CellRank for directed single-cell fate mapping.

Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank ( https://cellrank.org ) for single-cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease, for which direction is unknown. Our approach combines the robustness of trajectory inference with directional information from RNA velocity, taking into account the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in velocity vectors. On pancreas development data, CellRank automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage-traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes. CellRank also predicts a new dedifferentiation trajectory during postinjury lung regeneration, including previously unknown intermediate cell states, which we confirm experimentally.

Machine learning prediction of malaria vaccine efficacy based on antibody profiles.

Immunization through repeated direct venous inoculation of Plasmodium falciparum (Pf) sporozoites (PfSPZ) under chloroquine chemoprophylaxis, using the PfSPZ Chemoprophylaxis Vaccine (PfSPZ-CVac), induces high-level protection against controlled human malaria infection (CHMI). Humoral and cellular immunity contribute to vaccine efficacy but only limited information about the implicated Pf-specific antigens is available. Here, we examined Pf-specific antibody profiles, measured by protein arrays representing the full Pf proteome, of 40 placebo- and PfSPZ-immunized malaria-naïve volunteers from an earlier published PfSPZ-CVac dose-escalation trial. For this purpose, we both utilized and adapted supervised machine learning methods to identify predictive antibody profiles at two different time points: after immunization and before CHMI. We developed an adapted multitask support vector machine (SVM) approach and compared it to standard methods, i.e. single-task SVM, regularized logistic regression and random forests. Our results show, that the multitask SVM approach improved the classification performance to discriminate the protection status based on the underlying antibody-profiles while combining time- and dose-dependent data in the prediction model. Additionally, we developed the new fEature diStance exPlainabilitY (ESPY) method to quantify the impact of single antigens on the non-linear multitask SVM model and make it more interpretable. In conclusion, our multitask SVM model outperforms the studied standard approaches in regard of classification performance. Moreover, with our new explanation method ESPY, we were able to interpret the impact of Pf-specific antigen antibody responses that predict sterile protective immunity against CHMI after immunization. The identified Pf-specific antigens may contribute to a better understanding of immunity against human malaria and may foster vaccine development.

COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data.

MOTIVATION: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare, models that are optimized for large datasets usually operate as black boxes. In high-stakes scenarios, like healthcare, using a black-box model poses safety and security issues. Without an explanation about molecular factors and phenotypes that affected the prediction, healthcare providers are left with no choice but to blindly trust the models. We propose a new type of artificial neural network, named Convolutional Omics Kernel Network (COmic). By combining convolutional kernel networks with pathway-induced kernels, our method enables robust and interpretable end-to-end learning on omics datasets ranging in size from a few hundred to several hundreds of thousands of samples. Furthermore, COmic can be easily adapted to utilize multiomics data. RESULTS: We evaluated the performance capabilities of COmic on six different breast cancer cohorts. Additionally, we trained COmic models on multiomics data using the METABRIC cohort. Our models performed either better or similar to competitors on both tasks. We show how the use of pathway-induced Laplacian kernels opens the black-box nature of neural networks and results in intrinsically interpretable models that eliminate the need for post hoc explanation models. AVAILABILITY AND IMPLEMENTATION: Datasets, labels, and pathway-induced graph Laplacians used for the single-omics tasks can be downloaded at https://ibm.ent.box.com/s/ac2ilhyn7xjj27r0xiwtom4crccuobst/folder/48027287036. While datasets and graph Laplacians for the METABRIC cohort can be downloaded from the above mentioned repository, the labels have to be downloaded from cBioPortal at https://www.cbioportal.org/study/clinicalData?id=brca\_metabric. COmic source code as well as all scripts necessary to reproduce the experiments and analysis are publicly available at https://github.com/jditz/comics.

PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction.

MOTIVATION: Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently, no such dataset for the exploration of Plasmodium falciparum protein antigen candidates exists. The parasite P.falciparum causes the infectious disease malaria. Thus, identifying potential antigens is of utmost importance for the development of antimalarial drugs and vaccines. Since exploring antigen candidates experimentally is an expensive and time-consuming process, applying machine learning methods to support this process has the potential to accelerate the development of drugs and vaccines, which are needed for fighting and controlling malaria. RESULTS: We developed PlasmoFAB, a curated benchmark that can be used to train machine learning methods for the exploration of P.falciparum protein antigen candidates. We combined an extensive literature search with domain expertise to create high-quality labels for P.falciparum specific proteins that distinguish between antigen candidates and intracellular proteins. Additionally, we used our benchmark to compare different well-known prediction models and available protein localization prediction services on the task of identifying protein antigen candidates. We show that available general-purpose services are unable to provide sufficient performance on identifying protein antigen candidates and are outperformed by our models that were trained on this tailored data. AVAILABILITY AND IMPLEMENTATION: PlasmoFAB is publicly available on Zenodo with DOI 10.5281/zenodo.7433087. Furthermore, all scripts that were used in the creation of PlasmoFAB and the training and evaluation of machine learning models are open source and publicly available on GitHub here: https://github.com/msmdev/PlasmoFAB.

Generalized Markov modeling of nonreversible molecular kinetics.

Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems.

Inherently interpretable position-aware convolutional motif kernel networks for biological sequencing data.

Artificial neural networks show promising performance in detecting correlations within data that are associated with specific outcomes. However, the black-box nature of such models can hinder the knowledge advancement in research fields by obscuring the decision process and preventing scientist to fully conceptualize predicted outcomes. Furthermore, domain experts like healthcare providers need explainable predictions to assess whether a predicted outcome can be trusted in high stakes scenarios and to help them integrating a model into their own routine. Therefore, interpretable models play a crucial role for the incorporation of machine learning into high stakes scenarios like healthcare. In this paper we introduce Convolutional Motif Kernel Networks, a neural network architecture that involves learning a feature representation within a subspace of the reproducing kernel Hilbert space of the position-aware motif kernel function. The resulting model enables to directly interpret and evaluate prediction outcomes by providing a biologically and medically meaningful explanation without the need for additional post-hoc analysis. We show that our model is able to robustly learn on small datasets and reaches state-of-the-art performance on relevant healthcare prediction tasks. Our proposed method can be utilized on DNA and protein sequences. Furthermore, we show that the proposed method learns biologically meaningful concepts directly from data using an end-to-end learning scheme.

Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid ß Conformational Dynamics Driven by an Oscillating Electric Field.

Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems. To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid ß (1-40) peptide, periodically driven by an oscillating electric field.