MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

EVENet: Evidence-based Ensemble Learning for Uncertainty-aware Brain Parcellation Using Diffusion MRI

In this study, we developed an Evidence-based Ensemble Neural Network, namely EVENet, for anatomical brain parcellation using diffusion MRI. The key innovation of EVENet is the design of an evidential deep learning framework to quantify predictive uncertainty at each voxel during a single inference. Using EVENet, we obtained accurate parcellation and uncertainty estimates across different datasets from healthy and clinical populations and with different imaging acquisitions. The overall network includes five parallel subnetworks, where each is dedicated to learning the FreeSurfer parcellation for a certain diffusion MRI parameter. An evidence-based ensemble methodology is then proposed to fuse the individual outputs. We perform experimental evaluations on large-scale datasets from multiple imaging sources, including high-quality diffusion MRI data from healthy adults and clinically diffusion MRI data from participants with various brain diseases (schizophrenia, bipolar disorder, attention-deficit/hyperactivity disorder, Parkinson's disease, cerebral small vessel disease, and neurosurgical patients with brain tumors). Compared to several state-of-the-art methods, our experimental results demonstrate highly improved parcellation accuracy across the multiple testing datasets despite the differences in dMRI acquisition protocols and health conditions. Furthermore, thanks to the uncertainty estimation, our EVENet approach demonstrates a good ability to detect abnormal brain regions in patients with lesions, enhancing the interpretability and reliability of the segmentation results.

Reliable Deep Diffusion Tensor Estimation: Rethinking the Power of Data-Driven Optimization Routine

Diffusion tensor imaging (DTI) holds significant importance in clinical diagnosis and neuroscience research. However, conventional model-based fitting methods often suffer from sensitivity to noise, leading to decreased accuracy in estimating DTI parameters. While traditional data-driven deep learning methods have shown potential in terms of accuracy and efficiency, their limited generalization to out-of-training-distribution data impedes their broader application due to the diverse scan protocols used across centers, scanners, and studies. This work aims to tackle these challenges and promote the use of DTI by introducing a data-driven optimization-based method termed DoDTI. DoDTI combines the weighted linear least squares fitting algorithm and regularization by denoising technique. The former fits DW images from diverse acquisition settings into diffusion tensor field, while the latter applies a deep learning-based denoiser to regularize the diffusion tensor field instead of the DW images, which is free from the limitation of fixed-channel assignment of the network. The optimization object is solved using the alternating direction method of multipliers and then unrolled to construct a deep neural network, leveraging a data-driven strategy to learn network parameters. Extensive validation experiments are conducted utilizing both internally simulated datasets and externally obtained in-vivo datasets. The results, encompassing both qualitative and quantitative analyses, showcase that the proposed method attains state-of-the-art performance in DTI parameter estimation. Notably, it demonstrates superior generalization, accuracy, and efficiency, rendering it highly reliable for widespread application in the field.

A Split-and-Privatize Framework for Large Language Model Fine-Tuning

Fine-tuning is a prominent technique to adapt a pre-trained language model to downstream scenarios. In parameter-efficient fine-tuning, only a small subset of modules are trained over the downstream datasets, while leaving the rest of the pre-trained model frozen to save computation resources. In recent years, a popular productization form arises as Model-as-a-Service (MaaS), in which vendors provide abundant pre-trained language models, server resources and core functions, and customers can fine-tune, deploy and invoke their customized model by accessing the one-stop MaaS with their own private dataset. In this paper, we identify the model and data privacy leakage risks in MaaS fine-tuning, and propose a Split-and-Privatize (SAP) framework, which manage to mitigate the privacy issues by adapting the existing split learning architecture. The proposed SAP framework is sufficiently investigated by experiments, and the results indicate that it can enhance the empirical privacy by 62% at the cost of 1% model performance degradation on the Stanford Sentiment Treebank dataset.

Segment Anything Model-guided Collaborative Learning Network for Scribble-supervised Polyp Segmentation

Polyp segmentation plays a vital role in accurately locating polyps at an early stage, which holds significant clinical importance for the prevention of colorectal cancer. Various polyp segmentation methods have been developed using fully-supervised deep learning techniques. However, pixel-wise annotation for polyp images by physicians during the diagnosis is both time-consuming and expensive. Moreover, visual foundation models such as the Segment Anything Model (SAM) have shown remarkable performance. Nevertheless, directly applying SAM to medical segmentation may not produce satisfactory results due to the inherent absence of medical knowledge. In this paper, we propose a novel SAM-guided Collaborative Learning Network (SAM-CLNet) for scribble-supervised polyp segmentation, enabling a collaborative learning process between our segmentation network and SAM to boost the model performance. Specifically, we first propose a Cross-level Enhancement and Aggregation Network (CEA-Net) for weakly-supervised polyp segmentation. Within CEA-Net, we propose a Cross-level Enhancement Module (CEM) that integrates the adjacent features to enhance the representation capabilities of different resolution features. Additionally, a Feature Aggregation Module (FAM) is employed to capture richer features across multiple levels. Moreover, we present a box-augmentation strategy that combines the segmentation maps generated by CEA-Net with scribble annotations to create more precise prompts. These prompts are then fed into SAM, generating segmentation SAM-guided masks, which can provide additional supervision to train CEA-Net effectively. Furthermore, we present an Image-level Filtering Mechanism to filter out unreliable SAM-guided masks. Extensive experimental results show that our SAM-CLNet outperforms state-of-the-art weakly-supervised segmentation methods.

A Survey on Deep Learning for Polyp Segmentation: Techniques, Challenges and Future Trends

Early detection and assessment of polyps play a crucial role in the prevention and treatment of colorectal cancer (CRC). Polyp segmentation provides an effective solution to assist clinicians in accurately locating and segmenting polyp regions. In the past, people often relied on manually extracted lower-level features such as color, texture, and shape, which often had issues capturing global context and lacked robustness to complex scenarios. With the advent of deep learning, more and more outstanding medical image segmentation algorithms based on deep learning networks have emerged, making significant progress in this field. This paper provides a comprehensive review of polyp segmentation algorithms. We first review some traditional algorithms based on manually extracted features and deep segmentation algorithms, then detail benchmark datasets related to the topic. Specifically, we carry out a comprehensive evaluation of recent deep learning models and results based on polyp sizes, considering the pain points of research topics and differences in network structures. Finally, we discuss the challenges of polyp segmentation and future trends in this field. The models, benchmark datasets, and source code links we collected are all published at https://github.com/taozh2017/Awesome-Polyp-Segmentation.

Hawkeye: A PyTorch-based Library for Fine-Grained Image Recognition with Deep Learning

Fine-Grained Image Recognition (FGIR) is a fundamental and challenging task in computer vision and multimedia that plays a crucial role in Intellectual Economy and Industrial Internet applications. However, the absence of a unified open-source software library covering various paradigms in FGIR poses a significant challenge for researchers and practitioners in the field. To address this gap, we present Hawkeye, a PyTorch-based library for FGIR with deep learning. Hawkeye is designed with a modular architecture, emphasizing high-quality code and human-readable configuration, providing a comprehensive solution for FGIR tasks. In Hawkeye, we have implemented 16 state-of-the-art fine-grained methods, covering 6 different paradigms, enabling users to explore various approaches for FGIR. To the best of our knowledge, Hawkeye represents the first open-source PyTorch-based library dedicated to FGIR. It is publicly available at https://github.com/Hawkeye-FineGrained/Hawkeye/, providing researchers and practitioners with a powerful tool to advance their research and development in the field of FGIR.

Edge-aware Feature Aggregation Network for Polyp Segmentation

Precise polyp segmentation is vital for the early diagnosis and prevention of colorectal cancer (CRC) in clinical practice. However, due to scale variation and blurry polyp boundaries, it is still a challenging task to achieve satisfactory segmentation performance with different scales and shapes. In this study, we present a novel Edge-aware Feature Aggregation Network (EFA-Net) for polyp segmentation, which can fully make use of cross-level and multi-scale features to enhance the performance of polyp segmentation. Specifically, we first present an Edge-aware Guidance Module (EGM) to combine the low-level features with the high-level features to learn an edge-enhanced feature, which is incorporated into each decoder unit using a layer-by-layer strategy. Besides, a Scale-aware Convolution Module (SCM) is proposed to learn scale-aware features by using dilated convolutions with different ratios, in order to effectively deal with scale variation. Further, a Cross-level Fusion Module (CFM) is proposed to effectively integrate the cross-level features, which can exploit the local and global contextual information. Finally, the outputs of CFMs are adaptively weighted by using the learned edge-aware feature, which are then used to produce multiple side-out segmentation maps. Experimental results on five widely adopted colonoscopy datasets show that our EFA-Net outperforms state-of-the-art polyp segmentation methods in terms of generalization and effectiveness.

VideoGen: A Reference-Guided Latent Diffusion Approach for High Definition Text-to-Video Generation

In this paper, we present VideoGen, a text-to-video generation approach, which can generate a high-definition video with high frame fidelity and strong temporal consistency using reference-guided latent diffusion. We leverage an off-the-shelf text-to-image generation model, e.g., Stable Diffusion, to generate an image with high content quality from the text prompt, as a reference image to guide video generation. Then, we introduce an efficient cascaded latent diffusion module conditioned on both the reference image and the text prompt, for generating latent video representations, followed by a flow-based temporal upsampling step to improve the temporal resolution. Finally, we map latent video representations into a high-definition video through an enhanced video decoder. During training, we use the first frame of a ground-truth video as the reference image for training the cascaded latent diffusion module. The main characterises of our approach include: the reference image generated by the text-to-image model improves the visual fidelity; using it as the condition makes the diffusion model focus more on learning the video dynamics; and the video decoder is trained over unlabeled video data, thus benefiting from high-quality easily-available videos. VideoGen sets a new state-of-the-art in text-to-video generation in terms of both qualitative and quantitative evaluation. See \url{https://videogen.github.io/VideoGen/} for more samples.

SamDSK: Combining Segment Anything Model with Domain-Specific Knowledge for Semi-Supervised Learning in Medical Image Segmentation

The Segment Anything Model (SAM) exhibits a capability to segment a wide array of objects in natural images, serving as a versatile perceptual tool for various downstream image segmentation tasks. In contrast, medical image segmentation tasks often rely on domain-specific knowledge (DSK). In this paper, we propose a novel method that combines the segmentation foundation model (i.e., SAM) with domain-specific knowledge for reliable utilization of unlabeled images in building a medical image segmentation model. 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. These two stages are repeated until no more samples are added to the labeled set. A novel optimal-matching-based method is developed for combining the SAM-generated segmentation proposals and pixel-level and image-level DSK for constructing annotations of unlabeled images in the iterative stage (2). In experiments, we demonstrate the effectiveness of our proposed method for breast cancer segmentation in ultrasound images, polyp segmentation in endoscopic images, and skin lesion segmentation in dermoscopic images. Our work initiates a new direction of semi-supervised learning for medical image segmentation: the segmentation foundation model can be harnessed as a valuable tool for label-efficient segmentation learning in medical image segmentation.