Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nikola Rieke, Samuel Joutard, et al. (2023). CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation. MIA - Medical Image Analysis, 83, 102628.
Abstract: Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice – VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice – VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.
Keywords: Domain Adaptation; Segmen tation; Vestibular Schwnannoma
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Lei Li, Fuping Wu, Sihan Wang, Xinzhe Luo, Carlos Martin-Isla, Shuwei Zhai, et al. (2023). MyoPS: A benchmark of myocardial pathology segmentation combining three-sequence cardiac magnetic resonance images. MIA - Medical Image Analysis, 87, 102808.
Abstract: Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on the myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. Note that MyoPS refers to both myocardial pathology segmentation and the challenge in this paper. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore the potential of solutions, as well as to provide a benchmark for future research. The average Dice scores of submitted algorithms were and for myocardial scars and edema, respectively. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/).
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Shiqi Yang, Yaxing Wang, Luis Herranz, Shangling Jui, & Joost Van de Weijer. (2023). Casting a BAIT for offline and online source-free domain adaptation. CVIU - Computer Vision and Image Understanding, 234, 103747.
Abstract: We address the source-free domain adaptation (SFDA) problem, where only the source model is available during adaptation to the target domain. We consider two settings: the offline setting where all target data can be visited multiple times (epochs) to arrive at a prediction for each target sample, and the online setting where the target data needs to be directly classified upon arrival. Inspired by diverse classifier based domain adaptation methods, in this paper we introduce a second classifier, but with another classifier head fixed. When adapting to the target domain, the additional classifier initialized from source classifier is expected to find misclassified features. Next, when updating the feature extractor, those features will be pushed towards the right side of the source decision boundary, thus achieving source-free domain adaptation. Experimental results show that the proposed method achieves competitive results for offline SFDA on several benchmark datasets compared with existing DA and SFDA methods, and our method surpasses by a large margin other SFDA methods under online source-free domain adaptation setting.
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Bhalaji Nagarajan, Marc Bolaños, Eduardo Aguilar, & Petia Radeva. (2023). Deep ensemble-based hard sample mining for food recognition. JVCIR - Journal of Visual Communication and Image Representation, 95, 103905.
Abstract: Deep neural networks represent a compelling technique to tackle complex real-world problems, but are over-parameterized and often suffer from over- or under-confident estimates. Deep ensembles have shown better parameter estimations and often provide reliable uncertainty estimates that contribute to the robustness of the results. In this work, we propose a new metric to identify samples that are hard to classify. Our metric is defined as coincidence score for deep ensembles which measures the agreement of its individual models. The main hypothesis we rely on is that deep learning algorithms learn the low-loss samples better compared to large-loss samples. In order to compensate for this, we use controlled over-sampling on the identified ”hard” samples using proper data augmentation schemes to enable the models to learn those samples better. We validate the proposed metric using two public food datasets on different backbone architectures and show the improvements compared to the conventional deep neural network training using different performance metrics.
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Pau Cano, Alvaro Caravaca, Debora Gil, & Eva Musulen. (2023). Diagnosis of Helicobacter pylori using AutoEncoders for the Detection of Anomalous Staining Patterns in Immunohistochemistry Images.
Abstract: This work addresses the detection of Helicobacter pylori a bacterium classified since 1994 as class 1 carcinogen to humans. By its highest specificity and sensitivity, the preferred diagnosis technique is the analysis of histological images with immunohistochemical staining, a process in which certain stained antibodies bind to antigens of the biological element of interest. This analysis is a time demanding task, which is currently done by an expert pathologist that visually inspects the digitized samples.
We propose to use autoencoders to learn latent patterns of healthy tissue and detect H. pylori as an anomaly in image staining. Unlike existing classification approaches, an autoencoder is able to learn patterns in an unsupervised manner (without the need of image annotations) with high performance. In particular, our model has an overall 91% of accuracy with 86\% sensitivity, 96% specificity and 0.97 AUC in the detection of H. pylori.
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Juan Borrego-Carazo, Carles Sanchez, David Castells, Jordi Carrabina, & Debora Gil. (2023). BronchoPose: an analysis of data and model configuration for vision-based bronchoscopy pose estimation. CMPB - Computer Methods and Programs in Biomedicine, 228, 107241.
Abstract: Vision-based bronchoscopy (VB) models require the registration of the virtual lung model with the frames from the video bronchoscopy to provide effective guidance during the biopsy. The registration can be achieved by either tracking the position and orientation of the bronchoscopy camera or by calibrating its deviation from the pose (position and orientation) simulated in the virtual lung model. Recent advances in neural networks and temporal image processing have provided new opportunities for guided bronchoscopy. However, such progress has been hindered by the lack of comparative experimental conditions.
In the present paper, we share a novel synthetic dataset allowing for a fair comparison of methods. Moreover, this paper investigates several neural network architectures for the learning of temporal information at different levels of subject personalization. In order to improve orientation measurement, we also present a standardized comparison framework and a novel metric for camera orientation learning. Results on the dataset show that the proposed metric and architectures, as well as the standardized conditions, provide notable improvements to current state-of-the-art camera pose estimation in video bronchoscopy.
Keywords: Videobronchoscopy guiding; Deep learning; Architecture optimization; Datasets; Standardized evaluation framework; Pose estimation
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Parichehr Behjati, Pau Rodriguez, Carles Fernandez, Isabelle Hupont, Armin Mehri, & Jordi Gonzalez. (2023). Single image super-resolution based on directional variance attention network. PR - Pattern Recognition, 133, 108997.
Abstract: Recent advances in single image super-resolution (SISR) explore the power of deep convolutional neural networks (CNNs) to achieve better performance. However, most of the progress has been made by scaling CNN architectures, which usually raise computational demands and memory consumption. This makes modern architectures less applicable in practice. In addition, most CNN-based SR methods do not fully utilize the informative hierarchical features that are helpful for final image recovery. In order to address these issues, we propose a directional variance attention network (DiVANet), a computationally efficient yet accurate network for SISR. Specifically, we introduce a novel directional variance attention (DiVA) mechanism to capture long-range spatial dependencies and exploit inter-channel dependencies simultaneously for more discriminative representations. Furthermore, we propose a residual attention feature group (RAFG) for parallelizing attention and residual block computation. The output of each residual block is linearly fused at the RAFG output to provide access to the whole feature hierarchy. In parallel, DiVA extracts most relevant features from the network for improving the final output and preventing information loss along the successive operations inside the network. Experimental results demonstrate the superiority of DiVANet over the state of the art in several datasets, while maintaining relatively low computation and memory footprint. The code is available at https://github.com/pbehjatii/DiVANet.
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Souhail Bakkali, Zuheng Ming, Mickael Coustaty, Marçal Rusiñol, & Oriol Ramos Terrades. (2023). VLCDoC: Vision-Language Contrastive Pre-Training Model for Cross-Modal Document Classification. PR - Pattern Recognition, 139, 109419.
Abstract: Multimodal learning from document data has achieved great success lately as it allows to pre-train semantically meaningful features as a prior into a learnable downstream approach. In this paper, we approach the document classification problem by learning cross-modal representations through language and vision cues, considering intra- and inter-modality relationships. Instead of merging features from different modalities into a common representation space, the proposed method exploits high-level interactions and learns relevant semantic information from effective attention flows within and across modalities. The proposed learning objective is devised between intra- and inter-modality alignment tasks, where the similarity distribution per task is computed by contracting positive sample pairs while simultaneously contrasting negative ones in the common feature representation space}. Extensive experiments on public document classification datasets demonstrate the effectiveness and the generalization capacity of our model on both low-scale and large-scale datasets.
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Xavier Soria, Angel Sappa, Patricio Humanante, & Arash Akbarinia. (2023). Dense extreme inception network for edge detection. PR - Pattern Recognition, 139, 109461.
Abstract: Edge detection is the basis of many computer vision applications. State of the art predominantly relies on deep learning with two decisive factors: dataset content and network architecture. Most of the publicly available datasets are not curated for edge detection tasks. Here, we address this limitation. First, we argue that edges, contours and boundaries, despite their overlaps, are three distinct visual features requiring separate benchmark datasets. To this end, we present a new dataset of edges. Second, we propose a novel architecture, termed Dense Extreme Inception Network for Edge Detection (DexiNed), that can be trained from scratch without any pre-trained weights. DexiNed outperforms other algorithms in the presented dataset. It also generalizes well to other datasets without any fine-tuning. The higher quality of DexiNed is also perceptually evident thanks to the sharper and finer edges it outputs.
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Mohammad Momeny, Ali Asghar Neshat, Ahmad Jahanbakhshi, Majid Mahmoudi, Yiannis Ampatzidis, & Petia Radeva. (2023). Grading and fraud detection of saffron via learning-to-augment incorporated Inception-v4 CNN. FC - Food Control, 147, 109554.
Abstract: Saffron is a well-known product in the food industry. It is one of the spices that are sometimes adulterated with the sole motive of gaining more economic profit. Today, machine vision systems are widely used in controlling the quality of food and agricultural products as a new, non-destructive, and inexpensive approach. In this study, a machine vision system based on deep learning was used to detect fraud and saffron quality. A dataset of 1869 images was created and categorized in 6 classes including: dried saffron stigma using a dryer; dried saffron stigma using pressing method; pure stem of saffron; sunflower; saffron stem mixed with food coloring; and corn silk mixed with food coloring. A Learning-to-Augment incorporated Inception-v4 Convolutional Neural Network (LAII-v4 CNN) was developed for grading and fraud detection of saffron in images captured by smartphones. The best policies of data augmentation were selected with the proposed LAII-v4 CNN using images corrupted by Gaussian, speckle, and impulse noise to address overfitting the model. The proposed LAII-v4 CNN compared with regular CNN-based methods and traditional classifiers. Ensemble of Bagged Decision Trees, Ensemble of Boosted Decision Trees, k-Nearest Neighbor, Random Under-sampling Boosted Trees, and Support Vector Machine were used for classification of the features extracted by Histograms of Oriented Gradients and Local Binary Patterns, and selected by the Principal Component Analysis. The results showed that the proposed LAII-v4 CNN with an accuracy of 99.5% has achieved the best performance by employing batch normalization, Dropout, and leaky ReLU.
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Ruben Tito, Dimosthenis Karatzas, & Ernest Valveny. (2023). Hierarchical multimodal transformers for Multi-Page DocVQA. PR - Pattern Recognition, 144, 109834.
Abstract: Document Visual Question Answering (DocVQA) refers to the task of answering questions from document images. Existing work on DocVQA only considers single-page documents. However, in real scenarios documents are mostly composed of multiple pages that should be processed altogether. In this work we extend DocVQA to the multi-page scenario. For that, we first create a new dataset, MP-DocVQA, where questions are posed over multi-page documents instead of single pages. Second, we propose a new hierarchical method, Hi-VT5, based on the T5 architecture, that overcomes the limitations of current methods to process long multi-page documents. The proposed method is based on a hierarchical transformer architecture where the encoder summarizes the most relevant information of every page and then, the decoder takes this summarized information to generate the final answer. Through extensive experimentation, we demonstrate that our method is able, in a single stage, to answer the questions and provide the page that contains the relevant information to find the answer, which can be used as a kind of explainability measure.
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