Graph machine learning

Graphs are a natural way to represent data from various domains such as social networks, molecules, text, code, etc. We develop and analyze algorithms for graph-structured data.

Area 6. Graph machine learning.svg

Posts

Publications

  • A Critical Look at the Evaluation of GNNs under Heterophily: Are We Really Making Progress?

    Graph machine learning
    Oleg Platonov
    Denis Kuznedelev
    Michael Diskin
    Artem Babenko
    Liudmila Prokhorenkova
    ICLR,
    2023

    Node classification is a classical graph representation learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs

  • Graph-based Nearest Neighbor Search in Hyperbolic Spaces

    RepresentationsMachine learning theoryGraph machine learningNearest neighbor search
    Liudmila Prokhorenkova
    Dmitry Baranchuk
    Nikolay Bogachev
    Yury Demidovich
    Alexander Kolpakov
    ICLR,
    2022

    The nearest neighbor search (NNS) problem is widely studied in Euclidean space, and graph-based algorithms are known to outperform other approaches for this task. However, hyperbolic geometry often allows for better data representation in various domains, including graphs, words, and images. In this paper, we show that graph-based approaches are also well suited for hyperbolic geometry. From a theoretical perspective, we rigorously analyze the time and space complexity of graph-based NNS, assuming that an n-element dataset is uniformly distributed within a d-dimensional ball of radius R in the hyperbolic space of curvature -1. Under some conditions on R and d, we derive the time and space complexity of graph-based NNS and compare the obtained results with known guarantees for the Euclidean case. Interestingly, in the dense setting (d << log(n)) and under some assumptions on the radius R, graph-based NNS has lower time complexity in the hyperbolic space. This agrees with our experiments: we consider datasets embedded in hyperbolic and Euclidean spaces and show that graph-based NNS can be more efficient in the hyperbolic space. We also demonstrate that graph-based methods outperform other existing baselines for hyperbolic NNS. Overall, our theoretical and empirical analysis suggests that graph-based NNS can be considered a default approach for similarity search in hyperbolic spaces.

  • Overlapping Spaces for Compact Graph Representations

    RepresentationsGraph machine learning
    Kirill Shevkunov
    Liudmila Prokhorenkova
    NeurIPS,
    2021

    Various non-trivial spaces are becoming popular for embedding structured data such as graphs, texts, or images. Following spherical and hyperbolic spaces, more general product spaces have been proposed. However, searching for the best configuration of a product space is a resource-intensive procedure, which reduces the practical applicability of the idea. We generalize the concept of product space and introduce an overlapping space that does not have the configuration search problem. The main idea is to allow subsets of coordinates to be shared between spaces of different types (Euclidean, hyperbolic, spherical). As a result, we often need fewer coordinates to store the objects. Additionally, we propose an optimization algorithm that automatically learns the optimal configuration. Our experiments confirm that overlapping spaces outperform the competitors in graph embedding tasks with different evaluation metrics. We also perform an empirical analysis in a realistic information retrieval setup, where we compare all spaces by incorporating them into DSSM. In this case, the proposed overlapping space consistently achieves nearly optimal results without any configuration tuning. This allows for reducing training time, which can be essential in large-scale applications.

Datasets

  • Heterophilous graph datasets

    Graph machine learning
    Oleg Platonov
    Denis Kuznedelev
    Michael Diskin
    Artem Babenko
    Liudmila Prokhorenkova

    A graph dataset is called heterophilous if nodes prefer to connect to other nodes that are not similar to them. For example, in financial transaction networks, fraudsters often perform transactions with non-fraudulent users, and in dating networks, most connections are between people of opposite genders. Learning under heterophily is an important subfield of graph ML. Thus, having diverse and reliable benchmarks is essential.

    We propose a benchmark of five diverse heterophilous graphs that come from different domains and exhibit a variety of structural properties. Our benchmark includes a word dependency graph Roman-empire, a product co-purchasing network Amazon-ratings, a synthetic graph emulating the minesweeper game Minesweeper, a crowdsourcing platform worker network Tolokers, and a question-answering website interaction network Questions.