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1. A comparison of statistical relational learning and graph neural networks for aggregate graph queries

   https://doi.org/10.1007/s10994-021-06007-5  

   Embar, Varun; Srinivasan, Sriram; Getoor, Lise (June 2021, Machine Learning)

   Abstract Statistical relational learning (SRL) and graph neural networks (GNNs) are two powerful approaches for learning and inference over graphs. Typically, they are evaluated in terms of simple metrics such as accuracy over individual node labels. Complexaggregate graph queries(AGQ) involving multiple nodes, edges, and labels are common in the graph mining community and are used to estimate important network properties such as social cohesion and influence. While graph mining algorithms support AGQs, they typically do not take into account uncertainty, or when they do, make simplifying assumptions and do not build full probabilistic models. In this paper, we examine the performance of SRL and GNNs on AGQs over graphs with partially observed node labels. We show that, not surprisingly, inferring the unobserved node labels as a first step and then evaluating the queries on the fully observed graph can lead to sub-optimal estimates, and that a better approach is to compute these queries as an expectation under the joint distribution. We propose a sampling framework to tractably compute the expected values of AGQs. Motivated by the analysis of subgroup cohesion in social networks, we propose a suite of AGQs that estimate the community structure in graphs. In our empirical evaluation, we show that by estimating these queries as an expectation, SRL-based approaches yield up to a 50-fold reduction in average error when compared to existing GNN-based approaches. 

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2. An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation

   https://doi.org/10.1093/bioinformatics/btac142  

   Almodaresi, Fatemeh; Khan, Jamshed; Madaminov, Sergey; Ferdman, Michael; Johnson, Rob; Pandey, Prashant; Patro, Rob; Boeva, ed., Valentina (March 2022, Bioinformatics)

   Abstract MotivationIn the past few years, researchers have proposed numerous indexing schemes for searching large datasets of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes—Mantis, VariMerge and Bifrost—that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data. ResultsIn this paper, we show how to build a scalable and updatable exact raw sequence-search index. Specifically, we extend Mantis using the Bentley–Saxe transformation to support efficient updates, called Dynamic Mantis. We demonstrate Dynamic Mantis’s scalability by constructing an index of ≈40K samples from SRA by adding samples one at a time to an initial index of 10K samples. Compared to VariMerge and Bifrost, Dynamic Mantis is more efficient in terms of index-construction time and memory, query time and memory and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Dynamic Mantis scaled to more than 39K samples. Queries were over 24× faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Dynamic Mantis indexes were about 2.5× smaller than Bifrost’s indexes and about half as big as VariMerge’s indexes. Availability and implementationDynamic Mantis implementation is available at https://github.com/splatlab/mantis/tree/mergeMSTs. Supplementary informationSupplementary data are available at Bioinformatics online. 

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3. Compression algorithm for colored de Bruijn graphs

   https://doi.org/10.1186/s13015-024-00254-6  

   Rahman, Amatur; Dufresne, Yoann; Medvedev, Paul (December 2024, Algorithms for Molecular Biology)

   Abstract A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead. The software is available athttp://github.com/medvedevgroup/ESSColor. 

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4. Combining Graph Convolutional Neural Networks and Label Propagation

   https://doi.org/10.1145/3490478  

   Wang, Hongwei; Leskovec, Jure (October 2022, ACM Transactions on Information Systems)

   Label Propagation Algorithm (LPA) and Graph Convolutional Neural Networks (GCN) are both message passing algorithms on graphs. Both solve the task of node classification, but LPA propagates node label information across the edges of the graph, while GCN propagates and transforms node feature information. However, while conceptually similar, theoretical relationship between LPA and GCN has not yet been systematically investigated. Moreover, it is unclear how LPA and GCN can be combined under a unified framework to improve the performance. Here we study the relationship between LPA and GCN in terms of feature/label influence , in which we characterize how much the initial feature/label of one node influences the final feature/label of another node in GCN/LPA. Based on our theoretical analysis, we propose an end-to-end model that combines GCN and LPA. In our unified model, edge weights are learnable, and the LPA serves as regularization to assist the GCN in learning proper edge weights that lead to improved performance. Our model can also be seen as learning the weights of edges based on node labels, which is more direct and efficient than existing feature-based attention models or topology-based diffusion models. In a number of experiments for semi-supervised node classification and knowledge-graph-aware recommendation, our model shows superiority over state-of-the-art baselines. 

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5. GraphZip: Mining Graph Streams using Dictionary-based Compression

   Packer, Charles; Holder, Lawrence B (August 2017, SIGKDD Workshop on Mining and Learning in Graphs (MLG))

   A massive amount of data generated today on platforms such as social networks, telecommunication networks, and the internet in general can be represented as graph streams. Activity in a network’s underlying graph generates a sequence of edges in the form of a stream; for example, a social network may generate a graph stream based on the interactions (edges) between different users (nodes) over time. While many graph mining algorithms have already been developed for analyzing relatively small graphs, graphs that begin to approach the size of real-world networks stress the limitations of such methods due to their dynamic nature and the substantial number of nodes and connections involved. In this paper we present GraphZip, a scalable method for mining interesting patterns in graph streams. GraphZip is inspired by the Lempel-Ziv (LZ) class of compression algorithms, and uses a novel dictionary-based compression approach to discover maximally- compressing patterns in a graph stream. We experimentally show that GraphZip is able to retrieve complex and insightful patterns from large real-world graphs and artificially-generated graphs with ground truth patterns. Additionally, our results demonstrate that GraphZip is both highly efficient and highly effective compared to existing state-of-the-art methods for mining graph streams. 

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