arXiv subjects

Zongwei Zhou

Publications and source records attributed to Zongwei Zhou.

At least 55 records · Page 3Linked to original sources

arXiv2025

Medical World Model: Generative Simulation of Tumor Evolution for Treatment Planning

Providing effective treatment and making informed clinical decisions are essential goals of modern medicine and clinical care. We are interested in simulating disease dynamics for clinical decision-making, leveraging recent advances in large generative models. To this end, we introduce the Medical World Model (MeWM), the first world model in medicine that visually predicts future disease states based on clinical decisions. MeWM comprises (i) vision-language models to serve as policy models, and (ii) tumor generative models as dynamics models. The policy model generates action plans, such as clinical treatments, while the dynamics model simulates tumor progression or regression under given treatment conditions. Building on this, we propose the inverse dynamics model that applies survival analysis to the simulated post-treatment tumor, enabling the evaluation of treatment efficacy and the selection of the optimal clinical action plan. As a result, the proposed MeWM simulates disease dynamics by synthesizing post-treatment tumors, with state-of-the-art specificity in Turing tests evaluated by radiologists. Simultaneously, its inverse dynamics model outperforms medical-specialized GPTs in optimizing individualized treatment protocols across all metrics. Notably, MeWM improves clinical decision-making for interventional physicians, boosting F1-score in selecting the optimal TACE protocol by 13%, paving the way for future integration of medical world models as the second readers.

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arXiv2025

Are Vision Language Models Ready for Clinical Diagnosis? A 3D Medical Benchmark for Tumor-centric Visual Question Answering

Vision-Language Models (VLMs) have shown promise in various 2D visual tasks, yet their readiness for 3D clinical diagnosis remains unclear due to stringent demands for recognition precision, reasoning ability, and domain knowledge. To systematically evaluate these dimensions, we present DeepTumorVQA, a diagnostic visual question answering (VQA) benchmark targeting abdominal tumors in CT scans. It comprises 9,262 CT volumes (3.7M slices) from 17 public datasets, with 395K expert-level questions spanning four categories: Recognition, Measurement, Visual Reasoning, and Medical Reasoning. DeepTumorVQA introduces unique challenges, including small tumor detection and clinical reasoning across 3D anatomy. Benchmarking four advanced VLMs (RadFM, M3D, Merlin, CT-CHAT), we find current models perform adequately on measurement tasks but struggle with lesion recognition and reasoning, and are still not meeting clinical needs. Two key insights emerge: (1) large-scale multimodal pretraining plays a crucial role in DeepTumorVQA testing performance, making RadFM stand out among all VLMs. (2) Our dataset exposes critical differences in VLM components, where proper image preprocessing and design of vision modules significantly affect 3D perception. To facilitate medical multimodal research, we have released DeepTumorVQA as a rigorous benchmark: https://github.com/Schuture/DeepTumorVQA.

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arXiv2025

Text2CT: Towards 3D CT Volume Generation from Free-text Descriptions Using Diffusion Model

Generating 3D CT volumes from descriptive free-text inputs presents a transformative opportunity in diagnostics and research. In this paper, we introduce Text2CT, a novel approach for synthesizing 3D CT volumes from textual descriptions using the diffusion model. Unlike previous methods that rely on fixed-format text input, Text2CT employs a novel prompt formulation that enables generation from diverse, free-text descriptions. The proposed framework encodes medical text into latent representations and decodes them into high-resolution 3D CT scans, effectively bridging the gap between semantic text inputs and detailed volumetric representations in a unified 3D framework. Our method demonstrates superior performance in preserving anatomical fidelity and capturing intricate structures as described in the input text. Extensive evaluations show that our approach achieves state-of-the-art results, offering promising potential applications in diagnostics, and data augmentation.

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arXiv2025

Machine Learning Fleet Efficiency: Analyzing and Optimizing Large-Scale Google TPU Systems with ML Productivity Goodput

Recent years have seen the emergence of machine learning (ML) workloads deployed in warehouse-scale computing (WSC) settings, also known as ML fleets. As the computational demands placed on ML fleets have increased due to the rise of large models and growing demand for ML applications, it has become increasingly critical to measure and improve the efficiency of such systems. However, there is not yet an established methodology to characterize ML fleet performance and identify potential performance optimizations accordingly. This paper presents a large-scale analysis of an ML fleet based on Google's TPUs, introducing a framework to capture fleet-wide efficiency, systematically evaluate performance characteristics, and identify optimization strategies for the fleet. We begin by defining an ML fleet, outlining its components, and analyzing an example Google ML fleet in production comprising thousands of accelerators running diverse workloads. Our study reveals several critical insights: first, ML fleets extend beyond the hardware layer, with model, data, framework, compiler, and scheduling layers significantly impacting performance; second, the heterogeneous nature of ML fleets poses challenges in characterizing individual workload performance; and third, traditional utilization-based metrics prove insufficient for ML fleet characterization. To address these challenges, we present the "ML Productivity Goodput" (MPG) metric to measure ML fleet efficiency. We show how to leverage this metric to characterize the fleet across the ML system stack. We also present methods to identify and optimize performance bottlenecks using MPG, providing strategies for managing warehouse-scale ML systems in general. Lastly, we demonstrate quantitative evaluations from applying these methods to a real ML fleet for internal-facing Google TPU workloads, where we observed tangible improvements.

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arXiv2025

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

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arXiv2025

How Well Do Supervised 3D Models Transfer to Medical Imaging Tasks?

The pre-training and fine-tuning paradigm has become prominent in transfer learning. For example, if the model is pre-trained on ImageNet and then fine-tuned to PASCAL, it can significantly outperform that trained on PASCAL from scratch. While ImageNet pre-training has shown enormous success, it is formed in 2D, and the learned features are for classification tasks; when transferring to more diverse tasks, like 3D image segmentation, its performance is inevitably compromised due to the deviation from the original ImageNet context. A significant challenge lies in the lack of large, annotated 3D datasets rivaling the scale of ImageNet for model pre-training. To overcome this challenge, we make two contributions. Firstly, we construct AbdomenAtlas 1.1 that comprises 9,262 three-dimensional computed tomography (CT) volumes with high-quality, per-voxel annotations of 25 anatomical structures and pseudo annotations of seven tumor types. Secondly, we develop a suite of models that are pre-trained on our AbdomenAtlas 1.1 for transfer learning. Our preliminary analyses indicate that the model trained only with 21 CT volumes, 672 masks, and 40 GPU hours has a transfer learning ability similar to the model trained with 5,050 (unlabeled) CT volumes and 1,152 GPU hours. More importantly, the transfer learning ability of supervised models can further scale up with larger annotated datasets, achieving significantly better performance than preexisting pre-trained models, irrespective of their pre-training methodologies or data sources. We hope this study can facilitate collective efforts in constructing larger 3D medical datasets and more releases of supervised pre-trained models.

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arXiv2024

Text-Driven Tumor Synthesis

Tumor synthesis can generate examples that AI often misses or over-detects, improving AI performance by training on these challenging cases. However, existing synthesis methods, which are typically unconditional -- generating images from random variables -- or conditioned only by tumor shapes, lack controllability over specific tumor characteristics such as texture, heterogeneity, boundaries, and pathology type. As a result, the generated tumors may be overly similar or duplicates of existing training data, failing to effectively address AI's weaknesses. We propose a new text-driven tumor synthesis approach, termed TextoMorph, that provides textual control over tumor characteristics. This is particularly beneficial for examples that confuse the AI the most, such as early tumor detection (increasing Sensitivity by +8.5%), tumor segmentation for precise radiotherapy (increasing DSC by +6.3%), and classification between benign and malignant tumors (improving Sensitivity by +8.2%). By incorporating text mined from radiology reports into the synthesis process, we increase the variability and controllability of the synthetic tumors to target AI's failure cases more precisely. Moreover, TextoMorph uses contrastive learning across different texts and CT scans, significantly reducing dependence on scarce image-report pairs (only 141 pairs used in this study) by leveraging a large corpus of 34,035 radiology reports. Finally, we have developed rigorous tests to evaluate synthetic tumors, including Text-Driven Visual Turing Test and Radiomics Pattern Analysis, showing that our synthetic tumors is realistic and diverse in texture, heterogeneity, boundaries, and pathology.

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arXiv2024

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).

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arXiv2024

Radiative Gaussian Splatting for Efficient X-ray Novel View Synthesis

X-ray is widely applied for transmission imaging due to its stronger penetration than natural light. When rendering novel view X-ray projections, existing methods mainly based on NeRF suffer from long training time and slow inference speed. In this paper, we propose a 3D Gaussian splatting-based framework, namely X-Gaussian, for X-ray novel view synthesis. Firstly, we redesign a radiative Gaussian point cloud model inspired by the isotropic nature of X-ray imaging. Our model excludes the influence of view direction when learning to predict the radiation intensity of 3D points. Based on this model, we develop a Differentiable Radiative Rasterization (DRR) with CUDA implementation. Secondly, we customize an Angle-pose Cuboid Uniform Initialization (ACUI) strategy that directly uses the parameters of the X-ray scanner to compute the camera information and then uniformly samples point positions within a cuboid enclosing the scanned object. Experiments show that our X-Gaussian outperforms state-of-the-art methods by 6.5 dB while enjoying less than 15% training time and over 73x inference speed. The application on sparse-view CT reconstruction also reveals the practical values of our method. Code is publicly available at https://github.com/caiyuanhao1998/X-Gaussian . A video demo of the training process visualization is at https://www.youtube.com/watch?v=gDVf_Ngeghg .

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arXiv2024

Analyzing Tumors by Synthesis

Computer-aided tumor detection has shown great potential in enhancing the interpretation of over 80 million CT scans performed annually in the United States. However, challenges arise due to the rarity of CT scans with tumors, especially early-stage tumors. Developing AI with real tumor data faces issues of scarcity, annotation difficulty, and low prevalence. Tumor synthesis addresses these challenges by generating numerous tumor examples in medical images, aiding AI training for tumor detection and segmentation. Successful synthesis requires realistic and generalizable synthetic tumors across various organs. This chapter reviews AI development on real and synthetic data and summarizes two key trends in synthetic data for cancer imaging research: modeling-based and learning-based approaches. Modeling-based methods, like Pixel2Cancer, simulate tumor development over time using generic rules, while learning-based methods, like DiffTumor, learn from a few annotated examples in one organ to generate synthetic tumors in others. Reader studies with expert radiologists show that synthetic tumors can be convincingly realistic. We also present case studies in the liver, pancreas, and kidneys reveal that AI trained on synthetic tumors can achieve performance comparable to, or better than, AI only trained on real data. Tumor synthesis holds significant promise for expanding datasets, enhancing AI reliability, improving tumor detection performance, and preserving patient privacy.

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arXiv2024

From Pixel to Cancer: Cellular Automata in Computed Tomography

AI for cancer detection encounters the bottleneck of data scarcity, annotation difficulty, and low prevalence of early tumors. Tumor synthesis seeks to create artificial tumors in medical images, which can greatly diversify the data and annotations for AI training. However, current tumor synthesis approaches are not applicable across different organs due to their need for specific expertise and design. This paper establishes a set of generic rules to simulate tumor development. Each cell (pixel) is initially assigned a state between zero and ten to represent the tumor population, and a tumor can be developed based on three rules to describe the process of growth, invasion, and death. We apply these three generic rules to simulate tumor development--from pixel to cancer--using cellular automata. We then integrate the tumor state into the original computed tomography (CT) images to generate synthetic tumors across different organs. This tumor synthesis approach allows for sampling tumors at multiple stages and analyzing tumor-organ interaction. Clinically, a reader study involving three expert radiologists reveals that the synthetic tumors and their developing trajectories are convincingly realistic. Technically, we analyze and simulate tumor development at various stages using 9,262 raw, unlabeled CT images sourced from 68 hospitals worldwide. The performance in segmenting tumors in the liver, pancreas, and kidneys exceeds prevailing literature benchmarks, underlining the immense potential of tumor synthesis, especially for earlier cancer detection. The code and models are available at https://github.com/MrGiovanni/Pixel2Cancer

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arXiv2024

Embracing Massive Medical Data

As massive medical data become available with an increasing number of scans, expanding classes, and varying sources, prevalent training paradigms -- where AI is trained with multiple passes over fixed, finite datasets -- face significant challenges. First, training AI all at once on such massive data is impractical as new scans/sources/classes continuously arrive. Second, training AI continuously on new scans/sources/classes can lead to catastrophic forgetting, where AI forgets old data as it learns new data, and vice versa. To address these two challenges, we propose an online learning method that enables training AI from massive medical data. Instead of repeatedly training AI on randomly selected data samples, our method identifies the most significant samples for the current AI model based on their data uniqueness and prediction uncertainty, then trains the AI on these selective data samples. Compared with prevalent training paradigms, our method not only improves data efficiency by enabling training on continual data streams, but also mitigates catastrophic forgetting by selectively training AI on significant data samples that might otherwise be forgotten, outperforming by 15% in Dice score for multi-organ and tumor segmentation. The code is available at https://github.com/MrGiovanni/OnlineLearning

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arXiv2024

Quality Sentinel: Estimating Label Quality and Errors in Medical Segmentation Datasets

An increasing number of public datasets have shown a transformative impact on automated medical segmentation. However, these datasets are often with varying label quality, ranging from manual expert annotations to AI-generated pseudo-annotations. There is no systematic, reliable, and automatic quality control (QC). To fill in this bridge, we introduce a regression model, Quality Sentinel, to estimate label quality compared with manual annotations in medical segmentation datasets. This regression model was trained on over 4 million image-label pairs created by us. Each pair presents a varying but quantified label quality based on manual annotations, which enable us to predict the label quality of any image-label pairs in the inference. Our Quality Sentinel can predict the label quality of 142 body structures. The predicted label quality quantified by Dice Similarity Coefficient (DSC) shares a strong correlation with ground truth quality, with a positive correlation coefficient (r=0.902). Quality Sentinel has found multiple impactful use cases. (I) We evaluated label quality in publicly available datasets, where quality highly varies across different datasets. Our analysis also uncovers that male and younger subjects exhibit significantly higher quality. (II) We identified and corrected poorly annotated labels, achieving 1/3 reduction in annotation costs with optimal budgeting on TotalSegmentator. (III) We enhanced AI training efficiency and performance by focusing on high-quality pseudo labels, resulting in a 33%--88% performance boost over entropy-based methods, with a cost of 31% time and 4.5% memory. The data and model are released.

cs.CV↗

arXiv2024

Universal and Extensible Language-Vision Models for Organ Segmentation and Tumor Detection from Abdominal Computed Tomography

The advancement of artificial intelligence (AI) for organ segmentation and tumor detection is propelled by the growing availability of computed tomography (CT) datasets with detailed, per-voxel annotations. However, these AI models often struggle with flexibility for partially annotated datasets and extensibility for new classes due to limitations in the one-hot encoding, architectural design, and learning scheme. To overcome these limitations, we propose a universal, extensible framework enabling a single model, termed Universal Model, to deal with multiple public datasets and adapt to new classes (e.g., organs/tumors). Firstly, we introduce a novel language-driven parameter generator that leverages language embeddings from large language models, enriching semantic encoding compared with one-hot encoding. Secondly, the conventional output layers are replaced with lightweight, class-specific heads, allowing Universal Model to simultaneously segment 25 organs and six types of tumors and ease the addition of new classes. We train our Universal Model on 3,410 CT volumes assembled from 14 publicly available datasets and then test it on 6,173 CT volumes from four external datasets. Universal Model achieves first place on six CT tasks in the Medical Segmentation Decathlon (MSD) public leaderboard and leading performance on the Beyond The Cranial Vault (BTCV) dataset. In summary, Universal Model exhibits remarkable computational efficiency (6x faster than other dataset-specific models), demonstrates strong generalization across different hospitals, transfers well to numerous downstream tasks, and more importantly, facilitates the extensibility to new classes while alleviating the catastrophic forgetting of previously learned classes. Codes, models, and datasets are available at https://github.com/ljwztc/CLIP-Driven-Universal-Model

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arXiv2024

Towards Generalizable Tumor Synthesis

Tumor synthesis enables the creation of artificial tumors in medical images, facilitating the training of AI models for tumor detection and segmentation. However, success in tumor synthesis hinges on creating visually realistic tumors that are generalizable across multiple organs and, furthermore, the resulting AI models being capable of detecting real tumors in images sourced from different domains (e.g., hospitals). This paper made a progressive stride toward generalizable tumor synthesis by leveraging a critical observation: early-stage tumors (< 2cm) tend to have similar imaging characteristics in computed tomography (CT), whether they originate in the liver, pancreas, or kidneys. We have ascertained that generative AI models, e.g., Diffusion Models, can create realistic tumors generalized to a range of organs even when trained on a limited number of tumor examples from only one organ. Moreover, we have shown that AI models trained on these synthetic tumors can be generalized to detect and segment real tumors from CT volumes, encompassing a broad spectrum of patient demographics, imaging protocols, and healthcare facilities.

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arXiv2024

Structure-Aware Sparse-View X-ray 3D Reconstruction

X-ray, known for its ability to reveal internal structures of objects, is expected to provide richer information for 3D reconstruction than visible light. Yet, existing neural radiance fields (NeRF) algorithms overlook this important nature of X-ray, leading to their limitations in capturing structural contents of imaged objects. In this paper, we propose a framework, Structure-Aware X-ray Neural Radiodensity Fields (SAX-NeRF), for sparse-view X-ray 3D reconstruction. Firstly, we design a Line Segment-based Transformer (Lineformer) as the backbone of SAX-NeRF. Linefomer captures internal structures of objects in 3D space by modeling the dependencies within each line segment of an X-ray. Secondly, we present a Masked Local-Global (MLG) ray sampling strategy to extract contextual and geometric information in 2D projection. Plus, we collect a larger-scale dataset X3D covering wider X-ray applications. Experiments on X3D show that SAX-NeRF surpasses previous NeRF-based methods by 12.56 and 2.49 dB on novel view synthesis and CT reconstruction. Code, models, and data are released at https://github.com/caiyuanhao1998/SAX-NeRF

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arXiv2024

Exploiting Structural Consistency of Chest Anatomy for Unsupervised Anomaly Detection in Radiography Images

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. Exploiting this structured information could potentially ease the detection of anomalies from radiography images. To this end, we propose a Simple Space-Aware Memory Matrix for In-painting and Detecting anomalies from radiography images (abbreviated as SimSID). We formulate anomaly detection as an image reconstruction task, consisting of a space-aware memory matrix and an in-painting block in the feature space. During the training, SimSID can taxonomize the ingrained anatomical structures into recurrent visual patterns, and in the inference, it can identify anomalies (unseen/modified visual patterns) from the test image. Our SimSID surpasses the state of the arts in unsupervised anomaly detection by +8.0%, +5.0%, and +9.9% AUC scores on ZhangLab, COVIDx, and CheXpert benchmark datasets, respectively. Code: https://github.com/MrGiovanni/SimSID

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arXiv2024

Leveraging AI Predicted and Expert Revised Annotations in Interactive Segmentation: Continual Tuning or Full Training?

Interactive segmentation, an integration of AI algorithms and human expertise, premises to improve the accuracy and efficiency of curating large-scale, detailed-annotated datasets in healthcare. Human experts revise the annotations predicted by AI, and in turn, AI improves its predictions by learning from these revised annotations. This interactive process continues to enhance the quality of annotations until no major revision is needed from experts. The key challenge is how to leverage AI predicted and expert revised annotations to iteratively improve the AI. Two problems arise: (1) The risk of catastrophic forgetting--the AI tends to forget the previously learned classes if it is only retrained using the expert revised classes. (2) Computational inefficiency when retraining the AI using both AI predicted and expert revised annotations; moreover, given the dominant AI predicted annotations in the dataset, the contribution of newly revised annotations--often account for a very small fraction--to the AI training remains marginal. This paper proposes Continual Tuning to address the problems from two perspectives: network design and data reuse. Firstly, we design a shared network for all classes followed by class-specific networks dedicated to individual classes. To mitigate forgetting, we freeze the shared network for previously learned classes and only update the class-specific network for revised classes. Secondly, we reuse a small fraction of data with previous annotations to avoid over-computing. The selection of such data relies on the importance estimate of each data. The importance score is computed by combining the uncertainty and consistency of AI predictions. Our experiments demonstrate that Continual Tuning achieves a speed 16x greater than repeatedly training AI from scratch without compromising the performance.

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