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In the field of Alzheimer's disease diagnosis, segmentation and classification tasks are inherently interconnected. Sharing knowledge between models for these tasks can significantly improve training efficiency, particularly when training data is scarce. However, traditional knowledge distillation techniques often struggle to bridge the gap between segmentation and classification due to the distinct nature of tasks and different model architectures. To address this challenge, we propose a dual-stream pipeline that facilitates cross-task and cross-architecture knowledge sharing. Our approach introduces a dual-stream embedding module that unifies feature representations from segmentation and classification models, enabling dimensional integration of these features to guide the classification model. We validated our method on multiple 3D datasets for Alzheimer's disease diagnosis, demonstrating significant improvements in classification performance, especially on small datasets. Furthermore, we extended our pipeline with a residual temporal attention mechanism for early diagnosis, utilizing images taken before the atrophy of patients' brain mass. This advancement shows promise in enabling diagnosis approximately six months earlier in mild and asymptomatic stages, offering critical time for intervention., Comment: 8 pages, 3 figures, 3 tables

Explainable fake news detection predicts the authenticity of news items with annotated explanations. Today, Large Language Models (LLMs) are known for their powerful natural language understanding and explanation generation abilities. However, presenting LLMs for explainable fake news detection remains two main challenges. Firstly, fake news appears reasonable and could easily mislead LLMs, leaving them unable to understand the complex news-faking process. Secondly, utilizing LLMs for this task would generate both correct and incorrect explanations, which necessitates abundant labor in the loop. In this paper, we propose LLM-GAN, a novel framework that utilizes prompting mechanisms to enable an LLM to become Generator and Detector and for realistic fake news generation and detection. Our results demonstrate LLM-GAN's effectiveness in both prediction performance and explanation quality. We further showcase the integration of LLM-GAN to a cloud-native AI platform to provide better fake news detection service in the cloud.

Deep learning has achieved impressive results in nuclei segmentation, but the massive requirement for pixel-wise labels remains a significant challenge. To alleviate the annotation burden, existing methods generate pseudo masks for model training using point labels. However, the generated masks are inevitably different from the ground truth, and these dissimilarities are not handled reasonably during the network training, resulting in the subpar performance of the segmentation model. To tackle this issue, we propose a framework named DoNuSeg, enabling \textbf{D}ynamic pseudo label \textbf{O}ptimization in point-supervised \textbf{Nu}clei \textbf{Seg}mentation. Specifically, DoNuSeg takes advantage of class activation maps (CAMs) to adaptively capture regions with semantics similar to annotated points. To leverage semantic diversity in the hierarchical feature levels, we design a dynamic selection module to choose the optimal one among CAMs from different encoder blocks as pseudo masks. Meanwhile, a CAM-guided contrastive module is proposed to further enhance the accuracy of pseudo masks. In addition to exploiting the semantic information provided by CAMs, we consider location priors inherent to point labels, developing a task-decoupled structure for effectively differentiating nuclei. Extensive experiments demonstrate that DoNuSeg outperforms state-of-the-art point-supervised methods. The code is available at https://github.com/shinning0821/MICCAI24-DoNuSeg., Comment: early accepted by MICCAI2024

Survival prediction, utilizing pathological images and genomic profiles, is increasingly important in cancer analysis and prognosis. Despite significant progress, precise survival analysis still faces two main challenges: (1) The massive pixels contained in whole slide images (WSIs) complicate the process of pathological images, making it difficult to generate an effective representation of the tumor microenvironment (TME). (2) Existing multimodal methods often rely on alignment strategies to integrate complementary information, which may lead to information loss due to the inherent heterogeneity between pathology and genes. In this paper, we propose a Multimodal Cross-Task Interaction (MCTI) framework to explore the intrinsic correlations between subtype classification and survival analysis tasks. Specifically, to capture TME-related features in WSIs, we leverage the subtype classification task to mine tumor regions. Simultaneously, multi-head attention mechanisms are applied in genomic feature extraction, adaptively performing genes grouping to obtain task-related genomic embedding. With the joint representation of pathological images and genomic data, we further introduce a Transport-Guided Attention (TGA) module that uses optimal transport theory to model the correlation between subtype classification and survival analysis tasks, effectively transferring potential information. Extensive experiments demonstrate the superiority of our approaches, with MCTI outperforming state-of-the-art frameworks on three public benchmarks. \href{https://github.com/jsh0792/MCTI}{https://github.com/jsh0792/MCTI}.

Correlating neuropathology with neuroimaging findings provides a multiscale view of pathologic changes in the human organ spanning the meso- to micro-scales, and is an emerging methodology expected to shed light on numerous disease states. To gain the most information from this multimodal, multiscale approach, it is desirable to identify precisely where a histologic tissue section was taken from within the organ in order to correlate with the tissue features in exactly the same organ region. Histology-to-organ registration poses an extra challenge, as any given histologic section can capture only a small portion of a human organ. Making use of the capabilities of state-of-the-art deep learning models, we unlock the potential to address and solve such intricate challenges. Therefore, we create the ATOM benchmark dataset, sourced from diverse institutions, with the primary objective of transforming this challenge into a machine learning problem and delivering outstanding outcomes that enlighten the biomedical community. The performance of our RegisMCAN model demonstrates the potential of deep learning to accurately predict where a subregion extracted from an organ image was obtained from within the overall 3D volume. The code and dataset can be found at: https://github.com/haizailache999/Image-Registration/tree/main

Weakly supervised segmentation methods have gained significant attention due to their ability to reduce the reliance on costly pixel-level annotations during model training. However, the current weakly supervised nuclei segmentation approaches typically follow a two-stage pseudo-label generation and network training process. The performance of the nuclei segmentation heavily relies on the quality of the generated pseudo-labels, thereby limiting its effectiveness. This paper introduces a novel domain-adaptive weakly supervised nuclei segmentation framework using cross-task interaction strategies to overcome the challenge of pseudo-label generation. Specifically, we utilize weakly annotated data to train an auxiliary detection task, which assists the domain adaptation of the segmentation network. To enhance the efficiency of domain adaptation, we design a consistent feature constraint module integrating prior knowledge from the source domain. Furthermore, we develop pseudo-label optimization and interactive training methods to improve the domain transfer capability. To validate the effectiveness of our proposed method, we conduct extensive comparative and ablation experiments on six datasets. The results demonstrate the superiority of our approach over existing weakly supervised approaches. Remarkably, our method achieves comparable or even better performance than fully supervised methods. Our code will be released in https://github.com/zhangye-zoe/DAWN., Comment: 13 pages, 11 figures, 8 tables

Recently, pathological diagnosis, the gold standard for cancer diagnosis, has achieved superior performance by combining the Transformer with the multiple instance learning (MIL) framework using whole slide images (WSIs). However, the giga-pixel nature of WSIs poses a great challenge for the quadratic-complexity self-attention mechanism in Transformer to be applied in MIL. Existing studies usually use linear attention to improve computing efficiency but inevitably bring performance bottlenecks. To tackle this challenge, we propose a MamMIL framework for WSI classification by cooperating the selective structured state space model (i.e., Mamba) with MIL for the first time, enabling the modeling of instance dependencies while maintaining linear complexity. Specifically, to solve the problem that Mamba can only conduct unidirectional one-dimensional (1D) sequence modeling, we innovatively introduce a bidirectional state space model and a 2D context-aware block to enable MamMIL to learn the bidirectional instance dependencies with 2D spatial relationships. Experiments on two datasets show that MamMIL can achieve advanced classification performance with smaller memory footprints than the state-of-the-art MIL frameworks based on the Transformer. The code will be open-sourced if accepted., Comment: 11 pages, 2 figures

Semi-supervised segmentation methods have demonstrated promising results in natural scenarios, providing a solution to reduce dependency on manual annotation. However, these methods face significant challenges when directly applied to pathological images due to the subtle color differences between nuclei and tissues, as well as the significant morphological variations among nuclei. Consequently, the generated pseudo-labels often contain much noise, especially at the nuclei boundaries. To address the above problem, this paper proposes a boundary-aware contrastive learning network to denoise the boundary noise in a semi-supervised nuclei segmentation task. The model has two key designs: a low-resolution denoising (LRD) module and a cross-RoI contrastive learning (CRC) module. The LRD improves the smoothness of the nuclei boundary by pseudo-labels denoising, and the CRC enhances the discrimination between foreground and background by boundary feature contrastive learning. We conduct extensive experiments to demonstrate the superiority of our proposed method over existing semi-supervised instance segmentation methods., Comment: 12 pages, 3 figures, 6 tables

Automated diagnosis of Alzheimer Disease(AD) from brain imaging, such as magnetic resonance imaging (MRI), has become increasingly important and has attracted the community to contribute many deep learning methods. However, many of these methods are facing a trade-off that 3D models tend to be complicated while 2D models cannot capture the full 3D intricacies from the data. In this paper, we introduce a new model structure for diagnosing AD, and it can complete with performances of 3D models while essentially is a 2D method (thus computationally efficient). While the core idea lies in new perspective of cutting the 3D images into multiple 2D slices from three dimensions, we introduce multiple components that can further benefit the model in this new perspective, including adaptively selecting the number of sclices in each dimension, and the new attention mechanism. In addition, we also introduce a morphology augmentation, which also barely introduces new computational loads, but can help improve the diagnosis performances due to its alignment to the pathology of AD. We name our method ADAPT, which stands for Alzheimer Diagnosis through Adaptive Profiling Transformers. We test our model from a practical perspective (the testing domains do not appear in the training one): the diagnosis accuracy favors our ADAPT, while ADAPT uses less parameters than most 3D models use.

As attitude and motion sensing components, inertial sensors are widely used in various portable devices. But the severe errors of inertial sensors restrain their function, especially the trajectory recovery and semantic recognition. As a mainstream signal processing method, wavelet is hailed as the mathematical microscope of signal due to the plentiful and diverse wavelet basis functions. However, complicated noise types and application scenarios of inertial sensors make selecting wavelet basis perplexing. To this end, we propose a wavelet dynamic selection network (WDSNet), which intelligently selects the appropriate wavelet basis for variable inertial signals. In addition, existing deep learning architectures excel at extracting features from input data but neglect to learn the characteristics of target categories, which is essential to enhance the category awareness capability, thereby improving the selection of wavelet basis. Therefore, we propose a category representation mechanism (CRM), which enables the network to extract and represent category features without increasing trainable parameters. Furthermore, CRM transforms the common fully connected network into category representations, which provide closer supervision to the feature extractor than the far and trivial one-hot classification labels. We call this process of imposing interpretability on a network and using it to supervise the feature extractor the feature supervision mechanism, and its effectiveness is demonstrated experimentally and theoretically in this paper. The enhanced inertial signal can perform impracticable tasks with regard to the original signal, such as trajectory reconstruction. Both quantitative and visual results show that WDSNet outperforms the existing methods. Remarkably, WDSNet, as a weakly-supervised method, achieves the state-of-the-art performance of all the compared fully-supervised methods., Comment: Accepted by AAAI 2024 - Association for the Advancement of Artificial Intelligence

Biomarker detection is an indispensable part in the diagnosis and treatment of low-grade glioma (LGG). However, current LGG biomarker detection methods rely on expensive and complex molecular genetic testing, for which professionals are required to analyze the results, and intra-rater variability is often reported. To overcome these challenges, we propose an interpretable deep learning pipeline, a Multi-Biomarker Histomorphology Discoverer (Multi-Beholder) model based on the multiple instance learning (MIL) framework, to predict the status of five biomarkers in LGG using only hematoxylin and eosin-stained whole slide images and slide-level biomarker status labels. Specifically, by incorporating the one-class classification into the MIL framework, accurate instance pseudo-labeling is realized for instance-level supervision, which greatly complements the slide-level labels and improves the biomarker prediction performance. Multi-Beholder demonstrates superior prediction performance and generalizability for five LGG biomarkers (AUROC=0.6469-0.9735) in two cohorts (n=607) with diverse races and scanning protocols. Moreover, the excellent interpretability of Multi-Beholder allows for discovering the quantitative and qualitative correlations between biomarker status and histomorphology characteristics. Our pipeline not only provides a novel approach for biomarker prediction, enhancing the applicability of molecular treatments for LGG patients but also facilitates the discovery of new mechanisms in molecular functionality and LGG progression., Comment: 47 pages, 6 figures

The success of Computer Vision (CV) relies heavily on manually annotated data. However, it is prohibitively expensive to annotate images in key domains such as healthcare, where data labeling requires significant domain expertise and cannot be easily delegated to crowd workers. To address this challenge, we propose a neuro-symbolic approach called Rapid, which infers image labeling rules from a small amount of labeled data provided by domain experts and automatically labels unannotated data using the rules. Specifically, Rapid combines pre-trained CV models and inductive logic learning to infer the logic-based labeling rules. Rapid achieves a labeling accuracy of 83.33% to 88.33% on four image labeling tasks with only 12 to 39 labeled samples. In particular, Rapid significantly outperforms finetuned CV models in two highly specialized tasks. These results demonstrate the effectiveness of Rapid in learning from small data and its capability to generalize among different tasks. Code and our dataset are publicly available at https://github.com/Neural-Symbolic-Image-Labeling/, Comment: This paper was accepted by the 2023 ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Collecting annotations from multiple independent sources could mitigate the impact of potential noises and biases from a single source, which is a common practice in medical image segmentation. Learning segmentation networks from multi-source annotations remains a challenge due to the uncertainties brought by the variance of annotations and the quality of images. In this paper, we propose an Uncertainty-guided Multi-source Annotation Network (UMA-Net), which guides the training process by uncertainty estimation at both the pixel and the image levels. First, we developed the annotation uncertainty estimation module (AUEM) to learn the pixel-wise uncertainty of each annotation, which then guided the network to learn from reliable pixels by weighted segmentation loss. Second, a quality assessment module (QAM) was proposed to assess the image-level quality of the input samples based on the former assessed annotation uncertainties. Importantly, we introduced an auxiliary predictor to learn from the low-quality samples instead of discarding them, which ensured the preservation of their representation knowledge in the backbone without directly accumulating errors within the primary predictor. Extensive experiments demonstrated the effectiveness and feasibility of our proposed UMA-Net on various datasets, including 2D chest X-ray segmentation, fundus image segmentation, and 3D breast DCE-MRI segmentation.

Multiple Instance Learning (MIL), a powerful strategy for weakly supervised learning, is able to perform various prediction tasks on gigapixel Whole Slide Images (WSIs). However, the tens of thousands of patches in WSIs usually incur a vast computational burden for image augmentation, limiting the MIL model's improvement in performance. Currently, the feature augmentation-based MIL framework is a promising solution, while existing methods such as Mixup often produce unrealistic features. To explore a more efficient and practical augmentation method, we introduce the Diffusion Model (DM) into MIL for the first time and propose a feature augmentation framework called AugDiff. Specifically, we employ the generation diversity of DM to improve the quality of feature augmentation and the step-by-step generation property to control the retention of semantic information. We conduct extensive experiments over three distinct cancer datasets, two different feature extractors, and three prevalent MIL algorithms to evaluate the performance of AugDiff. Ablation study and visualization further verify the effectiveness. Moreover, we highlight AugDiff's higher-quality augmented feature over image augmentation and its superiority over self-supervised learning. The generalization over external datasets indicates its broader applications.

Body Mass Index (BMI), age, height and weight are important indicators of human health conditions, which can provide useful information for plenty of practical purposes, such as health care, monitoring and re-identification. Most existing methods of health indicator prediction mainly use front-view body or face images. These inputs are hard to be obtained in daily life and often lead to the lack of robustness for the models, considering their strict requirements on view and pose. In this paper, we propose to employ gait videos to predict health indicators, which are more prevalent in surveillance and home monitoring scenarios. However, the study of health indicator prediction from gait videos using deep learning was hindered due to the small amount of open-sourced data. To address this issue, we analyse the similarity and relationship between pose estimation and health indicator prediction tasks, and then propose a paradigm enabling deep learning for small health indicator datasets by pre-training on the pose estimation task. Furthermore, to better suit the health indicator prediction task, we bring forward Global-Local Aware aNd Centrosymmetric Encoder (GLANCE) module. It first extracts local and global features by progressive convolutions and then fuses multi-level features by a centrosymmetric double-path hourglass structure in two different ways. Experiments demonstrate that the proposed paradigm achieves state-of-the-art results for predicting health indicators on MoVi, and that the GLANCE module is also beneficial for pose estimation on 3DPW.

In low-permeability porous media, the velocity of a fluid flow exhibits a nonlinear dependence on the imposed pressure gradient. This non-Darcian flow behavior has important implications to geological disposal of nuclear waste, hydrocarbon extraction from shale, and flow and transport in clay-rich aquifers. Temperature has been postulated to affect the threshold pressure gradient of a non-Darcian flow; however, the supporting data is very limited. In this study we for the first time report a systematic measurement of the threshold pressure gradient under various permeabilities and temperatures. The results show that a higher temperature leads to a lower threshold pressure gradient under the same permeability and a faster reduction of the threshold pressure gradient with increasing permeability. The experimental data are fitted to a two-parameter model to determine the parameters, h0 and a, which characterize the interfacial fluid-solid interactions and the transition between the Darcy and non-Darcian regimes.

With the development of computational pathology, deep learning methods for Gleason grading through whole slide images (WSIs) have excellent prospects. Since the size of WSIs is extremely large, the image label usually contains only slide-level label or limited pixel-level labels. The current mainstream approach adopts multi-instance learning to predict Gleason grades. However, some methods only considering the slide-level label ignore the limited pixel-level labels containing rich local information. Furthermore, the method of additionally considering the pixel-level labels ignores the inaccuracy of pixel-level labels. To address these problems, we propose a mixed supervision Transformer based on the multiple instance learning framework. The model utilizes both slide-level label and instance-level labels to achieve more accurate Gleason grading at the slide level. The impact of inaccurate instance-level labels is further reduced by introducing an efficient random masking strategy in the mixed supervision training process. We achieve the state-of-the-art performance on the SICAPv2 dataset, and the visual analysis shows the accurate prediction results of instance level. The source code is available at https://github.com/bianhao123/Mixed_supervision., Comment: Accepted by MICCAI 2022