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  1. Hierarchical relations are prevalent and indispensable for organizing human knowledge captured by a knowledge graph (KG). The key property of hierarchical relations is that they induce a partial ordering over the entities, which needs to be modeled in order to allow for hierarchical reasoning. However, current KG embeddings can model only a single global hierarchy (single global partial ordering) and fail to model multiple heterogeneous hierarchies that exist in a single KG. Here we present ConE (Cone Embedding), a KG embedding model that is able to simultaneously model multiple hierarchical as well as non-hierarchical relations in a knowledge graph. ConEmore »embeds entities into hyperbolic cones and models relations as transformations between the cones. In particular, ConE uses cone containment constraints in different subspaces of the hyperbolic embedding space to capture multiple heterogeneous hierarchies. Experiments on standard knowledge graph benchmarks show that ConE obtains state-of-the-art performance on hierarchical reasoning tasks as well as knowledge graph completion task on hierarchical graphs. In particular, our approach yields new state-of-the-art Hits@1 of 45.3% on WN18RR and 16.1% on DDB14 (0.231 MRR). As for hierarchical reasoning task, our approach outperforms previous best results by an average of 20% across the three datasets.« less
    Free, publicly-accessible full text available December 6, 2022
  2. The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 38% reduction in embedding RMSE against the best competing geometry. The capacity of themore »framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.« less
    Free, publicly-accessible full text available December 6, 2022
  3. Graph Neural Networks (GNNs) are based on repeated aggregations of information from nodes’ neighbors in a graph. However, because nodes share many neighbors, a naive implementation leads to repeated and inefficient aggregations and represents significant computational overhead. Here we propose Hierarchically Aggregated computation Graphs (HAGs), a new GNN representation technique that explicitly avoids redundancy by managing intermediate aggregation results hierarchically and eliminates repeated computations and unnecessary data transfers in GNN training and inference. HAGs perform the same computations and give the same models/accuracy as traditional GNNs, but in a much shorter time due to optimized computations. To identify redundant computations,more »we introduce an accurate cost function and use a novel search algorithm to find optimized HAGs. Experiments show that the HAG representation significantly outperforms the standard GNN by increasing the end-to-end training throughput by up to 2.8× and reducing the aggregations and data transfers in GNN training by up to 6.3× and 5.6×, with only 0.1% memory overhead. Overall, our results represent an important advancement in speeding-up and scaling-up GNNs without any loss in model predictive performance.« less
  4. Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework—which we term “Graph Network-based Simulators” (GNS)—represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model wasmore »robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.« less
  5. Graph convolutional neural networks (GCNs) embed nodes in a graph into Euclidean space, which has been shown to incur a large distortion when embedding real-world graphs with scale-free or hierarchical structure. Hyperbolic geometry offers an exciting alternative, as it enables embeddings with much smaller distortion. However, extending GCNs to hyperbolic geometry presents several unique challenges because it is not clear how to define neural network operations, such as feature transformation and aggregation, in hyperbolic space. Furthermore, since input features are often Euclidean, it is unclear how to transform the features into hyperbolic embeddings with the right amount of curvature. Heremore »we propose Hyperbolic Graph Convolutional Neural Network (HGCN), the first inductive hyperbolic GCN that leverages both the expressiveness of GCNs and hyperbolic geometry to learn inductive node representations for hierarchical and scale-free graphs. We derive GCNs operations in the hyperboloid model of hyperbolic space and map Euclidean input features to embeddings in hyperbolic spaces with different trainable curvature at each layer. Experiments demonstrate that HGCN learns embeddings that preserve hierarchical structure, and leads to improved performance when compared to Euclidean analogs, even with very low dimensional embeddings: compared to state-of-the-art GCNs, HGCN achieves an error reduction of up to 63.1% in ROC AUC for link prediction and of up to 47.5% in F1 score for node classification, also improving state-of-the art on the PubMed dataset.« less
  6. Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models and explaining predictions made by GNNs remains unsolved. Here we propose GNNEXPLAINER, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNEXPLAINER identifies a compact subgraph structure and a small subset of node features that have a crucial role inmore »GNN’s prediction. Further, GNNEXPLAINER can generate consistent and concise explanations for an entire class of instances. We formulate GNNEXPLAINER as an optimization task that maximizes the mutual information between a GNN’s prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms alternative baseline approaches by up to 43.0% in explanation accuracy. GNNEXPLAINER provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.« less