Graph (abstract data type) | EPFL Graph Search

In computer science, a graph is an abstract data type that is meant to implement the undirected graph and directed graph concepts from the field of graph theory within mathematics. A graph data structure consists of a finite (and possibly mutable) set of vertices (also called nodes or points), together with a set of unordered pairs of these vertices for an undirected graph or a set of ordered pairs for a directed graph. These pairs are known as edges (also called links or lines), and for a directed graph are also known as edges but also sometimes arrows or arcs. The vertices may be part of the graph structure, or may be external entities represented by integer indices or references. A graph data structure may also associate to each edge some edge value, such as a symbolic label or a numeric attribute (cost, capacity, length, etc.). Operations The basic operations provided by a graph data structure G usually include:

: tests whether there is an edge from the vertex x to

Graph Representation Learning with Optimal Transport: Analysis and Applications

Effrosyni Simou

In several machine learning settings, the data of interest are well described by graphs. Examples include data pertaining to transportation networks or social networks. Further, biological data, such as proteins or molecules, lend themselves well to graph-structured descriptions. In such settings, it is desirable to design representation learning algorithms that can take into account the information captured by the underlying structure. This thesis focuses on providing new methods to ingrain geometrical information in end-to-end deep learning architectures for graphs through the use of elements from Optimal Transport theory.First, we consider the setting where the data can be described by a fixed graph. In this setting, each datapoint corresponds to a node of the graph and the edges among nodes signify their pairwise relations. We propose an autoencoder architecture that consists of a linear layer in the encoder and a novel Wasserstein barycentric layer at the decoder. Our proposed barycentric layer takes into account the underlying geometry through the diffusion distance of the graph and provides a way to obtain structure-aware, non-linear interpolations, which lead to directly interpretable node embeddings that are stable to perturbations of the graph structure. Further, the embeddings obtained with our proposed autoencoder achieve competitive or superior results compared to state-of-the-art methods in node classification tasks.Second, we consider the setting where the data consist of multiple graphs. In that setting, the graphs can be of varying size and, therefore, a global pooling operation is needed in order to obtain representations of fixed size and enable end-to-end learning with deep networks. We propose a global pooling operation that optimally preserves the statistical properties of the representations. In order to do so, we take into account the geometry of the representation space and introduce a global pooling layer that minimizes the Wasserstein distance between a graph representation and its pooled counterpart, of fixed size. This is achieved by performing a Wasserstein gradient flow with respect to the pooled representation. Our proposed method demonstrates promising results in the task of graph classification.Overall, in this thesis we provide new methods for incorporating geometrical information in end-to-end deep learning architectures for graph structured data. We believe that our proposals will contribute to the development of algorithms that learn meaningful representations and that take fully into account the geometry of the data under consideration.

EPFL2022

Graph Signal Processing

Ntorina Thanou

Over the past few decades we have been experiencing an explosion of information generated by large networks of sensors and other data sources. Much of this data is intrinsically structured, such as traffic evolution in a transportation network, temperature values in different geographical locations, information diffusion in social networks, functional activities in the brain, or 3D meshes in computer graphics. The representation, analysis, and compression of such data is a challenging task and requires the development of new tools that can identify and properly exploit the data structure. In this thesis, we formulate the processing and analysis of structured data using the emerging framework of graph signal processing. Graphs are generic data representation forms, suitable for modeling the geometric structure of signals that live on topologically complicated domains. The vertices of the graph represent the discrete data domain, and the edge weights capture the pairwise relationships between the vertices. A graph signal is then defined as a function that assigns a real value to each vertex. Graph signal processing is a useful framework for handling efficiently such data as it takes into consideration both the signal and the graph structure. In this work, we develop new methods and study several important problems related to the representation and structure-aware processing of graph signals in both centralized and distributed settings. We focus in particular in the theory of sparse graph signal representation and its applications and we bring some insights towards better understanding the interplay between graphs and signals on graphs. First, we study a novel yet natural application of the graph signal processing framework for the representation of 3D point cloud sequences. We exploit graph-based transform signal representations for addressing the challenging problem of compression of data that is characterized by dynamic 3D positions and color attributes. Next, we depart from graph-based transform signal representations to design new overcomplete representations, or dictionaries, which are adapted to specific classes of graph signals. In particular, we address the problem of sparse representation of graph signals residing on weighted graphs by learning graph structured dictionaries that incorporate the intrinsic geometric structure of the irregular data domain and are adapted to the characteristics of the signals. Then, we move to the efficient processing of graph signals in distributed scenarios, such as sensor or camera networks, which brings important constraints in terms of communication and computation in realistic settings. In particular, we study the effect of quantization in the distributed processing of graph signals that are represented by graph spectral dictionaries and we show that the impact of the quantization depends on the graph geometry and on the structure of the spectral dictionaries. Finally, we focus on a widely used graph process, the problem of distributed average consensus in a sensor network where sensors exchange quantized information with their neighbors. We propose a novel quantization scheme that depends on the graph topology and exploits the increasing correlation between the values exchanged by the sensors throughout the iterations of the consensus algorithm.

EPFL2016

FlowPool: Pooling Graph Representations with Wasserstein Gradient Flows

Effrosyni Simou

In several machine learning tasks for graph structured data, the graphs under consideration may be composed of a varying number of nodes. Therefore, it is necessary to design pooling methods that aggregate the graph representations of varying size to representations of fixed size which can be used in downstream tasks, such as graph classification. Existing graph pooling methods offer no guarantee with regards to the similarity of a graph representation and its pooled version. In this work we address this limitation by proposing FlowPool, a pooling method that optimally preserves the statistics of a graph representation to its pooled counterpart by minimizing their Wasserstein distance. This is achieved by performing a Wasserstein gradient flow with respect to the pooled graph representation. We propose a versatile implementation of our method which can take into account the geometry of the representation space through any ground cost. This implementation relies on the computation of the gradient of the Wasserstein distance with recently proposed implicit differentiation schemes. Our pooling method is amenable to automatic differentiation and can be integrated in end-to-end deep learning architectures. Further, FlowPool is invariant to permutations and can therefore be combined with permutation equivariant feature extraction layers in GNNs in order to obtain predictions that are independent of the ordering of the nodes. Experimental results demonstrate that our method leads to an increase in performance compared to existing pooling methods when evaluated in graph classification tasks.

2021

Graph Signal Processing

Ntorina Thanou

EPFL2016

Graph Representation Learning with Optimal Transport: Analysis and Applications

Effrosyni Simou

EPFL2022