An official website of the United States government
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.
more »
« less
Fairness without Imputation: A Decision Tree Approach for Fair Prediction with Missing Values
We investigate the fairness concerns of training a machine learning model using data with missing values. Even though there are a number of fairness intervention methods in the literature, most of them require a complete training set as input. In practice, data can have missing values, and data missing patterns can depend on group attributes (e.g. gender or race). Simply applying off-the-shelf fair learning algorithms to an imputed dataset may lead to an unfair model. In this paper, we first theoretically analyze different sources of discrimination risks when training with an imputed dataset. Then, we propose an integrated approach based on decision trees that does not require a separate process of imputation and learning. Instead, we train a tree with missing incorporated as attribute (MIA), which does not require explicit imputation, and we optimize a fairness-regularized objective function. We demonstrate that our approach outperforms existing fairness intervention methods applied to an imputed dataset, through several experiments on real-world datasets.
more »
« less
- PAR ID:
- 10339230
- Date Published:
- Journal Name:
- Proceedings of the AAAI Conference on Artificial Intelligence
- Volume:
- 36
- Issue:
- 9
- ISSN:
- 2159-5399
- Page Range / eLocation ID:
- 9558 to 9566
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Genotype imputation, where missing genotypes can be computationally imputed, is an essential tool in genomic analysis ranging from genome wide associations to phenotype prediction. Traditional genotype imputation methods are typically based on haplotype-clustering algorithms, hidden Markov models (HMMs), and statistical inference. Deep learning-based methods have been recently reported to suitably address the missing data problems in various fields. To explore the performance of deep learning for genotype imputation, in this study, we propose a deep model called a sparse convolutional denoising autoencoder (SCDA) to impute missing genotypes. We constructed the SCDA model using a convolutional layer that can extract various correlation or linkage patterns in the genotype data and applying a sparse weight matrix resulted from the L1 regularization to handle high dimensional data. We comprehensively evaluated the performance of the SCDA model in different scenarios for genotype imputation on the yeast and human genotype data, respectively. Our results showed that SCDA has strong robustness and significantly outperforms popular reference-free imputation methods. This study thus points to another novel application of deep learning models for missing data imputation in genomic studies.more » « less
-
Regional morphological analysis represents a crucial step in most neuroimaging studies. Results from brain segmentation techniques are intrinsically prone to certain degrees of variability, mainly as results of suboptimal segmentation. To reduce this inherent variability, the errors are often identified through visual inspection and then corrected (semi)manually. Identification and correction of incorrect segmentation could be very expensive for large-scale studies. While identification of the incorrect results can be done relatively fast even with manual inspection, the correction step is extremely time-consuming, as it requires training staff to perform laborious manual corrections. Here we frame the correction phase of this problem as a missing data problem. Instead of manually adjusting the segmentation outputs, our computational approach aims to derive accurate morphological measures by machine learning imputation. Data imputation techniques may be used to replace missing or incorrect region average values with carefully chosen imputed values, all of which are computed based on other available multivariate informa- tion. We examined our approach of correcting segmentation outputs on a cohort of 970 subjects, which were undergone an extensive, time-consuming, manual post-segmentation correction. A random forest imputation technique recovered the gold standard results with a significant accuracy (r = 0.93, p < 0.0001; when 30% of the segmentations were considered incorrect in a non-random fashion). The random forest technique proved to be most effective for big data studies (N > 250).more » « less
-
This paper develops a query-time missing value imputation framework, entitled ZIP, that modifies relational operators to be imputation aware in order to minimize the joint cost of imputing and query processing. The modified operators use a cost-based decision function to determine whether to invoke imputation or to defer to downstream operators to resolve missing values. The modified query processing logic ensures results with deferred imputations are identical to those produced if all missing values were imputed first. ZIP includes a novel outer-join based approach to preserve missing values during execution, and a bloom filter based index to optimize the space and running overhead. Extensive experiments on both real and synthetic data sets demonstrate 10 to 25 times improvement when augmenting the state-of-the-art technology, ImputeDB, with ZIP-based deferred imputation. ZIP also outperforms the offline approach by up to 19607 times in a real data set.more » « less
-
Abstract Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplete, a deep learning-based imputation method to impute or ‘fill-in’ missing phenotypes in population-scale biobank datasets. When applied to collections of phenotypes measured across ~300,000 individuals from the UK Biobank, AutoComplete substantially improved imputation accuracy over existing methods. On three traits with notable amounts of missingness, we show that AutoComplete yields imputed phenotypes that are genetically similar to the originally observed phenotypes while increasing the effective sample size by about twofold on average. Further, genome-wide association analyses on the resulting imputed phenotypes led to a substantial increase in the number of associated loci. Our results demonstrate the utility of deep learning-based phenotype imputation to increase power for genetic discoveries in existing biobank datasets.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1609/aaai.v36i9.21189
