scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features.

The abundance of unpaired multimodal single-cell data has motivated a growing body of research into the development of diagonal integration methods. However, the state-of-the-art suffers from the loss of biological information due to feature conversion and struggles with modality-specific populations. To overcome these crucial limitations, we here introduce scConfluence, a method for single-cell diagonal integration. scConfluence combines uncoupled autoencoders on the complete set of features with regularized Inverse Optimal Transport on weakly connected features. We extensively benchmark scConfluence in several single-cell integration scenarios proving that it outperforms the state-of-the-art. We then demonstrate the biological relevance of scConfluence in three applications. We predict spatial patterns for Scgn, Synpr and Olah in scRNA-smFISH integration. We improve the classification of B cells and Monocytes in highly heterogeneous scRNA-scATAC-CyTOF integration. Finally, we reveal the joint contribution of Fezf2 and apical dendrite morphology in Intra Telencephalic neurons, based on morphological images and scRNA.

An Evaluation of Anomaly Detection and Diagnosis in Multivariate Time Series.

Several techniques for multivariate time series anomaly detection have been proposed recently, but a systematic comparison on a common set of datasets and metrics is lacking. This article presents a systematic and comprehensive evaluation of unsupervised and semisupervised deep-learning-based methods for anomaly detection and diagnosis on multivariate time series data from cyberphysical systems. Unlike previous works, we vary the model and post-processing of model errors, i.e., the scoring functions independently of each other, through a grid of ten models and four scoring functions, comparing these variants to state-of-the-art methods. In time-series anomaly detection, detecting anomalous events is more important than detecting individual anomalous time points. Through experiments, we find that the existing evaluation metrics either do not take events into account or cannot distinguish between a good detector and trivial detectors, such as a random or an all-positive detector. We propose a new metric to overcome these drawbacks, namely, the composite F-score (Fc1), for evaluating time-series anomaly detection. Our study highlights that dynamic scoring functions work much better than static ones for multivariate time series anomaly detection, and the choice of scoring functions often matters more than the choice of the underlying model. We also find that a simple, channel-wise model-the univariate fully connected auto-encoder, with the dynamic Gaussian scoring function emerges as a winning candidate for both anomaly detection and diagnosis, beating state-of-the-art algorithms.