Domenec Puig

Kelly Payette, Hongwei Li, Priscille de Dumast et al.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Mayank Anand, Ujair Alam, Surya Prakash et al.

Clinical ultrasound acquisition is highly operator-dependent, where rapid probe motion and brightness fluctuations often lead to reconstruction errors that reduce trust and clinical utility. We present UltrasODM, a dual-stream framework that assists sonographers during acquisition through calibrated per-frame uncertainty, saliency-based diagnostics, and actionable prompts. UltrasODM integrates (i) a contrastive ranking module that groups frames by motion similarity, (ii) an optical-flow stream fused with Dual-Mamba temporal modules for robust 6-DoF pose estimation, and (iii) a Human-in-the-Loop (HITL) layer combining Bayesian uncertainty, clinician-calibrated thresholds, and saliency maps highlighting regions of low confidence. When uncertainty exceeds the threshold, the system issues unobtrusive alerts suggesting corrective actions such as re-scanning highlighted regions or slowing the sweep. Evaluated on a clinical freehand ultrasound dataset, UltrasODM reduces drift by 15.2%, distance error by 12.1%, and Hausdorff distance by 10.1% relative to UltrasOM, while producing per-frame uncertainty and saliency outputs. By emphasizing transparency and clinician feedback, UltrasODM improves reconstruction reliability and supports safer, more trustworthy clinical workflows. Our code is publicly available at https://github.com/AnandMayank/UltrasODM.

Eddardaa Ben Loussaief, Hatem Rashwan, Mohammed Ayad et al.

With numerous medical tasks, the performance of deep models has recently experienced considerable improvements. These models are often adept learners. Yet, their intricate architectural design and high computational complexity make deploying them in clinical settings challenging, particularly with devices with limited resources. To deal with this issue, Knowledge Distillation (KD) has been proposed as a compression method and an acceleration technology. KD is an efficient learning strategy that can transfer knowledge from a burdensome model (i.e., teacher model) to a lightweight model (i.e., student model). Hence we can obtain a compact model with low parameters with preserving the teacher's performance. Therefore, we develop a KD-based deep model for prostate MRI segmentation in this work by combining features-based distillation with Kullback-Leibler divergence, Lovasz, and Dice losses. We further demonstrate its effectiveness by applying two compression procedures: 1) distilling knowledge to a student model from a single well-trained teacher, and 2) since most of the medical applications have a small dataset, we train multiple teachers that each one trained with a small set of images to learn an adaptive student model as close to the teachers as possible considering the desired accuracy and fast inference time. Extensive experiments were conducted on a public multi-site prostate tumor dataset, showing that the proposed adaptation KD strategy improves the dice similarity score by 9%, outperforming all tested well-established baseline models.

Ezequiel de la Rosa, Mauricio Reyes, Sook-Lei Liew et al.

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

Armin Masoumian, Hatem A. Rashwan, Saddam Abdulwahab et al.

Depth estimation is a challenging task of 3D reconstruction to enhance the accuracy sensing of environment awareness. This work brings a new solution with a set of improvements, which increase the quantitative and qualitative understanding of depth maps compared to existing methods. Recently, a convolutional neural network (CNN) has demonstrated its extraordinary ability in estimating depth maps from monocular videos. However, traditional CNN does not support topological structure and they can work only on regular image regions with determined size and weights. On the other hand, graph convolutional networks (GCN) can handle the convolution on non-Euclidean data and it can be applied to irregular image regions within a topological structure. Therefore, in this work in order to preserve object geometric appearances and distributions, we aim at exploiting GCN for a self-supervised depth estimation model. Our model consists of two parallel auto-encoder networks: the first is an auto-encoder that will depend on ResNet-50 and extract the feature from the input image and on multi-scale GCN to estimate the depth map. In turn, the second network will be used to estimate the ego-motion vector (i.e., 3D pose) between two consecutive frames based on ResNet-18. Both the estimated 3D pose and depth map will be used for constructing a target image. A combination of loss functions related to photometric, projection, and smoothness is used to cope with bad depth prediction and preserve the discontinuities of the objects. In particular, our method provided comparable and promising results with a high prediction accuracy of 89% on the publicly KITTI and Make3D datasets along with a reduction of 40% in the number of trainable parameters compared to the state of the art solutions. The source code is publicly available at https://github.com/ArminMasoumian/GCNDepth.git

Muhammad Mursil, Hatem A. Rashwan, Luis Santos-Calderon et al.

Birth weight (BW) is a key indicator of neonatal health, with low birth weight (LBW) linked to increased mortality and morbidity. Early prediction of BW enables timely interventions; however, current methods like ultrasonography have limitations, including reduced accuracy before 20 weeks and operator dependent variability. Existing models often neglect nutritional and genetic influences, focusing mainly on physiological and lifestyle factors. This study presents an attention-based transformer model with a multi-encoder architecture for early (less than 12 weeks of gestation) BW prediction. Our model effectively integrates diverse maternal data such as physiological, lifestyle, nutritional, and genetic, addressing limitations seen in prior attention-based models such as TabNet. The model achieves a Mean Absolute Error (MAE) of 122 grams and an R-squared value of 0.94, demonstrating high predictive accuracy and interoperability with our in-house private dataset. Independent validation confirms generalizability (MAE: 105 grams, R-squared: 0.95) with the IEEE children dataset. To enhance clinical utility, predicted BW is classified into low and normal categories, achieving a sensitivity of 97.55% and a specificity of 94.48%, facilitating early risk stratification. Model interpretability is reinforced through feature importance and SHAP analyses, highlighting significant influences of maternal age, tobacco exposure, and vitamin B12 status, with genetic factors playing a secondary role. Our results emphasize the potential of advanced deep-learning models to improve early BW prediction, offering clinicians a robust, interpretable, and personalized tool for identifying pregnancies at risk and optimizing neonatal outcomes.

Saif Khalid, Hatem A. Rashwan, Saddam Abdulwahab et al.

The performance of diagnostic Computer-Aided Design (CAD) systems for retinal diseases depends on the quality of the retinal images being screened. Thus, many studies have been developed to evaluate and assess the quality of such retinal images. However, most of them did not investigate the relationship between the accuracy of the developed models and the quality of the visualization of interpretability methods for distinguishing between gradable and non-gradable retinal images. Consequently, this paper presents a novel framework called FGR-Net to automatically assess and interpret underlying fundus image quality by merging an autoencoder network with a classifier network. The FGR-Net model also provides an interpretable quality assessment through visualizations. In particular, FGR-Net uses a deep autoencoder to reconstruct the input image in order to extract the visual characteristics of the input fundus images based on self-supervised learning. The extracted features by the autoencoder are then fed into a deep classifier network to distinguish between gradable and ungradable fundus images. FGR-Net is evaluated with different interpretability methods, which indicates that the autoencoder is a key factor in forcing the classifier to focus on the relevant structures of the fundus images, such as the fovea, optic disk, and prominent blood vessels. Additionally, the interpretability methods can provide visual feedback for ophthalmologists to understand how our model evaluates the quality of fundus images. The experimental results showed the superiority of FGR-Net over the state-of-the-art quality assessment methods, with an accuracy of 89% and an F1-score of 87%.

Armin Masoumian, David G. F. Marei, Saddam Abdulwahab et al.

Determining the distance between the objects in a scene and the camera sensor from 2D images is feasible by estimating depth images using stereo cameras or 3D cameras. The outcome of depth estimation is relative distances that can be used to calculate absolute distances to be applicable in reality. However, distance estimation is very challenging using 2D monocular cameras. This paper presents a deep learning framework that consists of two deep networks for depth estimation and object detection using a single image. Firstly, objects in the scene are detected and localized using the You Only Look Once (YOLOv5) network. In parallel, the estimated depth image is computed using a deep autoencoder network to detect the relative distances. The proposed object detection based YOLO was trained using a supervised learning technique, in turn, the network of depth estimation was self-supervised training. The presented distance estimation framework was evaluated on real images of outdoor scenes. The achieved results show that the proposed framework is promising and it yields an accuracy of 96% with RMSE of 0.203 of the correct absolute distance.

Syeda Furruka Banu, Md. Mostafa Kamal Sarker, Mohamed Abdel-Nasser et al.

Lung cancer is deadly cancer that causes millions of deaths every year around the world. Accurate lung nodule detection and segmentation in computed tomography (CT) images is the most important part of diagnosing lung cancer in the early stage. Most of the existing systems are semi-automated and need to manually select the lung and nodules regions to perform the segmentation task. To address these challenges, we proposed a fully automated end-to-end lung nodule detection and segmentation system based on a deep learning approach. In this paper, we used Optimized Faster R-CNN; a state-of-the-art detection model to detect the lung nodule regions in the CT scans. Furthermore, we proposed an attention-aware weight excitation U-Net, called AWEU-Net, for lung nodule segmentation and boundaries detection. To achieve more accurate nodule segmentation, in AWEU-Net, we proposed position attention-aware weight excitation (PAWE), and channel attention-aware weight excitation (CAWE) blocks to highlight the best aligned spatial and channel features in the input feature maps. The experimental results demonstrate that our proposed model yields a Dice score of 89.79% and 90.35%, and an intersection over union (IoU) of 82.34% and 83.21% on the publicly LUNA16 and LIDC-IDRI datasets, respectively.

Farhan Akram, Vivek Kumar Singh, Hatem A. Rashwan et al.

In this paper, we propose an efficient blood vessel segmentation method for the eye fundus images using adversarial learning with multiscale features and kernel factorization. In the generator network of the adversarial framework, spatial pyramid pooling, kernel factorization and squeeze excitation block are employed to enhance the feature representation in spatial domain on different scales with reduced computational complexity. In turn, the discriminator network of the adversarial framework is formulated by combining convolutional layers with an additional squeeze excitation block to differentiate the generated segmentation mask from its respective ground truth. Before feeding the images to the network, we pre-processed them by using edge sharpening and Gaussian regularization to reach an optimized solution for vessel segmentation. The output of the trained model is post-processed using morphological operations to remove the small speckles of noise. The proposed method qualitatively and quantitatively outperforms state-of-the-art vessel segmentation methods using DRIVE and STARE datasets.

Vivek Kumar Singh, Hatem A. Rashwan, Mohamed Abdel-Nasser et al.

This paper proposes an efficient solution for tumor segmentation and classification in breast ultrasound (BUS) images. We propose to add an atrous convolution layer to the conditional generative adversarial network (cGAN) segmentation model to learn tumor features at different resolutions of BUS images. To automatically re-balance the relative impact of each of the highest level encoded features, we also propose to add a channel-wise weighting block in the network. In addition, the SSIM and L1-norm loss with the typical adversarial loss are used as a loss function to train the model. Our model outperforms the state-of-the-art segmentation models in terms of the Dice and IoU metrics, achieving top scores of 93.76% and 88.82%, respectively. In the classification stage, we show that few statistics features extracted from the shape of the boundaries of the predicted masks can properly discriminate between benign and malignant tumors with an accuracy of 85%$

Md. Mostafa Kamal Sarker, Hatem A. Rashwan, Farhan Akram et al.

The determination of precise skin lesion boundaries in dermoscopic images using automated methods faces many challenges, most importantly, the presence of hair, inconspicuous lesion edges and low contrast in dermoscopic images, and variability in the color, texture and shapes of skin lesions. Existing deep learning-based skin lesion segmentation algorithms are expensive in terms of computational time and memory. Consequently, running such segmentation algorithms requires a powerful GPU and high bandwidth memory, which are not available in dermoscopy devices. Thus, this article aims to achieve precise skin lesion segmentation with minimum resources: a lightweight, efficient generative adversarial network (GAN) model called SLSNet, which combines 1-D kernel factorized networks, position and channel attention, and multiscale aggregation mechanisms with a GAN model. The 1-D kernel factorized network reduces the computational cost of 2D filtering. The position and channel attention modules enhance the discriminative ability between the lesion and non-lesion feature representations in spatial and channel dimensions, respectively. A multiscale block is also used to aggregate the coarse-to-fine features of input skin images and reduce the effect of the artifacts. SLSNet is evaluated on two publicly available datasets: ISBI 2017 and the ISIC 2018. Although SLSNet has only 2.35 million parameters, the experimental results demonstrate that it achieves segmentation results on a par with the state-of-the-art skin lesion segmentation methods with an accuracy of 97.61%, and Dice and Jaccard similarity coefficients of 90.63% and 81.98%, respectively. SLSNet can run at more than 110 frames per second (FPS) in a single GTX1080Ti GPU, which is faster than well-known deep learning-based image segmentation models, such as FCN. Therefore, SLSNet can be used for practical dermoscopic applications.

Estefania Talavera, Maria Leyva-Vallina, Md. Mostafa Kamal Sarker et al.

Recent studies have shown that the environment where people eat can affect their nutritional behaviour. In this work, we provide automatic tools for a personalised analysis of a person's health habits by the examination of daily recorded egocentric photo-streams. Specifically, we propose a new automatic approach for the classification of food-related environments, that is able to classify up to 15 such scenes. In this way, people can monitor the context around their food intake in order to get an objective insight into their daily eating routine. We propose a model that classifies food-related scenes organized in a semantic hierarchy. Additionally, we present and make available a new egocentric dataset composed of more than 33000 images recorded by a wearable camera, over which our proposed model has been tested. Our approach obtains an accuracy and F-score of 56\% and 65\%, respectively, clearly outperforming the baseline methods.

Jordi de la Torre, Aida Valls, Domenec Puig et al.

Interpretability is a key factor in the design of automatic classifiers for medical diagnosis. Deep learning models have been proven to be a very effective classification algorithm when trained in a supervised way with enough data. The main concern is the difficulty of inferring rationale interpretations from them. Different attempts have been done in last years in order to convert deep learning classifiers from high confidence statistical black box machines into self-explanatory models. In this paper we go forward into the generation of explanations by identifying the independent causes that use a deep learning model for classifying an image into a certain class. We use a combination of Independent Component Analysis with a Score Visualization technique. In this paper we study the medical problem of classifying an eye fundus image into 5 levels of Diabetic Retinopathy. We conclude that only 3 independent components are enough for the differentiation and correct classification between the 5 disease standard classes. We propose a method for visualizing them and detecting lesions from the generated visual maps.

Vivek Kumar Singh, Hatem A. Rashwan, Santiago Romani et al.

Mammogram inspection in search of breast tumors is a tough assignment that radiologists must carry out frequently. Therefore, image analysis methods are needed for the detection and delineation of breast masses, which portray crucial morphological information that will support reliable diagnosis. In this paper, we proposed a conditional Generative Adversarial Network (cGAN) devised to segment a breast mass within a region of interest (ROI) in a mammogram. The generative network learns to recognize the breast mass area and to create the binary mask that outlines the breast mass. In turn, the adversarial network learns to distinguish between real (ground truth) and synthetic segmentations, thus enforcing the generative network to create binary masks as realistic as possible. The cGAN works well even when the number of training samples are limited. Therefore, the proposed method outperforms several state-of-the-art approaches. This hypothesis is corroborated by diverse experiments performed on two datasets, the public INbreast and a private in-house dataset. The proposed segmentation model provides a high Dice coefficient and Intersection over Union (IoU) of 94% and 87%, respectively. In addition, a shape descriptor based on a Convolutional Neural Network (CNN) is proposed to classify the generated masks into four mass shapes: irregular, lobular, oval and round. The proposed shape descriptor was trained on Digital Database for Screening Mammography (DDSM) yielding an overall accuracy of 80%, which outperforms the current state-of-the-art.

Md. Mostafa Kamal Sarker, Hatem A. Rashwan, Estefania Talavera et al.

First-person (wearable) camera continually captures unscripted interactions of the camera user with objects, people, and scenes reflecting his personal and relational tendencies. One of the preferences of people is their interaction with food events. The regulation of food intake and its duration has a great importance to protect against diseases. Consequently, this work aims to develop a smart model that is able to determine the recurrences of a person on food places during a day. This model is based on a deep end-to-end model for automatic food places recognition by analyzing egocentric photo-streams. In this paper, we apply multi-scale Atrous convolution networks to extract the key features related to food places of the input images. The proposed model is evaluated on an in-house private dataset called "EgoFoodPlaces". Experimental results shows promising results of food places classification recognition in egocentric photo-streams.

Vivek Kumar Singh, Hatem Rashwan, Farhan Akram et al.

This paper proposed a retinal image segmentation method based on conditional Generative Adversarial Network (cGAN) to segment optic disc. The proposed model consists of two successive networks: generator and discriminator. The generator learns to map information from the observing input (i.e., retinal fundus color image), to the output (i.e., binary mask). Then, the discriminator learns as a loss function to train this mapping by comparing the ground-truth and the predicted output with observing the input image as a condition.Experiments were performed on two publicly available dataset; DRISHTI GS1 and RIM-ONE. The proposed model outperformed state-of-the-art-methods by achieving around 0.96% and 0.98% of Jaccard and Dice coefficients, respectively. Moreover, an image segmentation is performed in less than a second on recent GPU.

Md. Mostafa Kamal Sarker, Mohammed Jabreel, Hatem A. Rashwan et al.

Diversity of food and its attributes represents the culinary habits of peoples from different countries. Thus, this paper addresses the problem of identifying food culture of people around the world and its flavor by classifying two main food attributes, cuisine and flavor. A deep learning model based on multi-scale convotuional networks is proposed for extracting more accurate features from input images. The aggregation of multi-scale convolution layers with different kernel size is also used for weighting the features results from different scales. In addition, a joint loss function based on Negative Log Likelihood (NLL) is used to fit the model probability to multi labeled classes for multi-modal classification task. Furthermore, this work provides a new dataset for food attributes, so-called Yummly48K, extracted from the popular food website, Yummly. Our model is assessed on the constructed Yummly48K dataset. The experimental results show that our proposed method yields 65% and 62% average F1 score on validation and test set which outperforming the state-of-the-art models.

Md. Mostafa Kamal Sarker, Hatem A. Rashwan, Farhan Akram et al.

Skin lesion segmentation (SLS) in dermoscopic images is a crucial task for automated diagnosis of melanoma. In this paper, we present a robust deep learning SLS model, so-called SLSDeep, which is represented as an encoder-decoder network. The encoder network is constructed by dilated residual layers, in turn, a pyramid pooling network followed by three convolution layers is used for the decoder. Unlike the traditional methods employing a cross-entropy loss, we investigated a loss function by combining both Negative Log Likelihood (NLL) and End Point Error (EPE) to accurately segment the melanoma regions with sharp boundaries. The robustness of the proposed model was evaluated on two public databases: ISBI 2016 and 2017 for skin lesion analysis towards melanoma detection challenge. The proposed model outperforms the state-of-the-art methods in terms of segmentation accuracy. Moreover, it is capable to segment more than $100$ images of size 384x384 per second on a recent GPU.

Vivek Kumar Singh, Santiago Romani, Hatem A. Rashwan et al.

This paper proposes a novel approach based on conditional Generative Adversarial Networks (cGAN) for breast mass segmentation in mammography. We hypothesized that the cGAN structure is well-suited to accurately outline the mass area, especially when the training data is limited. The generative network learns intrinsic features of tumors while the adversarial network enforces segmentations to be similar to the ground truth. Experiments performed on dozens of malignant tumors extracted from the public DDSM dataset and from our in-house private dataset confirm our hypothesis with very high Dice coefficient and Jaccard index (>94% and >89%, respectively) outperforming the scores obtained by other state-of-the-art approaches. Furthermore, in order to detect portray significant morphological features of the segmented tumor, a specific Convolutional Neural Network (CNN) have also been designed for classifying the segmented tumor areas into four types (irregular, lobular, oval and round), which provides an overall accuracy about 72% with the DDSM dataset.

Jordi de la Torre, Aida Valls, Domenec Puig

Deep neural network models have been proven to be very successful in image classification tasks, also for medical diagnosis, but their main concern is its lack of interpretability. They use to work as intuition machines with high statistical confidence but unable to give interpretable explanations about the reported results. The vast amount of parameters of these models make difficult to infer a rationale interpretation from them. In this paper we present a diabetic retinopathy interpretable classifier able to classify retine images into the different levels of disease severity and of explaining its results by assigning a score for every point in the hidden and input space, evaluating its contribution to the final classification in a linear way. The generated visual maps can be interpreted by an expert in order to compare its own knowledge with the interpretation given by the model.

Elnaz J. Heravi, Hamed H. Aghdam, Domenec Puig

Understanding the internal process of ConvNets is commonly done using visualization techniques. However, these techniques do not usually provide a tool for estimating the stability of a ConvNet against noise. In this paper, we show how to analyze a ConvNet in the frequency domain using a 4-dimensional visualization technique. Using the frequency domain analysis, we show the reason that a ConvNet might be sensitive to a very low magnitude additive noise. Our experiments on a few ConvNets trained on different datasets revealed that convolution kernels of a trained ConvNet usually pass most of the frequencies and they are not able to effectively eliminate the effect of high frequencies. Our next experiments shows that a convolution kernel which has a more concentrated frequency response could be more stable. Finally, we show that fine-tuning a ConvNet using a training set augmented with noisy images can produce more stable ConvNets.