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Register a new userLearnt Sparsification for Interpretable Graph Neural Networks
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Added by
Mandeep Rathee
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Graph neural networks (GNNs) have achieved great success on various tasks and fields that require relational modeling. GNNs aggregate node features using the graph structure as inductive biases resulting in flexible and powerful models. However, GNNs remain hard to interpret as the interplay between node features and graph structure is only implicitly learned. In this paper, we propose a novel method called Kedge for explicitly sparsifying the underlying graph by removing unnecessary neighbors. Our key idea is based on a tractable method for sparsification using the Hard Kumaraswamy distribution that can be used in conjugation with any GNN model. Kedge learns edge masks in a modular fashion trained with any GNN allowing for gradient based optimization in an end-to-end fashion. We demonstrate through extensive experiments that our model Kedge can prune a large proportion of the edges with only a minor effect on the test accuracy. Specifically, in the PubMed dataset, Kedge learns to drop more than 80% of the edges with an accuracy drop of merely 2% showing that graph structure has only a small contribution in comparison to node features. Finally, we also show that Kedge effectively counters the over-smoothing phenomena in deep GNNs by maintaining good task performance with increasing GNN layers.
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The attention mechanism has demonstrated superior performance for inference over nodes in graph neural networks (GNNs), however, they result in a high computational burden during both training and inference. We propose FastGAT, a method to make attention based GNNs lightweight by using spectral sparsification to generate an optimal pruning of the input graph. This results in a per-epoch time that is almost linear in the number of graph nodes as opposed to quadratic. We theoretically prove that spectral sparsification preserves the features computed by the GAT model, thereby justifying our algorithm. We experimentally evaluate FastGAT on several large real world graph datasets for node classification tasks under both inductive and transductive settings. FastGAT can dramatically reduce (up to textbf{10x}) the computational time and memory requirements, allowing the usage of attention based GNNs on large graphs.
We show implicit filter level sparsity manifests in convolutional neural networks (CNNs) which employ Batch Normalization and ReLU activation, and are trained with adaptive gradient descent techniques and L2 regularization or weight decay. Through an extensive empirical study (Mehta et al., 2019) we hypothesize the mechanism behind the sparsification process, and find surprising links to certain filter sparsification heuristics proposed in literature. Emergence of, and the subsequent pruning of selective features is observed to be one of the contributing mechanisms, leading to feature sparsity at par or better than certain explicit sparsification / pruning approaches. In this workshop article we summarize our findings, and point out corollaries of selective-featurepenalization which could also be employed as heuristics for filter pruning
We investigate molecular mechanisms of resistant or sensitive response of cancer drug combination therapies in an inductive and interpretable manner. Though deep learning algorithms are widely used in the drug synergy prediction problem, it is still an open problem to formulate the prediction model with biological meaning to investigate the mysterious mechanisms of synergy (MoS) for the human-AI collaboration in healthcare systems. To address the challenges, we propose a deep graph neural network, IDSP (Interpretable Deep Signaling Pathways), to incorporate the gene-gene as well as gene-drug regulatory relationships in synergic drug combination predictions. IDSP automatically learns weights of edges based on the gene and drug node relations, i.e., signaling interactions, by a multi-layer perceptron (MLP) and aggregates information in an inductive manner. The proposed architecture generates interpretable drug synergy prediction by detecting important signaling interactions, and can be implemented when the underlying molecular mechanism encounters unseen genes or signaling pathways. We test IDWSP on signaling networks formulated by genes from 46 core cancer signaling pathways and drug combinations from NCI ALMANAC drug combination screening data. The experimental results demonstrated that 1) IDSP can learn from the underlying molecular mechanism to make prediction without additional drug chemical information while achieving highly comparable performance with current state-of-art methods; 2) IDSP show superior generality and flexibility to implement the synergy prediction task on both transductive tasks and inductive tasks. 3) IDSP can generate interpretable results by detecting different salient signaling patterns (i.e. MoS) for different cell lines.
The graph Laplacian regularization term is usually used in semi-supervised representation learning to provide graph structure information for a model $f(X)$. However, with the recent popularity of graph neural networks (GNNs), directly encoding graph structure $A$ into a model, i.e., $f(A, X)$, has become the more common approach. While we show that graph Laplacian regularization brings little-to-no benefit to existing GNNs, and propose a simple but non-trivial variant of graph Laplacian regularization, called Propagation-regularization (P-reg), to boost the performance of existing GNN models. We provide formal analyses to show that P-reg not only infuses extra information (that is not captured by the traditional graph Laplacian regularization) into GNNs, but also has the capacity equivalent to an infinite-depth graph convolutional network. We demonstrate that P-reg can effectively boost the performance of existing GNN models on both node-level and graph-level tasks across many different datasets.
Weight pruning is an effective technique to reduce the model size and inference time for deep neural networks in real-world deployments. However, since magnitudes and relative importance of weights are very different for different layers of a neural network, existing methods rely on either manual tuning or handcrafted heuristic rules to find appropriate pruning rates individually for each layer. This approach generally leads to suboptimal performance. In this paper, by directly working on the probability space, we propose an effective network sparsification method called {it probabilistic masking} (ProbMask), which solves a natural sparsification formulation under global sparsity constraint. The key idea is to use probability as a global criterion for all layers to measure the weight importance. An appealing feature of ProbMask is that the amounts of weight redundancy can be learned automatically via our constraint and thus we avoid the problem of tuning pruning rates individually for different layers in a network. Extensive experimental results on CIFAR-10/100 and ImageNet demonstrate that our method is highly effective, and can outperform previous state-of-the-art methods by a significant margin, especially in the high pruning rate situation. Notably, the gap of Top-1 accuracy between our ProbMask and existing methods can be up to 10%. As a by-product, we show ProbMask is also highly effective in identifying supermasks, which are subnetworks with high performance in a randomly weighted dense neural network.
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