Missing Value Imputation With Unsupervised Backpropagation

Many data mining and data analysis techniques operate on dense matrices or complete tables of data. Real-world data sets, however, often contain unknown values. Even many classification algorithms that are designed to operate with missing values still exhibit deteriorated accuracy. One approach to handling missing values is to fill in (impute) the missing values. In this paper, we present a technique for unsupervised learning called Unsupervised Backpropagation (UBP), which trains a multi-layer perceptron to fit to the manifold sampled by a set of observed point-vectors. We evaluate UBP with the task of imputing missing values in datasets, and show that UBP is able to predict missing values with significantly lower sum-squared error than other collaborative filtering and imputation techniques. We also demonstrate with 24 datasets and 9 supervised learning algorithms that classification accuracy is usually higher when randomly-withheld values are imputed using UBP, rather than with other methods

Recommending Learning Algorithms and Their Associated Hyperparameters

The success of machine learning on a given task dependson, among other things, which learning algorithm is selected and its associated hyperparameters. Selecting an appropriate learning algorithm and setting its hyperparameters for a given data set can be a challenging task, especially for users who are not experts in machine learning. Previous work has examined using meta-features to predict which learning algorithm and hyperparameters should be used. However, choosing a set of meta-features that are predictive of algorithm performance is difficult. Here, we propose to apply collaborative filtering techniques to learning algorithm and hyperparameter selection, and find that doing so avoids determining which meta-features to use and outperforms traditional meta-learning approaches in many cases.Comment: Short paper--2 pages, 2 table

Simultaneous Measurement Imputation and Outcome Prediction for Achilles Tendon Rupture Rehabilitation

Achilles Tendon Rupture (ATR) is one of the typical soft tissue injuries. Rehabilitation after such a musculoskeletal injury remains a prolonged process with a very variable outcome. Accurately predicting rehabilitation outcome is crucial for treatment decision support. However, it is challenging to train an automatic method for predicting the ATR rehabilitation outcome from treatment data, due to a massive amount of missing entries in the data recorded from ATR patients, as well as complex nonlinear relations between measurements and outcomes. In this work, we design an end-to-end probabilistic framework to impute missing data entries and predict rehabilitation outcomes simultaneously. We evaluate our model on a real-life ATR clinical cohort, comparing with various baselines. The proposed method demonstrates its clear superiority over traditional methods which typically perform imputation and prediction in two separate stages

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues