Everything is Connected: Graph Neural Networks

In many ways, graphs are the main modality of data we receive from nature. This is due to the fact that most of the patterns we see, both in natural and artificial systems, are elegantly representable using the language of graph structures. Prominent examples include molecules (represented as graphs of atoms and bonds), social networks and transportation networks. This potential has already been seen by key scientific and industrial groups, with already-impacted application areas including traffic forecasting, drug discovery, social network analysis and recommender systems. Further, some of the most successful domains of application for machine learning in previous years -- images, text and speech processing -- can be seen as special cases of graph representation learning, and consequently there has been significant exchange of information between these areas. The main aim of this short survey is to enable the reader to assimilate the key concepts in the area, and position graph representation learning in a proper context with related fields.Comment: To appear in Current Opinion in Structural Biology. 14 pages, 1 figur

ANALYZING PULMONARY ABNORMALITY WITH SUPERPIXEL BASED GRAPH NEURAL NETWORKS IN CHEST X-RAY

In recent years, the utilization of graph-based deep learning has gained prominence, yet its potential in the realm of medical diagnosis remains relatively unexplored. Convolutional Neural Network (CNN) has achieved state-of-the-art performance in areas such as computer vision, particularly for grid-like data such as images. However, they require a huge dataset to achieve top level of performance and challenge arises when learning from the inherent irregular/unordered nature of physiological data. In this thesis, the research primarily focuses on abnormality screening: classification of Chest X-Ray (CXR) as Tuberculosis positive or negative, using Graph Neural Networks (GNN) that uses Region Adjacency Graphs (RAGs), and each superpixel serves as a dedicated graph node. For graph classification, provided that the different classes are distinct enough GNN often classify graphs using just the graph structures. This study delves into the inquiry of whether the incorporation of node features, such as coordinate points and pixel intensity, along with structured data representing graph can enhance the learning process. By integration of residual and concatenation structures, this methodology adeptly captures essential features and relationships among superpixels, thereby contributing to advancements in tuberculosis identification. We achieved the best performance: accuracy of 0.80 and AUC of 0.79, through the union of state-of-the-art neural network architectures and innovative graph-based representations. This work introduces a new perspective to medical image analysis

Deep Learning Methods for 3D Aerial and Satellite Data

Recent advances in digital electronics have led to an overabundance of observations from electro-optical (EO) imaging sensors spanning high spatial, spectral and temporal resolution. This unprecedented volume, variety, and velocity is overwhelming our capacity to manage and translate that data into actionable information. Although decades of image processing research have taken the human out of the loop for many important tasks, the human analyst is still an irreplaceable link in the image exploitation chain, especially for more complex tasks requiring contextual understanding, memory, discernment, and learning. If knowledge discovery is to keep pace with the growing availability of data, new processing paradigms are needed in order to automate the analysis of earth observation imagery and ease the burden of manual interpretation. To address this gap, this dissertation advances fundamental and applied research in deep learning for aerial and satellite imagery. We show how deep learning---a computational model inspired by the human brain---can be used for (1) tracking, (2) classifying, and (3) modeling from a variety of data sources including full-motion video (FMV), Light Detection and Ranging (LiDAR), and stereo photogrammetry. First we assess the ability of a bio-inspired tracking method to track small targets using aerial videos. The tracker uses three kinds of saliency maps: appearance, location, and motion. Our approach achieves the best overall performance, including being the only method capable of handling long-term occlusions. Second, we evaluate the classification accuracy of a multi-scale fully convolutional network to label individual points in LiDAR data. Our method uses only the 3D-coordinates and corresponding low-dimensional spectral features for each point. Evaluated using the ISPRS 3D Semantic Labeling Contest, our method scored second place with an overall accuracy of 81.6\%. Finally, we validate the prediction capability of our neighborhood-aware network to model the bare-earth surface of LiDAR and stereo photogrammetry point clouds. The network bypasses traditionally-used ground classifications and seamlessly integrate neighborhood features with point-wise and global features to predict a per point Digital Terrain Model (DTM). We compare our results with two widely used softwares for DTM extraction, ENVI and LAStools. Together, these efforts have the potential to alleviate the manual burden associated with some of the most challenging and time-consuming geospatial processing tasks, with implications for improving our response to issues of global security, emergency management, and disaster response