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1. A Quotient Space Formulation for Generative Statistical Analysis of Graphical Data

   https://doi.org/10.1007%2Fs10851-021-01027-1  

   Guo, X.; Srivastava, A.; Sarkar, S (March 2021, Journal of mathematical imaging and vision)

   null (Ed.)

   Complex analyses involving multiple, dependent random quantities often lead to graphical models—a set of nodes denoting variables of interest, and corresponding edges denoting statistical interactions between nodes. To develop statistical analyses for graphical data, especially towards generative modeling, one needs mathematical representations and metrics for matching and comparing graphs, and subsequent tools, such as geodesics, means, and covariances. This paper utilizes a quotient structure to develop efficient algorithms for computing these quantities, leading to useful statistical tools, including principal component analysis, statistical testing, and modeling. We demonstrate the efficacy of this framework using datasets taken from several problem areas, including letters, biochemical structures, and social networks. 

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2. Can Language Models Solve Graph Problems in Natural Language?

   Wang, Heng; Feng, Shangbin; He, Tianxing; Tan, Zhaoxuan; Han, Xiaochuang; Tsvetkov, Yulia (December 2023, Conference on Neural Information Processing Systems)

   Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. 

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3. Inference of regulatory networks through temporally sparse data

   https://doi.org/10.3389/fcteg.2022.1017256  

   Alali, Mohammad; Imani, Mahdi (December 2022, Frontiers in Control Engineering)

   A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses, including diagnosis or prognosis of diseases and finding effective treatments for chronic diseases such as cancer. Boolean networks have emerged as a successful class of models for capturing the behavior of GRNs. In most practical settings, inference of GRNs should be achieved through limited and temporally sparse genomics data. A large number of genes in GRNs leads to a large possible topology candidate space, which often cannot be exhaustively searched due to the limitation in computational resources. This paper develops a scalable and efficient topology inference for GRNs using Bayesian optimization and kernel-based methods. Rather than an exhaustive search over possible topologies, the proposed method constructs a Gaussian Process (GP) with a topology-inspired kernel function to account for correlation in the likelihood function. Then, using the posterior distribution of the GP model, the Bayesian optimization efficiently searches for the topology with the highest likelihood value by optimally balancing between exploration and exploitation. The performance of the proposed method is demonstrated through comprehensive numerical experiments using a well-known mammalian cell-cycle network. 

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4. 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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5. Generalization of graph network inferences in higher-order graphical models

   https://doi.org/10.1007/s41468-023-00147-4  

   Fei, Yicheng; Pitkow, Xaq (November 2023, Journal of Applied and Computational Topology)

   Abstract Probabilistic graphical models provide a powerful tool to describe complex statistical structure, with many real-world applications in science and engineering from controlling robotic arms to understanding neuronal computations. A major challenge for these graphical models is that inferences such as marginalization are intractable for general graphs. These inferences are often approximated by a distributed message-passing algorithm such as Belief Propagation, which does not always perform well on graphs with cycles, nor can it always be easily specified for complex continuous probability distributions. Such difficulties arise frequently in expressive graphical models that include intractable higher-order interactions. In this paper we define the Recurrent Factor Graph Neural Network (RF-GNN) to achieve fast approximate inference on graphical models that involve many-variable interactions. Experimental results on several families of graphical models demonstrate the out-of-distribution generalization capability of our method to different sized graphs, and indicate the domain in which our method outperforms Belief Propagation (BP). Moreover, we test the RF-GNN on a real-world Low-Density Parity-Check dataset as a benchmark along with other baseline models including BP variants and other GNN methods. Overall we find that RF-GNNs outperform other methods under high noise levels. 

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