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.

What If We Recaption Billions of Web Images with LLaMA-3?

Web-crawled image-text pairs are inherently noisy. Prior studies demonstrate that semantically aligning and enriching textual descriptions of these pairs can significantly enhance model training across various vision-language tasks, particularly text-to-image generation. However, large-scale investigations in this area remain predominantly closed-source. Our paper aims to bridge this community effort, leveraging the powerful and \textit{open-sourced} LLaMA-3, a GPT-4 level LLM. Our recaptioning pipeline is simple: first, we fine-tune a LLaMA-3-8B powered LLaVA-1.5 and then employ it to recaption 1.3 billion images from the DataComp-1B dataset. Our empirical results confirm that this enhanced dataset, Recap-DataComp-1B, offers substantial benefits in training advanced vision-language models. For discriminative models like CLIP, we observe enhanced zero-shot performance in cross-modal retrieval tasks. For generative models like text-to-image Diffusion Transformers, the generated images exhibit a significant improvement in alignment with users' text instructions, especially in following complex queries. Our project page is https://www.haqtu.me/Recap-Datacomp-1B/

Autoregressive Pretraining with Mamba in Vision

The vision community has started to build with the recently developed state space model, Mamba, as the new backbone for a range of tasks. This paper shows that Mamba's visual capability can be significantly enhanced through autoregressive pretraining, a direction not previously explored. Efficiency-wise, the autoregressive nature can well capitalize on the Mamba's unidirectional recurrent structure, enabling faster overall training speed compared to other training strategies like mask modeling. Performance-wise, autoregressive pretraining equips the Mamba architecture with markedly higher accuracy over its supervised-trained counterparts and, more importantly, successfully unlocks its scaling potential to large and even huge model sizes. For example, with autoregressive pretraining, a base-size Mamba attains 83.2\% ImageNet accuracy, outperforming its supervised counterpart by 2.0\%; our huge-size Mamba, the largest Vision Mamba to date, attains 85.0\% ImageNet accuracy (85.5\% when finetuned with $384\times384$ inputs), notably surpassing all other Mamba variants in vision. The code is available at \url{https://github.com/OliverRensu/ARM}.

Medical Vision Generalist: Unifying Medical Imaging Tasks in Context

This study presents Medical Vision Generalist (MVG), the first foundation model capable of handling various medical imaging tasks -- such as cross-modal synthesis, image segmentation, denoising, and inpainting -- within a unified image-to-image generation framework. Specifically, MVG employs an in-context generation strategy that standardizes the handling of inputs and outputs as images. By treating these tasks as an image generation process conditioned on prompt image-label pairs and input images, this approach enables a flexible unification of various tasks, even those spanning different modalities and datasets. To capitalize on both local and global context, we design a hybrid method combining masked image modeling with autoregressive training for conditional image generation. This hybrid approach yields the most robust performance across all involved medical imaging tasks. To rigorously evaluate MVG's capabilities, we curated the first comprehensive generalist medical vision benchmark, comprising 13 datasets and spanning four imaging modalities (CT, MRI, X-ray, and micro-ultrasound). Our results consistently establish MVG's superior performance, outperforming existing vision generalists, such as Painter and LVM. Furthermore, MVG exhibits strong scalability, with its performance demonstrably improving when trained on a more diverse set of tasks, and can be effectively adapted to unseen datasets with only minimal task-specific samples. The code is available at \url{https://github.com/OliverRensu/MVG}.

Scaling White-Box Transformers for Vision

CRATE, a white-box transformer architecture designed to learn compressed and sparse representations, offers an intriguing alternative to standard vision transformers (ViTs) due to its inherent mathematical interpretability. Despite extensive investigations into the scaling behaviors of language and vision transformers, the scalability of CRATE remains an open question which this paper aims to address. Specifically, we propose CRATE-$\alpha$, featuring strategic yet minimal modifications to the sparse coding block in the CRATE architecture design, and a light training recipe designed to improve the scalability of CRATE. Through extensive experiments, we demonstrate that CRATE-$\alpha$ can effectively scale with larger model sizes and datasets. For example, our CRATE-$\alpha$-B substantially outperforms the prior best CRATE-B model accuracy on ImageNet classification by 3.7%, achieving an accuracy of 83.2%. Meanwhile, when scaling further, our CRATE-$\alpha$-L obtains an ImageNet classification accuracy of 85.1%. More notably, these model performance improvements are achieved while preserving, and potentially even enhancing the interpretability of learned CRATE models, as we demonstrate through showing that the learned token representations of increasingly larger trained CRATE-$\alpha$ models yield increasingly higher-quality unsupervised object segmentation of images. The project page is https://rayjryang.github.io/CRATE-alpha/.

3D-TransUNet for Brain Metastases Segmentation in the BraTS2023 Challenge

Segmenting brain tumors is complex due to their diverse appearances and scales. Brain metastases, the most common type of brain tumor, are a frequent complication of cancer. Therefore, an effective segmentation model for brain metastases must adeptly capture local intricacies to delineate small tumor regions while also integrating global context to understand broader scan features. The TransUNet model, which combines Transformer self-attention with U-Net's localized information, emerges as a promising solution for this task. In this report, we address brain metastases segmentation by training the 3D-TransUNet model on the Brain Tumor Segmentation (BraTS-METS) 2023 challenge dataset. Specifically, we explored two architectural configurations: the Encoder-only 3D-TransUNet, employing Transformers solely in the encoder, and the Decoder-only 3D-TransUNet, utilizing Transformers exclusively in the decoder. For Encoder-only 3D-TransUNet, we note that Masked-Autoencoder pre-training is required for a better initialization of the Transformer Encoder and thus accelerates the training process. We identify that the Decoder-only 3D-TransUNet model should offer enhanced efficacy in the segmentation of brain metastases, as indicated by our 5-fold cross-validation on the training set. However, our use of the Encoder-only 3D-TransUNet model already yield notable results, with an average lesion-wise Dice score of 59.8\% on the test set, securing second place in the BraTS-METS 2023 challenge.

Revisiting Adversarial Training at Scale

The machine learning community has witnessed a drastic change in the training pipeline, pivoted by those ''foundation models'' with unprecedented scales. However, the field of adversarial training is lagging behind, predominantly centered around small model sizes like ResNet-50, and tiny and low-resolution datasets like CIFAR-10. To bridge this transformation gap, this paper provides a modern re-examination with adversarial training, investigating its potential benefits when applied at scale. Additionally, we introduce an efficient and effective training strategy to enable adversarial training with giant models and web-scale data at an affordable computing cost. We denote this newly introduced framework as AdvXL. Empirical results demonstrate that AdvXL establishes new state-of-the-art robust accuracy records under AutoAttack on ImageNet-1K. For example, by training on DataComp-1B dataset, our AdvXL empowers a vanilla ViT-g model to substantially surpass the previous records of $l_{\infty}$-, $l_{2}$-, and $l_{1}$-robust accuracy by margins of 11.4%, 14.2% and 12.9%, respectively. This achievement posits AdvXL as a pioneering approach, charting a new trajectory for the efficient training of robust visual representations at significantly larger scales. Our code is available at https://github.com/UCSC-VLAA/AdvXL.

3D TransUNet: Advancing Medical Image Segmentation through Vision Transformers

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

CLIPA-v2: Scaling CLIP Training with 81.1% Zero-shot ImageNet Accuracy within a \$10,000 Budget; An Extra \$4,000 Unlocks 81.8% Accuracy

The recent work CLIPA presents an inverse scaling law for CLIP training -- whereby the larger the image/text encoders used, the shorter the sequence length of image/text tokens that can be applied in training. This finding enables us to train high-performance CLIP models with significantly reduced computations. Building upon this work, we hereby present CLIPA-v2 with two key contributions. Technically, we find this inverse scaling law is also applicable in the finetuning stage, enabling further reduction in computational needs. Empirically, we explore CLIPA at scale, extending the experiments up to the H/14 model with ~13B image-text pairs seen during training. Our results are exciting -- by only allocating a budget of \$10,000, our CLIP model achieves an impressive zero-shot ImageNet accuracy of 81.1%, surpassing the prior best CLIP model (from OpenCLIP, 80.1%) by 1.0% and meanwhile reducing the computational cost by ~39X. Moreover, with an additional investment of $4,000, we can further elevate the zero-shot ImageNet accuracy to 81.8%. Our code and models are available at https://github.com/UCSC-VLAA/CLIPA.