Machine learning with missing data has been approached in two different ways, including feature imputation where missing feature values are estimated based on observed values and label prediction where downstream labels are learned directly from incomplete data. However, existing imputation models tend to have strong prior assumptions and cannot learn from downstream tasks, while models targeting label prediction often involve heuristics and can encounter scalability issues. Here we propose GRAPE, a graph-based framework for feature imputation as well as label prediction. GRAPE tackles the missing data problem using a graph representation, where the observations and features are viewed as two types of nodes in a bipartite graph, and the observed feature values as edges. Under the GRAPE framework, the feature imputation is formulated as an edge-level prediction task and the label prediction as a node-level prediction task. These tasks are then solved with Graph Neural Networks. Experimental results on nine benchmark datasets show that GRAPE yields 20% lower mean absolute error for imputation tasks and 10% lower for label prediction tasks, compared with existing state-of-the-art methods.
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On the Discrimination Risk of Mean Aggregation Feature Imputation in Graphs
In human networks, nodes belonging to a marginalized group often have a disproportionate rate of unknown or missing features. This, in conjunction with graph structure and known feature biases, can cause graph feature imputation algorithms to predict values for unknown features that make the marginalized group's feature values more distinct from the the dominant group's feature values than they are in reality. We call this distinction the discrimination risk. We prove that a higher discrimination risk can amplify the unfairness of a machine learning model applied to the imputed data. We then formalize a general graph feature imputation framework called mean aggregation imputation and theoretically and empirically characterize graphs in which applying this framework can yield feature values with a high discrimination risk. We propose a simple algorithm to ensure mean aggregation-imputed features provably have a low discrimination risk, while minimally sacrificing reconstruction error (with respect to the imputation objective). We evaluate the fairness and accuracy of our solution on synthetic and real-world credit networks.
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- Award ID(s):
- 1937599
- PAR ID:
- 10464919
- Date Published:
- Journal Name:
- 36th Conference on Neural Information Processing Systems (NeurIPS 2022)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
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