Estimation of missing values in astronomical survey data: An improved local approach using cluster directed neighbor selection

Imputation of cancer proteomics data with a deep model that learns from many datasets

Missing values are a major challenge in the analysis of mass spectrometry proteomics data. Missing values hinder reproducibility, decrease statistical power for identifying differentially expressed (DE) proteins and make it challenging to analyze low-abundance proteins. We present Lupine, a deep learning-based method for imputing, or estimating, missing values in tandem mass tag (TMT) proteomics data. Lupine is, to our knowledge, the first imputation method that is designed to learn jointly from many datasets, and we provide evidence that this approach leads to more accurate predictions. We validated Lupine by applying it to TMT data from >1,000 cancer patient samples spanning ten cancer types from the Clinical Proteomics Tumor Atlas Consortium (CPTAC). Lupine outperforms the state of the art for TMT imputation, identifies more DE proteins than other methods, corrects for TMT batch effects, and learns a meaningful representation of proteins and patient samples. Lupine is implemented as an open source Python package.

Evaluating Proteomics Imputation Methods with Improved Criteria

Quantitative measurements produced by tandem mass spectrometry proteomics experiments typically contain a large proportion of missing values. Missing values hinder reproducibility, reduce statistical power, and make it difficult to compare across samples or experiments. Although many methods exist for imputing missing values, in practice, the most commonly used methods are among the worst performing. Furthermore, previous benchmarking studies have focused on relatively simple measurements of error such as the mean-squared error between imputed and held-out values. Here we evaluate the performance of commonly used imputation methods using three practical, "downstream-centric" criteria. These criteria measure the ability to identify differentially expressed peptides, generate new quantitative peptides, and improve the peptide lower limit of quantification. Our evaluation comprises several experiment types and acquisition strategies, including data-dependent and data-independent acquisition. We find that imputation does not necessarily improve the ability to identify differentially expressed peptides but that it can identify new quantitative peptides and improve the peptide lower limit of quantification. We find that MissForest is generally the best performing method per our downstream-centric criteria. We also argue that existing imputation methods do not properly account for the variance of peptide quantifications and highlight the need for methods that do.

Strengthening intrusion detection system for adversarial attacks: improved handling of imbalance classification problem

Most defence mechanisms such as a network-based intrusion detection system (NIDS) are often sub-optimal for the detection of an unseen malicious pattern. In response, a number of studies attempt to empower a machine-learning-based NIDS to improve the ability to recognize adversarial attacks. Along this line of research, the present work focuses on non-payload connections at the TCP stack level, which is generalized and applicable to different network applications. As a compliment to the recently published investigation that searches for the most informative feature space for classifying obfuscated connections, the problem of class imbalance is examined herein. In particular, a multiple-clustering-based undersampling framework is proposed to determine the set of cluster centroids that best represent the majority class, whose size is reduced to be on par with that of the minority. Initially, a pool of centroids is created using the concept of ensemble clustering that aims to obtain a collection of accurate and diverse clusterings. From that, the final set of representatives is selected from this pool. Three different objective functions are formed for this optimization driven process, thus leading to three variants of FF-Majority, FF-Minority and FF-Overall. Based on the thorough evaluation of a published dataset, four classification models and different settings, these new methods often exhibit better predictive performance than its baseline, the single-clustering undersampling counterpart and state-of-the-art techniques. Parameter analysis and implication for analyzing an extreme case are also provided as a guideline for future applications.