Ziheng Zhao

Chaoyi Wu, Jiayu Lei, Qiaoyu Zheng et al. · harvard

Driven by the large foundation models, the development of artificial intelligence has witnessed tremendous progress lately, leading to a surge of general interest from the public. In this study, we aim to assess the performance of OpenAI's newest model, GPT-4V(ision), specifically in the realm of multimodal medical diagnosis. Our evaluation encompasses 17 human body systems, including Central Nervous System, Head and Neck, Cardiac, Chest, Hematology, Hepatobiliary, Gastrointestinal, Urogenital, Gynecology, Obstetrics, Breast, Musculoskeletal, Spine, Vascular, Oncology, Trauma, Pediatrics, with images taken from 8 modalities used in daily clinic routine, e.g., X-ray, Computed Tomography (CT), Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), Digital Subtraction Angiography (DSA), Mammography, Ultrasound, and Pathology. We probe the GPT-4V's ability on multiple clinical tasks with or without patent history provided, including imaging modality and anatomy recognition, disease diagnosis, report generation, disease localisation. Our observation shows that, while GPT-4V demonstrates proficiency in distinguishing between medical image modalities and anatomy, it faces significant challenges in disease diagnosis and generating comprehensive reports. These findings underscore that while large multimodal models have made significant advancements in computer vision and natural language processing, it remains far from being used to effectively support real-world medical applications and clinical decision-making. All images used in this report can be found in https://github.com/chaoyi-wu/GPT-4V_Medical_Evaluation.

Weixiong Lin, Ziheng Zhao, Xiaoman Zhang et al. · harvard

Foundation models trained on large-scale dataset gain a recent surge in CV and NLP. In contrast, development in biomedical domain lags far behind due to data scarcity. To address this issue, we build and release PMC-OA, a biomedical dataset with 1.6M image-caption pairs collected from PubMedCentral's OpenAccess subset, which is 8 times larger than before. PMC-OA covers diverse modalities or diseases, with majority of the image-caption samples aligned at finer-grained level, i.e., subfigure and subcaption. While pretraining a CLIP-style model on PMC-OA, our model named PMC-CLIP achieves state-of-the-art results on various downstream tasks, including image-text retrieval on ROCO, MedMNIST image classification, Medical VQA, i.e. +8.1% R@10 on image-text retrieval, +3.9% accuracy on image classification.

Tengfei Zhang, Ziheng Zhao, Lisong Dai et al.

Medical imaging artificial intelligence has achieved strong performance in isolated image interpretation, but remains poorly aligned with radiological practice, where diagnosis and follow-up rely on comparison across prior studies and analogous reference cases. Here we formulate radiological comparison as an entity-aware cross-image reasoning problem and introduce a framework that supports both reference-case retrieval and temporal comparative interpretation. We construct MedReCo-DB, a large-scale comparative imaging resource derived from routine image-report pairs, comprising more than 690,000 images from over 160,000 patients across eight institutions, four countries and seven imaging modalities. Reports are decomposed into anatomical structures, abnormal findings and pathological conditions to provide supervision for entity-conditioned retrieval and comparative visual question answering. Using this resource, we develop MedReCo, an entity-aware visual encoder for controllable retrieval of clinically analogous cases, and MedReCo-VLM, a vision--language extension for generative interpretation of interval change. Across internal, external and cross-center evaluations, MedReCo achieved the highest Recall@1 in all 12 internal retrieval settings and improved external retrieval by a mean of 6.0 percentage points. In clinically confusable differential groups, it consistently outperformed the strongest baselines. MedReCo-VLM achieved the best performance across all comparative generation evaluations and improved longitudinal follow-up accuracy by 14.5-46.5 percentage points on chest radiographs and 13.0-27.9 percentage points on CT. These findings suggest that entity-aware comparative reasoning can be learned from routine clinical data at scale and may provide a more clinically aligned foundation for medical imaging AI.

Haolin Li, Yuhang Zhou, Ziheng Zhao et al.

The widespread adoption of large-scale pre-training techniques has significantly advanced the development of medical foundation models, enabling them to serve as versatile tools across a broad range of medical tasks. However, despite their strong generalization capabilities, medical foundation models pre-trained on large-scale datasets tend to suffer from domain gaps between heterogeneous data, leading to suboptimal performance on specific tasks compared to specialist models, as evidenced by previous studies. In this paper, we explore a new perspective called "Knowledge Decomposition" to improve the performance on specific medical tasks, which deconstructs the foundation model into multiple lightweight expert models, each dedicated to a particular anatomical region, with the aim of enhancing specialization and simultaneously reducing resource consumption. To accomplish the above objective, we propose a novel framework named Low-Rank Knowledge Decomposition (LoRKD), which explicitly separates gradients from different tasks by incorporating low-rank expert modules and efficient knowledge separation convolution. The low-rank expert modules resolve gradient conflicts between heterogeneous data from different anatomical regions, providing strong specialization at lower costs. The efficient knowledge separation convolution significantly improves algorithm efficiency by achieving knowledge separation within a single forward propagation. Extensive experimental results on segmentation and classification tasks demonstrate that our decomposed models not only achieve state-of-the-art performance but also exhibit superior transferability on downstream tasks, even surpassing the original foundation models in task-specific evaluations. The code is available at here.

Haifeng Wang, Hua Wu, Tian Wu et al.

In this report, we introduce ERNIE 5.0, a natively autoregressive foundation model desinged for unified multimodal understanding and generation across text, image, video, and audio. All modalities are trained from scratch under a unified next-group-of-tokens prediction objective, based on an ultra-sparse mixture-of-experts (MoE) architecture with modality-agnostic expert routing. To address practical challenges in large-scale deployment under diverse resource constraints, ERNIE 5.0 adopts a novel elastic training paradigm. Within a single pre-training run, the model learns a family of sub-models with varying depths, expert capacities, and routing sparsity, enabling flexible trade-offs among performance, model size, and inference latency in memory- or time-constrained scenarios. Moreover, we systematically address the challenges of scaling reinforcement learning to unified foundation models, thereby guaranteeing efficient and stable post-training under ultra-sparse MoE architectures and diverse multimodal settings. Extensive experiments demonstrate that ERNIE 5.0 achieves strong and balanced performance across multiple modalities. To the best of our knowledge, among publicly disclosed models, ERNIE 5.0 represents the first production-scale realization of a trillion-parameter unified autoregressive model that supports both multimodal understanding and generation. To facilitate further research, we present detailed visualizations of modality-agnostic expert routing in the unified model, alongside comprehensive empirical analysis of elastic training, aiming to offer profound insights to the community.

Ziheng Zhao, Tianjiao Zhang, Weidi Xie et al.

This paper considers the problem of undersampled MRI reconstruction. We propose a novel Transformer-based framework for directly processing signal in k-space, going beyond the limitation of regular grids as ConvNets do. We adopt an implicit representation of k-space spectrogram, treating spatial coordinates as inputs, and dynamically query the sparsely sampled points to reconstruct the spectrogram, i.e. learning the inductive bias in k-space. To strike a balance between computational cost and reconstruction quality, we build the decoder with hierarchical structure to generate low-resolution and high-resolution outputs respectively. To validate the effectiveness of our proposed method, we have conducted extensive experiments on two public datasets, and demonstrate superior or comparable performance to state-of-the-art approaches.

Xiaoman Zhang, Chaoyi Wu, Ziheng Zhao et al. · harvard

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Ziheng Zhao, Yao Zhang, Chaoyi Wu et al. · harvard

This paper aims to build a model that can Segment Anything in 3D medical images, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three-fold: (i) We construct the first multimodal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build the largest and most comprehensive segmentation dataset for training, collecting over 22K 3D scans from 72 datasets, across 497 classes, with careful standardization on both image and label space; (ii) We propose to inject medical knowledge into a text encoder via contrastive learning and formulate a large-vocabulary segmentation model that can be prompted by medical terminologies in text form; (iii) We train SAT-Nano (110M parameters) and SAT-Pro (447M parameters). SAT-Pro achieves comparable performance to 72 nnU-Nets -- the strongest specialist models trained on each dataset (over 2.2B parameters combined) -- over 497 categories. Compared with the interactive approach MedSAM, SAT-Pro consistently outperforms across all 7 human body regions with +7.1% average Dice Similarity Coefficient (DSC) improvement, while showing enhanced scalability and robustness. On 2 external (cross-center) datasets, SAT-Pro achieves higher performance than all baselines (+3.7% average DSC), demonstrating superior generalization ability.

Ziheng Zhao, Lisong Dai, Ya Zhang et al.

Automated interpretation of CT images-particularly localizing and describing abnormal findings across multi-plane and whole-body scans-remains a significant challenge in clinical radiology. This work aims to address this challenge through four key contributions: (i) On taxonomy, we collaborate with senior radiologists to propose a comprehensive hierarchical classification system, with 404 representative abnormal findings across all body regions; (ii) On data, we contribute a dataset containing over 14.5K CT images from multiple planes and all human body regions, and meticulously provide grounding annotations for over 19K abnormalities, each linked to the detailed description and cast into the taxonomy; (iii) On model development, we propose OmniAbnorm-CT, which can automatically ground and describe abnormal findings on multi-plane and whole-body CT images based on text queries, while also allowing flexible interaction through visual prompts; (iv) On evaluation, we establish three representative tasks based on real clinical scenarios, and introduce a clinically grounded metric to assess abnormality descriptions. Through extensive experiments, we show that OmniAbnorm-CT can significantly outperform existing methods in both internal and external validations, and across all the tasks.

Tengfei Zhang, Ziheng Zhao, Chaoyi Wu et al.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Jinghao Feng, Qiaoyu Zheng, Chaoyi Wu et al.

Agentic AI systems have gained significant attention for their ability to autonomously perform complex tasks. However, their reliance on well-prepared tools limits their applicability in the medical domain, which requires to train specialized models. In this paper, we make three contributions: (i) We present M3Builder, a novel multi-agent system designed to automate machine learning (ML) in medical imaging. At its core, M3Builder employs four specialized agents that collaborate to tackle complex, multi-step medical ML workflows, from automated data processing and environment configuration to self-contained auto debugging and model training. These agents operate within a medical imaging ML workspace, a structured environment designed to provide agents with free-text descriptions of datasets, training codes, and interaction tools, enabling seamless communication and task execution. (ii) To evaluate progress in automated medical imaging ML, we propose M3Bench, a benchmark comprising four general tasks on 14 training datasets, across five anatomies and three imaging modalities, covering both 2D and 3D data. (iii) We experiment with seven state-of-the-art large language models serving as agent cores for our system, such as Claude series, GPT-4o, and DeepSeek-V3. Compared to existing ML agentic designs, M3Builder shows superior performance on completing ML tasks in medical imaging, achieving a 94.29% success rate using Claude-3.7-Sonnet as the agent core, showing huge potential towards fully automated machine learning in medical imaging.

Haoning Wu, Ziheng Zhao, Ya Zhang et al.

Training medical image segmentation models for rare yet clinically important imaging modalities is challenging due to the scarcity of annotated data, and manual mask annotations can be costly and labor-intensive to acquire. This paper investigates leveraging generative models to synthesize data, for training segmentation models for underrepresented modalities, particularly on annotation-scarce MRI. Concretely, our contributions are threefold: (i) we introduce MRGen-DB, a large-scale radiology image-text dataset comprising extensive samples with rich metadata, including modality labels, attributes, regions, and organs information, with a subset featuring pixel-wise mask annotations; (ii) we present MRGen, a diffusion-based data engine for controllable medical image synthesis, conditioned on text prompts and segmentation masks. MRGen can generate realistic images for diverse MRI modalities lacking mask annotations, facilitating segmentation training in low-source domains; (iii) extensive experiments across multiple modalities demonstrate that MRGen significantly improves segmentation performance on unannotated modalities by providing high-quality synthetic data. We believe that our method bridges a critical gap in medical image analysis, extending segmentation capabilities to scenarios that are challenging to acquire manual annotations. The codes, models, and data will be publicly available at https://haoningwu3639.github.io/MRGen/

Xiaoman Zhang, Chaoyi Wu, Ziheng Zhao et al.

Medical Visual Question Answering (MedVQA) presents a significant opportunity to enhance diagnostic accuracy and healthcare delivery by leveraging artificial intelligence to interpret and answer questions based on medical images. In this study, we reframe the problem of MedVQA as a generation task that naturally follows the human-machine interaction and propose a generative-based model for medical visual understanding by aligning visual information from a pre-trained vision encoder with a large language model. We establish a scalable pipeline to construct a large-scale medical visual question-answering dataset, named PMC-VQA, which contains 227k VQA pairs of 149k images that cover various modalities or diseases. We train the proposed model on PMC-VQA and then fine-tune it on multiple public benchmarks, e.g., VQA-RAD, SLAKE, and Image-Clef-2019, significantly outperforming existing MedVQA models in generating relevant, accurate free-form answers. In addition, we propose a test set that has undergone manual verification, which is significantly more challenging, serving to better monitor the development of generative MedVQA methods. To facilitate comprehensive evaluation and comparison, we have maintained a leaderboard at https://paperswithcode.com/paper/pmc-vqa-visual-instruction-tuning-for-medical, offering a centralized resource for tracking progress and benchmarking state-of-the-art approaches. The PMC-VQA dataset emerges as a vital resource for the field of research, and the MedVInT presents a significant breakthrough in the area of MedVQA.