no code implementations • 9 Mar 2025 • Lin Zhang, Yuteng Zhang, Dusit Niyato, Lei Ren, Pengfei Gu, Zhen Chen, Yuanjun Laili, Wentong Cai, Agostino Bruzzone
Generative AI (GenAI) has demonstrated remarkable capabilities in code generation, and its integration into complex product modeling and simulation code generation can significantly enhance the efficiency of the system design phase in Model-Based Systems Engineering (MBSE).
1 code implementation • 18 Jan 2025 • Delin An, Pan Du, Pengfei Gu, Jian-Xun Wang, Chaoli Wang
Accurate segmentation of the aorta and its associated arch branches is crucial for diagnosing aortic diseases.
1 code implementation • 21 Nov 2024 • Delin An, Pengfei Gu, Milan Sonka, Chaoli Wang, Danny Z. Chen
To address these challenges, in this work, we propose a new SSF, called \proposed, {for segmenting any anatomical structures in 3D medical images using only a single annotated slice per training and testing volume.}
1 code implementation • 23 Jul 2024 • Yunfei Lu, Pengfei Gu, Chaoli Wang
We present FCNR, a fast compressive neural representation for tens of thousands of visualization images under varying viewpoints and timesteps.
no code implementations • 16 Jun 2024 • Pengfei Gu, Zihan Zhao, Hongxiao Wang, Yaopeng Peng, Yizhe Zhang, Nishchal Sapkota, Chaoli Wang, Danny Z. Chen
The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images.
no code implementations • 15 Jun 2024 • Pengfei Gu, Yejia Zhang, Huimin Li, Chaoli Wang, Danny Z. Chen
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.
no code implementations • 18 Mar 2024 • Hongxiao Wang, Yang Yang, Zhuo Zhao, Pengfei Gu, Nishchal Sapkota, Danny Z. Chen
For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e. g., bulk RNA-seq) for quantifying gene expressions.
no code implementations • 15 Sep 2023 • Marinka Zitnik, Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T. M. Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z. Chen, Lenore Cowen, Kapil Devkota, Anthony Gitter, Sara Gosline, Pengfei Gu, Pietro H. Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R. Pico, Nataša Pržulj, Teresa M. Przytycka, Benjamin J. Raphael, Anna Ritz, Roded Sharan, Yang shen, Mona Singh, Donna K. Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales.
1 code implementation • 26 Aug 2023 • Yizhe Zhang, Tao Zhou, Shuo Wang, Ye Wu, Pengfei Gu, Danny Z. Chen
Our new method is iterative and consists of two main stages: (1) segmentation model training; (2) expanding the labeled set by using the trained segmentation model, an unlabeled set, SAM, and domain-specific knowledge.
1 code implementation • 23 Jul 2023 • Yejia Zhang, Pengfei Gu, Nishchal Sapkota, Danny Z. Chen
Modern medical image segmentation methods primarily use discrete representations in the form of rasterized masks to learn features and generate predictions.
no code implementations • 27 Jan 2023 • Xu Wang, Pengfei Gu, Pengkun Wang, Binwu Wang, Zhengyang Zhou, Lei Bai, Yang Wang
In this paper, with extensive and deep-going experiments, we comprehensively analyze existing spatiotemporal graph learning models and reveal that extracting adjacency matrices with carefully design strategies, which are viewed as the key of enhancing performance on graph learning, are largely ineffective.
no code implementations • 16 Nov 2022 • Yejia Zhang, Nishchal Sapkota, Pengfei Gu, Yaopeng Peng, Hao Zheng, Danny Z. Chen
Understanding of spatial attributes is central to effective 3D radiology image analysis where crop-based learning is the de facto standard.
no code implementations • 15 Nov 2022 • Pengfei Gu, Yejia Zhang, Chaoli Wang, Danny Z. Chen
(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.
no code implementations • 15 Nov 2022 • Yejia Zhang, Pengfei Gu, Nishchal Sapkota, Hao Zheng, Peixian Liang, Danny Z. Chen
High annotation costs and limited labels for dense 3D medical imaging tasks have recently motivated an assortment of 3D self-supervised pretraining methods that improve transfer learning performance.