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1. QA-GNN: Reasoning with Language Models and Knowledge Graphs for Question Answering

   Yasunaga, Michihiro ; Ren, Hongyu ; Bosselut, Antoine ; Liang, Percy ; Leskovec, Jure ( January 2021 , North American Chapter of the Association for Computational Linguistics (NAACL))

   null (Ed.)

   The problem of answering questions using knowledge from pre-trained language models (LMs) and knowledge graphs (KGs) presents two challenges: given a QA context (question and answer choice), methods need to (i) identify relevant knowledge from large KGs, and (ii) perform joint reasoning over the QA context and KG. Here we propose a new model, QA-GNN, which addresses the above challenges through two key innovations: (i) relevance scoring, where we use LMs to estimate the importance of KG nodes relative to the given QA context, and (ii) joint reasoning, where we connect the QA context and KG to form a joint graph, and mutually update their representations through graph-based message passing. We evaluate QA-GNN on the CommonsenseQA and OpenBookQA datasets, and show its improvement over existing LM and LM+KG models, as well as its capability to perform interpretable and structured reasoning, e.g., correctly handling negation in questions. 

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2. Efficient Contrastive Learning for Fast and Accurate Inference on Graphs

   Xiao, Teng ; Zhu, Huaisheng ; Zhang, Zhiwei ; Guo, Zhimeng ; Aggarwal, Charu C ; Wang, Suhang ; Honavar, Vasant G ( July 2024 , Proceedings of Machine Learning Research: International Conference on Machine Learning)

   Graph contrastive learning has made remarkable advances in settings where there is a scarcity of task-specific labels. Despite these advances, the significant computational overhead for representation inference incurred by existing methods that rely on intensive message passing makes them unsuitable for latency-constrained applications. In this paper, we present GraphECL, a simple and efficient contrastive learning method for fast inference on graphs. GraphECL does away with the need for expensive message passing during inference. Specifically, it introduces a novel coupling of the MLP and GNN models, where the former learns to computationally efficiently mimic the computations performed by the latter. We provide a theoretical analysis showing why MLP can capture essential structural information in neighbors well enough to match the performance of GNN in downstream tasks. The extensive experiments on widely used real-world benchmarks that show that GraphECL achieves superior performance and inference efficiency compared to state-of-the-art graph constrastive learning (GCL) methods on homophilous and heterophilous graphs. Code is available at: https: //github.com/tengxiao1/GraphECL. 

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3. High dimensional, tabular deep learning with an auxiliary knowledge graph

   Ruiz, Camilo ; Ren, Hongyu ; Huang, Kexin ; Leskovec, Jure ( December 2023 , Advances in neural information processing systems)

   Machine learning models exhibit strong performance on datasets with abundant labeled samples. However, for tabular datasets with extremely high d-dimensional features but limited n samples (i.e. d ≫ n), machine learning models struggle to achieve strong performance due to the risk of overfitting. Here, our key insight is that there is often abundant, auxiliary domain information describing input features which can be structured as a heterogeneous knowledge graph (KG). We propose PLATO, a method that achieves strong performance on tabular data with d ≫ n by using an auxiliary KG describing input features to regularize a multilayer perceptron (MLP). In PLATO, each input feature corresponds to a node in the auxiliary KG. In the MLP’s first layer, each input feature also corresponds to a weight vector. PLATO is based on the inductive bias that two input features corresponding to similar nodes in the auxiliary KG should have similar weight vectors in the MLP’s first layer. PLATO captures this inductive bias by inferring the weight vector for each input feature from its corresponding node in the KG via a trainable message-passing function. Across 6 d ≫ n datasets, PLATO outperforms 13 state-of-the-art baselines by up to 10.19%. 

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4. Long Range Graph Benchmark

   Dwivedi, Vijay Prakash ; Rampasek, Ladislav ; Galkin, Michael ; Parviz, Ali ; Wolf, Guy ; Luu, Anh Tuan ; Beaini, Dominique ( December 2022 , NeurIPS)

   Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB)1 with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI. 

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5. Learning local equivariant representations for large-scale atomistic dynamics

   https://doi.org/10.1038/s41467-023-36329-y  

   Musaelian, Albert ; Batzner, Simon ; Johansson, Anders ; Sun, Lixin ; Owen, Cameron J. ; Kornbluth, Mordechai ; Kozinsky, Boris ( February 2023 , Nature Communications)

   A simultaneously accurate and computationally efficient parametrization of the potential energy surface of molecules and materials is a long-standing goal in the natural sciences. While atom-centered message passing neural networks (MPNNs) have shown remarkable accuracy, their information propagation has limited the accessible length-scales. Local methods, conversely, scale to large simulations but have suffered from inferior accuracy. This work introduces Allegro, a strictly local equivariant deep neural network interatomic potential architecture that simultaneously exhibits excellent accuracy and scalability. Allegro represents a many-body potential using iterated tensor products of learned equivariant representations without atom-centered message passing. Allegro obtains improvements over state-of-the-art methods on QM9 and revMD17. A single tensor product layer outperforms existing deep MPNNs and transformers on QM9. Furthermore, Allegro displays remarkable generalization to out-of-distribution data. Molecular simulations using Allegro recover structural and kinetic properties of an amorphous electrolyte in excellent agreement with ab-initio simulations. Finally, we demonstrate parallelization with a simulation of 100 million atoms.

    

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