Chaoli Wang

Pengfei Gu, Yejia Zhang, Chaoli Wang et al.

Convolutional neural network (CNN) based methods have achieved great successes in medical image segmentation, but their capability to learn global representations is still limited due to using small effective receptive fields of convolution operations. Transformer based methods are capable of modelling long-range dependencies of information for capturing global representations, yet their ability to model local context is lacking. Integrating CNN and Transformer to learn both local and global representations while exploring multi-scale features is instrumental in further improving medical image segmentation. In this paper, we propose a hierarchical CNN and Transformer hybrid architecture, called ConvFormer, for medical image segmentation. ConvFormer is based on several simple yet effective designs. (1) A feed forward module of Deformable Transformer (DeTrans) is re-designed to introduce local information, called Enhanced DeTrans. (2) A residual-shaped hybrid stem based on a combination of convolutions and Enhanced DeTrans is developed to capture both local and global representations to enhance representation ability. (3) Our encoder utilizes the residual-shaped hybrid stem in a hierarchical manner to generate feature maps in different scales, and an additional Enhanced DeTrans encoder with residual connections is built to exploit multi-scale features with feature maps of different scales as input. Experiments on several datasets show that our ConvFormer, trained from scratch, outperforms various CNN- or Transformer-based architectures, achieving state-of-the-art performance.

Delin An, Chaoli Wang

Unlike their line-based counterparts, surface-based techniques have yet to be thoroughly investigated in flow visualization due to their significant placement, speed, perception, and evaluation challenges. This paper presents SurfPatch, a novel framework supporting exploratory stream surface visualization. To begin with, we translate the issue of surface placement to surface selection and trace a large number of stream surfaces from a given flow field dataset. Then, we introduce a three-stage process: vertex-level classification, patch-level matching, and surface-level clustering that hierarchically builds the connection between vertices and patches and between patches and surfaces. This bottom-up approach enables fine-grained, multiscale patch-level matching, sharply contrasts surface-level matching offered by existing works, and provides previously unavailable flexibility during querying. We design an intuitive visual interface for users to conveniently visualize and analyze the underlying collection of stream surfaces in an exploratory manner. SurfPatch is not limited to stream surfaces traced from steady flow datasets. We demonstrate its effectiveness through experiments on stream surfaces produced from steady and unsteady flows as well as isosurfaces extracted from scalar fields. The code is available at https://github.com/adlsn/SurfPatch.

Kuangshi Ai, Haichao Miao, Zhimin Li et al.

Recent advances in multi-modal large language models (MLLMs) have enabled increasingly sophisticated autonomous visualization agents capable of translating user intentions into data visualizations. However, measuring progress and comparing different agents remains challenging, particularly in scientific visualization (SciVis), due to the absence of comprehensive, large-scale benchmarks for evaluating real-world capabilities. This position paper examines the various types of evaluation required for SciVis agents, outlines the associated challenges, provides a simple proof-of-concept evaluation example, and discusses how evaluation benchmarks can facilitate agent self-improvement. We advocate for a broader collaboration to develop a SciVis agentic evaluation benchmark that would not only assess existing capabilities but also drive innovation and stimulate future development in the field.

Pengfei Gu, Zihan Zhao, Hongxiao Wang et al.

The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images. Recently, SAM has gained a great deal of attention for its applications in medical image segmentation. However, to our best knowledge, no studies have shown how to harness the power of SAM for medical image classification. To fill this gap and make SAM a true ``foundation model'' for medical image analysis, it is highly desirable to customize SAM specifically for medical image classification. In this paper, we introduce SAMAug-C, an innovative augmentation method based on SAM for augmenting classification datasets by generating variants of the original images. The augmented datasets can be used to train a deep learning classification model, thereby boosting the classification performance. Furthermore, we propose a novel framework that simultaneously processes raw and SAMAug-C augmented image input, capitalizing on the complementary information that is offered by both. Experiments on three public datasets validate the effectiveness of our new approach.

Pengfei Gu, Huimin Li, Yejia Zhang et al.

Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can aggregate contextual information for downstream tasks. But, existing MAE pre-training methods, which were specifically developed with the ViT architecture, lack the ability to capture geometric shape and spatial information, which is critical for medical image segmentation tasks. In this paper, we propose a novel extension of known MAEs for self pre-training (i.e., models pre-trained on the same target dataset) for 3D medical image segmentation. (1) We propose a new topological loss to preserve geometric shape information by computing topological signatures of both the input and reconstructed volumes, learning geometric shape information. (2) We introduce a pre-text task that predicts the positions of the centers and eight corners of 3D crops, enabling the MAE to aggregate spatial information. (3) We extend the MAE pre-training strategy to a hybrid state-of-the-art (SOTA) medical image segmentation architecture and co-pretrain it alongside the ViT. (4) We develop a fine-tuned model for downstream segmentation tasks by complementing the pre-trained ViT encoder with our pre-trained SOTA model. Extensive experiments on five public 3D segmentation datasets show the effectiveness of our new approach.