MOTIVATION: Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. Chevrier et al. introduce an experimental and computational procedure to estimate and compensate for spillover implemented in their R package CATALYST. They assume spillover can be described by a spillover matrix that encodes the ratio between the signal in the unstained spillover receiving and stained spillover emitting channel. They estimate the spillover matrix from experiments with beads. We propose to skip the matrix estimation step and work directly with the full bead distributions. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. Spillover correction is often a pre-processing step followed by downstream analyses, and choosing a flexible model reduces the chance of introducing biases that can propagate downstream. RESULTS: We implement our method in an R package spillR using expectation-maximization to fit the mixture model. We test our method on simulated, semi-simulated, and real data from CATALYST. We find that our method compensates low counts accurately, does not introduce negative counts, avoids overcompensating high counts, and preserves correlations between markers that may be biologically meaningful. AVAILABILITY AND IMPLEMENTATION: Our new R package spillR is on bioconductor at bioconductor.org/packages/spillR. All experiments and plots can be reproduced by compiling the R markdown file spillR_paper.Rmd at github.com/ChristofSeiler/spillR_paper.

Additive Noise Models (ANMs) are a common model class for causal discovery from observational data. Due to a lack of real-world data for which an underlying ANM is known, ANMs with randomly sampled parameters are commonly used to simulate data for the evaluation of causal discovery algorithms. While some parameters may be fixed by explicit assumptions, fully specifying an ANM requires choosing all parameters. Reisach et al. (2021) show that, for many ANM parameter choices, sorting the variables by increasing variance yields an ordering close to a causal order and introduce ‘var-sortability’ to quantify this alignment. Since increasing variances may be unrealistic and cannot be exploited when data scales are arbitrary, ANM data are often rescaled to unit variance in causal discovery benchmarking. We show that synthetic ANM data are characterized by another pattern that is scale-invariant and thus persists even after standardization: the explainable fraction of a variable’s variance, as captured by the coefficient of determination $R^2$, tends to increase along the causal order. The result is high ‘$R^2$-sortability’, meaning that sorting the variables by increasing $R^2$ yields an ordering close to a causal order. We propose a computationally efficient baseline algorithm termed ‘$R^2$-SortnRegress’ that exploits high $R^2$-sortability and that can match and exceed the performance of established causal discovery algorithms. We show analytically that sufficiently high edge weights lead to a relative decrease of the noise contributions along causal chains, resulting in increasingly deterministic relationships and high $R^2$. We characterize $R^2$-sortability on synthetic data with different simulation parameters and find high values in common settings. Our findings reveal high $R^2$-sortability as an assumption about the data generating process relevant to causal discovery and implicit in many ANM sampling schemes. It should be made explicit, as its prevalence in real-world data is an open question. For causal discovery benchmarking, we provide implementations of $R^2$-sortability, the $R^2$-SortnRegress algorithm, and ANM simulation procedures in our library CausalDisco at https://causaldisco.github.io/CausalDisco/.

Simulated DAG models may exhibit properties that, perhaps inadvertently, render their structure identifiable and unexpectedly affect structure learning algorithms. Here, we show that marginal variance tends to increase along the causal order for generically sampled additive noise models. We introduce varsortability as a measure of the agreement between the order of increasing marginal variance and the causal order. For commonly sampled graphs and model parameters, we show that the remarkable performance of some continuous structure learning algorithms can be explained by high varsortability and matched by a simple baseline method. Yet, this performance may not transfer to real-world data where varsortability may be moderate or dependent on the choice of measurement scales. On standardized data, the same algorithms fail to identify the ground-truth DAG or its Markov equivalence class. While standardization removes the pattern in marginal variance, we show that data generating processes that incur high varsortability also leave a distinct covariance pattern that may be exploited even after standardization. Our findings challenge the significance of generic benchmarks with independently drawn parameters. The code is available at https://github.com/Scriddie/Varsortability.

BACKGROUND: Flow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell basis by studying differential expression of proteins. Most current data analysis tools compare expressions across many computationally discovered cell types. Our goal is to focus on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. RESULTS: Differential analysis of marker expressions can be difficult due to marker correlations and inter-subject heterogeneity, particularly for studies of human immunology. We address these challenges with two multiple regression strategies: a bootstrapped generalized linear model and a generalized linear mixed model. On simulated datasets, we compare the robustness towards marker correlations and heterogeneity of both strategies. For paired experiments, we find that both strategies maintain the target false discovery rate under medium correlations and that mixed models are statistically more powerful under the correct model specification. For unpaired experiments, our results indicate that much larger patient sample sizes are required to detect differences. We illustrate the CytoGLMM R package and workflow for both strategies on a pregnancy dataset. CONCLUSION: Our approach to finding differential proteins in flow and mass cytometry data reduces biases arising from marker correlations and safeguards against false discoveries induced by patient heterogeneity.

Given the observed abnormal motion dynamics of patients with heart conditions, quantifying cardiac motion in both normal and pathological cases can provide useful insights for therapy planning. In order to be able to analyse the motion over multiple subjects in a robust manner, it is desirable to represent the motion by a low number of parameters. We propose a reduced order cardiac motion model, reduced in space through a polyaffine model, and reduced in time by statistical model order reduction. The method is applied to a data-set of synthetic cases with known ground truth to validate the accuracy of the left ventricular motion tracking, and to validate a patient-specific reduced-order motion model. Population-based statistics are computed on a set of 15 healthy volunteers to obtain separate spatial and temporal bases. Results demonstrate that the reduced model can efficiently detect abnormal motion patterns and even allowed to retrospectively reveal abnormal unnoticed motion within the control subjects.