Can Zhao

Pengfei Guo, Can Zhao, Dong Yang et al.

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

Jeya Maria Jose Valanarasu, Yucheng Tang, Dong Yang et al.

Harnessing the power of pre-training on large-scale datasets like ImageNet forms a fundamental building block for the progress of representation learning-driven solutions in computer vision. Medical images are inherently different from natural images as they are acquired in the form of many modalities (CT, MR, PET, Ultrasound etc.) and contain granulated information like tissue, lesion, organs etc. These characteristics of medical images require special attention towards learning features representative of local context. In this work, we focus on designing an effective pre-training framework for 3D radiology images. First, we propose a new masking strategy called local masking where the masking is performed across channel embeddings instead of tokens to improve the learning of local feature representations. We combine this with classical low-level perturbations like adding noise and downsampling to further enable low-level representation learning. To this end, we introduce Disruptive Autoencoders, a pre-training framework that attempts to reconstruct the original image from disruptions created by a combination of local masking and low-level perturbations. Additionally, we also devise a cross-modal contrastive loss (CMCL) to accommodate the pre-training of multiple modalities in a single framework. We curate a large-scale dataset to enable pre-training of 3D medical radiology images (MRI and CT). The proposed pre-training framework is tested across multiple downstream tasks and achieves state-of-the-art performance. Notably, our proposed method tops the public test leaderboard of BTCV multi-organ segmentation challenge.

Jianbo Ma, Chuanming Tang, Fei Wu et al.

Multiple object tracking (MOT) in Unmanned Aerial Vehicle (UAV) videos is important for diverse applications in computer vision. Current MOT trackers rely on accurate object detection results and precise matching of target reidentification (ReID). These methods focus on optimizing target spatial attributes while overlooking temporal cues in modelling object relationships, especially for challenging tracking conditions such as object deformation and blurring, etc. To address the above-mentioned issues, we propose a novel Spatio-Temporal Cohesion Multiple Object Tracking framework (STCMOT), which utilizes historical embedding features to model the representation of ReID and detection features in a sequential order. Concretely, a temporal embedding boosting module is introduced to enhance the discriminability of individual embedding based on adjacent frame cooperation. While the trajectory embedding is then propagated by a temporal detection refinement module to mine salient target locations in the temporal field. Extensive experiments on the VisDrone2019 and UAVDT datasets demonstrate our STCMOT sets a new state-of-the-art performance in MOTA and IDF1 metrics. The source codes are released at https://github.com/ydhcg-BoBo/STCMOT.

Can Zhao, Pengfei Guo, Dong Yang et al.

Medical image synthesis is an important topic for both clinical and research applications. Recently, diffusion models have become a leading approach in this area. Despite their strengths, many existing methods struggle with (1) limited generalizability that only work for specific body regions or voxel spacings, (2) slow inference, which is a common issue for diffusion models, and (3) weak alignment with input conditions, which is a critical issue for medical imaging. MAISI, a previously proposed framework, addresses generalizability issues but still suffers from slow inference and limited condition consistency. In this work, we present MAISI-v2, the first accelerated 3D medical image synthesis framework that integrates rectified flow to enable fast and high quality generation. To further enhance condition fidelity, we introduce a novel region-specific contrastive loss to enhance the sensitivity to region of interest. Our experiments show that MAISI-v2 can achieve SOTA image quality with $33 \times$ acceleration for latent diffusion model. We also conducted a downstream segmentation experiment to show that the synthetic images can be used for data augmentation. We release our code, training details, model weights, and a GUI demo to facilitate reproducibility and promote further development within the community.

Yufan He, Pengfei Guo, Yucheng Tang et al.

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

Wentao Zhu, Can Zhao, Wenqi Li et al.

Deep Learning (DL) models are becoming larger, because the increase in model size might offer significant accuracy gain. To enable the training of large deep networks, data parallelism and model parallelism are two well-known approaches for parallel training. However, data parallelism does not help reduce memory footprint per device. In this work, we introduce Large deep 3D ConvNets with Automated Model Parallelism (LAMP) and investigate the impact of both input's and deep 3D ConvNets' size on segmentation accuracy. Through automated model parallelism, it is feasible to train large deep 3D ConvNets with a large input patch, even the whole image. Extensive experiments demonstrate that, facilitated by the automated model parallelism, the segmentation accuracy can be improved through increasing model size and input context size, and large input yields significant inference speedup compared with sliding window of small patches in the inference. Code is available\footnote{https://monai.io/research/lamp-automated-model-parallelism}.

Maoqi Liu, Quan Fang, Yuhao Wu et al.

Accurate interpretation of Notices to Airmen (NOTAMs) is critical for aviation safety, yet their condensed and cryptic language poses significant challenges to both manual and automated processing. Existing automated systems are typically limited to shallow parsing, failing to extract the actionable intelligence needed for operational decisions. We formalize the complete interpretation task as deep parsing, a dual-reasoning challenge requiring both dynamic knowledge grounding (linking the NOTAM to evolving real-world aeronautical data) and schema-based inference (applying static domain rules to deduce operational status). To tackle this challenge, we propose NOTAM-Evolve, a self-evolving framework that enables a large language model (LLM) to autonomously master complex NOTAM interpretation. Leveraging a knowledge graph-enhanced retrieval module for data grounding, the framework introduces a closed-loop learning process where the LLM progressively improves from its own outputs, minimizing the need for extensive human-annotated reasoning traces. In conjunction with this framework, we introduce a new benchmark dataset of 10,000 expert-annotated NOTAMs. Our experiments demonstrate that NOTAM-Evolve achieves a 30.4% absolute accuracy improvement over the base LLM, establishing a new state of the art on the task of structured NOTAM interpretation.

Vishwesh Nath, Wenqi Li, Dong Yang et al.

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data$-$features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

Jiawei Mao, Yuhan Wang, Lifeng Chen et al.

Recent advances in generative medical models are constrained by modality-specific scenarios that hinder the integration of complementary evidence from imaging, pathology, and clinical notes. This fragmentation limits their evolution into foundation models that can learn and reason across the full spectrum of biomedical data. We propose MeDiM, the first medical discrete diffusion model that learns shared distributions across modalities without modality-specific components. MeDiM unifies multiple generative tasks: translating between images and text, and jointly producing image-report pairs across domains in response to prompts. Built on a discrete diffusion framework, MeDiM bridges vision and language representations through a shared probabilistic space. To enable unified and flexible medical generation, we employ a multimodal large language model (MLLM) as the diffusion backbone, leveraging its prior knowledge and cross-modal reasoning. Two key designs are introduced: (1) removing the causal attention mask for bidirectional context, and (2) injecting continuous timestep embeddings for diffusion awareness. Experiments demonstrate high-fidelity medical generation (FID 16.60 on MIMIC-CXR and FID 24.19 on PathGen) and accurate report generation (METEOR 0.2650 and 0.2580). Jointly generated image-report pairs further enhance downstream performance (plus6.43 percent BLEU-1, plus18.57 percent BLEU-2, plus31.58 percent BLEU-3, plus4.80 percent METEOR), showing that MeDiM supports coherent and clinically grounded multimodal outputs.

Niklas Bubeck, Suprosanna Shit, Chen Chen et al.

Cardiac Magnetic Resonance (CMR) imaging is a critical tool for diagnosing and managing cardiovascular disease, yet its utility is often limited by the sparse acquisition of 2D short-axis slices, resulting in incomplete volumetric information. Accurate 3D reconstruction from these sparse slices is essential for comprehensive cardiac assessment, but existing methods face challenges, including reliance on predefined interpolation schemes (e.g., linear or spherical), computational inefficiency, and dependence on additional semantic inputs such as segmentation labels or motion data. To address these limitations, we propose a novel Cardiac Latent Interpolation Diffusion (CaLID) framework that introduces three key innovations. First, we present a data-driven interpolation scheme based on diffusion models, which can capture complex, non-linear relationships between sparse slices and improves reconstruction accuracy. Second, we design a computationally efficient method that operates in the latent space and speeds up 3D whole-heart upsampling time by a factor of 24, reducing computational overhead compared to previous methods. Third, with only sparse 2D CMR images as input, our method achieves SOTA performance against baseline methods, eliminating the need for auxiliary input such as morphological guidance, thus simplifying workflows. We further extend our method to 2D+T data, enabling the effective modeling of spatiotemporal dynamics and ensuring temporal coherence. Extensive volumetric evaluations and downstream segmentation tasks demonstrate that CaLID achieves superior reconstruction quality and efficiency. By addressing the fundamental limitations of existing approaches, our framework advances the state of the art for spatio and spatiotemporal whole-heart reconstruction, offering a robust and clinically practical solution for cardiovascular imaging.

Yufan He, Dong Yang, Holger Roth et al.

Recently, neural architecture search (NAS) has been applied to automatically search high-performance networks for medical image segmentation. The NAS search space usually contains a network topology level (controlling connections among cells with different spatial scales) and a cell level (operations within each cell). Existing methods either require long searching time for large-scale 3D image datasets, or are limited to pre-defined topologies (such as U-shaped or single-path). In this work, we focus on three important aspects of NAS in 3D medical image segmentation: flexible multi-path network topology, high search efficiency, and budgeted GPU memory usage. A novel differentiable search framework is proposed to support fast gradient-based search within a highly flexible network topology search space. The discretization of the searched optimal continuous model in differentiable scheme may produce a sub-optimal final discrete model (discretization gap). Therefore, we propose a topology loss to alleviate this problem. In addition, the GPU memory usage for the searched 3D model is limited with budget constraints during search. Our Differentiable Network Topology Search scheme (DiNTS) is evaluated on the Medical Segmentation Decathlon (MSD) challenge, which contains ten challenging segmentation tasks. Our method achieves the state-of-the-art performance and the top ranking on the MSD challenge leaderboard.

Heran Yang, Jian Sun, Aaron Carass et al.

The cycleGAN is becoming an influential method in medical image synthesis. However, due to a lack of direct constraints between input and synthetic images, the cycleGAN cannot guarantee structural consistency between these two images, and such consistency is of extreme importance in medical imaging. To overcome this, we propose a structure-constrained cycleGAN for brain MR-to-CT synthesis using unpaired data that defines an extra structure-consistency loss based on the modality independent neighborhood descriptor to constrain structural consistency. Additionally, we use a position-based selection strategy for selecting training images instead of a completely random selection scheme. Experimental results on synthesizing CT images from brain MR images demonstrate that our method is better than the conventional cycleGAN and approximates the cycleGAN trained with paired data.

Can Zhao, Aaron Carass, Blake E. Dewey et al.

High resolution magnetic resonance~(MR) imaging~(MRI) is desirable in many clinical applications, however, there is a trade-off between resolution, speed of acquisition, and noise. It is common for MR images to have worse through-plane resolution~(slice thickness) than in-plane resolution. In these MRI images, high frequency information in the through-plane direction is not acquired, and cannot be resolved through interpolation. To address this issue, super-resolution methods have been developed to enhance spatial resolution. As an ill-posed problem, state-of-the-art super-resolution methods rely on the presence of external/training atlases to learn the transform from low resolution~(LR) images to high resolution~(HR) images. For several reasons, such HR atlas images are often not available for MRI sequences. This paper presents a self super-resolution~(SSR) algorithm, which does not use any external atlas images, yet can still resolve HR images only reliant on the acquired LR image. We use a blurred version of the input image to create training data for a state-of-the-art super-resolution deep network. The trained network is applied to the original input image to estimate the HR image. Our SSR result shows a significant improvement on through-plane resolution compared to competing SSR methods.