Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.51 and an F1-detection score of 0.83. The code is publicly available at //github.com/TIO-IKIM/CellViT
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GHN-Q: Parameter Prediction for Unseen Quantized Convolutional Architectures via Graph Hypernetworks
Deep convolutional neural network (CNN) training via iterative optimization has had incredible success in finding optimal parameters. However, modern CNN architectures often contain millions of parameters. Thus, any given model for a single architecture resides in a massive parameter space. Models with similar loss could have drastically different characteristics such as adversarial robustness, generalizability, and quantization robustness. For deep learning on the edge, quantization robustness is often crucial. Finding a model that is quantization-robust can sometimes require significant efforts. Recent works using Graph Hypernetworks (GHN) have shown remarkable performance predicting high-performant parameters of varying CNN architectures. Inspired by these successes, we wonder if the graph representations of GHN-2 can be leveraged to predict quantization-robust parameters as well, which we call GHN-Q. We conduct the first-ever study exploring the use of graph hypernetworks for predicting parameters of unseen quantized CNN architectures. We focus on a reduced CNN search space and find that GHN-Q can in fact predict quantization-robust parameters for various 8-bit quantized CNNs. Decent quantized accuracies are observed even with 4-bit quantization despite GHN-Q not being trained on it. Quantized finetuning of GHN-Q at lower bitwidths may bring further improvements and is currently being explored.
Microscopy images are crucial for life science research, allowing detailed inspection and characterization of cellular and tissue-level structures and functions. However, microscopy data are unavoidably affected by image degradations, such as noise, blur, or others. Many such degradations also contribute to a loss of image contrast, which becomes especially pronounced in deeper regions of thick samples. Today, best performing methods to increase the quality of images are based on Deep Learning approaches, which typically require ground truth (GT) data during training. Our inability to counteract blurring and contrast loss when imaging deep into samples prevents the acquisition of such clean GT data. The fact that the forward process of blurring and contrast loss deep into tissue can be modeled, allowed us to propose a new method that can circumvent the problem of unobtainable GT data. To this end, we first synthetically degraded the quality of microscopy images even further by using an approximate forward model for deep tissue image degradations. Then we trained a neural network that learned the inverse of this degradation function from our generated pairs of raw and degraded images. We demonstrated that networks trained in this way can be used out-of-distribution (OOD) to improve the quality of less severely degraded images, e.g. the raw data imaged in a microscope. Since the absolute level of degradation in such microscopy images can be stronger than the additional degradation introduced by our forward model, we also explored the effect of iterative predictions. Here, we observed that in each iteration the measured image contrast kept improving while detailed structures in the images got increasingly removed. Therefore, dependent on the desired downstream analysis, a balance between contrast improvement and retention of image details has to be found.
Vessel image segmentation plays a pivotal role in medical diagnostics, aiding in the early detection and treatment of vascular diseases. While segmentation based on deep learning has shown promising results, effectively segmenting small structures and maintaining connectivity between them remains challenging. To address these limitations, we propose GAEI-UNet, a novel model that combines global attention and elastic interaction-based techniques. GAEI-UNet leverages global spatial and channel context information to enhance high-level semantic understanding within the U-Net architecture, enabling precise segmentation of small vessels. Additionally, we adopt an elastic interaction-based loss function to improve connectivity among these fine structures. By capturing the forces generated by misalignment between target and predicted shapes, our model effectively learns to preserve the correct topology of vessel networks. Evaluation on retinal vessel dataset -- DRIVE demonstrates the superior performance of GAEI-UNet in terms of SE and connectivity of small structures, without significantly increasing computational complexity. This research aims to advance the field of vessel image segmentation, providing more accurate and reliable diagnostic tools for the medical community. The implementation code is available on Code.
Experts use retinal images and vessel trees to detect and diagnose various eye, blood circulation, and brain-related diseases. However, manual segmentation of retinal images is a time-consuming process that requires high expertise and is difficult due to privacy issues. Many methods have been proposed to segment images, but the need for large retinal image datasets limits the performance of these methods. Several methods synthesize deep learning models based on Generative Adversarial Networks (GAN) to generate limited sample varieties. This paper proposes a novel Denoising Diffusion Probabilistic Model (DDPM) that outperformed GANs in image synthesis. We developed a Retinal Trees (ReTree) dataset consisting of retinal images, corresponding vessel trees, and a segmentation network based on DDPM trained with images from the ReTree dataset. In the first stage, we develop a two-stage DDPM that generates vessel trees from random numbers belonging to a standard normal distribution. Later, the model is guided to generate fundus images from given vessel trees and random distribution. The proposed dataset has been evaluated quantitatively and qualitatively. Quantitative evaluation metrics include Frechet Inception Distance (FID) score, Jaccard similarity coefficient, Cohen's kappa, Matthew's Correlation Coefficient (MCC), precision, recall, F1-score, and accuracy. We trained the vessel segmentation model with synthetic data to validate our dataset's efficiency and tested it on authentic data. Our developed dataset and source code is available at //github.com/AAleka/retree.
Ultrasound (US) imaging is indispensable in clinical practice. To diagnose certain diseases, sonographers must observe corresponding dynamic anatomic structures to gather comprehensive information. However, the limited availability of specific US video cases causes teaching difficulties in identifying corresponding diseases, which potentially impacts the detection rate of such cases. The synthesis of US videos may represent a promising solution to this issue. Nevertheless, it is challenging to accurately animate the intricate motion of dynamic anatomic structures while preserving image fidelity. To address this, we present a novel online feature-decoupling framework called OnUVS for high-fidelity US video synthesis. Our highlights can be summarized by four aspects. First, we introduced anatomic information into keypoint learning through a weakly-supervised training strategy, resulting in improved preservation of anatomical integrity and motion while minimizing the labeling burden. Second, to better preserve the integrity and textural information of US images, we implemented a dual-decoder that decouples the content and textural features in the generator. Third, we adopted a multiple-feature discriminator to extract a comprehensive range of visual cues, thereby enhancing the sharpness and fine details of the generated videos. Fourth, we constrained the motion trajectories of keypoints during online learning to enhance the fluidity of generated videos. Our validation and user studies on in-house echocardiographic and pelvic floor US videos showed that OnUVS synthesizes US videos with high fidelity.
Long-tailed distribution of semantic categories, which has been often ignored in conventional methods, causes unsatisfactory performance in semantic segmentation on tail categories. In this paper, we focus on the problem of long-tailed semantic segmentation. Although some long-tailed recognition methods (e.g., re-sampling/re-weighting) have been proposed in other problems, they can probably compromise crucial contextual information and are thus hardly adaptable to the problem of long-tailed semantic segmentation. To address this issue, we propose MEDOE, a novel framework for long-tailed semantic segmentation via contextual information ensemble-and-grouping. The proposed two-sage framework comprises a multi-expert decoder (MED) and a multi-expert output ensemble (MOE). Specifically, the MED includes several "experts". Based on the pixel frequency distribution, each expert takes the dataset masked according to the specific categories as input and generates contextual information self-adaptively for classification; The MOE adopts learnable decision weights for the ensemble of the experts' outputs. As a model-agnostic framework, our MEDOE can be flexibly and efficiently coupled with various popular deep neural networks (e.g., DeepLabv3+, OCRNet, and PSPNet) to improve their performance in long-tailed semantic segmentation. Experimental results show that the proposed framework outperforms the current methods on both Cityscapes and ADE20K datasets by up to 1.78% in mIoU and 5.89% in mAcc.
Click-through rate (CTR) prediction is a crucial task in the context of an online on-demand food delivery (OFD) platform for precisely estimating the probability of a user clicking on food items. Unlike universal e-commerce platforms such as Taobao and Amazon, user behaviors and interests on the OFD platform are more location and time-sensitive due to limited delivery ranges and regional commodity supplies. However, existing CTR prediction algorithms in OFD scenarios concentrate on capturing interest from historical behavior sequences, which fails to effectively model the complex spatiotemporal information within features, leading to poor performance. To address this challenge, this paper introduces the Contrastive Sres under different search states using three modules: contrastive spatiotemporal representation learning (CSRL), spatiotemporal preference extractor (StPE), and spatiotemporal information filter (StIF). CSRL utilizes a contrastive learning framework to generate a spatiotemporal activation representation (SAR) for the search action. StPE employs SAR to activate users' diverse preferences related to location and time from the historical behavior sequence field, using a multi-head attention mechanism. StIF incorporates SAR into a gating network to automatically capture important features with latent spatiotemporal effects. Extensive experiments conducted on two large-scale industrial datasets demonstrate the state-of-the-art performance of CSPM. Notably, CSPM has been successfully deployed in Alibaba's online OFD platform Ele.me, resulting in a significant 0.88% lift in CTR, which has substantial business implications.
Visual dialogue is a challenging task that needs to extract implicit information from both visual (image) and textual (dialogue history) contexts. Classical approaches pay more attention to the integration of the current question, vision knowledge and text knowledge, despising the heterogeneous semantic gaps between the cross-modal information. In the meantime, the concatenation operation has become de-facto standard to the cross-modal information fusion, which has a limited ability in information retrieval. In this paper, we propose a novel Knowledge-Bridge Graph Network (KBGN) model by using graph to bridge the cross-modal semantic relations between vision and text knowledge in fine granularity, as well as retrieving required knowledge via an adaptive information selection mode. Moreover, the reasoning clues for visual dialogue can be clearly drawn from intra-modal entities and inter-modal bridges. Experimental results on VisDial v1.0 and VisDial-Q datasets demonstrate that our model outperforms exiting models with state-of-the-art results.
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.
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