Trimmed Density Ratio Estimation

Density ratio estimation is a vital tool in both machine learning and statistical community. However, due to the unbounded nature of density ratio, the estimation procedure can be vulnerable to corrupted data points, which often pushes the estimated ratio toward infinity. In this paper, we present a robust estimator which automatically identifies and trims outliers. The proposed estimator has a convex formulation, and the global optimum can be obtained via subgradient descent. We analyze the parameter estimation error of this estimator under high-dimensional settings. Experiments are conducted to verify the effectiveness of the estimator.Comment: Made minor revisions. Restructured the introductory section

Trimming Stability Selection increases variable selection robustness

Contamination can severely distort an estimator unless the estimation procedure is suitably robust. This is a well-known issue and has been addressed in Robust Statistics, however, the relation of contamination and distorted variable selection has been rarely considered in literature. As for variable selection, many methods for sparse model selection have been proposed, including the Stability Selection which is a meta-algorithm based on some variable selection algorithm in order to immunize against particular data configurations. We introduce the variable selection breakdown point that quantifies the number of cases resp. cells that have to be contaminated in order to let no relevant variable be detected. We show that particular outlier configurations can completely mislead model selection and argue why even cell-wise robust methods cannot fix this problem. We combine the variable selection breakdown point with resampling, resulting in the Stability Selection breakdown point that quantifies the robustness of Stability Selection. We propose a trimmed Stability Selection which only aggregates the models with the lowest in-sample losses so that, heuristically, models computed on heavily contaminated resamples should be trimmed away. An extensive simulation study with non-robust regression and classification algorithms as well as with Sparse Least Trimmed Squares reveals both the potential of our approach to boost the model selection robustness as well as the fragility of variable selection using non-robust algorithms, even for an extremely small cell-wise contamination rate

Unconventional machine learning of genome-wide human cancer data

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data. Here we show for the first time the efficacy of multiple annealing-based ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using annealing-based ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing architectures in the biomedical sciences