Assessing invasiveness of subsolid lung adenocarcinomas with combined attenuation and geometric feature models

The aim of this study was to develop and test multiclass predictive models for assessing the invasiveness of individual lung adenocarcinomas presenting as subsolid nodules on computed tomography (CT). 227 lung adenocarcinomas were included: 31 atypical adenomatous hyperplasia and adenocarcinomas in situ (class H1), 64 minimally invasive adenocarcinomas (class H2) and 132 invasive adenocarcinomas (class H3). Nodules were segmented, and geometric and CT attenuation features including functional principal component analysis features (FPC1 and FPC2) were extracted. After a feature selection step, two predictive models were built with ordinal regression: Model 1 based on volume (log) (logarithm of the nodule volume) and FPC1, and Model 2 based on volume (log) and Q.875 (CT attenuation value at the 87.5% percentile). Using the 200-repeats Monte-Carlo cross-validation method, these models provided a multiclass classification of invasiveness with discriminative power AUCs of 0.83 to 0.87 and predicted the class probabilities with less than a 10% average error. The predictive modelling approach adopted in this paper provides a detailed insight on how the value of the main predictors contribute to the probability of nodule invasiveness and underlines the role of nodule CT attenuation features in the nodule invasiveness classification

Automated detection and classification of tumor histotypes on dynamic PET imaging data through machine-learning driven voxel classification

2-deoxy-2-fluorine-(18F)fluoro-D-glucose Positron Emission Tomography/Computed Tomography (18F-FDG-PET/CT) is widely used in oncology mainly for diagnosis and staging of various cancer types, including lung cancer, which is the most common cancer worldwide. Since histopathologic subtypes of lung cancer show different degree of 18F-FDG uptake, to date there are some diagnostic limits and uncertainties, hindering an 18F-FDG-PET-driven classification of histologic subtypes of lung cancers. On the other hand, since activated macrophages, neutrophils, fibroblasts and granulation tissues also show an increased 18F-FDG activity, infectious and/or inflammatory processes and post-surgical and post-radiation changes may cause false-positive results, especially for lymph-nodes assessment. Here we propose a model-free, machine-learning based algorithm for the automated classification of adenocarcinoma, the most common type of lung cancer, and other types of tumors. Input for the algorithm are dynamic acquisitions of PET data (dPET), providing for a spatially and temporally resolved characterization of the uptake kinetic. The algorithm consists in a trained Random Forest classifier which, relying contextually on several spatial and temporal features of 18F-FDG uptake, generates as an outcome probability maps allowing to distinguish adenocarcinoma from other lung histotype and to identify metastatic lymph-nodes, ultimately increasing the specificity of the technique. Its performance, evaluated on a dPET dataset of 19 patients affected by primary lung cancer, provides a probability 0.943 ± 0.090 for the detection of adenocarcinoma. The use of this algorithm will guarantee an automatic and more accurate localization and discrimination of tumors, also providing a powerful tool for detecting at which extent tumor has spread beyond a primary tumor into lymphatic system

EGFR and KRAS mutation prediction on lung cancer through medical image processing and artificial intelligence

Lung cancer causes more deaths globally than any other type of cancer. To determine the best treatment, detecting EGFR and KRAS mutations is of interest. However, non-invasive ways to obtain this information are not available. In this study, an ensemble approach is applied to increase the performance of EGFR and KRAS mutation prediction from CT images using a small dataset. A new voting scheme, Selective Class Average Voting (SCAV) is proposed and its performance is assessed both for machine learning models and Convolutional Neural Networks (CNNs). For the EGFR mutation, in the machine learning approach, there was an increase in the Sensitivity from 0.66 to 0.75, and an increase in AUC from 0.68 to 0.70. With the deep learning approach an AUC of 0.846 was obtained with custom CNNs, and with SCAV the Accuracy of the model was increased from 0.80 to 0.857. Finally, when combining the best Custom and Pre-trained CNNs using SCAV an AUC of 0.914 was obtained. For the KRAS mutation both in the machine learning models (0.65 to 0.71 AUC) and the deep learning models (0.739 to 0.778 AUC) a significant increase in performance was found. This increase was even greater with Ensembles of Pre-trained CNNs (0.809 AUC). The results obtained in this work show how to effectively learn from small image datasets to predict EGFR and KRAS mutations, and that using ensembles with SCAV increases the performance of machine learning classifiers and CNNs.DoctoradoDoctor en Ingeniería de Sistemas y Computació

Texture-based Deep Neural Network for Histopathology Cancer Whole Slide Image (WSI) Classification

Automatic histopathological Whole Slide Image (WSI) analysis for cancer classification has been highlighted along with the advancements in microscopic imaging techniques. However, manual examination and diagnosis with WSIs is time-consuming and tiresome. Recently, deep convolutional neural networks have succeeded in histopathological image analysis. In this paper, we propose a novel cancer texture-based deep neural network (CAT-Net) that learns scalable texture features from histopathological WSIs. The innovation of CAT-Net is twofold: (1) capturing invariant spatial patterns by dilated convolutional layers and (2) Reducing model complexity while improving performance. Moreover, CAT-Net can provide discriminative texture patterns formed on cancerous regions of histopathological images compared to normal regions. The proposed method outperformed the current state-of-the-art benchmark methods on accuracy, precision, recall, and F1 score

Lung cancer classification based on CT scan image by applying FCM segmentation and neural network technique

The number of people with lung cancer has reached approximately 2.09 million people worldwide. Out of 9.06 million cases of death, 1.76 million people die due to lung cancer. Lung cancer can be automatically identified using a computer-aided diagnosis system (CAD) such as image processing. The steps taken for early detection are pre-processing feature extraction, and classification. Pre-processing is carried out in several stages, namely grayscale images, noise removal, and contrast limited adaptive histogram equalization. This image feature extracted using GLCM and classified using 2 method of neural network which is feed forward neural network (FFNN) dan feed backward neural network (FBNN). This research aims to obtain the best neural network model to classify lung cancer a. Based on training time and accuracy, the best method of FFNN is kernel extreme learning machine (KELM), with a training time of 12 seconds and an accuracy of 93.45%, while the best method of FBNN is Backpropagation with a training time of 18 minutes 04 seconds and an accuracy of 97.5%

Heterogeneidad tumoral en imágenes PET-CT

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Físicas, Departamento de Estructura de la Materia, Física Térmica y Electrónica, leída el 28/01/2021Cancer is a leading cause of morbidity and mortality [1]. The most frequent cancers worldwide are non–small cell lung carcinoma (NSCLC) and breast cancer [2], being their management a challenging task [3]. Tumor diagnosis is usually made through biopsy [4]. However, medical imaging also plays an important role in diagnosis, staging, response to treatment, and recurrence assessment [5]. Tumor heterogeneity is recognized to be involved in cancer treatment failure, with worse clinical outcomes for highly heterogeneous tumors [6,7]. This leads to the existence of tumor sub-regions with different biological behavior (some more aggressive and treatment-resistant than others) [8-10]. Which are characterized by a different pattern of vascularization, vessel permeability, metabolism, cell proliferation, cell death, and other features, that can be measured by modern medical imaging techniques, including positron emission tomography/computed tomography (PET/CT) [10-12]. Thus, the assessment of tumor heterogeneity through medical images could allow the prediction of therapy response and long-term outcomes of patients with cancer [13]. PET/CT has become essential in oncology [14,15] and is usually evaluated through semiquantitative metabolic parameters, such as maximum/mean standard uptake value (SUVmax, SUVmean) or metabolic tumor volume (MTV), which are valuables as prognostic image-based biomarkers in several tumors [16-17], but these do not assess tumor heterogeneity. Likewise, fluorodeoxyglucose (18F-FDG) PET/CT is important to differentiate malignant from benign solitary pulmonary nodules (SPN), reducing so the number of patients who undergo unnecessary surgical biopsies. Several publications have shown that some quantitative image features, extracted from medical images, are suitable for diagnosis, tumor staging, the prognosis of treatment response, and long-term evolution of cancer patients [18-20]. The process of extracting and relating image features with clinical or biological variables is called “Radiomics” [9,20-24]. Radiomic parameters, such as textural features have been related directly to tumor heterogeneity [25]. This thesis investigated the relationships of the tumor heterogeneity, assessed by 18F-FDG-PET/CT texture analysis, with metabolic parameters and pathologic staging in patients with NSCLC, and explored the diagnostic performance of different metabolic, morphologic, and clinical criteria for classifying (malignant or not) of solitary pulmonary nodules (SPN). Furthermore, 18F-FDG-PET/CT radiomic features of patients with recurrent/metastatic breast cancer were used for constructing predictive models of response to the chemotherapy, based on an optimal combination of several feature selection and machine learning (ML) methods...El cáncer es una de las principales causas de morbilidad y mortalidad. Los más frecuentes son el carcinoma de pulmón de células no pequeñas (NSCLC) y el cáncer de mama, siendo su tratamiento un reto. El diagnóstico se suele realizar mediante biopsia. La heterogeneidad tumoral (HT) está implicada en el fracaso del tratamiento del cáncer, con peores resultados clínicos para tumores muy heterogéneos. Esta conduce a la existencia de subregiones tumorales con diferente comportamiento biológico (algunas más agresivas y resistentes al tratamiento); las cuales se caracterizan por diferentes patrones de vascularización, permeabilidad de los vasos sanguíneos, metabolismo, proliferación y muerte celular, que se pueden medir mediante imágenes médicas, incluida la tomografía por emisión de positrones/tomografía computarizada con fluorodesoxiglucosa (18F-FDG-PET/CT). La evaluación de la HT a través de imágenes médicas, podría mejorar la predicción de la respuesta al tratamiento y de los resultados a largo plazo, en pacientes con cáncer. La 18F-FDG-PET/CT es esencial en oncología, generalmente se evalúa con parámetros metabólicos semicuantitativos, como el valor de captación estándar máximo/medio (SUVmáx, SUVmedio) o el volumen tumoral metabólico (MTV), que tienen un gran valor pronóstico en varios tumores, pero no evalúan la HT. Asimismo, es importante para diferenciar los nódulos pulmonares solitarios (NPS) malignos de los benignos, reduciendo el número de pacientes que van a biopsias quirúrgicas innecesarias. Publicaciones recientes muestran que algunas características cuantitativas, extraídas de las imágenes médicas, son robustas para diagnóstico, estadificación, pronóstico de la respuesta al tratamiento y la evolución, de pacientes con cáncer. El proceso de extraer y relacionar estas características con variables clínicas o biológicas se denomina “Radiomica”. Algunos parámetros radiómicos, como la textura, se han relacionado directamente con la HT. Esta tesis investigó las relaciones entre HT, evaluada mediante análisis de textura (AT) de imágenes 18F-FDG-PET/CT, con parámetros metabólicos y estadificación patológica en pacientes con NSCLC, y exploró el rendimiento diagnóstico de diferentes criterios metabólicos, morfológicos y clínicos para la clasificación de NPS. Además, se usaron características radiómicas de imágenes 18F-FDG-PET/CT de pacientes con cáncer de mama recurrente/metastásico, para construir modelos predictivos de la respuesta a la quimioterapia, combinándose varios métodos de selección de características y aprendizaje automático (ML)...Fac. de Ciencias FísicasTRUEunpu

Lung Disease Classification using Dense Alex Net Framework with Contrast Normalisation and Five-Fold Geometric Transformation

lung disease is one of the leading causes of death worldwide. Most cases of lung diseases are found when the disease is in an advanced stage. Therefore, the development of systems and methods that begin to diagnose quickly and prematurely plays a vital role in today's world. Currently, in detecting differences in lung cancer, an accurate diagnosis of cancer types is needed. However, improving the accuracy and reducing training time of the diagnosis remains a challenge. In this study, we have developed an automated classification scheme for lung cancer presented in histopathological images using a dense Alex Net framework. The proposed methodology carries out several phases includes pre-processing, contrast normalization, data augmentation and classification. Initially, the pre-processing step is accompanied to diminish the noisy contents present in the image. Contrast normalization has been explored to maintain the same illumination factor among histopathological lung images next to pre-processing. Afterwards, data augmentation phase has been carried out to enhance the dataset further to avoid over-fitting problems. Finally, the Dense Alex Net is utilized for classification that comprises five convolutional layers, one multi-scale convolution layer, and three fully connected layers. In evaluation experiments, the proposed approach was trained using our original database to provide rich and meaningful features. The accuracy attained by the proposed methodology is93%, which is maximum compared with the existing algorithm