Knowledge-aware Deep Framework for Collaborative Skin Lesion Segmentation and Melanoma Recognition

Deep learning techniques have shown their superior performance in dermatologist clinical inspection. Nevertheless, melanoma diagnosis is still a challenging task due to the difficulty of incorporating the useful dermatologist clinical knowledge into the learning process. In this paper, we propose a novel knowledge-aware deep framework that incorporates some clinical knowledge into collaborative learning of two important melanoma diagnosis tasks, i.e., skin lesion segmentation and melanoma recognition. Specifically, to exploit the knowledge of morphological expressions of the lesion region and also the periphery region for melanoma identification, a lesion-based pooling and shape extraction (LPSE) scheme is designed, which transfers the structure information obtained from skin lesion segmentation into melanoma recognition. Meanwhile, to pass the skin lesion diagnosis knowledge from melanoma recognition to skin lesion segmentation, an effective diagnosis guided feature fusion (DGFF) strategy is designed. Moreover, we propose a recursive mutual learning mechanism that further promotes the inter-task cooperation, and thus iteratively improves the joint learning capability of the model for both skin lesion segmentation and melanoma recognition. Experimental results on two publicly available skin lesion datasets show the effectiveness of the proposed method for melanoma analysis.Comment: Pattern Recognitio

Separation and Concentration in Deep Networks

Numerical experiments demonstrate that deep neural network classifiers progressively separate class distributions around their mean, achieving linear separability on the training set, and increasing the Fisher discriminant ratio. We explain this mechanism with two types of operators. We prove that a rectifier without biases applied to sign-invariant tight frames can separate class means and increase Fisher ratios. On the opposite, a soft-thresholding on tight frames can reduce within-class variabilities while preserving class means. Variance reduction bounds are proved for Gaussian mixture models. For image classification, we show that separation of class means can be achieved with rectified wavelet tight frames that are not learned. It defines a scattering transform. Learning $1 \times 1$ convolutional tight frames along scattering channels and applying a soft-thresholding reduces within-class variabilities. The resulting scattering network reaches the classification accuracy of ResNet-18 on CIFAR-10 and ImageNet, with fewer layers and no learned biases

Detección de carcinoma basocelular utilizando red neuronal convolucional y Support Vector Machine

El cáncer de piel es uno de los tipos de cáncer más frecuente en los seres humanos, abarca cerca de un tercio total de las neoplasias. Dentro del cáncer de piel encontramos al carcinoma basocelular (CBC) siendo este el tipo de cáncer más frecuente a nivel mundial. Una serie de estudios que involucran enfoques de aprendizaje profundo ya se han desempeñado en un número considerable como la clasificación de imágenes. Los modelos utilizados en dichas tareas emplean la función Softmax (modelo clásico) en la capa de clasificación. Sin embargo, se han realizado estudios que utilizan una alternativa a la función Softmax para la clasificación: la máquina de vectores de soporte (SVM). El uso de SVM en una arquitectura de red neuronal artificial produce resultados relativamente mejores que el uso de la función Softmax convencional. Por este motivo se construyó un sistema que diagnostica el carcinoma basocelular implementando un modelo híbrido de red neuronal convolucional y máquina de vectores de soporte para clasificar el CBC. Los resultados obtenidos fueron medidos con las métricas de precisión, recall, f1-score y exactitud obteniendo 94.51%, 88.42%, 91.36% y 91.54% respectivamente

Symbiotic deep learning for medical image analysis with applications in real-time diagnosis for fetal ultrasound screening

The last hundred years have seen a monumental rise in the power and capability of machines to perform intelligent tasks in the stead of previously human operators. This rise is not expected to slow down any time soon and what this means for society and humanity as a whole remains to be seen. The overwhelming notion is that with the right goals in mind, the growing influence of machines on our every day tasks will enable humanity to give more attention to the truly groundbreaking challenges that we all face together. This will usher in a new age of human machine collaboration in which humans and machines may work side by side to achieve greater heights for all of humanity. Intelligent systems are useful in isolation, but the true benefits of intelligent systems come to the fore in complex systems where the interaction between humans and machines can be made seamless, and it is this goal of symbiosis between human and machine that may democratise complex knowledge, which motivates this thesis. In the recent past, datadriven methods have come to the fore and now represent the state-of-the-art in many different fields. Alongside the shift from rule-based towards data-driven methods we have also seen a shift in how humans interact with these technologies. Human computer interaction is changing in response to data-driven methods and new techniques must be developed to enable the same symbiosis between man and machine for data-driven methods as for previous formula-driven technology. We address five key challenges which need to be overcome for data-driven human-in-the-loop computing to reach maturity. These are (1) the ’Categorisation Challenge’ where we examine existing work and form a taxonomy of the different methods being utilised for data-driven human-in-the-loop computing; (2) the ’Confidence Challenge’, where data-driven methods must communicate interpretable beliefs in how confident their predictions are; (3) the ’Complexity Challenge’ where the aim of reasoned communication becomes increasingly important as the complexity of tasks and methods to solve also increases; (4) the ’Classification Challenge’ in which we look at how complex methods can be separated in order to provide greater reasoning in complex classification tasks; and finally (5) the ’Curation Challenge’ where we challenge the assumptions around bottleneck creation for the development of supervised learning methods.Open Acces

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Machine Learning in Image Analysis and Pattern Recognition

This book is to chart the progress in applying machine learning, including deep learning, to a broad range of image analysis and pattern recognition problems and applications. In this book, we have assembled original research articles making unique contributions to the theory, methodology and applications of machine learning in image analysis and pattern recognition

Developing statistical and bioinformatic analysis of genomic data from tumours

Previous prognostic signatures for melanoma based on tumour transcriptomic data were developed predominantly on cohorts of AJCC (American Joint Committee on Cancer) stages III and IV melanoma. Since 92% of melanoma patients are diagnosed at AJCC stages I and II, there is an urgent need for better prognostic biomarkers to allow patient stratification for receiving early adjuvant therapies. This study uses genome-wide tumour gene expression levels and clinico-histopathological characteristics of patients from the Leeds Melanoma Cohort (LMC). Several unsupervised and supervised classification approaches were applied to the transcriptomic data, to identify biological classes of melanoma, and to develop prognostic classification models respectively. Unsupervised clustering identified six biologically distinct primary melanoma classes (LMC classes). Unlike previous molecular classes of melanoma, the LMC classes were prognostic in both the whole LMC dataset and in stage I tumours. The prognostic value of the LMC classes was replicated in an independent dataset, but insufficient data were available to replicate in an AJCC stage I subset. Supervised classification using the Random Forest (RF) approach provided improved performances when adjustments were made to deal with class imbalance, while this did not improve performance of the Support Vector Machine (SVM). However, RF and SVM had similar results overall, with RF only marginally better. Combining clinical and transcriptomic information in the RF further improved the performance of the prediction model in comparison to using clinical information alone. Finally, the agnostically derived LMC classes and the supervised RF model showed convergence in their association with outcome in some groups of patients, but not in others. In conclusion, this study reports six molecular classes of primary melanoma with prognostic value in stage I disease and overall, and a prognostic classification model that predicts outcome in primary melanoma

Biomedical Image Processing and Classification

Biomedical image processing is an interdisciplinary field involving a variety of disciplines, e.g., electronics, computer science, physics, mathematics, physiology, and medicine. Several imaging techniques have been developed, providing many approaches to the study of the human body. Biomedical image processing is finding an increasing number of important applications in, for example, the study of the internal structure or function of an organ and the diagnosis or treatment of a disease. If associated with classification methods, it can support the development of computer-aided diagnosis (CAD) systems, which could help medical doctors in refining their clinical picture

Deep learning assisted MRI guided attenuation correction in PET

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological and functional details of the tissue at the molecular level. However, the acquired PET images have some limitations such as the attenuation. PET attenuation correction is an essential step to obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners, magnetic resonance (MR) images are used to address the problem of PET attenuation correction. The MR images segmentation is one simple and robust approach to create pseudo computed tomography (CT) images, which are used to generate attenuation coefficient maps to correct the PET attenuation. Recently, deep learning has been proposed and used as a promising technique to efficiently perform MR and various medical images segmentation. In this research work, deep learning guided segmentation approaches have been proposed to enhance the bone class segmentation of MR brain images in order to generate accurate pseudo-CT images. The first approach has introduced the combination of handcrafted features with deep learning features to enrich the set of features. Multiresolution analysis techniques, which generate multiscale and multidirectional coefficients of an image such as contourlet and shearlet transforms, are applied and combined with deep convolutional neural network (CNN) features. Different experiments have been conducted to investigate the number of selected coefficients and the insertion location of the handcrafted features. The second approach aims at reducing the segmentation algorithm’s complexity while maintaining the segmentation performance. An attention based convolutional encode-decoder network has been proposed to adaptively recalibrate the deep network features. This attention based network consists of two different squeeze and excitation blocks that excite the features spatially and channel wise. The two blocks are combined sequentially to decrease the number of network’s parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w images. Multiple fine tuning approaches and experiments have been conducted to study the best fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been used to carry an objective evaluation to measure the segmentation performance of the results obtained by the three proposed methods. The first and second approaches have been validated with other studies in the literature that applied deep network based segmentation technique to perform MR based attenuation correction for PET images. The proposed methods have shown an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC) from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%. The proposed excitation-based CNN has decreased the model complexity by decreasing the number of trainable parameters by more than 46% where less computing resources are required to train the model. The proposed hybrid transfer learning method has shown its superiority to build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied transfer learning methods especially with the bone class where the DSC is increased from 0.3841 to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than transfer learning using open and conservative fine tuning