectiveness of positional embeddings, we introduce the "Three Cell Experiment", a novel benchmarking framework that assesses the ability of PEs to retain relative and absolute positional information across different ViT architectures. Unlike standard evaluations, which typically report a performance gap of 4 to 6% between models with and without PE, our method reveals a striking 30 to 35% difference, offering a more sensitive diagnostic tool to measure the efficacy of PEs. Our experimental analysis confirms that the proposed LOOPE demonstrates enhanced effectiveness in retaining both relative and absolute positional information.

From a falcon detecting prey to humans recognizing faces, many species exhibit extraordinary abilities in rapid visual localization and classification. These are made possible by a specialized retinal region called the fovea, which provides high acuity at the center of vision while maintaining lower resolution in the periphery. This distinctive spatial organization, preserved along the early visual pathway through retinotopic mapping, is fundamental to biological vision, yet remains largely unexplored in machine learning. Our study investigates how incorporating foveated retinotopy may benefit deep convolutional neural networks (CNNs) in image classification tasks. By implementing a foveated retinotopic transformation in the input layer of standard ResNet models and re-training them, we maintain comparable classification accuracy while enhancing the network's robustness to scale and rotational perturbations. Although this architectural modification introduces increased sensitivity to fixation point shifts, we demonstrate how this apparent limitation becomes advantageous: variations in classification probabilities across different gaze positions serve as effective indicators for object localization. Our findings suggest that foveated retinotopic mapping encodes implicit knowledge about visual object geometry, offering an efficient solution to the visual search problem - a capability crucial for many living species.

Recent advances in Large Multi-modal Models (LMMs) have demonstrated their remarkable success as general-purpose multi-modal assistants, with particular focuses on holistic image- and video-language understanding. Conversely, less attention has been given to scaling fine-grained pixel-level understanding capabilities, where the models are expected to realize pixel-level alignment between visual signals and language semantics. Some previous studies have applied LMMs to related tasks such as region-level captioning and referring expression segmentation. However, these models are limited to performing either referring or segmentation tasks independently and fail to integrate these fine-grained perception capabilities into visual reasoning. To bridge this gap, we propose UniPixel, a large multi-modal model capable of flexibly comprehending visual prompt inputs and generating mask-grounded responses. Our model distinguishes itself by seamlessly integrating pixel-level perception with general visual understanding capabilities. Specifically, UniPixel processes visual prompts and generates relevant masks on demand, and performs subsequent reasoning conditioning on these intermediate pointers during inference, thereby enabling fine-grained pixel-level reasoning. The effectiveness of our approach has been verified on 10 benchmarks across a diverse set of tasks, including pixel-level referring/segmentation and object-centric understanding in images/videos. A novel PixelQA task that jointly requires referring, segmentation, and question answering is also designed to verify the flexibility of our method.

The crux of learning vision-language models is to extract semantically aligned information from visual and linguistic data. Existing attempts usually face the problem of coarse alignment, e.g., the vision encoder struggles in localizing an attribute-specified object. In this work, we propose an embarrassingly simple approach to better align image and text features with no need of additional data formats other than image-text pairs. Concretely, given an image and its paired text, we manage to parse objects (e.g., cat) and attributes (e.g., black) from the description, which are highly likely to exist in the image. It is noteworthy that the parsing pipeline is fully automatic and thus enjoys good scalability. With these parsed semantics as supervision signals, we can complement the commonly used image-text contrastive loss with the multi-tag classification loss. Extensive experimental results on a broad suite of semantic segmentation datasets substantiate the average 3.65\% improvement of our framework over existing alternatives. Furthermore, the visualization results indicate that attribute supervision makes vision-language models accurately localize attribute-specified objects. Project page and code can be found at https://qinying-liu.github.io/Tag-Align.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

The alignment of vision-language representations endows current Vision-Language Models (VLMs) with strong multi-modal reasoning capabilities. However, the interpretability of the alignment component remains uninvestigated due to the difficulty in mapping the semantics of multi-modal representations into a unified concept set. To address this problem, we propose VL-SAE, a sparse autoencoder that encodes vision-language representations into its hidden activations. Each neuron in its hidden layer correlates to a concept represented by semantically similar images and texts, thereby interpreting these representations with a unified concept set. To establish the neuron-concept correlation, we encourage semantically similar representations to exhibit consistent neuron activations during self-supervised training. First, to measure the semantic similarity of multi-modal representations, we perform their alignment in an explicit form based on cosine similarity. Second, we construct the VL-SAE with a distance-based encoder and two modality-specific decoders to ensure the activation consistency of semantically similar representations. Experiments across multiple VLMs (e.g., CLIP, LLaVA) demonstrate the superior capability of VL-SAE in interpreting and enhancing the vision-language alignment. For interpretation, the alignment between vision and language representations can be understood by comparing their semantics with concepts. For enhancement, the alignment can be strengthened by aligning vision-language representations at the concept level, contributing to performance improvements in downstream tasks, including zero-shot image classification and hallucination elimination. Codes are available at https://github.com/ssfgunner/VL-SAE.

Vision-Language Models (VLMs) combine a vision encoder and a large language model (LLM) through alignment training, showing strong performance on multimodal tasks. A central component in this architecture is the projection layer, which maps visual features into the LLM's embedding space. Despite its importance, its ability to generalize to unseen visual concepts has not been systematically evaluated. To address this, we propose a benchmark for evaluating projection-layer generalization. We adapt object detection datasets (rich in fine-grained annotations) into a prompting format and design train/test splits with disjoint label sets, enabling precise control over seen and unseen concept separation. Experimental results show that the projection layer retains about 79 to 88 percent of the performance on unseen classes compared to seen ones across various settings, suggesting a non-trivial level of generalization even without explicit alignment supervision on those concepts. We further analyze this behavior through a mechanistic interpretability lens. Our findings indicate that the feed-forward network in the projection layer functions like a key-value memory, processing seen and unseen tokens in similar ways. This study introduces a new evaluation framework for alignment generalization and highlights the potential for efficient VLM training with limited aligned data.

We study the task of extending the large language model (LLM) into a vision-language instruction-following model. This task is crucial but challenging since the LLM is trained on text modality only, making it hard to effectively digest the visual modality. To address this, existing methods typically train a visual adapter to align the representation between a pre-trained vision transformer (ViT) and the LLM by a generative image captioning loss. However, we find that the generative objective can only produce weak alignment for vision and language, making the aligned vision-language model very hungry for the instruction fine-tuning data. In this paper, we propose CG-VLM that applies both Contrastive and Generative alignment objectives to effectively align the representation of ViT and LLM. Different from image level and sentence level alignment in common contrastive learning settings, CG-VLM aligns the image-patch level features and text-token level embeddings, which, however, is very hard to achieve as no explicit grounding patch-token relation provided in standard image captioning datasets. To address this issue, we propose to maximize the averaged similarity between pooled image-patch features and text-token embeddings. Extensive experiments demonstrate that the proposed CG-VLM produces strong vision-language alignment and is an efficient instruction learner. For example, using only 10% instruction tuning data, we reach 95% performance of state-of-the-art method LLaVA [29] on the zero-shot ScienceQA-Image benchmark.

Vision foundation models have been explored recently to build general-purpose vision systems. However, predominant paradigms, driven by casting instance-level tasks as an object-word alignment, bring heavy cross-modality interaction, which is not effective in prompting object detection and visual grounding. Another line of work that focuses on pixel-level tasks often encounters a large annotation gap of things and stuff, and suffers from mutual interference between foreground-object and background-class segmentation. In stark contrast to the prevailing methods, we present APE, a universal visual perception model for aligning and prompting everything all at once in an image to perform diverse tasks, i.e., detection, segmentation, and grounding, as an instance-level sentence-object matching paradigm. Specifically, APE advances the convergence of detection and grounding by reformulating language-guided grounding as open-vocabulary detection, which efficiently scales up model prompting to thousands of category vocabularies and region descriptions while maintaining the effectiveness of cross-modality fusion. To bridge the granularity gap of different pixel-level tasks, APE equalizes semantic and panoptic segmentation to proxy instance learning by considering any isolated regions as individual instances. APE aligns vision and language representation on broad data with natural and challenging characteristics all at once without task-specific fine-tuning. The extensive experiments on over 160 datasets demonstrate that, with only one-suit of weights, APE outperforms (or is on par with) the state-of-the-art models, proving that an effective yet universal perception for anything aligning and prompting is indeed feasible. Codes and trained models are released at https://github.com/shenyunhang/APE.

Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired multimodal samples, which are prohibitively expensive or infeasible to obtain in many domains. In this work, we explore the feasibility of building multimodal models with limited amount of paired data by aligning pretrained unimodal foundation models. We show that high-quality alignment is possible with as few as tens of thousands of paired samplesx2013less than 1% of the data typically used in the field. To achieve this, we introduce STRUCTURE, an effective regularization technique that preserves the neighborhood geometry of the latent space of unimodal encoders. Additionally, we show that aligning last layers is often suboptimal and demonstrate the benefits of aligning the layers with the highest representational similarity across modalities. These two components can be readily incorporated into existing alignment methods, yielding substantial gains across 24 zero-shot image classification and retrieval benchmarks, with average relative improvement of 51.6% in classification and 91.8% in retrieval tasks. Our results highlight the effectiveness and broad applicability of our framework for limited-sample multimodal learning and offer a promising path forward for resource-constrained domains.

The alignment of representations from different modalities has recently been shown to provide insights on the structural similarities and downstream capabilities of different encoders across diverse data types. While significant progress has been made in aligning images with text, the temporal nature of video data remains largely unexplored in this context. In this work, we conduct the first comprehensive study of video-text representation alignment, probing the capabilities of modern video and language encoders. Our findings reveal several key insights. First, we demonstrate that cross-modal alignment highly depends on the richness of both visual (static images vs. multi-frame videos) and text (single caption vs. a collection) data provided at test time, especially when using state-of-the-art video encoders. We propose parametric test-time scaling laws that capture this behavior and show remarkable predictive power against empirical observations. Secondly, we investigate the correlation between semantic alignment and performance on both semantic and non-semantic downstream tasks, providing initial evidence that strong alignment against text encoders may be linked to general-purpose video representation and understanding. Finally, we correlate temporal reasoning with cross-modal alignment providing a challenging test-bed for vision and language models. Overall, our work introduces video-text alignment as an informative zero-shot way to probe the representation power of different encoders for spatio-temporal data. Project page can be found at https://video-prh.github.io/

Multimodal Large Language Models (MLLMs) have recently demonstrated remarkable perceptual and reasoning abilities, typically comprising a Vision Encoder, an Adapter, and a Large Language Model (LLM). The adapter serves as the critical bridge between the visual and language components. However, training adapters with image-level supervision often results in significant misalignment, undermining the LLMs' capabilities and limiting the potential of Multimodal LLMs. To address this, we introduce Supervised Embedding Alignment (SEA), a token-level alignment method that leverages vision-language pre-trained models, such as CLIP, to align visual tokens with the LLM's embedding space through contrastive learning. This approach ensures a more coherent integration of visual and language representations, enhancing the performance and interpretability of multimodal LLMs while preserving their inherent capabilities. Extensive experiments show that SEA effectively improves MLLMs, particularly for smaller models, without adding extra data or inference computation. SEA also lays the groundwork for developing more general and adaptable solutions to enhance multimodal systems.

Reconstructions of visual perception from brain activity have improved tremendously, but the practical utility of such methods has been limited. This is because such models are trained independently per subject where each subject requires dozens of hours of expensive fMRI training data to attain high-quality results. The present work showcases high-quality reconstructions using only 1 hour of fMRI training data. We pretrain our model across 7 subjects and then fine-tune on minimal data from a new subject. Our novel functional alignment procedure linearly maps all brain data to a shared-subject latent space, followed by a shared non-linear mapping to CLIP image space. We then map from CLIP space to pixel space by fine-tuning Stable Diffusion XL to accept CLIP latents as inputs instead of text. This approach improves out-of-subject generalization with limited training data and also attains state-of-the-art image retrieval and reconstruction metrics compared to single-subject approaches. MindEye2 demonstrates how accurate reconstructions of perception are possible from a single visit to the MRI facility. All code is available on GitHub.

Prompt tuning (PT), as an emerging resource-efficient fine-tuning paradigm, has showcased remarkable effectiveness in improving the task-specific transferability of vision-language models. This paper delves into a previously overlooked information asymmetry issue in PT, where the visual modality mostly conveys more context than the object-oriented textual modality. Correspondingly, coarsely aligning these two modalities could result in the biased attention, driving the model to merely focus on the context area. To address this, we propose DAPT, an effective PT framework based on an intuitive decouple-before-align concept. First, we propose to explicitly decouple the visual modality into the foreground and background representation via exploiting coarse-and-fine visual segmenting cues, and then both of these decoupled patterns are aligned with the original foreground texts and the hand-crafted background classes, thereby symmetrically strengthening the modal alignment. To further enhance the visual concentration, we propose a visual pull-push regularization tailored for the foreground-background patterns, directing the original visual representation towards unbiased attention on the region-of-interest object. We demonstrate the power of architecture-free DAPT through few-shot learning, base-to-novel generalization, and data-efficient learning, all of which yield superior performance across prevailing benchmarks. Our code will be released at https://github.com/Ferenas/DAPT.

With the introduction of transformer-based models for vision and language tasks, such as LLaVA and Chameleon, there has been renewed interest in the discrete tokenized representation of images. These models often treat image patches as discrete tokens, analogous to words in natural language, learning joint alignments between visual and human languages. However, little is known about the statistical behavior of these visual languages - whether they follow similar frequency distributions, grammatical structures, or topologies as natural languages. In this paper, we take a natural-language-centric approach to analyzing discrete visual languages and uncover striking similarities and fundamental differences. We demonstrate that, although visual languages adhere to Zipfian distributions, higher token innovation drives greater entropy and lower compression, with tokens predominantly representing object parts, indicating intermediate granularity. We also show that visual languages lack cohesive grammatical structures, leading to higher perplexity and weaker hierarchical organization compared to natural languages. Finally, we demonstrate that, while vision models align more closely with natural languages than other models, this alignment remains significantly weaker than the cohesion found within natural languages. Through these experiments, we demonstrate how understanding the statistical properties of discrete visual languages can inform the design of more effective computer vision models.

Image segmentation is a fundamental task in computer vision, aimed at partitioning an image into semantically meaningful regions. Referring image segmentation extends this task by using natural language expressions to localize specific objects, requiring effective integration of visual and linguistic information. In this work, we propose SegVLM, a vision-language model that incorporates architectural improvements to enhance segmentation accuracy and cross-modal alignment. The model integrates squeeze-and-excitation (SE) blocks for dynamic feature recalibration, deformable convolutions for geometric adaptability, and residual connections for deep feature learning. We also introduce a novel referring-aware fusion (RAF) loss that balances region-level alignment, boundary precision, and class imbalance. Extensive experiments and ablation studies demonstrate that each component contributes to consistent performance improvements. SegVLM also shows strong generalization across diverse datasets and referring expression scenarios.

Vision-language models, such as CLIP, have achieved significant success in aligning visual and textual representations, becoming essential components of many multi-modal large language models (MLLMs) like LLaVA and OpenFlamingo. However, numerous studies have identified CLIP's limited fine-grained perception as a critical drawback, leading to substantial failures in downstream MLLMs. In contrast, vision-centric foundation models like DINOv2 demonstrate remarkable capabilities in capturing fine details from images. In this work, we propose a novel kernel-based method to align CLIP's visual representation with that of DINOv2, ensuring that the resulting embeddings maintain compatibility with text embeddings while enhancing perceptual capabilities. Our alignment objective is designed for efficient stochastic optimization. Following this image-only alignment fine-tuning, the visual encoder retains compatibility with the frozen text encoder and exhibits significant improvements in zero-shot object recognition, fine-grained spatial reasoning, and localization. By integrating the aligned visual encoder, downstream MLLMs also demonstrate enhanced performance.

Cell painting is a popular technique for creating human-interpretable, high-contrast images of cell morphology. There are two major issues with cell paint: (1) it is labor-intensive and (2) it requires chemical fixation, making the study of cell dynamics impossible. We train a diffusion model (Morphological Observation Neural Enhancement Tool, or MONET) on a large dataset to predict cell paint channels from brightfield images. We show that model quality improves with scale. The model uses a consistency architecture to generate time-lapse videos, despite the impossibility of obtaining cell paint video training data. In addition, we show that this architecture enables a form of in-context learning, allowing the model to partially transfer to out-of-distribution cell lines and imaging protocols. Virtual cell painting is not intended to replace physical cell painting completely, but to act as a complementary tool enabling novel workflows in biological research.

We propose a novel framework for retinal feature point alignment, designed for learning cross-modality features to enhance matching and registration across multi-modality retinal images. Our model draws on the success of previous learning-based feature detection and description methods. To better leverage unlabeled data and constrain the model to reproduce relevant keypoints, we integrate a keypoint-based segmentation task. It is trained in a self-supervised manner by enforcing segmentation consistency between different augmentations of the same image. By incorporating a keypoint augmented self-supervised layer, we achieve robust feature extraction across modalities. Extensive evaluation on two public datasets and one in-house dataset demonstrates significant improvements in performance for modality-agnostic retinal feature alignment. Our code and model weights are publicly available at https://github.com/MedICL-VU/RetinaIPA.

What happens when we push audio-visual alignment to its absolute limits? To systematically investigate this question, we needed datasets with granular alignment quality annotations, but existing datasets treat alignment as binary, either synchronized or not. To address this limitation, we developed a comprehensive dataset featuring detailed alignment scores that reveal the hidden spectrum of audio-visual perceptual correspondence. Using these precise scores, we create "superaligned" representations by training exclusively on the most perfectly matched audio-visual pairs, then conduct our systematic investigation into how this extreme alignment transforms perceptual model behavior across retrieval and generation tasks. The encoders under study fall into two main groups consisting of image-centric encoders that were pretrained using visual modalities as intermediary hubs for connecting modalities, and text-centric encoders that were pretrained with direct audio-language alignment. We first measure the baseline performance of these encoders on two key tasks, namely cross-modal retrieval and text description generation in vision-language models. Subsequently, we realign all encoders with the CLIP space using highly coherent audio-visual data and observe the performance changes. Our findings reveal that the initial architectural type of the encoder determines how it responds to the alignment process. Image-centric encoders, which are inherently designed for alignment, demonstrate exceptional performance in cross-modal retrieval, but this intensive alignment causes compression of unique linguistic information and reduces the quality of their text description generation in vision-language models. In contrast, text-centric encoders, which possess stronger linguistic authenticity, are able to maintain a better balance between the two objectives.

The problem of visual metamerism is defined as finding a family of perceptually indistinguishable, yet physically different images. In this paper, we propose our NeuroFovea metamer model, a foveated generative model that is based on a mixture of peripheral representations and style transfer forward-pass algorithms. Our gradient-descent free model is parametrized by a foveated VGG19 encoder-decoder which allows us to encode images in high dimensional space and interpolate between the content and texture information with adaptive instance normalization anywhere in the visual field. Our contributions include: 1) A framework for computing metamers that resembles a noisy communication system via a foveated feed-forward encoder-decoder network -- We observe that metamerism arises as a byproduct of noisy perturbations that partially lie in the perceptual null space; 2) A perceptual optimization scheme as a solution to the hyperparametric nature of our metamer model that requires tuning of the image-texture tradeoff coefficients everywhere in the visual field which are a consequence of internal noise; 3) An ABX psychophysical evaluation of our metamers where we also find that the rate of growth of the receptive fields in our model match V1 for reference metamers and V2 between synthesized samples. Our model also renders metamers at roughly a second, presenting a times1000 speed-up compared to the previous work, which allows for tractable data-driven metamer experiments.

Diabetic Retinopathy (DR), induced by diabetes, poses a significant risk of visual impairment. Accurate and effective grading of DR aids in the treatment of this condition. Yet existing models experience notable performance degradation on unseen domains due to domain shifts. Previous methods address this issue by simulating domain style through simple visual transformation and mitigating domain noise via learning robust representations. However, domain shifts encompass more than image styles. They overlook biases caused by implicit factors such as ethnicity, age, and diagnostic criteria. In our work, we propose a novel framework where representations of paired data from different domains are decoupled into semantic features and domain noise. The resulting augmented representation comprises original retinal semantics and domain noise from other domains, aiming to generate enhanced representations aligned with real-world clinical needs, incorporating rich information from diverse domains. Subsequently, to improve the robustness of the decoupled representations, class and domain prototypes are employed to interpolate the disentangled representations while data-aware weights are designed to focus on rare classes and domains. Finally, we devise a robust pixel-level semantic alignment loss to align retinal semantics decoupled from features, maintaining a balance between intra-class diversity and dense class features. Experimental results on multiple benchmarks demonstrate the effectiveness of our method on unseen domains. The code implementations are accessible on https://github.com/richard-peng-xia/DECO.

We present a simple mathematical model for the mammalian low visual pathway, taking into account its key elements: retina, lateral geniculate nucleus (LGN), primary visual cortex (V1). The analogies between the cortical level of the visual system and the structure of popular CNNs, used in image classification tasks, suggests the introduction of an additional preliminary convolutional module inspired to precortical neuronal circuits to improve robustness with respect to global light intensity and contrast variations in the input images. We validate our hypothesis on the popular databases MNIST, FashionMNIST and SVHN, obtaining significantly more robust CNNs with respect to these variations, once such extra module is added.

Diffusion models excel at image generation. Recent studies have shown that these models not only generate high-quality images but also encode text-image alignment information through attention maps or loss functions. This information is valuable for various downstream tasks, including segmentation, text-guided image editing, and compositional image generation. However, current methods heavily rely on the assumption of perfect text-image alignment in diffusion models, which is not the case. In this paper, we propose using zero-shot referring image segmentation as a proxy task to evaluate the pixel-level image and class-level text alignment of popular diffusion models. We conduct an in-depth analysis of pixel-text misalignment in diffusion models from the perspective of training data bias. We find that misalignment occurs in images with small sized, occluded, or rare object classes. Therefore, we propose ELBO-T2IAlign, a simple yet effective method to calibrate pixel-text alignment in diffusion models based on the evidence lower bound (ELBO) of likelihood. Our method is training-free and generic, eliminating the need to identify the specific cause of misalignment and works well across various diffusion model architectures. Extensive experiments on commonly used benchmark datasets on image segmentation and generation have verified the effectiveness of our proposed calibration approach.

Aligning objects with corresponding textual descriptions is a fundamental challenge and a realistic requirement in vision-language understanding. While recent multimodal embedding models excel at global image-text alignment, they often struggle with fine-grained alignment between image regions and specific phrases. In this work, we present ObjEmbed, a novel MLLM embedding model that decomposes the input image into multiple regional embeddings, each corresponding to an individual object, along with global embeddings. It supports a wide range of visual understanding tasks like visual grounding, local image retrieval, and global image retrieval. ObjEmbed enjoys three key properties: (1) Object-Oriented Representation: It captures both semantic and spatial aspects of objects by generating two complementary embeddings for each region: an object embedding for semantic matching and an IoU embedding that predicts localization quality. The final object matching score combines semantic similarity with the predicted IoU, enabling more accurate retrieval. (2) Versatility: It seamlessly handles both region-level and image-level tasks. (3) Efficient Encoding: All objects in an image, along with the full image, are encoded in a single forward pass for high efficiency. Superior performance on 18 diverse benchmarks demonstrates its strong semantic discrimination.

Vision-Language (V-L) models trained with contrastive learning to align the visual and language modalities have been shown to be strong few-shot learners. Soft prompt learning is the method of choice for few-shot downstream adaptation aiming to bridge the modality gap caused by the distribution shift induced by the new domain. While parameter-efficient, prompt learning still requires access to the model weights and can be computationally infeasible for large models with billions of parameters. To address these shortcomings, in this work, we describe a black-box method for V-L few-shot adaptation that (a) operates on pre-computed image and text features and hence works without access to the model's weights, (b) it is orders of magnitude faster at training time, (c) it is amenable to both supervised and unsupervised training, and (d) it can be even used to align image and text features computed from uni-modal models. To achieve this, we propose Linear Feature Alignment (LFA), a simple linear approach for V-L re-alignment in the target domain. LFA is initialized from a closed-form solution to a least-squares problem and then it is iteratively updated by minimizing a re-ranking loss. Despite its simplicity, our approach can even surpass soft-prompt learning methods as shown by extensive experiments on 11 image and 2 video datasets.

Vision language models (VLMs) have seen growing adoption in recent years, but many still struggle with basic spatial reasoning errors. We hypothesize that this is due to VLMs adopting pre-trained vision backbones, specifically vision transformers (ViTs) trained with image-level supervision and minimal inductive biases. Such models may fail to encode the class contents at each position in the image, and our goal is to resolve this by ensuring that the vision backbone effectively captures both local and global image semantics. Our main insight is that we do not require new supervision to learn this capability -- pre-trained models contain significant knowledge of local semantics that we can extract and use for scalable self-supervision. We propose a new efficient post-training stage for ViTs called locality alignment and a novel fine-tuning procedure called MaskEmbed that uses a masked reconstruction loss to learn semantic contributions for each image patch. We first evaluate locality alignment with a vision-only benchmark, finding that it improves a model's performance at a patch-level semantic segmentation task, especially for strong backbones trained with image-caption pairs (e.g., CLIP and SigLIP). We then train a series of VLMs with and without locality alignment, and show that locality-aligned backbones improve performance across a range of benchmarks, particularly ones that involve spatial understanding (e.g., RefCOCO, OCID-Ref, TallyQA, VSR, AI2D). Overall, we demonstrate that we can efficiently learn local semantic extraction via a locality alignment stage, and that this procedure complements existing VLM training recipes that use off-the-shelf vision backbones.

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.

Assessing image-text alignment models such as CLIP is crucial for bridging visual and linguistic representations. Yet existing benchmarks rely on rule-based perturbations or short captions, limiting their ability to measure fine-grained alignment. We introduce AlignBench, a benchmark that provides a new indicator of image-text alignment by evaluating detailed image-caption pairs generated by diverse image-to-text and text-to-image models. Each sentence is annotated for correctness, enabling direct assessment of VLMs as alignment evaluators. Benchmarking a wide range of decoder-based VLMs reveals three key findings: (i) CLIP-based models, even those tailored for compositional reasoning, remain nearly blind; (ii) detectors systematically over-score early sentences; and (iii) they show strong self-preference, favoring their own outputs and harming detection performance. Our project page will be available at https://dahlian00.github.io/AlignBench/.

Vision-language representation learning largely benefits from image-text alignment through contrastive losses (e.g., InfoNCE loss). The success of this alignment strategy is attributed to its capability in maximizing the mutual information (MI) between an image and its matched text. However, simply performing cross-modal alignment (CMA) ignores data potential within each modality, which may result in degraded representations. For instance, although CMA-based models are able to map image-text pairs close together in the embedding space, they fail to ensure that similar inputs from the same modality stay close by. This problem can get even worse when the pre-training data is noisy. In this paper, we propose triple contrastive learning (TCL) for vision-language pre-training by leveraging both cross-modal and intra-modal self-supervision. Besides CMA, TCL introduces an intra-modal contrastive objective to provide complementary benefits in representation learning. To take advantage of localized and structural information from image and text input, TCL further maximizes the average MI between local regions of image/text and their global summary. To the best of our knowledge, ours is the first work that takes into account local structure information for multi-modality representation learning. Experimental evaluations show that our approach is competitive and achieves the new state of the art on various common down-stream vision-language tasks such as image-text retrieval and visual question answering.

Vision and Language (VL) models offer an effective method for aligning representation spaces of images and text, leading to numerous applications such as cross-modal retrieval, visual question answering, captioning, and more. However, the aligned image-text spaces learned by all the popular VL models are still suffering from the so-called `object bias' - their representations behave as `bags of nouns', mostly ignoring or downsizing the attributes, relations, and states of objects described/appearing in texts/images. Although some great attempts at fixing these `compositional reasoning' issues were proposed in the recent literature, the problem is still far from being solved. In this paper, we uncover two factors limiting the VL models' compositional reasoning performance. These two factors are properties of the paired VL dataset used for finetuning and pre-training the VL model: (i) the caption quality, or in other words `image-alignment', of the texts; and (ii) the `density' of the captions in the sense of mentioning all the details appearing on the image. We propose a fine-tuning approach for automatically treating these factors leveraging a standard VL dataset (CC3M). Applied to CLIP, we demonstrate its significant compositional reasoning performance increase of up to sim27% over the base model, up to sim20% over the strongest baseline, and by 6.7% on average.

Deep networks are increasingly being applied to problems involving image synthesis, e.g., generating images from textual descriptions and reconstructing an input image from a compact representation. Supervised training of image-synthesis networks typically uses a pixel-wise loss (PL) to indicate the mismatch between a generated image and its corresponding target image. We propose instead to use a loss function that is better calibrated to human perceptual judgments of image quality: the multiscale structural-similarity score (MS-SSIM). Because MS-SSIM is differentiable, it is easily incorporated into gradient-descent learning. We compare the consequences of using MS-SSIM versus PL loss on training deterministic and stochastic autoencoders. For three different architectures, we collected human judgments of the quality of image reconstructions. Observers reliably prefer images synthesized by MS-SSIM-optimized models over those synthesized by PL-optimized models, for two distinct PL measures (ell_1 and ell_2 distances). We also explore the effect of training objective on image encoding and analyze conditions under which perceptually-optimized representations yield better performance on image classification. Finally, we demonstrate the superiority of perceptually-optimized networks for super-resolution imaging. Just as computer vision has advanced through the use of convolutional architectures that mimic the structure of the mammalian visual system, we argue that significant additional advances can be made in modeling images through the use of training objectives that are well aligned to characteristics of human perception.

Cell instance segmentation is a fundamental task in digital pathology with broad clinical applications. Recently, vision foundation models, which are predominantly based on Vision Transformers (ViTs), have achieved remarkable success in pathology image analysis. However, their improvements in cell instance segmentation remain limited. A key challenge arises from the tokenization process in ViTs, which substantially reduces the spatial resolution of input images, leading to suboptimal segmentation quality, especially for small and densely packed cells. To address this problem, we propose CellVTA (Cell Vision Transformer with Adapter), a novel method that improves the performance of vision foundation models for cell instance segmentation by incorporating a CNN-based adapter module. This adapter extracts high-resolution spatial information from input images and injects it into the ViT through a cross-attention mechanism. Our method preserves the core architecture of ViT, ensuring seamless integration with pretrained foundation models. Extensive experiments show that CellVTA achieves 0.538 mPQ on the CoNIC dataset and 0.506 mPQ on the PanNuke dataset, which significantly outperforms the state-of-the-art cell segmentation methods. Ablation studies confirm the superiority of our approach over other fine-tuning strategies, including decoder-only fine-tuning and full fine-tuning. Our code and models are publicly available at https://github.com/JieZheng-ShanghaiTech/CellVTA.

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

Accurately predicting gene expression from histopathology images offers a scalable and non-invasive approach to molecular profiling, with significant implications for precision medicine and computational pathology. However, existing methods often underutilize the cross-modal representation alignment between histopathology images and gene expression profiles across multiple representational levels, thereby limiting their prediction performance. To address this, we propose Gene-DML, a unified framework that structures latent space through Dual-pathway Multi-Level discrimination to enhance correspondence between morphological and transcriptional modalities. The multi-scale instance-level discrimination pathway aligns hierarchical histopathology representations extracted at local, neighbor, and global levels with gene expression profiles, capturing scale-aware morphological-transcriptional relationships. In parallel, the cross-level instance-group discrimination pathway enforces structural consistency between individual (image/gene) instances and modality-crossed (gene/image, respectively) groups, strengthening the alignment across modalities. By jointly modelling fine-grained and structural-level discrimination, Gene-DML is able to learn robust cross-modal representations, enhancing both predictive accuracy and generalization across diverse biological contexts. Extensive experiments on public spatial transcriptomics datasets demonstrate that Gene-DML achieves state-of-the-art performance in gene expression prediction. The code and checkpoints will be released soon.

We introduce a benchmark to directly evaluate the alignment between human observers and vision models on a 3D shape inference task. We leverage an experimental design from the cognitive sciences which requires zero-shot visual inferences about object shape: given a set of images, participants identify which contain the same/different objects, despite considerable viewpoint variation. We draw from a diverse range of images that include common objects (e.g., chairs) as well as abstract shapes (i.e., procedurally generated `nonsense' objects). After constructing over 2000 unique image sets, we administer these tasks to human participants, collecting 35K trials of behavioral data from over 500 participants. This includes explicit choice behaviors as well as intermediate measures, such as reaction time and gaze data. We then evaluate the performance of common vision models (e.g., DINOv2, MAE, CLIP). We find that humans outperform all models by a wide margin. Using a multi-scale evaluation approach, we identify underlying similarities and differences between models and humans: while human-model performance is correlated, humans allocate more time/processing on challenging trials. All images, data, and code can be accessed via our project page.

Most existing methods in vision language pre-training rely on object-centric features extracted through object detection and make fine-grained alignments between the extracted features and texts. It is challenging for these methods to learn relations among multiple objects. To this end, we propose a new method called X-VLM to perform `multi-grained vision language pre-training.' The key to learning multi-grained alignments is to locate visual concepts in the image given the associated texts, and in the meantime align the texts with the visual concepts, where the alignments are in multi-granularity. Experimental results show that X-VLM effectively leverages the learned multi-grained alignments to many downstream vision language tasks and consistently outperforms state-of-the-art methods.

Spatial transcriptomics (ST) provides spatially resolved measurements of gene expression, enabling characterization of the molecular landscape of human tissue beyond histological assessment as well as localized readouts that can be aligned with morphology. Concurrently, the success of multimodal foundation models that integrate vision with complementary modalities suggests that morphomolecular coupling between local expression and morphology can be systematically used to improve histological representations themselves. We introduce Spatial Expression-Aligned Learning (SEAL), a vision-omics self-supervised learning framework that infuses localized molecular information into pathology vision encoders. Rather than training new encoders from scratch, SEAL is designed as a parameter-efficient vision-omics finetuning method that can be flexibly applied to widely used pathology foundation models. We instantiate SEAL by training on over 700,000 paired gene expression spot-tissue region examples spanning tumor and normal samples from 14 organs. Tested across 38 slide-level and 15 patch-level downstream tasks, SEAL provides a drop-in replacement for pathology foundation models that consistently improves performance over widely used vision-only and ST prediction baselines on slide-level molecular status, pathway activity, and treatment response prediction, as well as patch-level gene expression prediction tasks. Additionally, SEAL encoders exhibit robust domain generalization on out-of-distribution evaluations and enable new cross-modal capabilities such as gene-to-image retrieval. Our work proposes a general framework for ST-guided finetuning of pathology foundation models, showing that augmenting existing models with localized molecular supervision is an effective and practical step for improving visual representations and expanding their cross-modal utility.

Vision Transformers (ViTs) based vision foundation models (VFMs) have achieved remarkable performance across diverse vision tasks, but suffer from quadratic complexity that limits scalability to long sequences. Existing linear attention approaches for ViTs are typically trained from scratch, requiring substantial computational resources, while linearization-based methods developed for large language model decoders do not transfer well to ViTs. To address these challenges, we propose ViT-AdaLA, a novel framework for effectively adapting and transferring prior knowledge from VFMs to linear attention ViTs. ViT-AdaLA consists of three stages: attention alignment, feature alignment, and supervised fine-tuning. In the attention alignment stage, we align vanilla linear attention with the original softmax-based attention in each block to approximate the behavior of softmax attention. However, residual approximation errors inevitably accumulate across layers. We mitigate this by fine-tuning the linearized ViT to align its final-layer features with a frozen softmax VFM teacher. Finally, the adapted prior knowledge is transferred to downstream tasks through supervised fine-tuning. Extensive experiments on classification and segmentation tasks demonstrate the effectiveness and generality of ViT-AdaLA over various state-of-the-art linear attention counterpart.

Vision Transformers (ViTs) often degrade under distribution shifts because they rely on spurious correlations, such as background cues, rather than semantically meaningful features. Existing regularization methods, typically relying on simple foreground-background masks, which fail to capture the fine-grained semantic concepts that define an object (e.g., ``long beak'' and ``wings'' for a ``bird''). As a result, these methods provide limited robustness to distribution shifts. To address this limitation, we introduce a novel finetuning framework that steers model reasoning toward concept-level semantics. Our approach optimizes the model's internal relevance maps to align with spatially grounded concept masks. These masks are generated automatically, without manual annotation: class-relevant concepts are first proposed using an LLM-based, label-free method, and then segmented using a VLM. The finetuning objective aligns relevance with these concept regions while simultaneously suppressing focus on spurious background areas. Notably, this process requires only a minimal set of images and uses half of the dataset classes. Extensive experiments on five out-of-distribution benchmarks demonstrate that our method improves robustness across multiple ViT-based models. Furthermore, we show that the resulting relevance maps exhibit stronger alignment with semantic object parts, offering a scalable path toward more robust and interpretable vision models. Finally, we confirm that concept-guided masks provide more effective supervision for model robustness than conventional segmentation maps, supporting our central hypothesis.

A fundamental question in cognitive neuroscience is what shapes visual perception: the external world's structure or the brain's internal architecture. Although some perceptual variability can be traced to individual differences, brain responses to naturalistic stimuli evoke similar activity patterns across individuals, suggesting a convergent representational principle. Here, we test if this stimulus-driven convergence follows a common trajectory across people and deep neural networks (DNNs) during its transformation from sensory to high-level internal representations. We introduce a unified framework that traces representational flow by combining inter-subject similarity with alignment to model hierarchies. Applying this framework to three independent fMRI datasets of visual scene perception, we reveal a cortex-wide network, conserved across individuals, organized into two pathways: a medial-ventral stream for scene structure and a lateral-dorsal stream tuned for social and biological content. This functional organization is captured by the hierarchies of vision DNNs but not language models, reinforcing the specificity of the visual-to-semantic transformation. These findings show a convergent computational solution for visual encoding in both human and artificial vision, driven by the structure of the external world.

Weakly Supervised Semantic Segmentation (WSSS) with image-level labels aims to achieve pixel-level predictions using Class Activation Maps (CAMs). Recently, Contrastive Language-Image Pre-training (CLIP) has been introduced in WSSS. However, recent methods primarily focus on image-text alignment for CAM generation, while CLIP's potential in patch-text alignment remains unexplored. In this work, we propose ExCEL to explore CLIP's dense knowledge via a novel patch-text alignment paradigm for WSSS. Specifically, we propose Text Semantic Enrichment (TSE) and Visual Calibration (VC) modules to improve the dense alignment across both text and vision modalities. To make text embeddings semantically informative, our TSE module applies Large Language Models (LLMs) to build a dataset-wide knowledge base and enriches the text representations with an implicit attribute-hunting process. To mine fine-grained knowledge from visual features, our VC module first proposes Static Visual Calibration (SVC) to propagate fine-grained knowledge in a non-parametric manner. Then Learnable Visual Calibration (LVC) is further proposed to dynamically shift the frozen features towards distributions with diverse semantics. With these enhancements, ExCEL not only retains CLIP's training-free advantages but also significantly outperforms other state-of-the-art methods with much less training cost on PASCAL VOC and MS COCO.

Despite the success of multimodal contrastive learning in aligning visual and linguistic representations, a persistent geometric anomaly, the Modality Gap, remains: embeddings of distinct modalities expressing identical semantics occupy systematically offset regions. Prior approaches to bridge this gap are largely limited by oversimplified isotropic assumptions, hindering their application in large-scale scenarios. In this paper, we address these limitations by precisely characterizing the geometric shape of the modality gap and leveraging it for efficient model scaling. First, we propose the Fixed-frame Modality Gap Theory, which decomposes the modality gap within a frozen reference frame into stable biases and anisotropic residuals. Guided by this precise modeling, we introduce ReAlign, a training-free modality alignment strategy. Utilizing statistics from massive unpaired data, ReAlign aligns text representation into the image representation distribution via a three-step process comprising Anchor, Trace, and Centroid Alignment, thereby explicitly rectifying geometric misalignment. Building on ReAlign, we propose ReVision, a scalable training paradigm for Multimodal Large Language Models (MLLMs). ReVision integrates ReAlign into the pretraining stage, enabling the model to learn the distribution of visual representations from unpaired text before visual instruction tuning, without the need for large-scale, high-quality image-text pairs. Our framework demonstrates that statistically aligned unpaired data can effectively substitute for expensive image-text pairs, offering a robust path for the efficient scaling of MLLMs.

While existing image-text alignment models reach high quality binary assessments, they fall short of pinpointing the exact source of misalignment. In this paper, we present a method to provide detailed textual and visual explanation of detected misalignments between text-image pairs. We leverage large language models and visual grounding models to automatically construct a training set that holds plausible misaligned captions for a given image and corresponding textual explanations and visual indicators. We also publish a new human curated test set comprising ground-truth textual and visual misalignment annotations. Empirical results show that fine-tuning vision language models on our training set enables them to articulate misalignments and visually indicate them within images, outperforming strong baselines both on the binary alignment classification and the explanation generation tasks. Our method code and human curated test set are available at: https://mismatch-quest.github.io/

Human perception integrates multiple modalities, such as vision, hearing, and language, into a unified understanding of the surrounding reality. While recent multimodal models have achieved significant progress by aligning pairs of modalities via contrastive learning, their solutions are unsuitable when scaling to multiple modalities. These models typically align each modality to a designated anchor without ensuring the alignment of all modalities with each other, leading to suboptimal performance in tasks requiring a joint understanding of multiple modalities. In this paper, we structurally rethink the pairwise conventional approach to multimodal learning and we present the novel Gramian Representation Alignment Measure (GRAM), which overcomes the above-mentioned limitations. GRAM learns and then aligns n modalities directly in the higher-dimensional space in which modality embeddings lie by minimizing the Gramian volume of the k-dimensional parallelotope spanned by the modality vectors, ensuring the geometric alignment of all modalities simultaneously. GRAM can replace cosine similarity in any downstream method, holding for 2 to n modalities and providing more meaningful alignment with respect to previous similarity measures. The novel GRAM-based contrastive loss function enhances the alignment of multimodal models in the higher-dimensional embedding space, leading to new state-of-the-art performance in downstream tasks such as video-audio-text retrieval and audio-video classification. The project page, the code, and the pretrained models are available at https://ispamm.github.io/GRAM/.

Growing evidence indicates that only a sparse subset from a pool of sensory neurons is active for the encoding of visual stimuli at any instant in time. Traditionally, to replicate such biological sparsity, generative models have been using the ell_1 norm as a penalty due to its convexity, which makes it amenable to fast and simple algorithmic solvers. In this work, we use biological vision as a test-bed and show that the soft thresholding operation associated to the use of the ell_1 norm is highly suboptimal compared to other functions suited to approximating ell_q with 0 leq q < 1 (including recently proposed Continuous Exact relaxations), both in terms of performance and in the production of features that are akin to signatures of the primary visual cortex. We show that ell_1 sparsity produces a denser code or employs a pool with more neurons, i.e. has a higher degree of overcompleteness, in order to maintain the same reconstruction error as the other methods considered. For all the penalty functions tested, a subset of the neurons develop orientation selectivity similarly to V1 neurons. When their code is sparse enough, the methods also develop receptive fields with varying functionalities, another signature of V1. Compared to other methods, soft thresholding achieves this level of sparsity at the expense of much degraded reconstruction performance, that more likely than not is not acceptable in biological vision. Our results indicate that V1 uses a sparsity inducing regularization that is closer to the ell_0 pseudo-norm rather than to the ell_1 norm.

We present a method for joint alignment of sparse in-the-wild image collections of an object category. Most prior works assume either ground-truth keypoint annotations or a large dataset of images of a single object category. However, neither of the above assumptions hold true for the long-tail of the objects present in the world. We present a self-supervised technique that directly optimizes on a sparse collection of images of a particular object/object category to obtain consistent dense correspondences across the collection. We use pairwise nearest neighbors obtained from deep features of a pre-trained vision transformer (ViT) model as noisy and sparse keypoint matches and make them dense and accurate matches by optimizing a neural network that jointly maps the image collection into a learned canonical grid. Experiments on CUB and SPair-71k benchmarks demonstrate that our method can produce globally consistent and higher quality correspondences across the image collection when compared to existing self-supervised methods. Code and other material will be made available at https://kampta.github.io/asic.

We present a model that generates natural language descriptions of images and their regions. Our approach leverages datasets of images and their sentence descriptions to learn about the inter-modal correspondences between language and visual data. Our alignment model is based on a novel combination of Convolutional Neural Networks over image regions, bidirectional Recurrent Neural Networks over sentences, and a structured objective that aligns the two modalities through a multimodal embedding. We then describe a Multimodal Recurrent Neural Network architecture that uses the inferred alignments to learn to generate novel descriptions of image regions. We demonstrate that our alignment model produces state of the art results in retrieval experiments on Flickr8K, Flickr30K and MSCOCO datasets. We then show that the generated descriptions significantly outperform retrieval baselines on both full images and on a new dataset of region-level annotations.

Vision is a primary means of how humans perceive the environment, but Blind and Low-Vision (BLV) people need assistance understanding their surroundings, especially in unfamiliar environments. The emergence of semantic-based systems as assistance tools for BLV users has motivated many researchers to explore responses from Large Vision-Language Models (LVLMs). However, it has yet been studied preferences of BLV users on diverse types/styles of responses from LVLMs, specifically for navigational aid. To fill this gap, we first construct Eye4B dataset, consisting of human-validated 1.1k curated outdoor/indoor scenes with 5-10 relevant requests per scene. Then, we conduct an in-depth user study with eight BLV users to evaluate their preferences on six LVLMs from five perspectives: Afraidness, Nonactionability, Sufficiency, and Conciseness. Finally, we introduce Eye4B benchmark for evaluating alignment between widely used model-based image-text metrics and our collected BLV preferences. Our work can be set as a guideline for developing BLV-aware LVLMs towards a Barrier-Free AI system.

The Platonic Representation Hypothesis posits that neural networks trained on different modalities converge toward a shared statistical model of the world. Recent work exploits this convergence by aligning frozen pretrained vision and language models with lightweight alignment layers, but typically relies on contrastive losses and millions of paired samples. In this work, we ask whether meaningful alignment can be achieved with substantially less supervision. We introduce a semi-supervised setting in which pretrained unimodal encoders are aligned using a small number of image-text pairs together with large amounts of unpaired data. To address this challenge, we propose SOTAlign, a two-stage framework that first recovers a coarse shared geometry from limited paired data using a linear teacher, then refines the alignment on unpaired samples via an optimal-transport-based divergence that transfers relational structure without overconstraining the target space. Unlike existing semi-supervised methods, SOTAlign effectively leverages unpaired images and text, learning robust joint embeddings across datasets and encoder pairs, and significantly outperforming supervised and semi-supervised baselines.

The advent of large Vision-Language Models (VLMs) has significantly advanced multimodal tasks, enabling more sophisticated and accurate reasoning across various applications, including image and video captioning, visual question answering, and cross-modal retrieval. Despite their superior capabilities, VLMs struggle with fine-grained image regional composition information perception. Specifically, they have difficulty accurately aligning the segmentation masks with the corresponding semantics and precisely describing the compositional aspects of the referred regions. However, compositionality - the ability to understand and generate novel combinations of known visual and textual components - is critical for facilitating coherent reasoning and understanding across modalities by VLMs. To address this issue, we propose FINECAPTION, a novel VLM that can recognize arbitrary masks as referential inputs and process high-resolution images for compositional image captioning at different granularity levels. To support this endeavor, we introduce COMPOSITIONCAP, a new dataset for multi-grained region compositional image captioning, which introduces the task of compositional attribute-aware regional image captioning. Empirical results demonstrate the effectiveness of our proposed model compared to other state-of-the-art VLMs. Additionally, we analyze the capabilities of current VLMs in recognizing various visual prompts for compositional region image captioning, highlighting areas for improvement in VLM design and training.

While existing large vision-language multimodal models focus on whole image understanding, there is a prominent gap in achieving region-specific comprehension. Current approaches that use textual coordinates or spatial encodings often fail to provide a user-friendly interface for visual prompting. To address this challenge, we introduce a novel multimodal model capable of decoding arbitrary visual prompts. This allows users to intuitively mark images and interact with the model using natural cues like a "red bounding box" or "pointed arrow". Our simple design directly overlays visual markers onto the RGB image, eliminating the need for complex region encodings, yet achieves state-of-the-art performance on region-understanding tasks like Visual7W, PointQA, and Visual Commonsense Reasoning benchmark. Furthermore, we present ViP-Bench, a comprehensive benchmark to assess the capability of models in understanding visual prompts across multiple dimensions, enabling future research in this domain. Code, data, and model are publicly available.

Deep neural networks have reached human-level performance on many computer vision tasks. However, the objectives used to train these networks enforce only that similar images are embedded at similar locations in the representation space, and do not directly constrain the global structure of the resulting space. Here, we explore the impact of supervising this global structure by linearly aligning it with human similarity judgments. We find that a naive approach leads to large changes in local representational structure that harm downstream performance. Thus, we propose a novel method that aligns the global structure of representations while preserving their local structure. This global-local transform considerably improves accuracy across a variety of few-shot learning and anomaly detection tasks. Our results indicate that human visual representations are globally organized in a way that facilitates learning from few examples, and incorporating this global structure into neural network representations improves performance on downstream tasks.

Recent developments of vision large language models (LLMs) have seen remarkable progress, yet still encounter challenges towards multimodal generalists, such as coarse-grained instance-level understanding, lack of unified support for both images and videos, and insufficient coverage across various vision tasks. In this paper, we present VITRON, a universal pixel-level vision LLM designed for comprehensive understanding, generating, segmenting, and editing of both static images and dynamic videos. Building on top of an LLM backbone, VITRON incorporates encoders for images, videos, and pixel-level regional visuals within its frontend modules, while employing state-of-the-art visual specialists as its backend, via which VITRON supports a spectrum of vision end tasks, spanning visual comprehension to visual generation, from low level to high level. To ensure an effective and precise message passing from LLM to backend modules for function invocation, we propose a novel hybrid method by simultaneously integrating discrete textual instructions and continuous signal embeddings. Further, we design various pixel-level spatiotemporal vision-language alignment learning for VITRON to reach the best fine-grained visual capability. Finally, a cross-task synergy module is advised to learn to maximize the task-invariant fine-grained visual features, enhancing the synergy between different visual tasks. Demonstrated over 12 visual tasks and evaluated across 22 datasets, VITRON showcases its extensive capabilities in the four main vision task clusters. Overall, this work illuminates the great potential of developing a more unified multimodal generalist. Project homepage: https://vitron-llm.github.io/

Vision transformers (ViTs) are quickly becoming the de-facto architecture for computer vision, yet we understand very little about why they work and what they learn. While existing studies visually analyze the mechanisms of convolutional neural networks, an analogous exploration of ViTs remains challenging. In this paper, we first address the obstacles to performing visualizations on ViTs. Assisted by these solutions, we observe that neurons in ViTs trained with language model supervision (e.g., CLIP) are activated by semantic concepts rather than visual features. We also explore the underlying differences between ViTs and CNNs, and we find that transformers detect image background features, just like their convolutional counterparts, but their predictions depend far less on high-frequency information. On the other hand, both architecture types behave similarly in the way features progress from abstract patterns in early layers to concrete objects in late layers. In addition, we show that ViTs maintain spatial information in all layers except the final layer. In contrast to previous works, we show that the last layer most likely discards the spatial information and behaves as a learned global pooling operation. Finally, we conduct large-scale visualizations on a wide range of ViT variants, including DeiT, CoaT, ConViT, PiT, Swin, and Twin, to validate the effectiveness of our method.

Vision Language Models (VLMs) are increasingly adopted for AI-generated images (AIGI) detection, yet converting VLMs into detectors requires substantial resource, while the resulting models still exhibit severe hallucinations. To probe the core issue, we conduct an empirical analysis and observe two characteristic behaviors: (i) fine-tuning VLMs on high-level semantic supervision strengthens semantic discrimination and well generalize to unseen data; (ii) fine-tuning VLMs on low-level pixel-artifact supervision yields poor transfer. We attribute VLMs' underperformance to task-model misalignment: semantics-oriented VLMs inherently lack sensitivity to fine-grained pixel artifacts, and semantically non-discriminative pixel artifacts thus exceeds their inductive biases. In contrast, we observe that conventional pixel-artifact detectors capture low-level pixel artifacts yet exhibit limited semantic awareness relative to VLMs, highlighting that distinct models are better matched to distinct tasks. In this paper, we formalize AIGI detection as two complementary tasks--semantic consistency checking and pixel-artifact detection--and show that neglecting either induces systematic blind spots. Guided by this view, we introduce the Task-Model Alignment principle and instantiate it as a two-branch detector, AlignGemini, comprising a VLM fine-tuned exclusively with pure semantic supervision and a pixel-artifact expert trained exclusively with pure pixel-artifact supervision. By enforcing orthogonal supervision on two simplified datasets, each branch trains to its strengths, producing complementary discrimination over semantic and pixel cues. On five in-the-wild benchmarks, AlignGemini delivers a +9.5 gain in average accuracy, supporting task-model alignment as an effective path to generalizable AIGI detection.

Vision-Language Models (VLMs) have achieved remarkable progress on a wide range of challenging multimodal understanding and reasoning tasks. However, existing reasoning paradigms, such as the classical Chain-of-Thought (CoT), rely solely on textual information and often underutilize important visual cues. While prior work has incorporated pixel-level visual cues, these representations require precise spatial localization, introducing additional learning complexity. To address this, we propose PatchCue, a novel patch-based visual cue paradigm designed to significantly enhance the visual reasoning capabilities of VLMs. By partitioning images into patches and representing cues at the patch level, PatchCue aligns better with human perceptual habits and leverages the patch-tokenized input of modern VLMs. We train VLMs using a two-stage approach: cold-start supervised fine-tuning to output patch-level cues, followed by reinforcement learning with a process-supervised cue reward that guides intermediate visual reasoning steps. Extensive experiments on multiple VLMs and diverse benchmarks, including general visual question answering, complex reasoning, and document understanding, demonstrate that PatchCue consistently improves overall model performance. Our results show that patch-level cues outperform both pixel-level bounding boxes and point-based cues, providing a more effective and cognitively aligned visual reasoning paradigm.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

While recent advancements in generative modeling have significantly improved text-image alignment, some residual misalignment between text and image representations still remains. Although many approaches have attempted to address this issue by fine-tuning models using various reward models, etc., we revisit the challenge from the perspective of representation alignment-an approach that has gained popularity with the success of REPresentation Alignment (REPA). We first argue that conventional text-to-image (T2I) diffusion models, typically trained on paired image and text data (i.e., positive pairs) by minimizing score matching or flow matching losses, is suboptimal from the standpoint of representation alignment. Instead, a better alignment can be achieved through contrastive learning that leverages both positive and negative pairs. To achieve this efficiently even with pretrained models, we introduce a lightweight contrastive fine tuning strategy called SoftREPA that uses soft text tokens. This approach improves alignment with minimal computational overhead by adding fewer than 1M trainable parameters to the pretrained model. Our theoretical analysis demonstrates that our method explicitly increases the mutual information between text and image representations, leading to enhanced semantic consistency. Experimental results across text-to-image generation and text-guided image editing tasks validate the effectiveness of our approach in improving the semantic consistency of T2I generative models.

We present the "Law of Vision Representation" in multimodal large language models (MLLMs). It reveals a strong correlation between the combination of cross-modal alignment, correspondence in vision representation, and MLLM performance. We quantify the two factors using the cross-modal Alignment and Correspondence score (AC score). Through extensive experiments involving thirteen different vision representation settings and evaluations across eight benchmarks, we find that the AC score is linearly correlated to model performance. By leveraging this relationship, we are able to identify and train the optimal vision representation only, which does not require finetuning the language model every time, resulting in a 99.7% reduction in computational cost.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Large language models (LLMs) can handle a wide variety of general tasks with simple prompts, without the need for task-specific training. Multimodal Large Language Models (MLLMs), built upon LLMs, have demonstrated impressive potential in tackling complex tasks involving visual, auditory, and textual data. However, critical issues related to truthfulness, safety, o1-like reasoning, and alignment with human preference remain insufficiently addressed. This gap has spurred the emergence of various alignment algorithms, each targeting different application scenarios and optimization goals. Recent studies have shown that alignment algorithms are a powerful approach to resolving the aforementioned challenges. In this paper, we aim to provide a comprehensive and systematic review of alignment algorithms for MLLMs. Specifically, we explore four key aspects: (1) the application scenarios covered by alignment algorithms, including general image understanding, multi-image, video, and audio, and extended multimodal applications; (2) the core factors in constructing alignment datasets, including data sources, model responses, and preference annotations; (3) the benchmarks used to evaluate alignment algorithms; and (4) a discussion of potential future directions for the development of alignment algorithms. This work seeks to help researchers organize current advancements in the field and inspire better alignment methods. The project page of this paper is available at https://github.com/BradyFU/Awesome-Multimodal-Large-Language-Models/tree/Alignment.

Human vision organizes local cues into coherent global forms using Gestalt principles like closure, proximity, and figure-ground assignment -- functions reliant on global spatial structure. We investigate whether modern vision models show similar behaviors, and under what training conditions these emerge. We find that Vision Transformers (ViTs) trained with Masked Autoencoding (MAE) exhibit activation patterns consistent with Gestalt laws, including illusory contour completion, convexity preference, and dynamic figure-ground segregation. To probe the computational basis, we hypothesize that modeling global dependencies is necessary for Gestalt-like organization. We introduce the Distorted Spatial Relationship Testbench (DiSRT), which evaluates sensitivity to global spatial perturbations while preserving local textures. Using DiSRT, we show that self-supervised models (e.g., MAE, CLIP) outperform supervised baselines and sometimes even exceed human performance. ConvNeXt models trained with MAE also exhibit Gestalt-compatible representations, suggesting such sensitivity can arise without attention architectures. However, classification finetuning degrades this ability. Inspired by biological vision, we show that a Top-K activation sparsity mechanism can restore global sensitivity. Our findings identify training conditions that promote or suppress Gestalt-like perception and establish DiSRT as a diagnostic for global structure sensitivity across models.

In vision-language models (VLMs), misalignment between textual descriptions and visual coordinates often induces hallucinations. This issue becomes particularly severe in dense prediction tasks such as spatial-temporal video grounding (STVG). Prior approaches typically focus on enhancing visual-textual alignment or attaching auxiliary decoders. However, these strategies inevitably introduce additional trainable modules, leading to significant annotation costs and computational overhead. In this work, we propose a novel visual prompting paradigm that avoids the difficult problem of aligning coordinates across modalities. Specifically, we reformulate per-frame coordinate prediction as a compact instance-level identification problem by assigning each object a unique, temporally consistent ID. These IDs are embedded into the video as visual prompts, providing explicit and interpretable inputs to the VLMs. Furthermore, we introduce STVG-R1, the first reinforcement learning framework for STVG, which employs a task-driven reward to jointly optimize temporal accuracy, spatial consistency, and structural format regularization. Extensive experiments on six benchmarks demonstrate the effectiveness of our approach. STVG-R1 surpasses the baseline Qwen2.5-VL-7B by a remarkable margin of 20.9% on m_IoU on the HCSTVG-v2 benchmark, establishing a new state of the art (SOTA). Surprisingly, STVG-R1 also exhibits strong zero-shot generalization to multi-object referring video object segmentation tasks, achieving a SOTA 47.3% J&F on MeViS.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Vision language models (VLMs) have drastically changed the computer vision model landscape in only a few years, opening an exciting array of new applications from zero-shot image classification, over to image captioning, and visual question answering. Unlike pure vision models, they offer an intuitive way to access visual content through language prompting. The wide applicability of such models encourages us to ask whether they also align with human vision - specifically, how far they adopt human-induced visual biases through multimodal fusion, or whether they simply inherit biases from pure vision models. One important visual bias is the texture vs. shape bias, or the dominance of local over global information. In this paper, we study this bias in a wide range of popular VLMs. Interestingly, we find that VLMs are often more shape-biased than their vision encoders, indicating that visual biases are modulated to some extent through text in multimodal models. If text does indeed influence visual biases, this suggests that we may be able to steer visual biases not just through visual input but also through language: a hypothesis that we confirm through extensive experiments. For instance, we are able to steer shape bias from as low as 49% to as high as 72% through prompting alone. For now, the strong human bias towards shape (96%) remains out of reach for all tested VLMs.

Recent research has made significant progress in localizing and editing image regions based on text. However, most approaches treat these regions in isolation, relying solely on local cues without accounting for how each part contributes to the overall visual and semantic composition. This often results in inconsistent edits, unnatural transitions, or loss of coherence across the image. In this work, we propose Region in Context, a novel framework for text-conditioned image editing that performs multilevel semantic alignment between vision and language, inspired by the human ability to reason about edits in relation to the whole scene. Our method encourages each region to understand its role within the global image context, enabling precise and harmonized changes. At its core, the framework introduces a dual-level guidance mechanism: regions are represented with full-image context and aligned with detailed region-level descriptions, while the entire image is simultaneously matched to a comprehensive scene-level description generated by a large vision-language model. These descriptions serve as explicit verbal references of the intended content, guiding both local modifications and global structure. Experiments show that it produces more coherent and instruction-aligned results. Code is available at: https://github.com/thuyvuphuong/Region-in-Context.git

Object recognition plays a fundamental role in how biological organisms perceive and interact with their environment. While the human visual system performs this task with remarkable efficiency, reproducing similar capabilities in artificial systems remains challenging. This study investigates VisNet, a biologically inspired neural network model, and several enhanced variants incorporating radial basis function neurons, Mahalanobis distance based learning, and retinal like preprocessing for both general object recognition and symmetry classification. By leveraging principles of Hebbian learning and temporal continuity associating temporally adjacent views to build invariant representations. VisNet and its extensions capture robust and transformation invariant features. Experimental results across multiple datasets, including MNIST, CIFAR10, and custom symmetric object sets, show that these enhanced VisNet variants substantially improve recognition accuracy compared with the baseline model. These findings underscore the adaptability and biological relevance of VisNet inspired architectures, offering a powerful and interpretable framework for visual recognition in both neuroscience and artificial intelligence. Keywords: VisNet, Object Recognition, Symmetry Detection, Hebbian Learning, RBF Neurons, Mahalanobis Distance, Biologically Inspired Models, Invariant Representations

The emergence of foundational models has greatly improved performance across various downstream tasks, with fine-tuning often yielding even better results. However, existing fine-tuning approaches typically require access to model weights and layers, leading to challenges such as managing multiple model copies or inference pipelines, inefficiencies in edge device optimization, and concerns over proprietary rights, privacy, and exposure to unsafe model variants. In this paper, we address these challenges by exploring "Gray-box" fine-tuning approaches, where the model's architecture and weights remain hidden, allowing only gradient propagation. We introduce a novel yet simple and effective framework that adapts to new tasks using two lightweight learnable modules at the model's input and output. Additionally, we present a less restrictive variant that offers more entry points into the model, balancing performance with model exposure. We evaluate our approaches across several backbones on benchmarks such as text-image alignment, text-video alignment, and sketch-image alignment. Results show that our Gray-box approaches are competitive with full-access fine-tuning methods, despite having limited access to the model.

Our research aims to develop machines that learn to perceive visual motion as do humans. While recent advances in computer vision (CV) have enabled DNN-based models to accurately estimate optical flow in naturalistic images, a significant disparity remains between CV models and the biological visual system in both architecture and behavior. This disparity includes humans' ability to perceive the motion of higher-order image features (second-order motion), which many CV models fail to capture because of their reliance on the intensity conservation law. Our model architecture mimics the cortical V1-MT motion processing pathway, utilizing a trainable motion energy sensor bank and a recurrent graph network. Supervised learning employing diverse naturalistic videos allows the model to replicate psychophysical and physiological findings about first-order (luminance-based) motion perception. For second-order motion, inspired by neuroscientific findings, the model includes an additional sensing pathway with nonlinear preprocessing before motion energy sensing, implemented using a simple multilayer 3D CNN block. When exploring how the brain acquired the ability to perceive second-order motion in natural environments, in which pure second-order signals are rare, we hypothesized that second-order mechanisms were critical when estimating robust object motion amidst optical fluctuations, such as highlights on glossy surfaces. We trained our dual-pathway model on novel motion datasets with varying material properties of moving objects. We found that training to estimate object motion from non-Lambertian materials naturally endowed the model with the capacity to perceive second-order motion, as can humans. The resulting model effectively aligns with biological systems while generalizing to both first- and second-order motion phenomena in natural scenes.

We introduce the "single-life" learning paradigm, where we train a distinct vision model exclusively on egocentric videos captured by one individual. We leverage the multiple viewpoints naturally captured within a single life to learn a visual encoder in a self-supervised manner. Our experiments demonstrate three key findings. First, models trained independently on different lives develop a highly aligned geometric understanding. We demonstrate this by training visual encoders on distinct datasets each capturing a different life, both indoors and outdoors, as well as introducing a novel cross-attention-based metric to quantify the functional alignment of the internal representations developed by different models. Second, we show that single-life models learn generalizable geometric representations that effectively transfer to downstream tasks, such as depth estimation, in unseen environments. Third, we demonstrate that training on up to 30 hours from one week of the same person's life leads to comparable performance to training on 30 hours of diverse web data, highlighting the strength of single-life representation learning. Overall, our results establish that the shared structure of the world, both leads to consistency in models trained on individual lives, and provides a powerful signal for visual representation learning.

Recent studies have shown that Large Vision-Language Models (VLMs) tend to neglect image content and over-rely on language-model priors, resulting in errors in visually grounded tasks and hallucinations. We hypothesize that this issue arises because existing VLMs are not explicitly trained to generate texts that are accurately grounded in fine-grained image details. To enhance visual feedback during VLM training, we propose S-VCO (Symmetrical Visual Contrastive Optimization), a novel finetuning objective that steers the model toward capturing important visual details and aligning them with corresponding text tokens. To further facilitate this detailed alignment, we introduce MVC, a paired image-text dataset built by automatically filtering and augmenting visual counterfactual data to challenge the model with hard contrastive cases involving Minimal Visual Contrasts. Experiments show that our method consistently improves VLM performance across diverse benchmarks covering various abilities and domains, achieving up to a 22% reduction in hallucinations, and significant gains in vision-centric and general tasks. Notably, these improvements become increasingly pronounced in benchmarks with higher visual dependency. In short, S-VCO offers a significant enhancement of VLM's visually-dependent task performance while retaining or even improving the model's general abilities. We opensource our code at https://s-vco.github.io/

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

Large-scale contrastive vision-language pre-training has shown significant progress in visual representation learning. Unlike traditional visual systems trained by a fixed set of discrete labels, a new paradigm was introduced in radford2021learning to directly learn to align images with raw texts in an open-vocabulary setting. On downstream tasks, a carefully chosen text prompt is employed to make zero-shot predictions.~To avoid non-trivial prompt engineering, context optimization zhou2021coop has been proposed to learn continuous vectors as task-specific prompts with few-shot training examples.~In this paper, we show that there is an alternative path to achieve better vision-language models other than prompt tuning.~While prompt tuning is for the textual inputs, we propose CLIP-Adapter to conduct fine-tuning with feature adapters on either visual or language branch. Specifically, CLIP-Adapter adopts an additional bottleneck layer to learn new features and performs residual-style feature blending with the original pre-trained features.~As a consequence, CLIP-Adapter is able to outperform context optimization while maintains a simple design. Experiments and extensive ablation studies on various visual classification tasks demonstrate the effectiveness of our approach. Code is released at t https://github.com/gaopengcuhk/CLIP-Adapter.

Text-to-image diffusion models have shown great success in generating high-quality text-guided images. Yet, these models may still fail to semantically align generated images with the provided text prompts, leading to problems like incorrect attribute binding and/or catastrophic object neglect. Given the pervasive object-oriented structure underlying text prompts, we introduce a novel object-conditioned Energy-Based Attention Map Alignment (EBAMA) method to address the aforementioned problems. We show that an object-centric attribute binding loss naturally emerges by approximately maximizing the log-likelihood of a z-parameterized energy-based model with the help of the negative sampling technique. We further propose an object-centric intensity regularizer to prevent excessive shifts of objects attention towards their attributes. Extensive qualitative and quantitative experiments, including human evaluation, on several challenging benchmarks demonstrate the superior performance of our method over previous strong counterparts. With better aligned attention maps, our approach shows great promise in further enhancing the text-controlled image editing ability of diffusion models.

Detecting objects accurately from a large or open vocabulary necessitates the vision-language alignment on region representations. However, learning such a region-text alignment by obtaining high-quality box annotations with text labels or descriptions is expensive and infeasible. In contrast, collecting image-text pairs is simpler but lacks precise object location information to associate regions with texts. In this paper, we propose a novel approach called Contrastive Language-Image Mosaic (CLIM), which leverages large-scale image-text pairs effectively for aligning region and text representations. CLIM combines multiple images into a mosaicked image and treats each image as a `pseudo region'. The feature of each pseudo region is extracted and trained to be similar to the corresponding text embedding while dissimilar from others by a contrastive loss, enabling the model to learn the region-text alignment without costly box annotations. As a generally applicable approach, CLIM consistently improves different open-vocabulary object detection methods that use caption supervision. Furthermore, CLIM can effectively enhance the region representation of vision-language models, thus providing stronger backbones for open-vocabulary object detectors. Our experimental results demonstrate that CLIM improves different baseline open-vocabulary object detectors by a large margin on both OV-COCO and OV-LVIS benchmarks. The code is available at https://github.com/wusize/CLIM.

Vision Transformers rely on positional embeddings and class tokens that encode fixed spatial priors. While effective for natural images, these priors may hinder generalization when spatial layout is weakly informative or inconsistent, a frequent condition in medical imaging and edge-deployed clinical systems. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a compact Vision Transformer that removes both positional embeddings and the [CLS] token, achieving permutation invariance through global average pooling over patch representations. The term "Zero-token" specifically refers to removing the dedicated [CLS] aggregation token and positional embeddings; patch tokens remain unchanged and are processed normally. Adaptive residual projections preserve training stability in compact configurations while maintaining a strict parameter budget. Evaluation is performed across seven MedMNIST datasets spanning binary and multi-class tasks under a strict few-shot protocol (50 samples per class, fixed hyperparameters, five random seeds). The empirical analysis demonstrates regime-dependent behavior: ZACH-ViT (0.25M parameters, trained from scratch) achieves its strongest advantage on BloodMNIST and remains competitive with TransMIL on PathMNIST, while its relative advantage decreases on datasets with strong anatomical priors (OCTMNIST, OrganAMNIST), consistent with the architectural hypothesis. These findings support the view that aligning architectural inductive bias with data structure can be more important than pursuing universal benchmark dominance. Despite its minimal size and lack of pretraining, ZACH-ViT achieves competitive performance while maintaining sub-second inference times, supporting deployment in resource-constrained clinical environments. Code and models are available at https://github.com/Bluesman79/ZACH-ViT.

The emergence of large Vision Language Models (VLMs) has broadened the scope and capabilities of single-modal Large Language Models (LLMs) by integrating visual modalities, thereby unlocking transformative cross-modal applications in a variety of real-world scenarios. Despite their impressive performance, VLMs are prone to significant hallucinations, particularly in the form of cross-modal inconsistencies. Building on the success of Reinforcement Learning from Human Feedback (RLHF) in aligning LLMs, recent advancements have focused on applying direct preference optimization (DPO) on carefully curated datasets to mitigate these issues. Yet, such approaches typically introduce preference signals in a brute-force manner, neglecting the crucial role of visual information in the alignment process. In this paper, we introduce Re-Align, a novel alignment framework that leverages image retrieval to construct a dual-preference dataset, effectively incorporating both textual and visual preference signals. We further introduce rDPO, an extension of the standard direct preference optimization that incorporates an additional visual preference objective during fine-tuning. Our experimental results demonstrate that Re-Align not only mitigates hallucinations more effectively than previous methods but also yields significant performance gains in general visual question-answering (VQA) tasks. Moreover, we show that Re-Align maintains robustness and scalability across a wide range of VLM sizes and architectures. This work represents a significant step forward in aligning multimodal LLMs, paving the way for more reliable and effective cross-modal applications. We release all the code in https://github.com/taco-group/Re-Align.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

Multimodal large language models (MLLMs) integrate image features from visual encoders with LLMs, demonstrating advanced comprehension capabilities. However, mainstream MLLMs are solely supervised by the next-token prediction of textual tokens, neglecting critical vision-centric information essential for analytical abilities. To track this dilemma, we introduce VaCo, which optimizes MLLM representations through Vision-Centric activation and Coordination from multiple vision foundation models (VFMs). VaCo introduces visual discriminative alignment to integrate task-aware perceptual features extracted from VFMs, thereby unifying the optimization of both textual and visual outputs in MLLMs. Specifically, we incorporate the learnable Modular Task Queries (MTQs) and Visual Alignment Layers (VALs) into MLLMs, activating specific visual signals under the supervision of diverse VFMs. To coordinate representation conflicts across VFMs, the crafted Token Gateway Mask (TGM) restricts the information flow among multiple groups of MTQs. Extensive experiments demonstrate that VaCo significantly improves the performance of different MLLMs on various benchmarks, showcasing its superior capabilities in visual comprehension.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Visually linking matching cues is a crucial ability in daily life, such as identifying the same person in multiple photos based on their cues, even without knowing who they are. Despite the extensive knowledge that vision-language models (VLMs) possess, it remains largely unexplored whether they are capable of performing this fundamental task. To address this, we introduce VLM^2-Bench, a benchmark designed to assess whether VLMs can Visually Link Matching cues, with 9 subtasks and over 3,000 test cases. Comprehensive evaluation across eight open-source VLMs and GPT-4o, along with further analysis of various language-side and vision-side prompting methods, leads to a total of eight key findings. We identify critical challenges in models' ability to link visual cues, highlighting a significant performance gap where even GPT-4o lags 34.80% behind humans. Based on these insights, we advocate for (i) enhancing core visual capabilities to improve adaptability and reduce reliance on prior knowledge, (ii) establishing clearer principles for integrating language-based reasoning in vision-centric tasks to prevent unnecessary biases, and (iii) shifting vision-text training paradigms toward fostering models' ability to independently structure and infer relationships among visual cues.

The ability to accurately interpret complex visual information is a crucial topic of multimodal large language models (MLLMs). Recent work indicates that enhanced visual perception significantly reduces hallucinations and improves performance on resolution-sensitive tasks, such as optical character recognition and document analysis. A number of recent MLLMs achieve this goal using a mixture of vision encoders. Despite their success, there is a lack of systematic comparisons and detailed ablation studies addressing critical aspects, such as expert selection and the integration of multiple vision experts. This study provides an extensive exploration of the design space for MLLMs using a mixture of vision encoders and resolutions. Our findings reveal several underlying principles common to various existing strategies, leading to a streamlined yet effective design approach. We discover that simply concatenating visual tokens from a set of complementary vision encoders is as effective as more complex mixing architectures or strategies. We additionally introduce Pre-Alignment to bridge the gap between vision-focused encoders and language tokens, enhancing model coherence. The resulting family of MLLMs, Eagle, surpasses other leading open-source models on major MLLM benchmarks. Models and code: https://github.com/NVlabs/Eagle

Multi-modal large language models (MLLMs) have achieved remarkable success in fine-grained visual understanding across a range of tasks. However, they often encounter significant challenges due to inadequate alignment for fine-grained knowledge, which restricts their ability to accurately capture local details and attain a comprehensive global perception. While recent advancements have focused on aligning object expressions with grounding information, they typically lack explicit integration of object images, which contain affluent information beyond mere texts or coordinates. To bridge this gap, we introduce a novel fine-grained visual knowledge alignment method that effectively aligns and integrates multi-scale knowledge of objects, including texts, coordinates, and images. This innovative method is underpinned by our multi-scale fine-grained enhancement data synthesis pipeline, which provides over 300K essential training data to enhance alignment and improve overall performance. Furthermore, we present TinyGroundingGPT, a series of compact models optimized for high-level alignments. With a scale of approximately 3B parameters, TinyGroundingGPT achieves outstanding results in grounding tasks while delivering performance comparable to larger MLLMs in complex visual scenarios.

Recent advances in vision-language models (VLMs) have demonstrated remarkable zero-shot capabilities, yet adapting these models to specialized domains remains a significant challenge. Building on recent theoretical insights suggesting that independently trained VLMs are related by a canonical transformation, we extend this understanding to the concept of domains. We hypothesize that image features across disparate domains are related by a canonicalized geometric transformation that can be recovered using a small set of anchors. Few-shot classification provides a natural setting for this alignment, as the limited labeled samples serve as the anchors required to estimate this transformation. Motivated by this hypothesis, we introduce BiCLIP, a framework that applies a targeted transformation to multimodal features to enhance cross-modal alignment. Our approach is characterized by its extreme simplicity and low parameter footprint. Extensive evaluations across 11 standard benchmarks, including EuroSAT, DTD, and FGVCAircraft, demonstrate that BiCLIP consistently achieves state-of-the-art results. Furthermore, we provide empirical verification of existing geometric findings by analyzing the orthogonality and angular distribution of the learned transformations, confirming that structured alignment is the key to robust domain adaptation. Code is available at https://github.com/QuantitativeImagingLaboratory/BilinearCLIP

Multilingual Alignment is an effective and representative paradigm to enhance LLMs' multilingual capabilities, which transfers the capabilities from the high-resource languages to the low-resource languages. Meanwhile, some researches on language-specific neurons reveal that there are language-specific neurons that are selectively activated in LLMs when processing different languages. This provides a new perspective to analyze and understand LLMs' mechanisms more specifically in multilingual scenarios. In this work, we propose a new finer-grained neuron identification algorithm, which detects language neurons~(including language-specific neurons and language-related neurons) and language-agnostic neurons. Furthermore, based on the distributional characteristics of different types of neurons, we divide the LLMs' internal process for multilingual inference into four parts: (1) multilingual understanding, (2) shared semantic space reasoning, (3) multilingual output space transformation, and (4) vocabulary space outputting. Additionally, we systematically analyze the models before and after alignment with a focus on different types of neurons. We also analyze the phenomenon of ''Spontaneous Multilingual Alignment''. Overall, our work conducts a comprehensive investigation based on different types of neurons, providing empirical results and valuable insights for better understanding multilingual alignment and multilingual capabilities of LLMs.

We create a framework for bootstrapping visual representation learning from a primitive visual grouping capability. We operationalize grouping via a contour detector that partitions an image into regions, followed by merging of those regions into a tree hierarchy. A small supervised dataset suffices for training this grouping primitive. Across a large unlabeled dataset, we apply this learned primitive to automatically predict hierarchical region structure. These predictions serve as guidance for self-supervised contrastive feature learning: we task a deep network with producing per-pixel embeddings whose pairwise distances respect the region hierarchy. Experiments demonstrate that our approach can serve as state-of-the-art generic pre-training, benefiting downstream tasks. We additionally explore applications to semantic region search and video-based object instance tracking.

Current perceptual similarity metrics operate at the level of pixels and patches. These metrics compare images in terms of their low-level colors and textures, but fail to capture mid-level similarities and differences in image layout, object pose, and semantic content. In this paper, we develop a perceptual metric that assesses images holistically. Our first step is to collect a new dataset of human similarity judgments over image pairs that are alike in diverse ways. Critical to this dataset is that judgments are nearly automatic and shared by all observers. To achieve this we use recent text-to-image models to create synthetic pairs that are perturbed along various dimensions. We observe that popular perceptual metrics fall short of explaining our new data, and we introduce a new metric, DreamSim, tuned to better align with human perception. We analyze how our metric is affected by different visual attributes, and find that it focuses heavily on foreground objects and semantic content while also being sensitive to color and layout. Notably, despite being trained on synthetic data, our metric generalizes to real images, giving strong results on retrieval and reconstruction tasks. Furthermore, our metric outperforms both prior learned metrics and recent large vision models on these tasks.

Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.

Shapley value-based methods have become foundational in explainable artificial intelligence (XAI), offering theoretically grounded feature attributions through cooperative game theory. However, in practice, particularly in vision tasks, the assumption of feature independence breaks down, as features (i.e., pixels) often exhibit strong spatial and semantic dependencies. To address this, modern SHAP implementations now include the Owen value, a hierarchical generalization of the Shapley value that supports group attributions. While the Owen value preserves the foundations of Shapley values, its effectiveness critically depends on how feature groups are defined. We show that commonly used segmentations (e.g., axis-aligned or SLIC) violate key consistency properties, and propose a new segmentation approach that satisfies the T-property to ensure semantic alignment across hierarchy levels. This hierarchy enables computational pruning while improving attribution accuracy and interpretability. Experiments on image and tabular datasets demonstrate that O-Shap outperforms baseline SHAP variants in attribution precision, semantic coherence, and runtime efficiency, especially when structure matters.

The unsupervised task of Joint Alignment (JA) of images is beset by challenges such as high complexity, geometric distortions, and convergence to poor local or even global optima. Although Vision Transformers (ViT) have recently provided valuable features for JA, they fall short of fully addressing these issues. Consequently, researchers frequently depend on expensive models and numerous regularization terms, resulting in long training times and challenging hyperparameter tuning. We introduce the Spatial Joint Alignment Model (SpaceJAM), a novel approach that addresses the JA task with efficiency and simplicity. SpaceJAM leverages a compact architecture with only 16K trainable parameters and uniquely operates without the need for regularization or atlas maintenance. Evaluations on SPair-71K and CUB datasets demonstrate that SpaceJAM matches the alignment capabilities of existing methods while significantly reducing computational demands and achieving at least a 10x speedup. SpaceJAM sets a new standard for rapid and effective image alignment, making the process more accessible and efficient. Our code is available at: https://bgu-cs-vil.github.io/SpaceJAM/.

Recent approaches have shown that large-scale vision-language models such as CLIP can improve semantic segmentation performance. These methods typically aim for pixel-level vision-language alignment, but often rely on low resolution image features from CLIP, resulting in class ambiguities along boundaries. Moreover, the global scene representations in CLIP text embeddings do not directly correlate with the local and detailed pixel-level features, making meaningful alignment more difficult. To address these limitations, we introduce MTA-CLIP, a novel framework employing mask-level vision-language alignment. Specifically, we first propose Mask-Text Decoder that enhances the mask representations using rich textual data with the CLIP language model. Subsequently, it aligns mask representations with text embeddings using Mask-to-Text Contrastive Learning. Furthermore, we introduce MaskText Prompt Learning, utilizing multiple context-specific prompts for text embeddings to capture diverse class representations across masks. Overall, MTA-CLIP achieves state-of-the-art, surpassing prior works by an average of 2.8% and 1.3% on on standard benchmark datasets, ADE20k and Cityscapes, respectively.

Large-scale vision-language models (VLMs), such as CLIP, have achieved remarkable success in zero-shot learning (ZSL) by leveraging large-scale visual-text pair datasets. However, these methods often lack interpretability, as they compute the similarity between an entire query image and the embedded category words, making it difficult to explain their predictions. One approach to address this issue is to develop interpretable models by integrating language, where classifiers are built using discrete attributes, similar to human perception. This introduces a new challenge: how to effectively align local visual features with corresponding attributes based on pre-trained VLMs. To tackle this, we propose LaZSL, a locally-aligned vision-language model for interpretable ZSL. LaZSL employs local visual-semantic alignment via optimal transport to perform interaction between visual regions and their associated attributes, facilitating effective alignment and providing interpretable similarity without the need for additional training. Extensive experiments demonstrate that our method offers several advantages, including enhanced interpretability, improved accuracy, and strong domain generalization. Codes available at: https://github.com/shiming-chen/LaZSL.

Contrastive learning-based vision-language pre-training approaches, such as CLIP, have demonstrated great success in many vision-language tasks. These methods achieve cross-modal alignment by encoding a matched image-text pair with similar feature embeddings, which are generated by aggregating information from visual patches and language tokens. However, direct aligning cross-modal information using such representations is challenging, as visual patches and text tokens differ in semantic levels and granularities. To alleviate this issue, we propose a Finite Discrete Tokens (FDT) based multimodal representation. FDT is a set of learnable tokens representing certain visual-semantic concepts. Both images and texts are embedded using shared FDT by first grounding multimodal inputs to FDT space and then aggregating the activated FDT representations. The matched visual and semantic concepts are enforced to be represented by the same set of discrete tokens by a sparse activation constraint. As a result, the granularity gap between the two modalities is reduced. Through both quantitative and qualitative analyses, we demonstrate that using FDT representations in CLIP-style models improves cross-modal alignment and performance in visual recognition and vision-language downstream tasks. Furthermore, we show that our method can learn more comprehensive representations, and the learned FDT capture meaningful cross-modal correspondence, ranging from objects to actions and attributes.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Recently, Multimodal Large Language Models (MLLMs) that enable Large Language Models (LLMs) to interpret images through visual instruction tuning have achieved significant success. However, existing visual instruction tuning methods only utilize image-language instruction data to align the language and image modalities, lacking a more fine-grained cross-modal alignment. In this paper, we propose Position-enhanced Visual Instruction Tuning (PVIT), which extends the functionality of MLLMs by integrating an additional region-level vision encoder. This integration promotes a more detailed comprehension of images for the MLLM. In addition, to efficiently achieve a fine-grained alignment between the vision modules and the LLM, we design multiple data generation strategies to construct an image-region-language instruction dataset. Finally, we present both quantitative experiments and qualitative analysis that demonstrate the superiority of the proposed model. Code and data will be released at https://github.com/THUNLP-MT/PVIT.

Large Vision-Language Models (LVLMs) encode visual inputs as dense sequences of patch-level tokens to capture fine-grained semantics. These visual tokens often outnumber their textual counterparts by a large margin, leading to substantial computational overhead and limiting the scalability of LVLMs in practice. Previous efforts have explored visual token reduction either prior to or within the large language models (LLMs). However, most in-LLM reduction approaches rely on text-conditioned interactions, implicitly assuming that textual tokens can reliably capture the importance of visual tokens. In this work, we revisit this assumption and reveal causal, semantic, and spatial forms of cross-modal misalignment. These misalignments undermine the effectiveness of text-guided visual token reduction. To address this, we introduce VisionDrop, a training-free, visual-only pruning framework that selects informative visual tokens based on intra-modal (visual-to-visual) attention, without relying on textual signals. To further suppress redundancy throughout the model hierarchy, we treat the visual encoder and the LLM as a unified system and design a progressive pruning pipeline. Our method performs dominant token selection and lightweight contextual merging at multiple stages, enabling fine-grained visual information to be retained even under aggressive token budgets. Extensive experiments across diverse benchmarks show that VisionDrop achieves consistent improvements over existing approaches, despite requiring no additional training or complex modifications. Notably, when integrated with LLaVA-NeXT-7B, VisionDrop achieves a 2.7x reduction in inference latency and 6x in FLOPs, while retaining 95.71% of the original performance.

Aligned text-image encoders such as CLIP have become the de facto model for vision-language tasks. Furthermore, modality-specific encoders achieve impressive performances in their respective domains. This raises a central question: does an alignment exist between uni-modal vision and language encoders since they fundamentally represent the same physical world? Analyzing the latent spaces structure of vision and language models on image-caption benchmarks using the Centered Kernel Alignment (CKA), we find that the representation spaces of unaligned and aligned encoders are semantically similar. In the absence of statistical similarity in aligned encoders like CLIP, we show that a possible matching of unaligned encoders exists without any training. We frame this as a seeded graph-matching problem exploiting the semantic similarity between graphs and propose two methods - a Fast Quadratic Assignment Problem optimization, and a novel localized CKA metric-based matching/retrieval. We demonstrate the effectiveness of this on several downstream tasks including cross-lingual, cross-domain caption matching and image classification. Code available at github.com/mayug/0-shot-llm-vision.

Unsupervised domain adaptation for medical image segmentation remains a significant challenge due to substantial domain shifts across imaging modalities, such as CT and MRI. While recent vision-language representation learning methods have shown promise, their potential in UDA segmentation tasks remains underexplored. To address this gap, we propose TCSA-UDA, a Text-driven Cross-Semantic Alignment framework that leverages domain-invariant textual class descriptions to guide visual representation learning. Our approach introduces a vision-language covariance cosine loss to directly align image encoder features with inter-class textual semantic relations, encouraging semantically meaningful and modality-invariant feature representations. Additionally, we incorporate a prototype alignment module that aligns class-wise pixel-level feature distributions across domains using high-level semantic prototypes. This mitigates residual category-level discrepancies and enhances cross-modal consistency. Extensive experiments on challenging cross-modality cardiac, abdominal, and brain tumor segmentation benchmarks demonstrate that our TCSA-UDA framework significantly reduces domain shift and consistently outperforms state-of-the-art UDA methods, establishing a new paradigm for integrating language-driven semantics into domain-adaptive medical image analysis.

Large vision-language models (LVLMs) are markedly proficient in deriving visual representations guided by natural language. Recent explorations have utilized LVLMs to tackle zero-shot visual anomaly detection (VAD) challenges by pairing images with textual descriptions indicative of normal and abnormal conditions, referred to as anomaly prompts. However, existing approaches depend on static anomaly prompts that are prone to cross-semantic ambiguity, and prioritize global image-level representations over crucial local pixel-level image-to-text alignment that is necessary for accurate anomaly localization. In this paper, we present ALFA, a training-free approach designed to address these challenges via a unified model. We propose a run-time prompt adaptation strategy, which first generates informative anomaly prompts to leverage the capabilities of a large language model (LLM). This strategy is enhanced by a contextual scoring mechanism for per-image anomaly prompt adaptation and cross-semantic ambiguity mitigation. We further introduce a novel fine-grained aligner to fuse local pixel-level semantics for precise anomaly localization, by projecting the image-text alignment from global to local semantic spaces. Extensive evaluations on MVTec and VisA datasets confirm ALFA's effectiveness in harnessing the language potential for zero-shot VAD, achieving significant PRO improvements of 12.1% on MVTec and 8.9% on VisA compared to state-of-the-art approaches.