Genetic screens mediated via CRISPR-Cas9 combined with high-content readouts have emerged as powerful tools for biological discovery. However, computational analyses of these screens come with additional challenges beyond those found with standard scRNA-seq analyses. For example, perturbation-induced variations of interest may be subtle and masked by other dominant source of variation shared with controls, and variable guide efficiency results in some cells not undergoing genetic perturbation despite expressing a guide RNA. While a number of methods have been developed to address the former problem by explicitly disentangling perturbation-induced variations from those shared with controls, less attention has been paid to the latter problem of noisy perturbation labels. To address this issue, here we propose ContrastiveVI+, a generative modeling framework that both disentangles perturbation-induced from non-perturbation-related variations while also inferring whether cells truly underwent genomic edits. Applied to three large-scale Perturb-seq datasets, we find that ContrastiveVI+ better recovers known perturbation-induced variations compared to previous methods while successfully identifying cells that escaped the functional consequences of guide RNA expression. An open-source implementation of our model is available at https://github.

Contrastive analysis (CA) refers to the exploration of variations uniquely enriched in a target dataset as compared to a corresponding background dataset generated from sources of variation that are irrelevant to a given task. For example, a biomedical data analyst may wish to find a small set of genes to use as a proxy for variations in genomic data only present among patients with a given disease (target) as opposed to healthy control subjects (background). However, as of yet the problem of feature selection in the CA setting has received little attention from the machine learning community. In this work we present contrastive feature selection (CFS), a method for performing feature selection in the CA setting. We motivate our approach with a novel information-theoretic analysis of representation learning in the CA setting, and we empirically validate CFS on a semi-synthetic dataset and four real-world biomedical datasets. We find that our method consistently outperforms previously proposed state-of-the-art supervised and fully unsupervised feature selection methods not designed for the CA setting. An open-source implementation of our method is available at https://github.com/suinleelab/CFS.

We study the effectiveness of various approaches that defend against adversarial attacks on deep networks via manipulations based on basis function representations of images. Specifically, we experiment with low-pass filtering, PCA, JPEG compression, low resolution wavelet approximation, and soft-thresholding. We evaluate these defense techniques using three types of popular attacks in black, gray and white-box settings. Our results show JPEG compression tends to outperform the other tested defenses in most of the settings considered, in addition to soft-thresholding, which performs well in specific cases, and yields a more mild decrease in accuracy on benign examples. In addition, we also mathematically derive a novel white-box attack in which the adversarial perturbation is composed only of terms corresponding a to pre-determined subset of the basis functions, of which a "low frequency attack" is a special case.