GAN-based generative modelling for dermatological applications -- comparative study

The lack of sufficiently large open medical databases is one of the biggest challenges in AI-powered healthcare. Synthetic data created using Generative Adversarial Networks (GANs) appears to be a good solution to mitigate the issues with privacy policies. The other type of cure is decentralized protocol across multiple medical institutions without exchanging local data samples. In this paper, we explored unconditional and conditional GANs in centralized and decentralized settings. The centralized setting imitates studies on large but highly unbalanced skin lesion dataset, while the decentralized one simulates a more realistic hospital scenario with three institutions. We evaluated models' performance in terms of fidelity, diversity, speed of training, and predictive ability of classifiers trained on the generated synthetic data. In addition we provided explainability through exploration of latent space and embeddings projection focused both on global and local explanations. Calculated distance between real images and their projections in the latent space proved the authenticity and generalization of trained GANs, which is one of the main concerns in this type of applications. The open source code for conducted studies is publicly available at \url{https://github.com/aidotse/stylegan2-ada-pytorch}.Comment: 16 pages, 5 figures, 2 table

A multi-stage GAN for multi-organ chest X-ray image generation and segmentation

Multi-organ segmentation of X-ray images is of fundamental importance for computer aided diagnosis systems. However, the most advanced semantic segmentation methods rely on deep learning and require a huge amount of labeled images, which are rarely available due to both the high cost of human resources and the time required for labeling. In this paper, we present a novel multi-stage generation algorithm based on Generative Adversarial Networks (GANs) that can produce synthetic images along with their semantic labels and can be used for data augmentation. The main feature of the method is that, unlike other approaches, generation occurs in several stages, which simplifies the procedure and allows it to be used on very small datasets. The method has been evaluated on the segmentation of chest radiographic images, showing promising results. The multistage approach achieves state-of-the-art and, when very few images are used to train the GANs, outperforms the corresponding single-stage approach

SkinCAN AI: A deep learning-based skin cancer classification and segmentation pipeline designed along with a generative model

The rarity of Melanoma skin cancer accounts for the dataset collected to be limited and highly skewed, as benign moles can easily mimic the impression of the melanoma-affected area. Such an imbalanced dataset makes training any deep learning classifier network harder by affecting the training stability. We have an intuition that synthesizing such skin lesion medical images could help solve the issue of overfitting in training networks and assist in enforcing the anonymization of actual patients. Despite multiple previous attempts, none of the models were practical for the fast-paced clinical environment. In this thesis, we propose a novel pipeline named SkinCAN AI, inspired by StyleGAN but designed explicitly considering the limitations of the skin lesion dataset and emphasizing the requirement of a faster optimized diagnostic tool that can be easily inferred and integrated into the clinical environment. Our SkinCAN AI model is equipped with its module of adaptive discriminator augmentation that enables limited target data distribution to be learned and artificial data points to be sampled, which further assist the classifier network in learning semantic features. We elucidate the novelty of our SkinCAN AI pipeline by integrating the soft attention module in the classifier network. This module yields an attention mask analyzed by DenseNet201 to focus on learning relevant semantic features from skin lesion images without using any heavy computational burden of artifact removal software. The SkinGAN model achieves an FID score of 0.622 while allowing its synthetic samples to train the DenseNet201 model with an accuracy of 0.9494, AUC of 0.938, specificity of 0.969, and sensitivity of 0.695. We provide evidence in our thesis that our proposed pipelines outperform other state-of-the-art existing networks developed for this task of early diagnosis

Mathematical Modelling and Machine Learning Methods for Bioinformatics and Data Science Applications

Mathematical modeling is routinely used in physical and engineering sciences to help understand complex systems and optimize industrial processes. Mathematical modeling differs from Artificial Intelligence because it does not exclusively use the collected data to describe an industrial phenomenon or process, but it is based on fundamental laws of physics or engineering that lead to systems of equations able to represent all the variables that characterize the process. Conversely, Machine Learning methods require a large amount of data to find solutions, remaining detached from the problem that generated them and trying to infer the behavior of the object, material or process to be examined from observed samples. Mathematics allows us to formulate complex models with effectiveness and creativity, describing nature and physics. Together with the potential of Artificial Intelligence and data collection techniques, a new way of dealing with practical problems is possible. The insertion of the equations deriving from the physical world in the data-driven models can in fact greatly enrich the information content of the sampled data, allowing to simulate very complex phenomena, with drastically reduced calculation times. Combined approaches will constitute a breakthrough in cutting-edge applications, providing precise and reliable tools for the prediction of phenomena in biological macro/microsystems, for biotechnological applications and for medical diagnostics, particularly in the field of precision medicine