Artifact-Robust Graph-Based Learning in Digital Pathology

Whole slide images~(WSIs) are digitized images of tissues placed in glass slides using advanced scanners. The digital processing of WSIs is challenging as they are gigapixel images and stored in multi-resolution format. A common challenge with WSIs is that perturbations/artifacts are inevitable during storing the glass slides and digitizing them. These perturbations include motion, which often arises from slide movement during placement, and changes in hue and brightness due to variations in staining chemicals and the quality of digitizing scanners. In this work, a novel robust learning approach to account for these artifacts is presented. Due to the size and resolution of WSIs and to account for neighborhood information, graph-based methods are called for. We use graph convolutional network~(GCN) to extract features from the graph representing WSI. Through a denoiser {and pooling layer}, the effects of perturbations in WSIs are controlled and the output is followed by a transformer for the classification of different grades of prostate cancer. To compare the efficacy of the proposed approach, the model without denoiser is trained and tested with WSIs without any perturbation and then different perturbations are introduced in WSIs and passed through the network with the denoiser. The accuracy and kappa scores of the proposed model with prostate cancer dataset compared with non-robust algorithms show significant improvement in cancer diagnosis

Graph Based Learning for Building Prediction in Smart Cities

Anticipating pedestrians’ activity is a necessary task for providing a safe and energy efficient environment in an urban area. By locating strategically sensors throughout the city useful information could be obtained. By knowing the average activity of those throughout different days of the week we could identify the typology of the buildings neighboring those sensors. For these type of purposes, clustering methods show great capability forming groups of items that have great similarity intra clusters and dissimilarity inter cluster. Different approaches are made to classify sensors depending on the typology of buildings surrounding them and the mean pedestrians’ counts for different time intervals. By this way, sensors could be classified in different groups according to their activation patterns and the environment in which they are located through clustering processes and using graph convolutional networks. This study reveals that there is a close relationship between the activity pattern of the pedestrians’ and the type of environment sensors that collect pedestrians’ data are located. By this way, institutions could alleviate a great amount of effort needed to ensure safe and energy efficient urban areas, only knowing the typology of buildings of an urban zone

Graph-based learning under perturbations via total least-squares

Graphs are pervasive in different fields unveiling complex relationships between data. Two major graph-based learning tasks are topology identification and inference of signals over graphs. Among the possible models to explain data interdependencies, structural equation models (SEMs) accommodate a gamut of applications involving topology identification. Obtaining conventional SEMs though requires measurements across nodes. On the other hand, typical signal inference approaches “blindly trust” a given nominal topology. In practice however, signal or topology perturbations may be present in both tasks, due to model mismatch, outliers, outages or adversarial behavior. To cope with such perturbations, this work introduces a regularized total least-squares (TLS) approach and iterative algorithms with convergence guarantees to solve both tasks. Further generalizations are also considered relying on structured and/or weighted TLS when extra prior information on the perturbation is available. Analyses with simulated and real data corroborate the effectiveness of the novel TLS-based approaches

Flexible Graph-based Learning with Applications to Genetic Data Analysis

With the abundance of increasingly complex and high dimensional data in many scientific disciplines, graphical models have become an extremely useful statistical tool to explore data structures. In this dissertation, we study graphical models from two perspectives: i) to enhance supervised learning, classification in particular, and ii) graphical model estimation for specific data types. For classification, the optimal classifier is often connected with the feature structure within each class. In the first project, starting from the Gaussian population scenario, we aim to find an approach to utilize the graphical structure information of the features in classification. With respect to graphical models, many existing graphical estimation methods have been proposed based on a homogeneous Gaussian population. Due to the Gaussian assumption, these methods may not be suitable for many typical genetic data. For instance, the gene expression data may come from individuals of multiple populations with possibly distinct graphical structures. Another instance would be the single cell RNA-sequencing data, which are featured by substantial sample dependence and zero-inflation. In the second and the third project, we propose multiple graphical model estimation methods for these scenarios respectively. In particular, two dependent count-data graphical models are introduced for the latter case. Both numerical and theoretical studies are performed to demonstrate the effectiveness of these methods.Doctor of Philosoph