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Apr 23

TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks

Motivation: The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose TITAN (Tcr epITope bimodal Attention Networks), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes. Results: By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-distance-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures.

  • 3 authors
·
Apr 21, 2021

TiC: Exploring Vision Transformer in Convolution

While models derived from Vision Transformers (ViTs) have been phonemically surging, pre-trained models cannot seamlessly adapt to arbitrary resolution images without altering the architecture and configuration, such as sampling the positional encoding, limiting their flexibility for various vision tasks. For instance, the Segment Anything Model (SAM) based on ViT-Huge requires all input images to be resized to 1024times1024. To overcome this limitation, we propose the Multi-Head Self-Attention Convolution (MSA-Conv) that incorporates Self-Attention within generalized convolutions, including standard, dilated, and depthwise ones. Enabling transformers to handle images of varying sizes without retraining or rescaling, the use of MSA-Conv further reduces computational costs compared to global attention in ViT, which grows costly as image size increases. Later, we present the Vision Transformer in Convolution (TiC) as a proof of concept for image classification with MSA-Conv, where two capacity enhancing strategies, namely Multi-Directional Cyclic Shifted Mechanism and Inter-Pooling Mechanism, have been proposed, through establishing long-distance connections between tokens and enlarging the effective receptive field. Extensive experiments have been carried out to validate the overall effectiveness of TiC. Additionally, ablation studies confirm the performance improvement made by MSA-Conv and the two capacity enhancing strategies separately. Note that our proposal aims at studying an alternative to the global attention used in ViT, while MSA-Conv meets our goal by making TiC comparable to state-of-the-art on ImageNet-1K. Code will be released at https://github.com/zs670980918/MSA-Conv.

  • 4 authors
·
Oct 6, 2023

Bidirectional Hierarchical Protein Multi-Modal Representation Learning

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural context. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. This bidirectional and hierarchical (Bi-Hierarchical) fusion approach leverages the strengths of both modalities to capture richer and more comprehensive protein representations. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including enzyme EC classification, model quality assessment, protein-ligand binding affinity prediction, protein-protein binding site prediction, and B cell epitopes prediction. Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of Bi-Hierarchical Fusion in bridging sequence and structural modalities.

  • 5 authors
·
Apr 7, 2025

Token Coordinated Prompt Attention is Needed for Visual Prompting

Visual prompting techniques are widely used to efficiently fine-tune pretrained Vision Transformers (ViT) by learning a small set of shared prompts for all tokens. However, existing methods overlook the unique roles of different tokens in conveying discriminative information and interact with all tokens using the same prompts, thereby limiting the representational capacity of ViT. This often leads to indistinguishable and biased prompt-extracted features, hindering performance. To address this issue, we propose a plug-and-play Token Coordinated Prompt Attention (TCPA) module, which assigns specific coordinated prompts to different tokens for attention-based interactions. Firstly, recognizing the distinct functions of CLS and image tokens-global information aggregation and local feature extraction, we disentangle the prompts into CLS Prompts and Image Prompts, which interact exclusively with CLS tokens and image tokens through attention mechanisms. This enhances their respective discriminative abilities. Furthermore, as different image tokens correspond to distinct image patches and contain diverse information, we employ a matching function to automatically assign coordinated prompts to individual tokens. This enables more precise attention interactions, improving the diversity and representational capacity of the extracted features. Extensive experiments across various benchmarks demonstrate that TCPA significantly enhances the diversity and discriminative power of the extracted features. The code is available at https://github.com/zhoujiahuan1991/ICML2025-TCPA.

  • 4 authors
·
May 5, 2025

Cross-Modal Translation and Alignment for Survival Analysis

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

  • 2 authors
·
Sep 22, 2023

MODA: MOdular Duplex Attention for Multimodal Perception, Cognition, and Emotion Understanding

Multimodal large language models (MLLMs) recently showed strong capacity in integrating data among multiple modalities, empowered by a generalizable attention architecture. Advanced methods predominantly focus on language-centric tuning while less exploring multimodal tokens mixed through attention, posing challenges in high-level tasks that require fine-grained cognition and emotion understanding. In this work, we identify the attention deficit disorder problem in multimodal learning, caused by inconsistent cross-modal attention and layer-by-layer decayed attention activation. To address this, we propose a novel attention mechanism, termed MOdular Duplex Attention (MODA), simultaneously conducting the inner-modal refinement and inter-modal interaction. MODA employs a correct-after-align strategy to effectively decouple modality alignment from cross-layer token mixing. In the alignment phase, tokens are mapped to duplex modality spaces based on the basis vectors, enabling the interaction between visual and language modality. Further, the correctness of attention scores is ensured through adaptive masked attention, which enhances the model's flexibility by allowing customizable masking patterns for different modalities. Extensive experiments on 21 benchmark datasets verify the effectiveness of MODA in perception, cognition, and emotion tasks. Source code and demo are available in https://zzcheng.top/MODA.

  • 10 authors
·
Jul 6, 2025

Multimodal Optimal Transport-based Co-Attention Transformer with Global Structure Consistency for Survival Prediction

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

  • 2 authors
·
Jun 14, 2023

PatchCT: Aligning Patch Set and Label Set with Conditional Transport for Multi-Label Image Classification

Multi-label image classification is a prediction task that aims to identify more than one label from a given image. This paper considers the semantic consistency of the latent space between the visual patch and linguistic label domains and introduces the conditional transport (CT) theory to bridge the acknowledged gap. While recent cross-modal attention-based studies have attempted to align such two representations and achieved impressive performance, they required carefully-designed alignment modules and extra complex operations in the attention computation. We find that by formulating the multi-label classification as a CT problem, we can exploit the interactions between the image and label efficiently by minimizing the bidirectional CT cost. Specifically, after feeding the images and textual labels into the modality-specific encoders, we view each image as a mixture of patch embeddings and a mixture of label embeddings, which capture the local region features and the class prototypes, respectively. CT is then employed to learn and align those two semantic sets by defining the forward and backward navigators. Importantly, the defined navigators in CT distance model the similarities between patches and labels, which provides an interpretable tool to visualize the learned prototypes. Extensive experiments on three public image benchmarks show that the proposed model consistently outperforms the previous methods.

  • 7 authors
·
Jul 18, 2023

MoCa: Modality-aware Continual Pre-training Makes Better Bidirectional Multimodal Embeddings

Multimodal embedding models, built upon causal Vision Language Models (VLMs), have shown promise in various tasks. However, current approaches face three key limitations: the use of causal attention in VLM backbones is suboptimal for embedding tasks; scalability issues due to reliance on high-quality labeled paired data for contrastive learning; and limited diversity in training objectives and data. To address these issues, we propose MoCa, a two-stage framework for transforming pre-trained VLMs into effective bidirectional multimodal embedding models. The first stage, Modality-aware Continual Pre-training, introduces a joint reconstruction objective that simultaneously denoises interleaved text and image inputs, enhancing bidirectional context-aware reasoning. The second stage, Heterogeneous Contrastive Fine-tuning, leverages diverse, semantically rich multimodal data beyond simple image-caption pairs to enhance generalization and alignment. Our method addresses the stated limitations by introducing bidirectional attention through continual pre-training, scaling effectively with massive unlabeled datasets via joint reconstruction objectives, and utilizing diverse multimodal data for enhanced representation robustness. Experiments demonstrate that MoCa consistently improves performance across MMEB and ViDoRe-v2 benchmarks, achieving new state-of-the-art results, and exhibits strong scalability with both model size and training data on MMEB.

  • 7 authors
·
Jun 29, 2025 1

Multi-Granularity Cross-modal Alignment for Generalized Medical Visual Representation Learning

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.

  • 5 authors
·
Oct 12, 2022

MEDUSA: Multi-scale Encoder-Decoder Self-Attention Deep Neural Network Architecture for Medical Image Analysis

Medical image analysis continues to hold interesting challenges given the subtle characteristics of certain diseases and the significant overlap in appearance between diseases. In this work, we explore the concept of self-attention for tackling such subtleties in and between diseases. To this end, we introduce MEDUSA, a multi-scale encoder-decoder self-attention mechanism tailored for medical image analysis. While self-attention deep convolutional neural network architectures in existing literature center around the notion of multiple isolated lightweight attention mechanisms with limited individual capacities being incorporated at different points in the network architecture, MEDUSA takes a significant departure from this notion by possessing a single, unified self-attention mechanism with significantly higher capacity with multiple attention heads feeding into different scales in the network architecture. To the best of the authors' knowledge, this is the first "single body, multi-scale heads" realization of self-attention and enables explicit global context amongst selective attention at different levels of representational abstractions while still enabling differing local attention context at individual levels of abstractions. With MEDUSA, we obtain state-of-the-art performance on multiple challenging medical image analysis benchmarks including COVIDx, RSNA RICORD, and RSNA Pneumonia Challenge when compared to previous work. Our MEDUSA model is publicly available.

  • 7 authors
·
Oct 12, 2021

From Narrow to Panoramic Vision: Attention-Guided Cold-Start Reshapes Multimodal Reasoning

The cold-start initialization stage plays a pivotal role in training Multimodal Large Reasoning Models (MLRMs), yet its mechanisms remain insufficiently understood. To analyze this stage, we introduce the Visual Attention Score (VAS), an attention-based metric that quantifies how much a model attends to visual tokens. We find that reasoning performance is strongly correlated with VAS (r=0.9616): models with higher VAS achieve substantially stronger multimodal reasoning. Surprisingly, multimodal cold-start fails to elevate VAS, resulting in attention distributions close to the base model, whereas text-only cold-start leads to a clear increase. We term this counter-intuitive phenomenon Lazy Attention Localization. To validate its causal role, we design training-free interventions that directly modulate attention allocation during inference, performance gains of 1-2% without any retraining. Building on these insights, we further propose Attention-Guided Visual Anchoring and Reflection (AVAR), a comprehensive cold-start framework that integrates visual-anchored data synthesis, attention-guided objectives, and visual-anchored reward shaping. Applied to Qwen2.5-VL-7B, AVAR achieves an average gain of 7.0% across 7 multimodal reasoning benchmarks. Ablation studies further confirm that each component of AVAR contributes step-wise to the overall gains. The code, data, and models are available at https://github.com/lrlbbzl/Qwen-AVAR.

Qwen Qwen
·
Mar 4 2

Medical Image Classification with KAN-Integrated Transformers and Dilated Neighborhood Attention

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.

  • 5 authors
·
Feb 19, 2025 1

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

  • 16 authors
·
Jan 13, 2025 3

Seeing is Understanding: Unlocking Causal Attention into Modality-Mutual Attention for Multimodal LLMs

Recent Multimodal Large Language Models (MLLMs) have demonstrated significant progress in perceiving and reasoning over multimodal inquiries, ushering in a new research era for foundation models. However, vision-language misalignment in MLLMs has emerged as a critical challenge, where the textual responses generated by these models are not factually aligned with the given text-image inputs. Existing efforts to address vision-language misalignment have focused on developing specialized vision-language connectors or leveraging visual instruction tuning from diverse domains. In this paper, we tackle this issue from a fundamental yet unexplored perspective by revisiting the core architecture of MLLMs. Most MLLMs are typically built on decoder-only LLMs consisting of a causal attention mechanism, which limits the ability of earlier modalities (e.g., images) to incorporate information from later modalities (e.g., text). To address this problem, we propose AKI, a novel MLLM that unlocks causal attention into modality-mutual attention (MMA) to enable image tokens to attend to text tokens. This simple yet effective design allows AKI to achieve superior performance in 12 multimodal understanding benchmarks (+7.2% on average) without introducing additional parameters and increasing training time. Our MMA design is intended to be generic, allowing for application across various modalities, and scalable to accommodate diverse multimodal scenarios. The code is publicly available at https://github.com/sony/aki, and we will release our AKI-4B model to encourage further advancements in MLLMs across various directions.

  • 4 authors
·
Mar 4, 2025

BioD2C: A Dual-level Semantic Consistency Constraint Framework for Biomedical VQA

Biomedical visual question answering (VQA) has been widely studied and has demonstrated significant application value and potential in fields such as assistive medical diagnosis. Despite their success, current biomedical VQA models perform multimodal information interaction only at the model level within large language models (LLMs), leading to suboptimal multimodal semantic alignment when dealing with complex tasks. To address this issue, we propose BioD2C: a novel Dual-level Semantic Consistency Constraint Framework for Biomedical VQA, which achieves dual-level semantic interaction alignment at both the model and feature levels, enabling the model to adaptively learn visual features based on the question. Specifically, we firstly integrate textual features into visual features via an image-text fusion mechanism as feature-level semantic interaction, obtaining visual features conditioned on the given text; and then introduce a text-queue-based cross-modal soft semantic loss function to further align the image semantics with the question semantics. Specifically, in this work, we establish a new dataset, BioVGQ, to address inherent biases in prior datasets by filtering manually-altered images and aligning question-answer pairs with multimodal context, and train our model on this dataset. Extensive experimental results demonstrate that BioD2C achieves state-of-the-art (SOTA) performance across multiple downstream datasets, showcasing its robustness, generalizability, and potential to advance biomedical VQA research.

  • 5 authors
·
Mar 4, 2025

MedTrinity-25M: A Large-scale Multimodal Dataset with Multigranular Annotations for Medicine

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

  • 11 authors
·
Aug 5, 2024 2

Learning Modality-Aware Representations: Adaptive Group-wise Interaction Network for Multimodal MRI Synthesis

Multimodal MR image synthesis aims to generate missing modality images by effectively fusing and mapping from a subset of available MRI modalities. Most existing methods adopt an image-to-image translation paradigm, treating multiple modalities as input channels. However, these approaches often yield sub-optimal results due to the inherent difficulty in achieving precise feature- or semantic-level alignment across modalities. To address these challenges, we propose an Adaptive Group-wise Interaction Network (AGI-Net) that explicitly models both inter-modality and intra-modality relationships for multimodal MR image synthesis. Specifically, feature channels are first partitioned into predefined groups, after which an adaptive rolling mechanism is applied to conventional convolutional kernels to better capture feature and semantic correspondences between different modalities. In parallel, a cross-group attention module is introduced to enable effective feature fusion across groups, thereby enhancing the network's representational capacity. We validate the proposed AGI-Net on the publicly available IXI and BraTS2023 datasets. Experimental results demonstrate that AGI-Net achieves state-of-the-art performance in multimodal MR image synthesis tasks, confirming the effectiveness of its modality-aware interaction design. We release the relevant code at: https://github.com/zunzhumu/Adaptive-Group-wise-Interaction-Network-for-Multimodal-MRI-Synthesis.git.

  • 9 authors
·
Nov 21, 2024

BEVANet: Bilateral Efficient Visual Attention Network for Real-Time Semantic Segmentation

Real-time semantic segmentation presents the dual challenge of designing efficient architectures that capture large receptive fields for semantic understanding while also refining detailed contours. Vision transformers model long-range dependencies effectively but incur high computational cost. To address these challenges, we introduce the Large Kernel Attention (LKA) mechanism. Our proposed Bilateral Efficient Visual Attention Network (BEVANet) expands the receptive field to capture contextual information and extracts visual and structural features using Sparse Decomposed Large Separable Kernel Attentions (SDLSKA). The Comprehensive Kernel Selection (CKS) mechanism dynamically adapts the receptive field to further enhance performance. Furthermore, the Deep Large Kernel Pyramid Pooling Module (DLKPPM) enriches contextual features by synergistically combining dilated convolutions and large kernel attention. The bilateral architecture facilitates frequent branch communication, and the Boundary Guided Adaptive Fusion (BGAF) module enhances boundary delineation by integrating spatial and semantic features under boundary guidance. BEVANet achieves real-time segmentation at 33 FPS, yielding 79.3% mIoU without pretraining and 81.0% mIoU on Cityscapes after ImageNet pretraining, demonstrating state-of-the-art performance. The code and model is available at https://github.com/maomao0819/BEVANet.

  • 5 authors
·
Aug 10, 2025

Multimodal Data Integration for Oncology in the Era of Deep Neural Networks: A Review

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

  • 5 authors
·
Mar 11, 2023

Bi-Bimodal Modality Fusion for Correlation-Controlled Multimodal Sentiment Analysis

Multimodal sentiment analysis aims to extract and integrate semantic information collected from multiple modalities to recognize the expressed emotions and sentiment in multimodal data. This research area's major concern lies in developing an extraordinary fusion scheme that can extract and integrate key information from various modalities. However, one issue that may restrict previous work to achieve a higher level is the lack of proper modeling for the dynamics of the competition between the independence and relevance among modalities, which could deteriorate fusion outcomes by causing the collapse of modality-specific feature space or introducing extra noise. To mitigate this, we propose the Bi-Bimodal Fusion Network (BBFN), a novel end-to-end network that performs fusion (relevance increment) and separation (difference increment) on pairwise modality representations. The two parts are trained simultaneously such that the combat between them is simulated. The model takes two bimodal pairs as input due to the known information imbalance among modalities. In addition, we leverage a gated control mechanism in the Transformer architecture to further improve the final output. Experimental results on three datasets (CMU-MOSI, CMU-MOSEI, and UR-FUNNY) verifies that our model significantly outperforms the SOTA. The implementation of this work is available at https://github.com/declare-lab/multimodal-deep-learning.

  • 6 authors
·
Jul 28, 2021

Toward a Vision-Language Foundation Model for Medical Data: Multimodal Dataset and Benchmarks for Vietnamese PET/CT Report Generation

Vision-Language Foundation Models (VLMs), trained on large-scale multimodal datasets, have driven significant advances in Artificial Intelligence (AI) by enabling rich cross-modal reasoning. Despite their success in general domains, applying these models to medical imaging remains challenging due to the limited availability of diverse imaging modalities and multilingual clinical data. Most existing medical VLMs are trained on a subset of imaging modalities and focus primarily on high-resource languages, thus limiting their generalizability and clinical utility. To address these limitations, we introduce a novel Vietnamese-language multimodal medical dataset consisting of 2,757 whole-body PET/CT volumes from independent patients and their corresponding full-length clinical reports. This dataset is designed to fill two pressing gaps in medical AI development: (1) the lack of PET/CT imaging data in existing VLMs training corpora, which hinders the development of models capable of handling functional imaging tasks; and (2) the underrepresentation of low-resource languages, particularly the Vietnamese language, in medical vision-language research. To the best of our knowledge, this is the first dataset to provide comprehensive PET/CT-report pairs in Vietnamese. We further introduce a training framework to enhance VLMs' learning, including data augmentation and expert-validated test sets. We conduct comprehensive experiments benchmarking state-of-the-art VLMs on downstream tasks. The experimental results show that incorporating our dataset significantly improves the performance of existing VLMs. We believe this dataset and benchmark will serve as a pivotal step in advancing the development of more robust VLMs for medical imaging, especially for low-resource languages and clinical use in Vietnamese healthcare. The source code is available at https://github.com/AIoT-Lab-BKAI/ViPET-ReportGen.

  • 14 authors
·
Jan 31

ShizhenGPT: Towards Multimodal LLMs for Traditional Chinese Medicine

Despite the success of large language models (LLMs) in various domains, their potential in Traditional Chinese Medicine (TCM) remains largely underexplored due to two critical barriers: (1) the scarcity of high-quality TCM data and (2) the inherently multimodal nature of TCM diagnostics, which involve looking, listening, smelling, and pulse-taking. These sensory-rich modalities are beyond the scope of conventional LLMs. To address these challenges, we present ShizhenGPT, the first multimodal LLM tailored for TCM. To overcome data scarcity, we curate the largest TCM dataset to date, comprising 100GB+ of text and 200GB+ of multimodal data, including 1.2M images, 200 hours of audio, and physiological signals. ShizhenGPT is pretrained and instruction-tuned to achieve deep TCM knowledge and multimodal reasoning. For evaluation, we collect recent national TCM qualification exams and build a visual benchmark for Medicinal Recognition and Visual Diagnosis. Experiments demonstrate that ShizhenGPT outperforms comparable-scale LLMs and competes with larger proprietary models. Moreover, it leads in TCM visual understanding among existing multimodal LLMs and demonstrates unified perception across modalities like sound, pulse, smell, and vision, paving the way toward holistic multimodal perception and diagnosis in TCM. Datasets, models, and code are publicly available. We hope this work will inspire further exploration in this field.

  • 13 authors
·
Aug 20, 2025 1

Think Twice to See More: Iterative Visual Reasoning in Medical VLMs

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

  • 9 authors
·
Oct 11, 2025

MEDVISTAGYM: A Scalable Training Environment for Thinking with Medical Images via Tool-Integrated Reinforcement Learning

Vision language models (VLMs) achieve strong performance on general image understanding but struggle to think with medical images, especially when performing multi-step reasoning through iterative visual interaction. Medical VLMs often rely on static visual embeddings and single-pass inference, preventing models from re-examining, verifying, or refining visual evidence during reasoning. While tool-integrated reasoning offers a promising path forward, open-source VLMs lack the training infrastructure to learn effective tool selection, invocation, and coordination in multi-modal medical reasoning. We introduce MedVistaGym, a scalable and interactive training environment that incentivizes tool-integrated visual reasoning for medical image analysis. MedVistaGym equips VLMs to determine when and which tools to invoke, localize task-relevant image regions, and integrate single or multiple sub-image evidence into interleaved multimodal reasoning within a unified, executable interface for agentic training. Using MedVistaGym, we train MedVistaGym-R1 to interleave tool use with agentic reasoning through trajectory sampling and end-to-end reinforcement learning. Across six medical VQA benchmarks, MedVistaGym-R1-8B exceeds comparably sized tool-augmented baselines by 19.10% to 24.21%, demonstrating that structured agentic training--not tool access alone--unlocks effective tool-integrated reasoning for medical image analysis.

  • 9 authors
·
Jan 11

How Does Attention Work in Vision Transformers? A Visual Analytics Attempt

Vision transformer (ViT) expands the success of transformer models from sequential data to images. The model decomposes an image into many smaller patches and arranges them into a sequence. Multi-head self-attentions are then applied to the sequence to learn the attention between patches. Despite many successful interpretations of transformers on sequential data, little effort has been devoted to the interpretation of ViTs, and many questions remain unanswered. For example, among the numerous attention heads, which one is more important? How strong are individual patches attending to their spatial neighbors in different heads? What attention patterns have individual heads learned? In this work, we answer these questions through a visual analytics approach. Specifically, we first identify what heads are more important in ViTs by introducing multiple pruning-based metrics. Then, we profile the spatial distribution of attention strengths between patches inside individual heads, as well as the trend of attention strengths across attention layers. Third, using an autoencoder-based learning solution, we summarize all possible attention patterns that individual heads could learn. Examining the attention strengths and patterns of the important heads, we answer why they are important. Through concrete case studies with experienced deep learning experts on multiple ViTs, we validate the effectiveness of our solution that deepens the understanding of ViTs from head importance, head attention strength, and head attention pattern.

  • 8 authors
·
Mar 23, 2023

MoRE: Multi-Modal Contrastive Pre-training with Transformers on X-Rays, ECGs, and Diagnostic Report

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

  • 4 authors
·
Oct 21, 2024

The Linear Attention Resurrection in Vision Transformer

Vision Transformers (ViTs) have recently taken computer vision by storm. However, the softmax attention underlying ViTs comes with a quadratic complexity in time and memory, hindering the application of ViTs to high-resolution images. We revisit the attention design and propose a linear attention method to address the limitation, which doesn't sacrifice ViT's core advantage of capturing global representation like existing methods (e.g. local window attention of Swin). We further investigate the key difference between linear attention and softmax attention. Our empirical results suggest that linear attention lacks a fundamental property of concentrating the distribution of the attention matrix. Inspired by this observation, we introduce a local concentration module to enhance linear attention. By incorporating enhanced linear global attention and local window attention, we propose a new ViT architecture, dubbed L^2ViT. Notably, L^2ViT can effectively capture both global interactions and local representations while enjoying linear computational complexity. Extensive experiments demonstrate the strong performance of L^2ViT. On image classification, L^2ViT achieves 84.4% Top-1 accuracy on ImageNet-1K without any extra training data or label. By further pre-training on ImageNet-22k, it attains 87.0% when fine-tuned with resolution 384^2. For downstream tasks, L^2ViT delivers favorable performance as a backbone on object detection as well as semantic segmentation.

  • 1 authors
·
Jan 27, 2025

CRISP-SAM2: SAM2 with Cross-Modal Interaction and Semantic Prompting for Multi-Organ Segmentation

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

  • 8 authors
·
Jun 29, 2025 1

Croc: Pretraining Large Multimodal Models with Cross-Modal Comprehension

Recent advances in Large Language Models (LLMs) have catalyzed the development of Large Multimodal Models (LMMs). However, existing research primarily focuses on tuning language and image instructions, ignoring the critical pretraining phase where models learn to process textual and visual modalities jointly. In this paper, we propose a new pretraining paradigm for LMMs to enhance the visual comprehension capabilities of LLMs by introducing a novel cross-modal comprehension stage. Specifically, we design a dynamically learnable prompt token pool and employ the Hungarian algorithm to replace part of the original visual tokens with the most relevant prompt tokens. Then, we conceptualize visual tokens as analogous to a "foreign language" for the LLMs and propose a mixed attention mechanism with bidirectional visual attention and unidirectional textual attention to comprehensively enhance the understanding of visual tokens. Meanwhile, we integrate a detailed caption generation task, leveraging rich descriptions to further facilitate LLMs in understanding visual semantic information. After pretraining on 1.5 million publicly accessible data, we present a new foundation model called Croc. Experimental results demonstrate that Croc achieves new state-of-the-art performance on massive vision-language benchmarks. To support reproducibility and facilitate further research, we release the training code and pre-trained model weights at https://github.com/deepglint/Croc.

  • 11 authors
·
Oct 18, 2024

Epistemic-aware Vision-Language Foundation Model for Fetal Ultrasound Interpretation

Recent medical vision-language models have shown promise on tasks such as VQA, report generation, and anomaly detection. However, most are adapted to structured adult imaging and underperform in fetal ultrasound, which poses challenges of multi-view image reasoning, numerous diseases, and image diversity. To bridge this gap, we introduce FetalMind, a medical AI system tailored to fetal ultrasound for both report generation and diagnosis. Guided by clinical workflow, we propose Salient Epistemic Disentanglement (SED), which injects an expert-curated bipartite graph into the model to decouple view-disease associations and to steer preference selection along clinically faithful steps via reinforcement learning. This design mitigates variability across diseases and heterogeneity across views, reducing learning bottlenecks while aligning the model's inference with obstetric practice. To train FetalMind at scale, we curate FetalSigma-1M dataset, the first large-scale fetal ultrasound report corpus, comprising 20K reports from twelve medical centers, addressing the scarcity of domain data. Extensive experiments show that FetalMind outperforms open- and closed-source baselines across all gestational stages, achieving +14% average gains and +61.2% higher accuracy on critical conditions while remaining efficient, stable, and scalable. Project Page: https://hexiao0275.github.io/FetalMind.

  • 10 authors
·
Oct 14, 2025

Plug-and-Play Regulators for Image-Text Matching

Exploiting fine-grained correspondence and visual-semantic alignments has shown great potential in image-text matching. Generally, recent approaches first employ a cross-modal attention unit to capture latent region-word interactions, and then integrate all the alignments to obtain the final similarity. However, most of them adopt one-time forward association or aggregation strategies with complex architectures or additional information, while ignoring the regulation ability of network feedback. In this paper, we develop two simple but quite effective regulators which efficiently encode the message output to automatically contextualize and aggregate cross-modal representations. Specifically, we propose (i) a Recurrent Correspondence Regulator (RCR) which facilitates the cross-modal attention unit progressively with adaptive attention factors to capture more flexible correspondence, and (ii) a Recurrent Aggregation Regulator (RAR) which adjusts the aggregation weights repeatedly to increasingly emphasize important alignments and dilute unimportant ones. Besides, it is interesting that RCR and RAR are plug-and-play: both of them can be incorporated into many frameworks based on cross-modal interaction to obtain significant benefits, and their cooperation achieves further improvements. Extensive experiments on MSCOCO and Flickr30K datasets validate that they can bring an impressive and consistent R@1 gain on multiple models, confirming the general effectiveness and generalization ability of the proposed methods. Code and pre-trained models are available at: https://github.com/Paranioar/RCAR.

  • 5 authors
·
Mar 23, 2023

BiFormer: Vision Transformer with Bi-Level Routing Attention

As the core building block of vision transformers, attention is a powerful tool to capture long-range dependency. However, such power comes at a cost: it incurs a huge computation burden and heavy memory footprint as pairwise token interaction across all spatial locations is computed. A series of works attempt to alleviate this problem by introducing handcrafted and content-agnostic sparsity into attention, such as restricting the attention operation to be inside local windows, axial stripes, or dilated windows. In contrast to these approaches, we propose a novel dynamic sparse attention via bi-level routing to enable a more flexible allocation of computations with content awareness. Specifically, for a query, irrelevant key-value pairs are first filtered out at a coarse region level, and then fine-grained token-to-token attention is applied in the union of remaining candidate regions (\ie, routed regions). We provide a simple yet effective implementation of the proposed bi-level routing attention, which utilizes the sparsity to save both computation and memory while involving only GPU-friendly dense matrix multiplications. Built with the proposed bi-level routing attention, a new general vision transformer, named BiFormer, is then presented. As BiFormer attends to a small subset of relevant tokens in a query adaptive manner without distraction from other irrelevant ones, it enjoys both good performance and high computational efficiency, especially in dense prediction tasks. Empirical results across several computer vision tasks such as image classification, object detection, and semantic segmentation verify the effectiveness of our design. Code is available at https://github.com/rayleizhu/BiFormer.

  • 5 authors
·
Mar 15, 2023

VisRL: Intention-Driven Visual Perception via Reinforced Reasoning

Visual understanding is inherently intention-driven - humans selectively focus on different regions of a scene based on their goals. Recent advances in large multimodal models (LMMs) enable flexible expression of such intentions through natural language, allowing queries to guide visual reasoning processes. Frameworks like Visual Chain-of-Thought have demonstrated the benefit of incorporating explicit reasoning steps, where the model predicts a focus region before answering a query. However, existing approaches rely heavily on supervised training with annotated intermediate bounding boxes, which severely limits scalability due to the combinatorial explosion of intention-region pairs. To overcome this limitation, we propose VisRL, the first framework that applies reinforcement learning (RL) to the problem of intention-driven visual perception. VisRL optimizes the entire visual reasoning process using only reward signals. By treating intermediate focus selection as an internal decision optimized through trial-and-error, our method eliminates the need for costly region annotations while aligning more closely with how humans learn to perceive the world. Extensive experiments across multiple benchmarks show that VisRL consistently outperforms strong baselines, demonstrating both its effectiveness and its strong generalization across different LMMs. Our code is available at https://github.com/zhangquanchen/VisRL.

  • 3 authors
·
Mar 10, 2025

TextBraTS: Text-Guided Volumetric Brain Tumor Segmentation with Innovative Dataset Development and Fusion Module Exploration

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

  • 10 authors
·
Jun 20, 2025

Diagnosing and Mitigating Modality Interference in Multimodal Large Language Models

Multimodal Large Language Models have demonstrated impressive capabilities across tasks, yet they often exhibit difficulty in distinguishing task-relevant from irrelevant signals -- particularly in tasks like Visual Question Answering -- which can lead to susceptibility to misleading or spurious inputs. We refer to this broader limitation as the Cross-Modality Competency Problem -- the model's inability to fairly evaluate all modalities. This vulnerability becomes more evident in modality-specific tasks -- such as image classification or pure text question answering -- where models are expected to rely solely on one modality. In such tasks, spurious information from irrelevant modalities often leads to significant performance degradation. We refer to this failure as Modality Interference, which serves as a concrete and measurable instance of the cross-modality competency problem, and we further design a perturbation-based causal diagnostic experiment to verify and quantify this problem. To mitigate modality interference, we propose a novel framework to finetune MLLMs, including perturbation-based data augmentations with both heuristic perturbations and adversarial perturbations, and a consistency regularization strategy applying on model outputs with original and perturbed inputs. Experiments on multiple benchmark datasets (image-heavy, text-heavy and multimodal tasks) and multiple model families with different scales demonstrate significant improvements in robustness and cross-modality competency, indicating our method's effectiveness in boosting unimodal reasoning ability while enhancing performance on multimodal tasks.

ucdavis UC Davis
·
May 26, 2025

ViTGaze: Gaze Following with Interaction Features in Vision Transformers

Gaze following aims to interpret human-scene interactions by predicting the person's focal point of gaze. Prevailing approaches often adopt a two-stage framework, whereby multi-modality information is extracted in the initial stage for gaze target prediction. Consequently, the efficacy of these methods highly depends on the precision of the preceding modality extraction. Others use a single-modality approach with complex decoders, increasing network computational load. Inspired by the remarkable success of pre-trained plain vision transformers (ViTs), we introduce a novel single-modality gaze following framework called ViTGaze. In contrast to previous methods, it creates a novel gaze following framework based mainly on powerful encoders (relative decoder parameters less than 1%). Our principal insight is that the inter-token interactions within self-attention can be transferred to interactions between humans and scenes. Leveraging this presumption, we formulate a framework consisting of a 4D interaction encoder and a 2D spatial guidance module to extract human-scene interaction information from self-attention maps. Furthermore, our investigation reveals that ViT with self-supervised pre-training has an enhanced ability to extract correlation information. Many experiments have been conducted to demonstrate the performance of the proposed method. Our method achieves state-of-the-art (SOTA) performance among all single-modality methods (3.4% improvement in the area under curve (AUC) score, 5.1% improvement in the average precision (AP)) and very comparable performance against multi-modality methods with 59% number of parameters less.

  • 6 authors
·
Mar 19, 2024

BrainFLORA: Uncovering Brain Concept Representation via Multimodal Neural Embeddings

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

  • 5 authors
·
Jul 13, 2025

Remedying Target-Domain Astigmatism for Cross-Domain Few-Shot Object Detection

Cross-domain few-shot object detection (CD-FSOD) aims to adapt pretrained detectors from a source domain to target domains with limited annotations, suffering from severe domain shifts and data scarcity problems. In this work, we find a previously overlooked phenomenon: models exhibit dispersed and unfocused attention in target domains, leading to imprecise localization and redundant predictions, just like a human cannot focus on visual objects. Therefore, we call it the target-domain Astigmatism problem. Analysis on attention distances across transformer layers reveals that regular fine-tuning inherently shows a trend to remedy this problem, but results are still far from satisfactory, which we aim to enhance in this paper. Biologically inspired by the human fovea-style visual system, we enhance the fine-tuning's inherent trend through a center-periphery attention refinement framework, which contains (1) a Positive Pattern Refinement module to reshape attention toward semantic objects using class-specific prototypes, simulating the visual center region; (2) a Negative Context Modulation module to enhance boundary discrimination by modeling background context, simulating the visual periphery region; and (3) a Textual Semantic Alignment module to strengthen center-periphery distinction through cross-modal cues. Our bio-inspired approach transforms astigmatic attention into focused patterns, substantially improving adaptation to target domains. Experiments on six challenging CD-FSOD benchmarks consistently demonstrate improved detection accuracy and establish new state-of-the-art results.

  • 4 authors
·
Mar 18

See What You Are Told: Visual Attention Sink in Large Multimodal Models

Large multimodal models (LMMs) "see" images by leveraging the attention mechanism between text and visual tokens in the transformer decoder. Ideally, these models should focus on key visual information relevant to the text token. However, recent findings indicate that LMMs have an extraordinary tendency to consistently allocate high attention weights to specific visual tokens, even when these tokens are irrelevant to the corresponding text. In this study, we investigate the property behind the appearance of these irrelevant visual tokens and examine their characteristics. Our findings show that this behavior arises due to the massive activation of certain hidden state dimensions, which resembles the attention sink found in language models. Hence, we refer to this phenomenon as the visual attention sink. In particular, our analysis reveals that removing the irrelevant visual sink tokens does not impact model performance, despite receiving high attention weights. Consequently, we recycle the attention to these tokens as surplus resources, redistributing the attention budget to enhance focus on the image. To achieve this, we introduce Visual Attention Redistribution (VAR), a method that redistributes attention in image-centric heads, which we identify as innately focusing on visual information. VAR can be seamlessly applied across different LMMs to improve performance on a wide range of tasks, including general vision-language tasks, visual hallucination tasks, and vision-centric tasks, all without the need for additional training, models, or inference steps. Experimental results demonstrate that VAR enables LMMs to process visual information more effectively by adjusting their internal attention mechanisms, offering a new direction to enhancing the multimodal capabilities of LMMs.

  • 4 authors
·
Mar 5, 2025

VLMs Need Words: Vision Language Models Ignore Visual Detail In Favor of Semantic Anchors

Vision Language Models (VLMs) achieve impressive performance across a wide range of multimodal tasks. However, on some tasks that demand fine-grained visual perception, they often fail even when the required information is present in their internal representations. In this work, we demonstrate that this gap arises from their narrow training pipeline which focuses on moving visual information to the textual space. Consequently, VLMs can only reason about visual entities that can be mapped to known concepts in the language space, leaving vision-focused tasks such as visual correspondence and reasoning about novel visual entities poorly supported. As a result, VLMs are severely limited in several important multimodal capabilities because they rely on brittle, hallucinated textual descriptions of visual entities that they cannot map to textual representations. We verify this behavior through visual correspondence tasks, in which VLMs must detect matching entities between two images. Testing across semantic, shape, and face correspondence tasks, we find that VLMs perform much better when the relevant entities are nameable in language than when they are unnameable. Mechanistically, our Logit Lens analyses confirm that VLMs explicitly assign semantic labels to nameable entities and surface more unique corresponding tokens compared to unnameable entities. Furthermore, we show that teaching completely arbitrary names for unknown entities improves performance, yet task-specific finetuning yields even stronger generalization without relying on language priors. Our findings suggest that current VLM failures on visual tasks reflect learned shortcuts from their training, rather than a fundamental limitation of multimodal architectures.

  • 7 authors
·
Apr 1 2

MSM-Seg: A Modality-and-Slice Memory Framework with Category-Agnostic Prompting for Multi-Modal Brain Tumor Segmentation

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

  • 6 authors
·
Oct 12, 2025

Revealing Vision-Language Integration in the Brain with Multimodal Networks

We use (multi)modal deep neural networks (DNNs) to probe for sites of multimodal integration in the human brain by predicting stereoencephalography (SEEG) recordings taken while human subjects watched movies. We operationalize sites of multimodal integration as regions where a multimodal vision-language model predicts recordings better than unimodal language, unimodal vision, or linearly-integrated language-vision models. Our target DNN models span different architectures (e.g., convolutional networks and transformers) and multimodal training techniques (e.g., cross-attention and contrastive learning). As a key enabling step, we first demonstrate that trained vision and language models systematically outperform their randomly initialized counterparts in their ability to predict SEEG signals. We then compare unimodal and multimodal models against one another. Because our target DNN models often have different architectures, number of parameters, and training sets (possibly obscuring those differences attributable to integration), we carry out a controlled comparison of two models (SLIP and SimCLR), which keep all of these attributes the same aside from input modality. Using this approach, we identify a sizable number of neural sites (on average 141 out of 1090 total sites or 12.94%) and brain regions where multimodal integration seems to occur. Additionally, we find that among the variants of multimodal training techniques we assess, CLIP-style training is the best suited for downstream prediction of the neural activity in these sites.

  • 7 authors
·
Jun 20, 2024

Sparsifiner: Learning Sparse Instance-Dependent Attention for Efficient Vision Transformers

Vision Transformers (ViT) have shown their competitive advantages performance-wise compared to convolutional neural networks (CNNs) though they often come with high computational costs. To this end, previous methods explore different attention patterns by limiting a fixed number of spatially nearby tokens to accelerate the ViT's multi-head self-attention (MHSA) operations. However, such structured attention patterns limit the token-to-token connections to their spatial relevance, which disregards learned semantic connections from a full attention mask. In this work, we propose a novel approach to learn instance-dependent attention patterns, by devising a lightweight connectivity predictor module to estimate the connectivity score of each pair of tokens. Intuitively, two tokens have high connectivity scores if the features are considered relevant either spatially or semantically. As each token only attends to a small number of other tokens, the binarized connectivity masks are often very sparse by nature and therefore provide the opportunity to accelerate the network via sparse computations. Equipped with the learned unstructured attention pattern, sparse attention ViT (Sparsifiner) produces a superior Pareto-optimal trade-off between FLOPs and top-1 accuracy on ImageNet compared to token sparsity. Our method reduces 48% to 69% FLOPs of MHSA while the accuracy drop is within 0.4%. We also show that combining attention and token sparsity reduces ViT FLOPs by over 60%.

  • 6 authors
·
Mar 23, 2023

Envision: Benchmarking Unified Understanding & Generation for Causal World Process Insights

Current multimodal models aim to transcend the limitations of single-modality representations by unifying understanding and generation, often using text-to-image (T2I) tasks to calibrate semantic consistency. However, their reliance on static, single-image generation in training and evaluation leads to overfitting to static pattern matching and semantic fusion, while fundamentally hindering their ability to model dynamic processes that unfold over time. To address these constraints, we propose Envision-a causal event progression benchmark for chained text-to-multi-image generation. Grounded in world knowledge and structured by spatiotemporal causality, it reorganizes existing evaluation dimensions and includes 1,000 four-stage prompts spanning six scientific and humanities domains. To transition evaluation from single images to sequential frames and assess whether models truly internalize world knowledge while adhering to causal-temporal constraints, we introduce Envision-Score, a holistic metric integrating multi-dimensional consistency, physicality, and aesthetics. Comprehensive evaluation of 15 models (10 specialized T2I models, 5 unified models) uncovers: specialized T2I models demonstrate proficiency in aesthetic rendering yet lack intrinsic world knowledge. Unified multimodal models bridge this gap, consistently outperforming specialized counterparts in causal narrative coherence. However, even these unified architectures remain subordinate to closed-source models and struggle to overcome the core challenge of spatiotemporal consistency. This demonstrates that a focus on causally-isolated single images impedes multi-frame reasoning and generation, promoting static pattern matching over dynamic world modeling-ultimately limiting world knowledge internalization, generation.

opendatalab OpenDataLab
·
Dec 1, 2025 5

BiCLIP: Domain Canonicalization via Structured Geometric Transformation

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

CrossLMM: Decoupling Long Video Sequences from LMMs via Dual Cross-Attention Mechanisms

The advent of Large Multimodal Models (LMMs) has significantly enhanced Large Language Models (LLMs) to process and interpret diverse data modalities (e.g., image and video). However, as input complexity increases, particularly with long video sequences, the number of required tokens has grown significantly, leading to quadratically computational costs. This has made the efficient compression of video tokens in LMMs, while maintaining performance integrity, a pressing research challenge. In this paper, we introduce CrossLMM, decoupling long video sequences from LMMs via a dual cross-attention mechanism, which substantially reduces visual token quantity with minimal performance degradation. Specifically, we first implement a significant token reduction from pretrained visual encoders through a pooling methodology. Then, within LLM layers, we employ a visual-to-visual cross-attention mechanism, wherein the pooled visual tokens function as queries against the original visual token set. This module enables more efficient token utilization while retaining fine-grained informational fidelity. In addition, we introduce a text-to-visual cross-attention mechanism, for which the text tokens are enhanced through interaction with the original visual tokens, enriching the visual comprehension of the text tokens. Comprehensive empirical evaluation demonstrates that our approach achieves comparable or superior performance across diverse video-based LMM benchmarks, despite utilizing substantially fewer computational resources.

  • 8 authors
·
May 22, 2025

M3Net: Multimodal Multi-task Learning for 3D Detection, Segmentation, and Occupancy Prediction in Autonomous Driving

The perception system for autonomous driving generally requires to handle multiple diverse sub-tasks. However, current algorithms typically tackle individual sub-tasks separately, which leads to low efficiency when aiming at obtaining full-perception results. Some multi-task learning methods try to unify multiple tasks with one model, but do not solve the conflicts in multi-task learning. In this paper, we introduce M3Net, a novel multimodal and multi-task network that simultaneously tackles detection, segmentation, and 3D occupancy prediction for autonomous driving and achieves superior performance than single task model. M3Net takes multimodal data as input and multiple tasks via query-token interactions. To enhance the integration of multi-modal features for multi-task learning, we first propose the Modality-Adaptive Feature Integration (MAFI) module, which enables single-modality features to predict channel-wise attention weights for their high-performing tasks, respectively. Based on integrated features, we then develop task-specific query initialization strategies to accommodate the needs of detection/segmentation and 3D occupancy prediction. Leveraging the properly initialized queries, a shared decoder transforms queries and BEV features layer-wise, facilitating multi-task learning. Furthermore, we propose a Task-oriented Channel Scaling (TCS) module in the decoder to mitigate conflicts between optimizing for different tasks. Additionally, our proposed multi-task querying and TCS module support both Transformer-based decoder and Mamba-based decoder, demonstrating its flexibility to different architectures. M3Net achieves state-of-the-art multi-task learning performance on the nuScenes benchmarks.

  • 7 authors
·
Mar 23, 2025

Benchmarking Spatial Relationships in Text-to-Image Generation

Spatial understanding is a fundamental aspect of computer vision and integral for human-level reasoning about images, making it an important component for grounded language understanding. While recent text-to-image synthesis (T2I) models have shown unprecedented improvements in photorealism, it is unclear whether they have reliable spatial understanding capabilities. We investigate the ability of T2I models to generate correct spatial relationships among objects and present VISOR, an evaluation metric that captures how accurately the spatial relationship described in text is generated in the image. To benchmark existing models, we introduce a dataset, SR_{2D}, that contains sentences describing two or more objects and the spatial relationships between them. We construct an automated evaluation pipeline to recognize objects and their spatial relationships, and employ it in a large-scale evaluation of T2I models. Our experiments reveal a surprising finding that, although state-of-the-art T2I models exhibit high image quality, they are severely limited in their ability to generate multiple objects or the specified spatial relations between them. Our analyses demonstrate several biases and artifacts of T2I models such as the difficulty with generating multiple objects, a bias towards generating the first object mentioned, spatially inconsistent outputs for equivalent relationships, and a correlation between object co-occurrence and spatial understanding capabilities. We conduct a human study that shows the alignment between VISOR and human judgement about spatial understanding. We offer the SR_{2D} dataset and the VISOR metric to the community in support of T2I reasoning research.

  • 8 authors
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Dec 20, 2022

MolFM: A Multimodal Molecular Foundation Model

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

  • 5 authors
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Jun 6, 2023

MultiModN- Multimodal, Multi-Task, Interpretable Modular Networks

Predicting multiple real-world tasks in a single model often requires a particularly diverse feature space. Multimodal (MM) models aim to extract the synergistic predictive potential of multiple data types to create a shared feature space with aligned semantic meaning across inputs of drastically varying sizes (i.e. images, text, sound). Most current MM architectures fuse these representations in parallel, which not only limits their interpretability but also creates a dependency on modality availability. We present MultiModN, a multimodal, modular network that fuses latent representations in a sequence of any number, combination, or type of modality while providing granular real-time predictive feedback on any number or combination of predictive tasks. MultiModN's composable pipeline is interpretable-by-design, as well as innately multi-task and robust to the fundamental issue of biased missingness. We perform four experiments on several benchmark MM datasets across 10 real-world tasks (predicting medical diagnoses, academic performance, and weather), and show that MultiModN's sequential MM fusion does not compromise performance compared with a baseline of parallel fusion. By simulating the challenging bias of missing not-at-random (MNAR), this work shows that, contrary to MultiModN, parallel fusion baselines erroneously learn MNAR and suffer catastrophic failure when faced with different patterns of MNAR at inference. To the best of our knowledge, this is the first inherently MNAR-resistant approach to MM modeling. In conclusion, MultiModN provides granular insights, robustness, and flexibility without compromising performance.

  • 8 authors
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Sep 25, 2023

Label Critic: Design Data Before Models

As medical datasets rapidly expand, creating detailed annotations of different body structures becomes increasingly expensive and time-consuming. We consider that requesting radiologists to create detailed annotations is unnecessarily burdensome and that pre-existing AI models can largely automate this process. Following the spirit don't use a sledgehammer on a nut, we find that, rather than creating annotations from scratch, radiologists only have to review and edit errors if the Best-AI Labels have mistakes. To obtain the Best-AI Labels among multiple AI Labels, we developed an automatic tool, called Label Critic, that can assess label quality through tireless pairwise comparisons. Extensive experiments demonstrate that, when incorporated with our developed Image-Prompt pairs, pre-existing Large Vision-Language Models (LVLM), trained on natural images and texts, achieve 96.5% accuracy when choosing the best label in a pair-wise comparison, without extra fine-tuning. By transforming the manual annotation task (30-60 min/scan) into an automatic comparison task (15 sec/scan), we effectively reduce the manual efforts required from radiologists by an order of magnitude. When the Best-AI Labels are sufficiently accurate (81% depending on body structures), they will be directly adopted as the gold-standard annotations for the dataset, with lower-quality AI Labels automatically discarded. Label Critic can also check the label quality of a single AI Label with 71.8% accuracy when no alternatives are available for comparison, prompting radiologists to review and edit if the estimated quality is low (19% depending on body structures).

  • 7 authors
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Nov 4, 2024

Subspace Alignment for Vision-Language Model Test-time Adaptation

Vision-language models (VLMs), despite their extraordinary zero-shot capabilities, are vulnerable to distribution shifts. Test-time adaptation (TTA) emerges as a predominant strategy to adapt VLMs to unlabeled test data on the fly. However, existing TTA methods heavily rely on zero-shot predictions as pseudo-labels for self-training, which can be unreliable under distribution shifts and misguide adaptation due to two fundamental limitations. First (Modality Gap), distribution shifts induce gaps between visual and textual modalities, making cross-modal relations inaccurate. Second (Visual Nuisance), visual embeddings encode rich but task-irrelevant noise that often overwhelms task-specific semantics under distribution shifts. To address these limitations, we propose SubTTA, which aligns the semantic subspaces of both modalities to enhance zero-shot predictions to better guide the TTA process. To bridge the modality gap, SubTTA extracts the principal subspaces of both modalities and aligns the visual manifold to the textual semantic anchor by minimizing their chordal distance. To eliminate visual nuisance, SubTTA projects the aligned visual features onto the task-specific textual subspace, which filters out task-irrelevant noise by constraining visual embeddings within the valid semantic span, and standard TTA is further performed on the purified space to refine the decision boundaries. Extensive experiments on various benchmarks and VLM architectures demonstrate the effectiveness of SubTTA, yielding an average improvement of 2.24% over state-of-the-art TTA methods.

  • 11 authors
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Jan 12

SMMILE: An Expert-Driven Benchmark for Multimodal Medical In-Context Learning

Multimodal in-context learning (ICL) remains underexplored despite significant potential for domains such as medicine. Clinicians routinely encounter diverse, specialized tasks requiring adaptation from limited examples, such as drawing insights from a few relevant prior cases or considering a constrained set of differential diagnoses. While multimodal large language models (MLLMs) have shown advances in medical visual question answering (VQA), their ability to learn multimodal tasks from context is largely unknown. We introduce SMMILE, the first expert-driven multimodal ICL benchmark for medical tasks. Eleven medical experts curated problems, each including a multimodal query and multimodal in-context examples as task demonstrations. SMMILE encompasses 111 problems (517 question-image-answer triplets) covering 6 medical specialties and 13 imaging modalities. We further introduce SMMILE++, an augmented variant with 1038 permuted problems. A comprehensive evaluation of 15 MLLMs demonstrates that most models exhibit moderate to poor multimodal ICL ability in medical tasks. In open-ended evaluations, ICL contributes only 8% average improvement over zero-shot on SMMILE and 9.4% on SMMILE++. We observe a susceptibility for irrelevant in-context examples: even a single noisy or irrelevant example can degrade performance by up to 9.5%. Moreover, example ordering exhibits a recency bias, i.e., placing the most relevant example last can lead to substantial performance improvements by up to 71%. Our findings highlight critical limitations and biases in current MLLMs when learning multimodal medical tasks from context.

  • 12 authors
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Jun 26, 2025 1

Point, Detect, Count: Multi-Task Medical Image Understanding with Instruction-Tuned Vision-Language Models

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

  • 3 authors
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May 22, 2025

OLIVES Dataset: Ophthalmic Labels for Investigating Visual Eye Semantics

Clinical diagnosis of the eye is performed over multifarious data modalities including scalar clinical labels, vectorized biomarkers, two-dimensional fundus images, and three-dimensional Optical Coherence Tomography (OCT) scans. Clinical practitioners use all available data modalities for diagnosing and treating eye diseases like Diabetic Retinopathy (DR) or Diabetic Macular Edema (DME). Enabling usage of machine learning algorithms within the ophthalmic medical domain requires research into the relationships and interactions between all relevant data over a treatment period. Existing datasets are limited in that they neither provide data nor consider the explicit relationship modeling between the data modalities. In this paper, we introduce the Ophthalmic Labels for Investigating Visual Eye Semantics (OLIVES) dataset that addresses the above limitation. This is the first OCT and near-IR fundus dataset that includes clinical labels, biomarker labels, disease labels, and time-series patient treatment information from associated clinical trials. The dataset consists of 1268 near-IR fundus images each with at least 49 OCT scans, and 16 biomarkers, along with 4 clinical labels and a disease diagnosis of DR or DME. In total, there are 96 eyes' data averaged over a period of at least two years with each eye treated for an average of 66 weeks and 7 injections. We benchmark the utility of OLIVES dataset for ophthalmic data as well as provide benchmarks and concrete research directions for core and emerging machine learning paradigms within medical image analysis.

  • 6 authors
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Sep 22, 2022

True Multimodal In-Context Learning Needs Attention to the Visual Context

Multimodal Large Language Models (MLLMs), built on powerful language backbones, have enabled Multimodal In-Context Learning (MICL)-adapting to new tasks from a few multimodal demonstrations consisting of images, questions, and answers. Despite showing noticeable improvement on standard vision-language datasets, current MLLMs struggle to leverage visual information in the demonstrations. Specifically, they tend to neglect visual cues and over-rely on textual patterns, leading to mere text imitation rather than genuine multimodal adaptation. This behavior makes MICL still unimodal and largely restricts its practical utility. More importantly, this limitation is often concealed by the improved performance on tasks that do not require understanding the visual context. As a result, how to effectively enhance MICL ability and reliably evaluate the MICL performance remains underexplored. To address these issues, we first introduce Dynamic Attention Reallocation (DARA), an efficient fine-tuning strategy that encourages models to attend to the visual context by rebalancing attention across visual and textual tokens. In addition, we present TrueMICL, an MICL-dedicated dataset with both support and test sets that explicitly requires the integration of multimodal information-particularly visual content-for correct task completion. Extensive experiments demonstrate the effectiveness of our holistic solution, showcasing substantial improvements in the true multimodal in-context learning capabilities. Code and datasets are available at https://chenxshuo.github.io/true-micl-colm .

  • 8 authors
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Jul 21, 2025 2

[CLS] Token Tells Everything Needed for Training-free Efficient MLLMs

Multimodal Large Language Models (MLLMs) have recently demonstrated strong performance across a wide range of vision-language tasks, garnering significant attention in the computer vision. However, their efficient deployment remains a substantial challenge due to high computational costs and memory requirements. Recognizing the redundancy of information within the vision modality, recent studies have explored methods for compressing visual tokens in MLLMs to enhance efficiency in a training-free manner. Despite their effectiveness, existing methods like Fast rely on the attention between visual tokens and prompt text tokens as the importance indicator, overlooking the relevance to response text and thus introducing perception bias. In this paper, we demonstrate that in MLLMs, the [CLS] token in the visual encoder inherently knows which visual tokens are important for MLLMs. Building on this prior, we introduce a simple yet effective method for train-free visual token compression, called VTC-CLS. Firstly, it leverages the attention score of the [CLS] token on visual tokens as an importance indicator for pruning visual tokens. Besides, we also explore ensembling the importance scores derived by the [CLS] token from different layers to capture the key visual information more comprehensively. Extensive experiments demonstrate that our VTC-CLS achieves the state-of-the-art performance across various tasks compared with baseline methods. It also brings notably less computational costs in a training-free manner, highlighting its effectiveness and superiority. Code and models are available at https://github.com/THU-MIG/VTC-CLS.

  • 6 authors
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Dec 8, 2024

ZACH-ViT: Regime-Dependent Inductive Bias in Compact Vision Transformers for Medical Imaging

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.

  • 1 authors
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Feb 19

FancyVideo: Towards Dynamic and Consistent Video Generation via Cross-frame Textual Guidance

Synthesizing motion-rich and temporally consistent videos remains a challenge in artificial intelligence, especially when dealing with extended durations. Existing text-to-video (T2V) models commonly employ spatial cross-attention for text control, equivalently guiding different frame generations without frame-specific textual guidance. Thus, the model's capacity to comprehend the temporal logic conveyed in prompts and generate videos with coherent motion is restricted. To tackle this limitation, we introduce FancyVideo, an innovative video generator that improves the existing text-control mechanism with the well-designed Cross-frame Textual Guidance Module (CTGM). Specifically, CTGM incorporates the Temporal Information Injector (TII), Temporal Affinity Refiner (TAR), and Temporal Feature Booster (TFB) at the beginning, middle, and end of cross-attention, respectively, to achieve frame-specific textual guidance. Firstly, TII injects frame-specific information from latent features into text conditions, thereby obtaining cross-frame textual conditions. Then, TAR refines the correlation matrix between cross-frame textual conditions and latent features along the time dimension. Lastly, TFB boosts the temporal consistency of latent features. Extensive experiments comprising both quantitative and qualitative evaluations demonstrate the effectiveness of FancyVideo. Our approach achieves state-of-the-art T2V generation results on the EvalCrafter benchmark and facilitates the synthesis of dynamic and consistent videos. The video show results can be available at https://fancyvideo.github.io/, and we will make our code and model weights publicly available.

  • 7 authors
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Aug 15, 2024 3

EVA: Towards a universal model of the immune system

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

  • 11 authors
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Feb 10

OpenVid-1M: A Large-Scale High-Quality Dataset for Text-to-video Generation

Text-to-video (T2V) generation has recently garnered significant attention thanks to the large multi-modality model Sora. However, T2V generation still faces two important challenges: 1) Lacking a precise open sourced high-quality dataset. The previous popular video datasets, e.g. WebVid-10M and Panda-70M, are either with low quality or too large for most research institutions. Therefore, it is challenging but crucial to collect a precise high-quality text-video pairs for T2V generation. 2) Ignoring to fully utilize textual information. Recent T2V methods have focused on vision transformers, using a simple cross attention module for video generation, which falls short of thoroughly extracting semantic information from text prompt. To address these issues, we introduce OpenVid-1M, a precise high-quality dataset with expressive captions. This open-scenario dataset contains over 1 million text-video pairs, facilitating research on T2V generation. Furthermore, we curate 433K 1080p videos from OpenVid-1M to create OpenVidHD-0.4M, advancing high-definition video generation. Additionally, we propose a novel Multi-modal Video Diffusion Transformer (MVDiT) capable of mining both structure information from visual tokens and semantic information from text tokens. Extensive experiments and ablation studies verify the superiority of OpenVid-1M over previous datasets and the effectiveness of our MVDiT.

  • 9 authors
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Jul 2, 2024 6