An Explainable AI-Based Computer Aided Detection System for Diabetic Retinopathy Using Retinal Fundus Images

Diabetic patients have a high risk of developing diabetic retinopathy (DR), which is one of the major causes of blindness. With early detection and the right treatment patients may be spared from losing their vision. We propose a computer-aided detection system, which uses retinal fundus images as input and it detects all types of lesions that define diabetic retinopathy. The aim of our system is to assist eye specialists by automatically detecting the healthy retinas and referring the images of the unhealthy ones. For the latter cases, the system offers an interactive tool where the doctor can examine the local lesions that our system marks as suspicious. The final decision remains in the hands of the ophthalmologists. Our approach consists of a multi-class detector, that is able to locate and recognize all candidate DR-defining lesions. If the system detects at least one lesion, then the image is marked as unhealthy. The lesion detector is built on the faster R-CNN ResNet 101 architecture, which we train by transfer learning. We evaluate our approach on three benchmark data sets, namely Messidor-2, IDRiD, and E-Ophtha by measuring the sensitivity (SE) and specificity (SP) based on the binary classification of healthy and unhealthy images. The results that we obtain for Messidor-2 and IDRiD are (SE: 0.965, SP: 0.843), and (SE: 0.83, SP: 0.94), respectively. For the E-Ophtha data set we follow the literature and perform two experiments, one where we detect only lesions of the type micro aneurysms (SE: 0.939, SP: 0.82) and the other when we detect only exudates (SE: 0.851, SP: 0.971). Besides the high effectiveness that we achieve, the other important contribution of our work is the interactive tool, which we offer to the medical experts, highlighting all suspicious lesions detected by the proposed system.<br/

Hybrid Deep Learning Gaussian Process for Diabetic Retinopathy Diagnosis and Uncertainty Quantification

Diabetic Retinopathy (DR) is one of the microvascular complications of Diabetes Mellitus, which remains as one of the leading causes of blindness worldwide. Computational models based on Convolutional Neural Networks represent the state of the art for the automatic detection of DR using eye fundus images. Most of the current work address this problem as a binary classification task. However, including the grade estimation and quantification of predictions uncertainty can potentially increase the robustness of the model. In this paper, a hybrid Deep Learning-Gaussian process method for DR diagnosis and uncertainty quantification is presented. This method combines the representational power of deep learning, with the ability to generalize from small datasets of Gaussian process models. The results show that uncertainty quantification in the predictions improves the interpretability of the method as a diagnostic support tool. The source code to replicate the experiments is publicly available at https://github.com/stoledoc/DLGP-DR-Diagnosis

Mapping and characterization of structural variation in 17,795 human genomes

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0–11.2% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing

Hybrid Deep Learning Gaussian Process for Diabetic Retinopathy Diagnosis and Uncertainty Quantification

La retinopatía diabética (RD) es una de las complicaciones microvasculares de la diabetes mellitus, que sigue siendo una de las principales causas de ceguera en todo el mundo. Los modelos computacionales basados ​​en redes neuronales convolucionales representan el estado del arte para la detección automática de RD utilizando imágenes de fondo de ojo. La mayor parte del trabajo actual aborda este problema como una tarea de clasificación binaria. Sin embargo, incluir la estimación de leyes y la cuantificación de la incertidumbre de las predicciones puede aumentar potencialmente la solidez del modelo. En este artículo, se presenta un método de proceso híbrido de aprendizaje profundo y gaussiano para el diagnóstico de RD y la cuantificación de la incertidumbre. Este método combina el poder de representación del aprendizaje profundo con la capacidad de generalizar a partir de pequeños conjuntos de datos de modelos de procesos gaussianos. Los resultados muestran que la cuantificación de la incertidumbre en las predicciones mejora la interpretabilidad del método como herramienta de apoyo al diagnósticoDiabetic retinopathy (DR) is one of the microvascular complications of diabetes mellitus, which remains a leading cause of blindness worldwide. Computational models based on convolutional neural networks represent the state of the art for automatic detection of DR using fundus images. Most of the current work addresses this problem as a binary classification task. However, including law estimation and quantification of prediction uncertainty can potentially increase model robustness. In this paper, a hybrid deep learning and Gaussian process method for DR diagnosis and uncertainty quantification is presented. This method combines the representational power of deep learning with the ability to generalize from small data sets of Gaussian process models. The results show that the quantification of uncertainty in the predictions improves the interpretability of the method as a diagnostic support tool. Translated with www.DeepL.com/Translator (free version)Este trabajo fue parcialmente financiado por un premio de investigación de Google y por el proyecto Colciencias número 1101-807-63563

Segmentation of pigment signs in fundus images for retinitis pigmentosa analysis by using deep learning

The adoption of Deep Learning (DL) algorithms into the practice of ophthalmology could play an important role in screening and diagnosis of eye diseases in the coming years. In particular, DL tools interpreting ocular data derived from low-cost devices, as a fundus camera, could support massive screening also in resource limited countries. This paper explores a fully automatic method supporting the diagnosis of the Retinitis Pigmentosa by means of the segmentation of pigment signs in retinal fundus images. The proposed approach relies on an U-Net based deep convolutional network. At the present, this is the first approach for pigment signs segmentation in retinal fundus images that is not dependent on hand-crafted features, but automatically learns a hierarchy of increasingly complex features directly from data. We assess the performance by training the model on the public dataset RIPS and comparisons with the state of the art have been considered in accordance with approaches working on the same dataset. The experimental results show an improvement of 15% in F-measure score