One Signal-Noise Separation based Wiener Filter for Magnetogastrogram

Magnetogastrogram (MGG) signal frequency is about 0.05 Hz, the low-frequency environmental noise interference is serious and can be several times stronger in magnitude than the signals of interest and may severely impede the extraction of relevant information. Wiener filter is one classic denoising solution for biomagnetic applications. Since the reference channels are usually placed not far enough from the biomagnetic sources under test, they will inevitably detect the signals and the Wiener filters may produce ill-conditioned solutions. Considering the solutions to improve the signal-to-noise ratio (SNR) of Wiener filter output, there are few methods to separate the signals from the noises of the reference signal at the filter input. In this paper, a new signal processing framework called signal-noise separation based Wiener filter (SNSWF) is proposed that it separates the main noise as the input signal of the filter to improve the output SNR of Wiener filter. The filter was successfully applied to the noise suppression for MGG signal detection. Using the SNSWF, the filter SNR is 16.7 dB better than the classic Wiener filter.

Assessing the capacity of a denoising diffusion probabilistic model to reproduce spatial context

Diffusion models have emerged as a popular family of deep generative models (DGMs). In the literature, it has been claimed that one class of diffusion models -- denoising diffusion probabilistic models (DDPMs) -- demonstrate superior image synthesis performance as compared to generative adversarial networks (GANs). To date, these claims have been evaluated using either ensemble-based methods designed for natural images, or conventional measures of image quality such as structural similarity. However, there remains an important need to understand the extent to which DDPMs can reliably learn medical imaging domain-relevant information, which is referred to as `spatial context' in this work. To address this, a systematic assessment of the ability of DDPMs to learn spatial context relevant to medical imaging applications is reported for the first time. A key aspect of the studies is the use of stochastic context models (SCMs) to produce training data. In this way, the ability of the DDPMs to reliably reproduce spatial context can be quantitatively assessed by use of post-hoc image analyses. Error-rates in DDPM-generated ensembles are reported, and compared to those corresponding to a modern GAN. The studies reveal new and important insights regarding the capacity of DDPMs to learn spatial context. Notably, the results demonstrate that DDPMs hold significant capacity for generating contextually correct images that are `interpolated' between training samples, which may benefit data-augmentation tasks in ways that GANs cannot.

Semi-Supervised Semantic Segmentation of Cell Nuclei via Diffusion-based Large-Scale Pre-Training and Collaborative Learning

Automated semantic segmentation of cell nuclei in microscopic images is crucial for disease diagnosis and tissue microenvironment analysis. Nonetheless, this task presents challenges due to the complexity and heterogeneity of cells. While supervised deep learning methods are promising, they necessitate large annotated datasets that are time-consuming and error-prone to acquire. Semi-supervised approaches could provide feasible alternatives to this issue. However, the limited annotated data may lead to subpar performance of semi-supervised methods, regardless of the abundance of unlabeled data. In this paper, we introduce a novel unsupervised pre-training-based semi-supervised framework for cell-nuclei segmentation. Our framework is comprised of three main components. Firstly, we pretrain a diffusion model on a large-scale unlabeled dataset. The diffusion model's explicit modeling capability facilitates the learning of semantic feature representation from the unlabeled data. Secondly, we achieve semantic feature aggregation using a transformer-based decoder, where the pretrained diffusion model acts as the feature extractor, enabling us to fully utilize the small amount of labeled data. Finally, we implement a collaborative learning framework between the diffusion-based segmentation model and a supervised segmentation model to further enhance segmentation performance. Experiments were conducted on four publicly available datasets to demonstrate significant improvements compared to competitive semi-supervised segmentation methods and supervised baselines. A series of out-of-distribution tests further confirmed the generality of our framework. Furthermore, thorough ablation experiments and visual analysis confirmed the superiority of our proposed method.

Compact Twice Fusion Network for Edge Detection

The significance of multi-scale features has been gradually recognized by the edge detection community. However, the fusion of multi-scale features increases the complexity of the model, which is not friendly to practical application. In this work, we propose a Compact Twice Fusion Network (CTFN) to fully integrate multi-scale features while maintaining the compactness of the model. CTFN includes two lightweight multi-scale feature fusion modules: a Semantic Enhancement Module (SEM) that can utilize the semantic information contained in coarse-scale features to guide the learning of fine-scale features, and a Pseudo Pixel-level Weighting (PPW) module that aggregate the complementary merits of multi-scale features by assigning weights to all features. Notwithstanding all this, the interference of texture noise makes the correct classification of some pixels still a challenge. For these hard samples, we propose a novel loss function, coined Dynamic Focal Loss, which reshapes the standard cross-entropy loss and dynamically adjusts the weights to correct the distribution of hard samples. We evaluate our method on three datasets, i.e., BSDS500, NYUDv2, and BIPEDv2. Compared with state-of-the-art methods, CTFN achieves competitive accuracy with less parameters and computational cost. Apart from the backbone, CTFN requires only 0.1M additional parameters, which reduces its computation cost to just 60% of other state-of-the-art methods. The codes are available at https://github.com/Li-yachuan/CTFN-pytorch-master.

A quality assurance framework for real-time monitoring of deep learning segmentation models in radiotherapy

To safely deploy deep learning models in the clinic, a quality assurance framework is needed for routine or continuous monitoring of input-domain shift and the models' performance without ground truth contours. In this work, cardiac substructure segmentation was used as an example task to establish a QA framework. A benchmark dataset consisting of Computed Tomography (CT) images along with manual cardiac delineations of 241 patients were collected, including one 'common' image domain and five 'uncommon' domains. Segmentation models were tested on the benchmark dataset for an initial evaluation of model capacity and limitations. An image domain shift detector was developed by utilizing a trained Denoising autoencoder (DAE) and two hand-engineered features. Another Variational Autoencoder (VAE) was also trained to estimate the shape quality of the auto-segmentation results. Using the extracted features from the image/segmentation pair as inputs, a regression model was trained to predict the per-patient segmentation accuracy, measured by Dice coefficient similarity (DSC). The framework was tested across 19 segmentation models to evaluate the generalizability of the entire framework. As results, the predicted DSC of regression models achieved a mean absolute error (MAE) ranging from 0.036 to 0.046 with an averaged MAE of 0.041. When tested on the benchmark dataset, the performances of all segmentation models were not significantly affected by scanning parameters: FOV, slice thickness and reconstructions kernels. For input images with Poisson noise, CNN-based segmentation models demonstrated a decreased DSC ranging from 0.07 to 0.41, while the transformer-based model was not significantly affected.

On the impact of incorporating task-information in learning-based image denoising

A variety of deep neural network (DNN)-based image denoising methods have been proposed for use with medical images. These methods are typically trained by minimizing loss functions that quantify a distance between the denoised image, or a transformed version of it, and the defined target image (e.g., a noise-free or low-noise image). They have demonstrated high performance in terms of traditional image quality metrics such as root mean square error (RMSE), structural similarity index measure (SSIM), or peak signal-to-noise ratio (PSNR). However, it has been reported recently that such denoising methods may not always improve objective measures of image quality. In this work, a task-informed DNN-based image denoising method was established and systematically evaluated. A transfer learning approach was employed, in which the DNN is first pre-trained by use of a conventional (non-task-informed) loss function and subsequently fine-tuned by use of the hybrid loss that includes a task-component. The task-component was designed to measure the performance of a numerical observer (NO) on a signal detection task. The impact of network depth and constraining the fine-tuning to specific layers of the DNN was explored. The task-informed training method was investigated in a stylized low-dose X-ray computed tomography (CT) denoising study for which binary signal detection tasks under signal-known-statistically (SKS) with background-known-statistically (BKS) conditions were considered. The impact of changing the specified task at inference time to be different from that employed for model training, a phenomenon we refer to as "task-shift", was also investigated. The presented results indicate that the task-informed training method can improve observer performance while providing control over the trade off between traditional and task-based measures of image quality.

Joint localization and classification of breast tumors on ultrasound images using a novel auxiliary attention-based framework

Automatic breast lesion detection and classification is an important task in computer-aided diagnosis, in which breast ultrasound (BUS) imaging is a common and frequently used screening tool. Recently, a number of deep learning-based methods have been proposed for joint localization and classification of breast lesions using BUS images. In these methods, features extracted by a shared network trunk are appended by two independent network branches to achieve classification and localization. Improper information sharing might cause conflicts in feature optimization in the two branches and leads to performance degradation. Also, these methods generally require large amounts of pixel-level annotated data for model training. To overcome these limitations, we proposed a novel joint localization and classification model based on the attention mechanism and disentangled semi-supervised learning strategy. The model used in this study is composed of a classification network and an auxiliary lesion-aware network. By use of the attention mechanism, the auxiliary lesion-aware network can optimize multi-scale intermediate feature maps and extract rich semantic information to improve classification and localization performance. The disentangled semi-supervised learning strategy only requires incomplete training datasets for model training. The proposed modularized framework allows flexible network replacement to be generalized for various applications. Experimental results on two different breast ultrasound image datasets demonstrate the effectiveness of the proposed method. The impacts of various network factors on model performance are also investigated to gain deep insights into the designed framework.

Spectrally-Corrected and Regularized Linear Discriminant Analysis for Spiked Covariance Model

In this paper, we propose an improved linear discriminant analysis, called spectrally-corrected and regularized linear discriminant analysis (SCRLDA). This method integrates the design ideas of the sample spectrally-corrected covariance matrix and the regularized discriminant analysis. The SCRLDA method is specially designed for classification problems under the assumption that the covariance matrix follows a spiked model. Through the real and simulated data analysis, it is shown that our proposed classifier outperforms the classical R-LDA and can be as competitive as the KNN, SVM classifiers while requiring lower computational complexity.

The Counterfactual-Shapley Value: Attributing Change in System Metrics

Given an unexpected change in the output metric of a large-scale system, it is important to answer why the change occurred: which inputs caused the change in metric? A key component of such an attribution question is estimating the counterfactual: the (hypothetical) change in the system metric due to a specified change in a single input. However, due to inherent stochasticity and complex interactions between parts of the system, it is difficult to model an output metric directly. We utilize the computational structure of a system to break up the modelling task into sub-parts, such that each sub-part corresponds to a more stable mechanism that can be modelled accurately over time. Using the system's structure also helps to view the metric as a computation over a structural causal model (SCM), thus providing a principled way to estimate counterfactuals. Specifically, we propose a method to estimate counterfactuals using time-series predictive models and construct an attribution score, CF-Shapley, that is consistent with desirable axioms for attributing an observed change in the output metric. Unlike past work on causal shapley values, our proposed method can attribute a single observed change in output (rather than a population-level effect) and thus provides more accurate attribution scores when evaluated on simulated datasets. As a real-world application, we analyze a query-ad matching system with the goal of attributing observed change in a metric for ad matching density. Attribution scores explain how query volume and ad demand from different query categories affect the ad matching density, leading to actionable insights and uncovering the role of external events (e.g., "Cheetah Day") in driving the matching density.

Stereo Superpixel Segmentation Via Decoupled Dynamic Spatial-Embedding Fusion Network

Stereo superpixel segmentation aims at grouping the discretizing pixels into perceptual regions through left and right views more collaboratively and efficiently. Existing superpixel segmentation algorithms mostly utilize color and spatial features as input, which may impose strong constraints on spatial information while utilizing the disparity information in terms of stereo image pairs. To alleviate this issue, we propose a stereo superpixel segmentation method with a decoupling mechanism of spatial information in this work. To decouple stereo disparity information and spatial information, the spatial information is temporarily removed before fusing the features of stereo image pairs, and a decoupled stereo fusion module (DSFM) is proposed to handle the stereo features alignment as well as occlusion problems. Moreover, since the spatial information is vital to superpixel segmentation, we further design a dynamic spatiality embedding module (DSEM) to re-add spatial information, and the weights of spatial information will be adaptively adjusted through the dynamic fusion (DF) mechanism in DSEM for achieving a finer segmentation. Comprehensive experimental results demonstrate that our method can achieve the state-of-the-art performance on the KITTI2015 and Cityscapes datasets, and also verify the efficiency when applied in salient object detection on NJU2K dataset. The source code will be available publicly after paper is accepted.