Jie Tian

Zihan Li, Dihan Li, Cangbai Xu et al. · uw

Medical image segmentation is one of the most fundamental tasks concerning medical information analysis. Various solutions have been proposed so far, including many deep learning-based techniques, such as U-Net, FC-DenseNet, etc. However, high-precision medical image segmentation remains a highly challenging task due to the existence of inherent magnification and distortion in medical images as well as the presence of lesions with similar density to normal tissues. In this paper, we propose TFCNs (Transformers for Fully Convolutional denseNets) to tackle the problem by introducing ResLinear-Transformer (RL-Transformer) and Convolutional Linear Attention Block (CLAB) to FC-DenseNet. TFCNs is not only able to utilize more latent information from the CT images for feature extraction, but also can capture and disseminate semantic features and filter non-semantic features more effectively through the CLAB module. Our experimental results show that TFCNs can achieve state-of-the-art performance with dice scores of 83.72\% on the Synapse dataset. In addition, we evaluate the robustness of TFCNs for lesion area effects on the COVID-19 public datasets. The Python code will be made publicly available on https://github.com/HUANGLIZI/TFCNs.

Lingwei Meng, Di Dong, Xin Chen et al.

Objective: Radiomics, an emerging tool for medical image analysis, is potential towards precisely characterizing gastric cancer (GC). Whether using one-slice 2D annotation or whole-volume 3D annotation remains a long-time debate, especially for heterogeneous GC. We comprehensively compared 2D and 3D radiomic features' representation and discrimination capacity regarding GC, via three tasks. Methods: Four-center 539 GC patients were retrospectively enrolled and divided into the training and validation cohorts. From 2D or 3D regions of interest (ROIs) annotated by radiologists, radiomic features were extracted respectively. Feature selection and model construction procedures were customed for each combination of two modalities (2D or 3D) and three tasks. Subsequently, six machine learning models (Model_2D^LNM, Model_3D^LNM; Model_2D^LVI, Model_3D^LVI; Model_2D^pT, Model_3D^pT) were derived and evaluated to reflect modalities' performances in characterizing GC. Furthermore, we performed an auxiliary experiment to assess modalities' performances when resampling spacing is different. Results: Regarding three tasks, the yielded areas under the curve (AUCs) were: Model_2D^LNM's 0.712 (95% confidence interval, 0.613-0.811), Model_3D^LNM's 0.680 (0.584-0.775); Model_2D^LVI's 0.677 (0.595-0.761), Model_3D^LVI's 0.615 (0.528-0.703); Model_2D^pT's 0.840 (0.779-0.901), Model_3D^pT's 0.813 (0.747-0.879). Moreover, the auxiliary experiment indicated that Models_2D are statistically more advantageous than Models3D with different resampling spacings. Conclusion: Models constructed with 2D radiomic features revealed comparable performances with those constructed with 3D features in characterizing GC. Significance: Our work indicated that time-saving 2D annotation would be the better choice in GC, and provided a related reference to further radiomics-based researches.

Dandan Shan, Zihan Li, Wentao Chen et al. · uw

Segmentation of COVID-19 lesions can assist physicians in better diagnosis and treatment of COVID-19. However, there are few relevant studies due to the lack of detailed information and high-quality annotation in the COVID-19 dataset. To solve the above problem, we propose C2FVL, a Coarse-to-Fine segmentation framework via Vision-Language alignment to merge text information containing the number of lesions and specific locations of image information. The introduction of text information allows the network to achieve better prediction results on challenging datasets. We conduct extensive experiments on two COVID-19 datasets including chest X-ray and CT, and the results demonstrate that our proposed method outperforms other state-of-the-art segmentation methods.

Gen Shi, Hui Zhang, Jie Tian

Accurate segmentation of 3D vascular structures is essential for various medical imaging applications. The dispersed nature of vascular structures leads to inherent spatial uncertainty and necessitates location awareness, yet most current 3D medical segmentation models rely on the patch-wise training strategy that usually loses this spatial context. In this study, we introduce the Coordinate-aware Modulated Mamba Network (COMMA) and contribute a manually labeled dataset of 570 cases, the largest publicly available 3D vessel dataset to date. COMMA leverages both entire and cropped patch data through global and local branches, ensuring robust and efficient spatial location awareness. Specifically, COMMA employs a channel-compressed Mamba (ccMamba) block to encode entire image data, capturing long-range dependencies while optimizing computational costs. Additionally, we propose a coordinate-aware modulated (CaM) block to enhance interactions between the global and local branches, allowing the local branch to better perceive spatial information. We evaluate COMMA on six datasets, covering two imaging modalities and five types of vascular tissues. The results demonstrate COMMA's superior performance compared to state-of-the-art methods with computational efficiency, especially in segmenting small vessels. Ablation studies further highlight the importance of our proposed modules and spatial information. The code and data will be open source at https://github.com/shigen-StoneRoot/COMMA.

Liwen Zhang, Lianzhen Zhong, Fan Yang et al.

A core challenge in survival analysis is to model the distribution of censored time-to-event data, where the event of interest may be a death, failure, or occurrence of a specific event. Previous studies have showed that ranking and maximum likelihood estimation (MLE)loss functions are widely-used for survival analysis. However, ranking loss only focus on the ranking of survival time and does not consider potential effect of samples for exact survival time values. Furthermore, the MLE is unbounded and easily subject to outliers (e.g., censored data), which may cause poor performance of modeling. To handle the complexities of learning process and exploit valuable survival time values, we propose a time-adaptive coordinate loss function, TripleSurv, to achieve adaptive adjustments by introducing the differences in the survival time between sample pairs into the ranking, which can encourage the model to quantitatively rank relative risk of pairs, ultimately enhancing the accuracy of predictions. Most importantly, the TripleSurv is proficient in quantifying the relative risk between samples by ranking ordering of pairs, and consider the time interval as a trade-off to calibrate the robustness of model over sample distribution. Our TripleSurv is evaluated on three real-world survival datasets and a public synthetic dataset. The results show that our method outperforms the state-of-the-art methods and exhibits good model performance and robustness on modeling various sophisticated data distributions with different censor rates. Our code will be available upon acceptance.

Gen Shi, Hao Lu, Hui Hui et al.

The precise cerebrovascular segmentation in time-of-flight magnetic resonance angiography (TOF-MRA) data is crucial for clinically computer-aided diagnosis. However, the sparse distribution of cerebrovascular structures in TOF-MRA results in an exceedingly high cost for manual data labeling. The use of unlabeled TOF-MRA data holds the potential to enhance model performance significantly. In this study, we construct the largest preprocessed unlabeled TOF-MRA datasets (1510 subjects) to date. We also provide three additional labeled datasets totaling 113 subjects. Furthermore, we propose a simple yet effective pertraining strategy based on Frangi filtering, known for enhancing vessel-like structures, to fully leverage the unlabeled data for 3D cerebrovascular segmentation. Specifically, we develop a Frangi filtering-based preprocessing workflow to handle the large-scale unlabeled dataset, and a multi-task pretraining strategy is proposed to effectively utilize the preprocessed data. By employing this approach, we maximize the knowledge gained from the unlabeled data. The pretrained model is evaluated on four cerebrovascular segmentation datasets. The results have demonstrated the superior performance of our model, with an improvement of approximately 3\% compared to state-of-the-art semi- and self-supervised methods. Furthermore, the ablation studies also demonstrate the generalizability and effectiveness of the pretraining method regarding the backbone structures. The code and data have been open source at: \url{https://github.com/shigen-StoneRoot/FFPN}.

Bao Li, Zhenyu Liu, Lizhi Shao et al.

Directly predicting human epidermal growth factor receptor 2 (HER2) status from widely available hematoxylin and eosin (HE)-stained whole slide images (WSIs) can reduce technical costs and expedite treatment selection. Accurately predicting HER2 requires large collections of multi-site WSIs. Federated learning enables collaborative training of these WSIs without gigabyte-size WSIs transportation and data privacy concerns. However, federated learning encounters challenges in addressing label imbalance in multi-site WSIs from the real world. Moreover, existing WSI classification methods cannot simultaneously exploit local context information and long-range dependencies in the site-end feature representation of federated learning. To address these issues, we present a point transformer with federated learning for multi-site HER2 status prediction from HE-stained WSIs. Our approach incorporates two novel designs. We propose a dynamic label distribution strategy and an auxiliary classifier, which helps to establish a well-initialized model and mitigate label distribution variations across sites. Additionally, we propose a farthest cosine sampling based on cosine distance. It can sample the most distinctive features and capture the long-range dependencies. Extensive experiments and analysis show that our method achieves state-of-the-art performance at four sites with a total of 2687 WSIs. Furthermore, we demonstrate that our model can generalize to two unseen sites with 229 WSIs.

Chenghao Fan, Zhenyi Lu, Wei Wei et al.

Efficient fine-tuning of large language models for task-specific applications is imperative, yet the vast number of parameters in these models makes their training increasingly challenging. Despite numerous proposals for effective methods, a substantial memory overhead remains for gradient computations during updates. \thm{Can we fine-tune a series of task-specific small models and transfer their knowledge directly to a much larger model without additional training?} In this paper, we explore weak-to-strong specialization using logit arithmetic, facilitating a direct answer to this question. Existing weak-to-strong methods often employ a static knowledge transfer ratio and a single small model for transferring complex knowledge, which leads to suboptimal performance. % To address this, To surmount these limitations, we propose a dynamic logit fusion approach that works with a series of task-specific small models, each specialized in a different task. This method adaptively allocates weights among these models at each decoding step, learning the weights through Kullback-Leibler divergence constrained optimization problems. We conduct extensive experiments across various benchmarks in both single-task and multi-task settings, achieving leading results. By transferring expertise from the 7B model to the 13B model, our method closes the performance gap by 96.4\% in single-task scenarios and by 86.3\% in multi-task scenarios compared to full fine-tuning of the 13B model. Notably, we achieve surpassing performance on unseen tasks. Moreover, we further demonstrate that our method can effortlessly integrate in-context learning for single tasks and task arithmetic for multi-task scenarios.

Xiaoyan Liu, Zhiwei Xu, Yana Qin et al.

New intelligence applications are driving increasing interest in deploying deep neural networks (DNN) in a distributed way. To set up distributed deep learning involves alterations of a great number of the parameter configurations of network/edge devices and DNN models, which are crucial to achieve best performances. Simulations measure scalability of intelligence applications in the early stage, as well as to determine the effects of different configurations, thus highly desired. However, work on simulating the distributed intelligence environment is still in its infancy. The existing simulation frameworks, such as NS-3, etc., cannot extended in a straightforward way to support simulations of distributed learning. In this paper, we propose a novel discrete event simulator, sim4DistrDL, which includes a deep learning module and a network simulation module to facilitate simulation of DNN-based distributed applications. Specifically, we give the design and implementation of the proposed learning simulator and present an illustrative use case.