Abstract
Inferring cellular trajectories using a variety of omic data is a critical task in singlecell data science. However, accurate prediction of cell fates, and thereby biologically meaningful discovery, is challenged by the sheer size of singlecell data, the diversity of omic data types, and the complexity of their topologies. We present VIA, a scalable trajectory inference algorithm that overcomes these limitations by using lazyteleporting random walks to accurately reconstruct complex cellular trajectories beyond treelike pathways (e.g., cyclic or disconnected structures). We show that VIA robustly and efficiently unravels the finegrained subtrajectories in a 1.3millioncell transcriptomic mouse atlas without losing the global connectivity at such a high cell count. We further apply VIA to discovering elusive lineages and less populous cell fates missed by other methods across a variety of data types, including singlecell proteomic, epigenomic, multiomics datasets, and a new inhouse singlecell morphological dataset.
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Introduction
Singlecell omics data captures snapshots of cells that catalog cell types and molecular states with high precision. These highcontent readouts can be harnessed to model evolving cellular heterogeneity and track dynamical changes of cell fates in tissue, tumor, and cell population. However, current computational methods face four critical challenges. First, it remains difficult to accurately reconstruct highresolution cell trajectories and automatically detect the pertinent cell fates and lineages without relying on prior knowledge of input parameter settings. This is a foundational but unmet attribute of trajectory inference (TI) that could make lineage prediction less biased towards input parameters, and thus minimize the confounding factors that impact the underlying hypothesis testing. However, even the few algorithms which automate cell fate detection (e.g., SlingShot^{1}, Palantir^{2}, STREAM^{3}, and Monocle3^{4}) exhibit low sensitivity to cell fates and are highly susceptible to changes in input parameters. Second, current trajectory inference (TI) methods predominantly work well on treelike trajectories (e.g., Slingshot and STREAM), but lack the generalizability to infer disconnected, cyclic or hybrid topologies without imposing restrictions on transitions and causality^{5}. This attribute is crucial in enabling unbiased discovery of complex trajectories which are commonly not well known a priori, especially given the increasing diversity of singlecell omic datasets. Third, the growing scale of singlecell data, notably cell atlases of whole organisms^{4,6}, embryos^{7,8}, and human organs^{9}, exceeds the existing TI capacity, not just in runtime and memory, but in preserving both the finegrain resolution of the embedded trajectories and the global connectivity among them. Very often, such global information is lost in current TI methods after extensive and multiple rounds of dimension reduction or subsampling. Fourth, fueling the advance in singlecell technologies is the ongoing pursuit to understand cellular heterogeneity from a broader perspective beyond transcriptomics. A notable example is the emergence of singlecell imaging technologies that now allow informationrich profiling of morphological and biophysical phenotypes of single cells, and thus offer mechanistic cues to cellular functions that cannot be solely inferred by proteomic or sequencing data (e.g., in cancer^{10}, ageing^{11}, and drug responses^{12}). However, the applicability of TI to a broader spectrum of singlecell data has yet to be fully exploited.
To overcome these recurring challenges, we present VIA, a graphbased TI algorithm that uses a new strategy to compute pseudotime, and reconstruct cell lineages based on lazyteleporting random walks integrated with Markov chain Monte Carlo (MCMC) refinement (Fig. 1). VIA relaxes common constraints on traversing the graph, and thus allows capture of cellular trajectories not only in multifurcations and trees, but also in disconnected and cyclic topologies. The lazyteleporting MCMC characteristics also make VIA robust to a wide range of preprocessing and input algorithmic parameters, and allow VIA to consistently identify pertinent lineages that remain elusive or even lost in other topperforming and popular TI algorithms we benchmark^{5}, which are chosen for comparative analysis conditional on meeting several of the following criteria: automated lineage path and cell fate prediction, recovery of complex topologies not limited to trees, scalability and generalizability to multiple singlecellmodalities. We validate the performance of VIA and thus its ability to offer better interpretation of the underlying biology across a variety of transcriptomic, epigenomic, and integrated multiomic datasets (seven biological datasets with a further two datasets presented in Supplementary). Notably, we show in subsequent sections that VIA accurately detects minor dendritic subpopulations and their characteristic gene expression trends in human hematopoiesis; automatically identifies pancreatic islets including rare delta cells; and recovers endothelial and cardiomyocyte bifurcation in integrated data sets of singlecell RNAsequencing (scRNAseq) and singlecell sequencing assay for transposaseaccessible chromatin (scATACseq).
Another defining attribute of VIA is its resilience in handling the wide disparity in singlecell data size, structure and dimensionality across modalities. Specifically, VIA is highly scalable with respect to number of cells (10^{2} to >10^{6} cells) and features, without requiring extensive dimensionality reduction or subsampling which compromise global information. Most TI methods require two stages of dimensionality reduction in the form of PCA followed by a subsequent stage of UMAP, MLLE, or diffusion components. Only a low number of components from the second layer of dimensionality reduction is retained as an input to the TI method (e.g., STREAM, Monocle3, Slingshot, and even PAGA and Palantir which subset the diffusion components after PCA). In VIA, we show that for cytometry data there is no need for any dimensionality reduction, and for transcriptomic data we show that VIA does not need a second dimensionality reduction step but robustly infers lineages on a wide range of input principal components (PCs). Although PCA is a common step in analyzing transcriptomic data in order to strengthen the signal in the data, we also show that inprinciple, VIA can handle 1000 s of genes as direct inputs without any PCA at all (Supplementary Note 5 and Figs. 27–29). We showcase the scalability of sample size by analyzing the finegrained developmental subtrajectories in the 1.3millioncell mouse organogenesis atlas in terms of fast runtime and preservation of global celltype connectivity, which is otherwise lost in existing TI methods. We also show that VIA is robust against the dimensionality drop (down to 10’s–100’s antibodies or morphological features) in mass cytometry (proteomics) and imaging cytometry (morphological) data. For instance, VIA consistently reconstructs the pseudotime that recapitulates murine embryonic stem cells (ESCs) differentiation toward mesoderm cells in CyTOF data, where the lazyteleporting MCMCs contribute to the high accuracy of inference. Lastly, we hypothesize that VIA can also be applied to imaging cytometry for gaining a mechanistic biophysical understanding of cellular progress. To this end, we profiled the biophysical and morphological phenotypes of singlecell live breast cancer cells with our recently developed highthroughput imaging flow cytometer, called FACED^{13}. Validated with the in situ fluorescence (FL) image capture, we found that VIA reliably reconstructs the continuous cellcycle progressions from G1SG2/M phase, and reveals subtle changes in cell mass accumulation.
Results
Algorithm
VIA first represents the singlecell data as a cluster graph (i.e., each node is a cluster of single cells), computed by our recently developed datadriven communitydetection algorithm, PARC, which allows scalable clustering whilst preserving global properties of the topology needed for accurate TI^{14} (Step 1 in Fig. 1). The root (starting point) is designated by the user, either as a singlecell index or using group or cluster level labels. The cell fates and their lineage pathways are then computed by a twostage probabilistic method, which is the key algorithmic contribution of this work (Step 2 in Fig. 1, see “Methods” for detailed explanation). In the first stage of Step 2, VIA models the cellular process as a modified random walk that allows degrees of laziness (remaining at a node/state) and teleportation (jumping to any other node/state) with predefined probabilities. The pseudotime, and thus the graph directionality, can be computed based on the theoretical hitting times of nodes (see the theory and derivation in “Methods” and Supplementary Note 2). The lazyteleporting behavior prevents the expected hitting time from converging to a local distribution in the graph as otherwise occurs in regular random walks, especially when the sample size grows^{15}. More specifically, the laziness and teleportation factors regulate the weights given to each eigenvectorvalue pair in the expected hitting time formulation such that the stationary distribution (given by the localnode degreeproperties in regular walks) does not overwhelm the global information provided by other “eigenpairs”. Moreover, the computation does not require subsetting the first k eigenvectors (bypassing the need for the user to select a suitable threshold or subset of eigenvectors) since the dimensionality is not on the order of number of cells, but is equal to the number of clusters. Hence all eigenvalueeigenvector pairs can be incorporated without causing a bottleneck in runtime. Consequently in VIA, the modified walk on a clustergraph not only enables scalable pseudotime computation for large datasets in terms of runtime, but also preserves information about the global neighborhood relationships within the graph. In the second stage of Step 2, VIA infers the directionality of the graph by biasing the edgeweights with the initial pseudotime computations, and refines the pseudotime through lazyteleporting MCMC simulations on the forward biased graph.
Next (Step 3 in Fig. 1), the MCMCrefined graphedges of the lazyteleporting random walk enable accurate predictions of terminal cell fates through a consensus vote of various vertex connectivity properties derived from the directed graph. The cell fate predictions obtained using this approach are more accurate and robust to changes in input data and parameters compared to other TI methods (Fig. 2 simulated complex topologies and Supplementary Fig. 1 summary of lineage detection accuracy for all benchmarked real datasets). Trajectories towards identified terminal states are then resolved using lazyteleporting MCMC simulations (Step 4 in Fig. 1). The singlecell level KNN graph constructed in Step 1 is then used to project the lineage probabilities of trajectories (pathways from root to cell fate), and temporal ordering derived from the clustergraph topology onto a singlecell level. Together, these four steps facilitate holistic topological visualization of TI on the singlecell level (e.g., using UMAP or PHATE^{16,17}) and critically enable datadriven downstream analyses such as recovering gene expression trends and singlecell level pathways of lineages, that are essential to biological validation and discovery of lineage commitment (Methods) (Step 5 in Fig. 1).
VIA accurately captures complex topologies obscured in other TI methods
We first generate and analyze simulated datasets (see Methods) to demonstrate that VIA’s probabilistic approach to graphtraversal allows it to infer cell fates when the underlying data spans combinations of multifurcating trees and cyclic/disconnected topologies  topologies and lineages often obscured in existing TI methods. In VIA, the relaxation of edge constraints in computing lineage pathways and pseudotime enables accurate detection of cell fates and complex trajectories by avoiding prematurely imposing constraints on nodetonode mobility. Other methods resort to constraints such as reducing the graph to a tree, imposing unidirectionality by thresholding edges based on pseudotime directionality, removing outgoing edges from terminal states^{2,18}, and computing shortest paths for pseudotime^{1,2}.
The availability of a reference truth model for the synthetics datasets allows us to quantify TI accuracy using a composite metric which assesses multiple layers of the inferred trajectory including topology, pseudotime and lineage prediction. The metric assesses “local” graph similarity between the inferred and reference graphs using the Graph Edit Distance (GED) and an F1Branch score (which labels branches in the inferred topology as true or false positives, or the lack thereof as a false negative). “Global” graph similarity is computed using the Ipsen–Mikhailov metric^{19} (Methods), and pseudotime quality is captured by the Pearson correlation between the inferred and reference pseudotimes. Terminal cell fate prediction is evaluated using the F1score. The breakdown of the composite score and further detail on each metric is available in Supplementary Note 3 and Supplementary Figs. 2–5.
The differences in accuracy between VIA and other methods is most significant for complex topologies, particularly those with disconnected components comprising various connected topologies, whilst the ability to accurately detect cell fates is highlighted by multilineage furcating topologies. In the fourleaf multifurcation (Fig. 2a top), VIA accurately captures the two cascading bifurcations which lead to four leaf nodes. In particular, VIA detects the elusive “M2” terminal state whereas other methods (Palantir, PAGA, Slingshot, STREAM, and Monocle3) merge it with the “M8” lineage. Monocle3 and STREAM typically only capture a single bifurcation and thus merge the pairs of leaves that otherwise arise from the second layer of bifurcation (Fig. 2a). Even for the fairly simple cyclic topology (Fig. 2a), other methods tend to fragment the structure to varying degrees depending on the parameter choice whereas VIA consistently preserves the global cyclic structure (Supplementary Fig. 4c under various K (KNN)). This is not to say VIA is invariant to parameter choice, but rather that VIA predictably modulates the graph resolution across a wide range of K without disrupting the underlying global topology (see the increase in the number of nodes in K = 30 versus K = 5 in Supplementary Fig. 4c). This characteristic is important for robustly analyzing multiple levels of resolution in complex graph topologies, as also shown in our later investigation of the 1.3millioncell mouse atlas. The performance comparison for the disconnected hybrid topologies (Fig. 2) shows that VIA disentangles the cyclic and bifurcating lineages (that comprise Disconnected1) and captures the key leafstates in the bifurcation as well as the “tail” extending from the cyclic topology. Palantir overly fragments the two trajectories, whereas Monocle3 and Slingshot merge them, STREAM is not well suited to nontree trajectories given the underlying structure is assumed to be a spanning tree.
We also show that VIA is flexible to using clustering methods other than PARC by substituting PARC with Kmeans clustering to show that the lazyteleporting MCMCs still enable faithful recovery of various topologies as well as the associated cell fates (Supplementary Note 6 and Figs. 30–32). The main drawback of using Kmeans is that under or overclustering can occur based on the userchoice of K, whereas methods like PARC enable a more datadriven resolution of the data where the recovery of less populous cell types is not dependent on an adequately large number of clusters.
VIA reveals rare lineages in epigenomic and transcriptomic landscapes of human hematopoiesis
To assess the performance of VIA on inferring real cellular trajectory, we first considered a range of scRNAseq datasets, including hematopoiesis^{2,20}, endocrine genesis, Bcell differentiation^{21}, and embryonic stem (ES) cell differentiation in embryoid bodies^{17}. We present the analyses of CD34+ human hematopoiesis and endocrine differentiation here, whereas the generalizable performance of VIA on other scRNAseq datasets is presented in Supplementary Figs. 1, 6, 13. We highlight human hematopoiesis as it has been extensively studied not only with scRNAseq, but also other singlecell omics modalities, notably scATACseq. Hence, it allows us to reliably assess lineage identification performance and downstream analyses using VIA.
First, we show that VIA consistently reveals from the scRNAseq dataset the typical hierarchical bifurcations during hematopoiesis that result in key committed lineages of hematopoietic stem cells (HSCs) to monocytic, lymphoid, erythroid, classical and plasmacytoid dendritic cell (cDCs and pDCs) lineages and megakaryocytes (Fig. 3a). The automated detection of these terminal states in VIA, as quantified by F1scores on the annotated cells, remains robust to varying the number of neighbors in the KNN graph, and the number of PCs (Fig. 3c). Specifically, VIA’s sustained sensitivity to rarer cell types (e.g., DCs and megakaryocytes) can be attributed to a better underlying graph structure where nodes are well delineated by PARC (as rare cell types are well separated by graph pruning in the clustering stage) and edges governing the random walk pathways are not prematurely removed due to restrictions on causality.
In contrast, the sensitivity of Palantir and Slingshot in detecting rarer lineages drops significantly outside a favorable “sweet spot” of parameters. Slingshot can only recover the major cell populations (monocytes, erythroid, and B cells) and confuses the DC populations with the monocytes and the megakaryocytes with the erythroid cells. Palantir can only identify the DCs and megakaryocytes for a handful of parameter options, whereas VIA achieves this goal across a wider range of parameters (Fig. 3c). To verify that VIA reliably delineates the megakaryocyte, cDC and pDC lineages, we used VIA to automatically plot the lineage specific trends for selected marker genes. We showed that while both DC lineages exhibit elevated IRF8, the CSF1R is specific to the cDC, and the CD123 remains elevated for pDCs whereas it is first upregulated, then downregulated in cDCs (Fig. 3b and Supplementary Figs. 7–9). Marker genes known to increase along a specific lineage are correlated against the pseudotime along each lineage as an indicator of correct cell ordering (Fig. 3d). The gene trends inferred by each method are provided in Supplementary Fig. 9 to show a sidebyside comparison of nuances in the quality of plotted expressions, such as the presence of crosstalk between distinct lineages, or distortion of the trends due to unrelated cells assimilated into lineages.
We find that VIA’s interpretation of the human scATACseq profiles (Fig. 3e) mirrors the continuous landscape of scRNAseq human hematopoietic data (Fig. 3a). We use two common preprocessing pipelines^{20,22} (see Methods), intended to alleviate challenges posed by the sparsity of scATACseq data, to show that VIA consistently predicts the expected hierarchy of lineages furcating from hematopoietic progenitors to their descendants. The graph topology of VIA (colored by pseudotime) captures the progression of multipotent progenitors (MPPs) toward the lymphoidprimed MPPs (LMPP) and the common myeloid progenitors (CMPs) which in turn give rise to the CLP and MEP lineages respectively. The known joint contribution of LMPPs and CMPs towards the GMP lineage is also captured by the VIA graph. We verified the lineages identified by VIA by analyzing the changes in the accessibility of TF motifs associated with known regulators of the lineage commitments, e.g., GATA1 (erythroid), CEBPD (myeloid) and IRF8 (DCs) (Fig. 3e, Supplementary Fig. 10c). Again, we note that the detection of these lineages is less straightforward in other methods, which generally face a sharp drop in accuracy of detecting relevant cell fates as the input number of PCs exceeds ~50PCs (e.g., Palantir often misses the CLP and monocyte lineages, see Supplementary Fig. 6 for Palantir’s outputs across parameters and Fig. 3g for the corresponding prediction accuracy). The quality of the lineage pathways and gene trends is indicated in Fig. 3h by the correlation of lineage cell ordering against marker gene expression. Visual comparisons of the topologies and predicted gene trends of each method are shown in Supplementary Fig. 11. We emphasize that VIA’s robustness in handling both the scRNAseq and scATACseq datasets demonstrates its unique ability to achieve stable prediction and thus faithful query of the underlying biology without biasing specific sets of input parameters which nontrivially vary across datasets—as also evident from our series of “stress tests” on VIA’s performance and the genetrend comparisons (Supplementary Fig. 1).
VIA detects small endocrine Delta lineages and Beta subtypes
We use a scRNAseq dataset of E15.5 murine pancreatic cells to again examine whether VIA can automatically detect multiple lineages, in particular less populous ones. This data spans all developmental stages from initial endocrine progenitorprecursor (EP) state (low level of Ngn3, or Ngn3^{low}), to intermediate EP (high level of Ngn3, or Ngn3^{high}) and Fev^{+} states, to terminal states of hormoneproducing alpha, beta, epsilon and delta cells^{23} (Fig. 4a).
A key challenge in analyzing this dataset is the automated detection of the small deltacell population (a mere 3% of the total population), which otherwise requires manual assignment in CellRank and Palantir (see Supplementary Figs. 15, 16 for a comparison of topology and automated gene trend plots along predicted lineages by different methods). In contrast, the welldelineated nodes of the VIA clustergraph (a result of the accurate terminal state prediction enabled by the lazyteleporting MCMC property of VIA on the inferred topology) lends itself to automatically detecting this small population of delta cells, together with all other key lineages (alpha, beta and epsilon lineages) (Fig. 4a–c). As evidenced by the corresponding geneexpression trend analysis, VIA detects all of the hormoneproducing cells including delta cells which show exclusively elevated Hhex, Sst, and Cd24a (Fig. 4c–e). To show that this is not a coincidence of parameter choice, we verify that these populations can be identified for a wide range of chosen highly variable genes (HVGs prior to PCA) and number of PCs (see Supplementary Fig. 1c). Interestingly, consistent with an observation by BastidasPonce et al.^{23} we see two groups of Fev+ populations branching from the Ngn+ populations, which subsequently progress towards the distinct cell lines. We show consistency in predicted topology, cell fates and gene trends when applying VIA directly on 1000 s of HVGs without PCA for a wide range of HVGs (see Supplementary Fig. 29), and under artificial degradation of the data to test robustness to noise (see Supplementary Fig. 18 and Note 4 to see that VIA is more robust to the addition of noise than other methods which merge major lineages).
Interestingly, we find VIA often automatically detects two Betacell subpopulations (Beta1 and Beta2) (Fig. 4b–e) that express common Betacell markers, such as Dlk1, Pdx1, but differ in their expressions of Ins1 and Ins2 (Fig. 4c–e). The pseudotime order within this Betacell heterogeneity^{24,25}, undetectable by other TI methods (as shown in the gene correlation comparisons Supplementary Fig. 15), can further be reconciled in the VIA graph where the immature Beta2 population precedes the mature Beta1 population. We find that the immature Beta2 population strongly expresses Ins2, and weakly expresses Ins1, followed by the mature Beta1 cells which express both types of Ins^{25} (Fig. 4d–f). VIA graphs colored by Ins1 and Ins2 further show the difference in Ins expression by the two Beta populations).
VIA recovers Isl1+ cardiac progenitor bifurcation in multiomic data
We next demonstrate the applicability of VIA in singlecell multiomics analysis by investigating murine Ils1+ cardiac progenitor cells (CPC) which are known to bifurcate towards endothelial and cardiomyocyte fates (Fig. 5). VIA consistently uncovers the bifurcating lineages using both singlecell transcriptomic (scRNAseq) and chromatin accessibility (scATACseq) information^{26,27,28}, as well as their data integration (see “Methods” for data integration using Seurat). Other methods that are also applicable to nontranscriptomic data, fail to uncover the two main lineages.
Other methods typically only detect the cardiomyocyte lineage (the inability to detect a bifurcation is exacerbated when the number of input PCs increases), and instead falsely detect several intermediate and early stages as final cell fates. For instance STREAM consistently merges the cardiomyocyte and endothelial lineages and instead presents the intermediate stage as a separate bifurcation. See Supplementary Figs. 20, 21 for sample outputs across parameters, and Fig. 5g for the corresponding prediction accuracy of each method. PAGA does not offer automated cell fate prediction or lineage paths and is therefore not benchmarked for this dataset. The disparity in trajectory inference is evident in the scRNAseq and integrated data where Monocle3, Slingshot and Palantir do not resolve either of the two cell fates (Fig. 5g), and STREAM detects multiple spurious branches that fragment the structure entirely. We hypothesized that lowering the K (number of nearest neighbors) in Palantir and VIA would be more appropriate given the extremely low cell count (~200 cells) of the scRNAseq dataset. Whilst this approach did not alter the outcome for Palantir, we found that VIA is able to capture the transition from early to intermediate CPCs and finally lineage committed cells.
More importantly, VIA automatically generates a pseudotemporal ordering of relevant cells (without requiring manual selection of relevant cells as done in Jia et al.^{26}) along each lineage and their markerTF pairs (Fig. 5c and Supplementary Fig. 19f for differential gene expression analysis). Hence, VIA can be used to faithfully interpret relationships between transcription factor dynamics and gene expression in an unsupervised manner. The highlighted gene and TF pairs in the cardiac lineage show a strong correlation between expression and accessibility of Gata and Homeobox Hox genes which are known to be related to the regulation of cardiomyocyte proliferation^{29,30,31}. VIA’s reliable performance against userreconfiguration (number of PCs, individual or integrated omic data) suggests its utility in transferable interpretation between scRNAseq and scATACseq data.
VIA preserves global connectivity when scaling to millions of cells
VIA is designed to be highly scalable and offers automated lineage prediction without extensive dimension reduction or subsampling even at large cell counts. To showcase this, we use VIA to explore the 1.3million scRNAseq mouse organogenesis cell atlas (MOCA)^{7}. While this dataset is inaccessible to most TI methods from a runtime and memory perspective, VIA can efficiently resolve the underlying developmental heterogeneity, including nine major trajectories (Fig. 6a, b) with a runtime of ~40 min, compared to the next fastest method PAGA which has a runtime of 3 h, Palantir and STREAM which takes over 4 and 6.5 h respectively. Other methods like Slingshot and CellRank were deemed infeasible due to extremely long runtimes on much smaller datasets. (Supplementary Table 3 for a summary of runtimes). Going beyond the computational efficiency, VIA also preserves wider neighborhood information and reveals a globally connected topology of MOCA which is otherwise lost in the Monocle3 analysis which first reduces the input data dimensionality using UMAP.
The overall cluster graph of VIA consists of three main branches that concur with the known developmental process at early organogenesis^{32} (Fig. 6a). It starts from the root stem which has a high concentration of E9.5 early epithelial cells made of multiple subtrajectories (e.g., epidermis, and foregut/hindgut epithelial cells derived from the ectoderm and endoderm). The stem is connected to two distinct lineages: (1) mesenchymal cells originated from the mesoderm which arises from interactions between the ectoderm and endoderm^{27,28,32,33,34,35} and (2) neural tube/crest cells derived from neurulation when the ectoderm folds inwards^{34}.
The sparsity of early cells (only ~8% are E9.5) and the absence of earlier ancestral cells make it particularly challenging to capture the simultaneous development of trajectories. However, VIA is able to capture the overall pseudotime structure depicting early organogenesis (Fig. 6b). For instance, at the junction of the epithelialtomesenchymal branch, we find early mesenchymal cells from E9.5–E10.5. Cells from later mesenchymal developmental stages (e.g., myocytes from E12.5–E13.5) reside at the leaves of the branch. Similarly, at the junction of epithelialtoneural tube, we find dorsal tube neural cells and notochord plate cells which are predominantly from E9.5–E10.5 and more developed neural cells at branch tips (e.g., excitatory and inhibitory neurons appearing at E12.5–E13.5). In contrast, the pseudotime gradient of PAGA’s nodes offer little salient information at this scale, with 90% of cells predicted to be in the first 10% of the pseudotime color scale (see Supplementary Fig. 22c, d).
VIA also consistently places the other smaller dispersed groups of trajectories (e.g., endothelial, hematopoietic) in biologically relevant neighborhoods (see Supplementary Note 7 for a detailed explanation of VIA’s structural connections supported by known transitions in organogenesis literature). While VIA’s connected topology offers a coarsegrained holistic view, it does not compromise the ability to delineate individual lineage pathways, such as the erythroid and white blood cell lineages within the hematopoietic super group (consistent with annotations made by Cao et al.^{7}) as shown in Fig. 6c.
As such, TI using VIA uniquely preserves both the global and local structures of the data. Whilst manifoldlearning methods are often used to extensively reduce dimensionality to mitigate the computational burden of large singlecell datasets, they tend to incur loss of global information and be sensitive to input parameters. VIA is sufficiently scalable to bypass such a step, and therefore retains a higher degree of neighborhood information when mapping large datasets. This is in contrast to Monocle3’s^{7} UMAPreduced inputs that reveal different disconnected supergroups and fluctuating connectivity depending on input parameters. As shown in Fig. 6e (and Supplementary Fig. 22 for varying KNN), methods such as Monocle3 which require a very low dimensional representation (e.g., first 23 components of UMAP) for TI are susceptible to unpredictable changes in the composition of super cell groups, their relative positions and interconnectivity. For instance, in UMAP, the neural tube group is sometimes shown as a single super group, and other times fragmented across the embedding without context of neighboring groups. Similarly the hematopoietic supergroup is shown as a single, two or even three separate groups dispersed across the embedding landscape (Fig. 6e). In contrast, VIA uncovers biologically consistent structures across the same range of parameters. In VIA, the cells belonging to these finegrained supergroups remain connected and neighborhood relationships are preserved, for instance the neural crest cells (containing Peripheral Nervous System neurons and glial cells) remain adjacent to the neural tube (Figs. 6d, Supplementary Fig. 22a).
VIA’s lazyteleporting MCMCs delineate mesoderm differentiation in mass cytometry data
Broad applicability of TI beyond transcriptomic analysis is increasingly critical, but existing methods have limitations contending with the disparity in the data structure (e.g., sparsity and dimensionality) across a variety of singlecell data types. While we have shown that VIA can be used to successfully interrogate scATACseq, scRNAseq, and their integrated data, we further investigate whether VIA can cope with the significant drop in data dimensionality (10–100), as often presented in flow/mass cytometry data, and still delineate continuous biological processes.
We applied VIA on a timeseries mass cytometry data (28 antibodies, 90K cells) capturing murine ESCs differentiation toward mesoderm cells^{36}. The mESCs are captured at 12 intervals within the first 11 days and hence provide sufficiently granular temporal annotation to allow a correlation assessment of the inferred pseudotimes. We quantified that the pseudotimes computed by VIA shows a Pearson correlation of ~88% with the actual annotated days. We further verified that VIA’s performance is critically improved by the lazyteleporting MCMCs (Fig. 7d), without which the correlation drops closer to PAGA’s. Palantir and Monocle3 suffer from low connectivity of cells between the Day 0–1 and the subsequent early stages (finding disconnected trajectories even when increasing K in KNN), and thus result in loss of pseudotime gradient and low correlation to the true annotations.
More importantly, unlike previous analysis^{36} of the same data which required chronological labels to visualize the chronological developmental hierarchy, we ran VIA without such supervised adjustments and accurately captured the sequential development. Not only can it achieve faster runtime (running in 2 min on the full antibodyfeature set versus Slingshot which required 6 h even on a subset of first 5 PCs see Supplementary Table 3 for more runtime comparisons), VIA detects three terminal states corresponding to cells in the final developmental stages of Day 10–11 which are indicated by upregulation of Pdgfra, Cd44 and Gata4 mesodermal markers (Fig. 7e). In contrast, other methods struggle to identify the correct terminal states (e.g., Palantir, STREAM and Slingshot Fig. 7f) and do not depict salient structures (e.g., STREAM where the Day 10–11 branch is placed in between Day 0 and Day 5 branches).
VIA captures morphological trends of live cells in cell cycle progression
Apart from the omics technologies, optical microscopy is a powerful parallel advance in singlecell analysis for generating the “fingerprint” profiles of cell morphology. Such spatial information is typically obscured in sequencing data, but can effectively underpin cell states and functions without costly and timeconsuming sequencing protocols. However, trajectory predictions based on morphological profiles of single cells have only been scarcely studied until recently, but advancements in highthroughput imaging cytometry are now making largescale image data generation and related studies feasible. We thus sought to test if VIA can predict biologically relevant progress based on singlecell morphological snapshots captured by our recently developed highthroughput imaging flow cytometer, called FACED^{13}—a technology that is at least 100 times faster than stateoftheart imaging flow cytometry (IFC) (Fig. 8a).
Our FACED imaging platform captured multiple image contrasts of single cells, including FL, and quantitative phase images (QPI), which measure highresolution biophysical properties of cells, which are otherwise inaccessible in other methods^{37}. Using the QPIs captured by FACED, we first generated spatiallyresolved singlecell biophysical profiles of two live breast cancer cell types (MDAMB231 and MCF7) undergoing cell cycle progressions (38 features including cell shape, size, dry mass density, optical density and their subcellular textures (see Supplementary Tables 6, 7 for definitions of features)). The QPI together with the FL images of individual cells were also used to train a convolutional neural networkbased regression model for predicting the DNA content. We first validated that there is a high correlation (Pearson’s correlation coefficient r = 0.72) between the actual DNA content determined by the FL images and DNA content predicted by the QPI (Supplementary Fig. 24a). In addition, the predicted percentages of cells in each cell cycle phases (i.e., G1, S and G2/M) by the biophysical profile are highly consistent with the ground truth defined by the DNA dye (Supplementary Fig. 24b). Based on the biophysical profiles as validated by the above tests, VIA reliably reconstructed the continuous cellcycle progressions from G1SG2/M phase of both types of live breast cancer cells (Methods) (Fig. 8b–g).
Intriguingly, according to the pseudotime ordered by VIA, not only does it reveal the known cell growth in size and mass^{38}, and general conservation of cell mass density^{39} (as derived from the FACED images (Methods)) throughout the G1/S/G2 phases, but also a slowdown trend during the G1/S transition in both cell types, consistent with the lower proteinaccumulation rate during S phase^{40} (Fig. 8f, g). The variation in biophysical textures (e.g., peak phase, and phase fiber radial distribution) along the VIA pseudotime likely relates to known architectural changes of chromosomes and cytoskeletons during the cell cycles (Fig. 8f, g). We find other methods on this dataset to be sensitive to the choice of early cells and detecting intermediate cells as terminal cell fates (e.g., Palantir, Slingshot), and often adding additional edges or branches (e.g., STREAM, PAGA), see Supplementary Fig. 23 for Palantir, Slingshot, Monocle3, STREAM and PAGA outputs. The slowdown during the Sphase is missed by the gene trend prediction available in other methods. To probe subsets of the morphological features, we remove volume and volume related features (e.g., Dry Mass, Area) and test whether this can still be used to infer the topology and cell ordering that reveals the slowdown observed in the Sphase. We found that VIA is consistently able to reveal these trends in both cell lines, whereas other methods struggle to maintain the linear progression expected along the cellcycle with spurious linkages emerging (see Supplementary Figs. 25, 26) and intermediate states being selected as final G2 stages. These results further substantiate the growing body of work^{41,42,43,44} on imaging biophysical cytometry for gaining a mechanistic understanding of biological systems, especially when combined with omics analysis^{45}.
Discussion
With the growing scale and complexity of singlecell datasets, there is an unmet need for accurate cell fate prediction and lineage detection in complex topologies manifested in biology (not limited to trees). This challenge, broadly faced by the current TI methods, is compounded by susceptibility to algorithmic parameter changes, limited scalability to large data size; and insufficient generalizability to multiomic data beyond transcriptomic data. We introduced VIA, which alleviates these challenges by fast and scalable construction of clustergraph of cells, followed by pseudotime, and reconstructing cell lineages based on lazyteleporting random walks and MCMC simulations. This strategy critically relaxes common constraints on graph traversal and causality that impede accurate prediction of elusive lineages and less populous cell fates. We validated the efficacy of these measures in terms of detecting various challenging topologies on simulated data, as well as robust prediction of cell fates and temporally changing feature trends on a variety biological processes (spanning epigenomic, transcriptomic, integrated omic, as well as imaging and mass cytometric data) to show that VIA detects pertinent biological lineages and their pathways that remain undetected by other methods.
Notably, VIA distinguished between dendritic subtypes in an scRNAseq hematopoiesis dataset; identified the rare delta cell islet in pancreatic development, a population requiring manual assignment in other TI methods; and revealed the bifurcation towards cardiomyocyte and endothelial lineage commitment in a multiomic scATACseq and scRNAseq dataset which proved challenging for other methods. In order to demonstrate that these biological findings are robust to user parameter tuning, we conducted a series of ‘stress tests’ of the inferred topology and cell fates on both simulated and biological data, which show that VIA behaves more predictably (allowing controllable degrees of analytical granularity) and accurately than other methods with regards to topology and lineage prediction. In other methods, user parameter choice can incur fragmentation or spurious linkages in the modeled topology, and consequently only yield biologically sensible lineages for a narrow sweet spot of parameters (see the summary in Supplementary Fig. 1 and sample outputs by other methods in Supplementary Figs. 6, 9, 11–13, 15–18, 20–21, 22, and 23).
We also demonstrated on the 1.3 million MOCA dataset that VIA is highly scalable with a runtime of ~40 min (compared to 3–4 h on the next fastest method). Importantly, VIA not only recovers the finegrained subtrajectories, but also maintains global connectivity between related cell types and thus captures key relationships among lineages in early embryogenesis. It also computes a more salient pseudotime measure supported by lazyteleporting MCMCs, compared to other methods whose pseudotime scale was distorted at such high cell counts (Supplementary Fig. 22c, d). We showed that methods which require UMAP (or tSNE) before parsing MOCA are highly susceptible to user defined input parameters that can significantly and unpredictably fragment the global topology.
We also assessed whether VIA can be generalized to nontranscriptomic singlecell datasets, especially those with significant dimensionality disparity compared to sequencing data. We first applied VIA to the mESC CyTOF dataset and showed that the lazyteleporting MCMCs strategy in VIA enables it to outperform other methods in correctly correlating the pseudotime of the mesoderm development to the annotated dates. We finally explored the utility of VIA in analyzing emerging imagebased singlecell biophysical profile data. We showed that VIA not only successfully identified the progression of G1/S/G2 stages, but also revealed the subtle changes in biophysicalrelated cellular properties, which are otherwise obscured in other methods. VIA could thus motivate new strategies in singlecell analysis that link cellular biophysical phenotypes and biochemical/biomolecular information, to discover how molecular signatures translate into the emergent cellular biophysical properties, which has already shown effective in studies of cancer, ageing, and drug responses. Overall, VIA offers an advancement to TI methods to robustly study a diverse range of singlecell data. Together with its scalable computation and efficient runtime, VIA could be useful for multifaceted exploratory analysis to uncover biological processes, potentially those deviated from the healthy trajectories
Methods
VIA algorithm
VIA applies a scalable probabilistic method to infer cell state dynamics and differentiation hierarchies by organizing cells into trajectories along a pseudotime axis in a nearestneighbor graph which is the basis for subsequent random walks. Single cells are represented by graph nodes that are connected based on their feature similarity, e.g., gene expression, transcription factor accessibility motif, protein expression, or morphological features of cell images. A typical routine in VIA mainly consists of four steps:
Accelerated and scalable clustergraph construction
VIA first represents the singlecell data in a knearestneighbor (KNN) graph where each node is a cluster of single cells. The clusters are computed by our recently developed clustering algorithm, PARC^{14}. In brief, PARC is built on hierarchical navigable small world^{46} accelerated KNN graph construction and a fast communitydetection algorithm (Leiden method^{47}), which is further refined by datadriven pruning. The combination of these steps enables PARC to outperform other clustering algorithms in computational runtime, scalability in data size and dimension (without relying on subsampling of largescale, highdimensional singlecell data (>1 million cells)), and sensitivity of rarecell detection. We employ the clusterlevel topology, instead of a singlecelllevel graph, for TI as it provides a coarser but clearer view of the key linkages and pathways of the underlying cell dynamics without imposing constraints on the graph edges. Together with the strength of PARC in clustering scalability and sensitivity, this step critically allows VIA to faithfully reveal complex topologies namely cyclic, disconnected and multifurcating trajectories (Fig. 2). If the user prefers to use another clustering method or grouplabels of cell types according to apriori information, VIA can easily accommodate such a substitution and the robustness of the lazyteleporting random walks to different clustering approaches is shown in Supplementary Note 6 and Figs. S30–32 for real and synthetic data. The root cell is initialized by the user in one of two ways: If for instance there are some cell type/group/cluster level labels available in advance, the desired starting group can be indicated to VIA, which will then automatically select a cluster in its clustergraph that contains a majority of this particular cell type/group classification. In the case of many clusters satisfying this criteria, it subsequently proceeds to select the cluster in the VIA graph that has connectivity metrics indicative of a root (leaf) node (such as high out degree, low betweenness and low centrality). The user can also choose to provide a specific single cell as the root node. In the case that the user wishes to select the root based on the VIA graph, one would save the VIAclustergraph labels and use them to guide selection of the root node as described in the first approach.
Probabilistic pseudotime computation
The trajectories are then modeled in VIA as: (i) lazyteleporting random walk paths along which the pseudotime is computed and further refined by (ii) MCMC simulations. The root is a single cell chosen by the user.These two substeps are detailed as follows:
Lazyteleporting random walk
We first compute the pseudotime as the expected hitting time of a lazyteleporting random walk on an undirected clustergraph generated in Step 1. The lazyteleporting nature of this random walk ensures that as the sample size grows, the expected hitting time of each node does not converge to the stationary probability given by local node properties, but instead continues to incorporate the wider global neighborhood information^{15}. Here we highlight the derivation of the closed form expression of the hitting time of this modified random walk with a detailed derivation in Supplementary Note 2.
The cluster graph constructed in VIA is defined as a weighted connected graph G (V, E, W) with a vertex set V of n vertices (or nodes), i.e., \(V\,=\,\{{v}_{1},\cdots ,{v}_{n}\}\) and an edge set E, i.e., a set of ordered pairs of distinct nodes. W is an \(n\,\times\, n\) weight matrix that describes a set of edge weights between node i and j, \({w}_{ij}\,\ge\, 0\) are assigned to the edges \(({v}_{i},{v}_{j})\). For an undirected graph, \({w}_{ij}\,=\,{w}_{ji}\), the \(n\,\times\, n\) probability transition matrix, P, of a standard random walk on G is given by
where D is the n × n degree matrix, which is a diagonal matrix of the weighted sum of the degree of each node, i.e., the matrix elements are expressed as
where k are the neighboring nodes connected to node i. Hence, \({d}_{ii}\) (which can be reduced as \({d}_{i}\)) is the degree of node i. We next consider a lazy random walk, defined as Z, with probability (\(1\,\,x\)) of being lazy (where \(0 \, < \, x \, < \, 1\)), i.e., staying at the same node, then
where I is the identity matrix. When teleportation occurs with a probability (\(1\,\,\alpha\)), the modified lazyteleporting random walk Z′ can be written as follows, where \(J\)is an \(n\,\times\, n\) matrix of ones.
Here we adapt the concept of personalized PageRank vector, originally used for recording (or ranking) personal preferences of a websurfer toward particular website pages^{48}, to rank the importance of other nodes (clusters of cells) to a given node, depending on the similarities among nodes (related to P in the graph), and the lazyteleporting random walk characteristics in the graph (set by probabilities of teleporting and being lazy). Based on this concept, one could model the likelihood to transit from one node (cluster of cells) to another, and thus construct the pseudotime based on the hitting time, which is a parameter describing the expected number of steps it takes for a random walk that starts at node i and visit node j for the first time. Consider the teleporting probability of (\(1\,\,\alpha\)) and a seed vector s specifying the initial probability distribution across the n nodes (such that \(\mathop{\sum}\nolimits_{m}{s}_{m}\,=\,1\), where s_{m} is the probability of starting at node m) the personalized PageRank vector \(p{r}_{\alpha }(s)\) (which is defined as a column vector) is the unique solution to^{49}
Substituting Z (Eq. (3)) into Eq. (5), we can express the personalized PageRank vector \(p{r}_{\alpha }(s)\) in terms of the inverse of the \({{{{{\boldsymbol{\beta }}}}}}\)normalized Laplacian, \({R}_{\beta ,NL}\) of the modified random walk (Supplementary Note 2), i.e.,
where \(\beta \,=\,\frac{2(1\,\,\alpha )}{(2\,\,\alpha )}\), and \({{{{{{\bf{R}}}}}}}_{{{{{{\boldsymbol{\beta }}}}}},{{{{{\bf{N}}}}}}{{{{{\bf{L}}}}}}}\,=\,\mathop{\sum}\nolimits_{m\,=\,1}\frac{{{{{{{\boldsymbol{\Phi }}}}}}}_{{{{{{\rm{m}}}}}}}{{{{{{\boldsymbol{\Phi }}}}}}}_{{{{{{\rm{m}}}}}}}^{{{{{{\rm{T}}}}}}}}{[\beta \,+\,2x(1\,\,\beta ){{{{{{\boldsymbol{\eta }}}}}}}_{{{{{{\bf{m}}}}}}}]}\). \({{{{{{\boldsymbol{\Phi }}}}}}}_{{{{{{\bf{m}}}}}}}\) and \({{{{{{\boldsymbol{\eta }}}}}}}_{{{{{{\bf{m}}}}}}}\) are the m^{th} eigenvector and eigenvalue of the normalized Laplacian. In the expression of \({{{{{{\bf{R}}}}}}}_{{{{{{\boldsymbol{\beta }}}}}},{{{{{\bf{N}}}}}}{{{{{\bf{L}}}}}}}\), the \(\,{{{{{\boldsymbol{\beta }}}}}}\) and x regulate the weight of contribution in each eigenvalueeigenvector pair of the summation such that the first eigenvalueeigenvector pair (corresponding to the stationary distribution and given by the localnode degreeproperties) remains included in the overall expression, but does not overwhelm the global information provided by subsequent “eigenpairs”. Moreover, computation of \({{{{{{\bf{R}}}}}}}_{{{{{{\boldsymbol{\beta }}}}}},{{{{{\bf{N}}}}}}{{{{{\bf{L}}}}}}}\) is not limited to a subset of the first k eigenvectors (bypassing the need for the user to select a suitable threshold or subset of eigenvectors) since the dimensionality is not on the order of number of cells, but equal to the number of clusters and hence all eigenvalue–eigenvector pairs can be incorporated without causing a bottleneck in runtime.
The expected hitting time from node q to node r is given by^{50},
where \({e}_{i}\)is an indicator vector with 1 in the i^{th} entry and 0 elsewhere (i.e., \({s}_{m}\,=\,1\) if \(m\,=\,i\,\) and \({s}_{m}\,=\,0\) if \(m\,\ne\, i\)). We can substitute Eq. (6) into Eq. (7), making use of the fact that \(\frac{1}{{d}_{r}}\,=\,[{{{{{{\bf{D}}}}}}}^{1}{{{{{{\bf{e}}}}}}}_{{{{{{\bf{r}}}}}}}](r)\), and \({{{{{{\bf{D}}}}}}}^{0.5}{{{{{{\bf{R}}}}}}}_{{{{{{\boldsymbol{\beta }}}}}},{{{{{\bf{N}}}}}}{{{{{\bf{L}}}}}}}{{{{{{\bf{D}}}}}}}^{0.5}\) is symmetric, to obtain a closed form expression of the hitting time in terms of \({{{{{{\bf{R}}}}}}}_{{{{{{\boldsymbol{\beta }}}}}},{{{{{\bf{N}}}}}}{{{{{\bf{L}}}}}}}\)
MCMC simulation
The hitting time metric computed in Step1 is used to infer graphdirectionality. Instead of pruning edges in the “reverse” direction, edgeweights are biased based on the time difference between nodes using the logistic function with growth factor b = 1.
We then recompute the pseudotimes on the forward biased graph: Since there is no closed form solution of hitting times on a directed graph, we perform MCMC simulations (parallely processed to enable fast simulations of 1000 s of teleporting, lazy random walks starting at the root node of the cluster graph) and use the first quartile of the simulated pseudotime values for a respective node as the refined pseudotime for that node relative to the root. This refinement step ensures that the pseudotime is robust to the spurious links (or conversely, links that are too weakly weighted) that can distort calculations based purely on the closed form solution of hitting times (Supplementary Fig. 7d). By using this 2step pseudotime computation, VIA mitigates the issues of convergence issues and spurious edgeweights, both of which are common in randomwalk pseudotime computation on large and complex datasets^{15}.
Automated terminalstate detection
The algorithm uses the refined directed and weighted graph (edges are reweighted using the refined pseudotimes) to predict which nodes represent the terminal states based on a consensus vote of pseudotime and multiple vertex connectivity properties, including outdegree (i.e., the number of edges directed out of a node), closeness C(q), and betweenness B(q).
\(l(q,r)\) is the distance between node q and node r (i.e., the sum of edges in a shortest path connecting them). \({\sigma }_{rt}\) is the total number of shortest paths from node r to node t. \({\sigma }_{rt}(q)\) is the number of these paths passing through node q. The consensus vote is performed on nodes that score above (or below for outdegree) the median in terms of connectivity properties. We show on multiple simulated and real biological datasets that VIA more accurately predicts the terminal states, across a range of input data dimensions and key algorithm parameters, than other methods attempting the same (Supplementary Fig. 1).
Automated trajectory reconstruction
VIA then identifies the most likely path of each lineage by computing the likelihood of a node traversing towards a particular terminal state (e.g., differentiation). These lineage likelihoods are computed as the visitation frequency under lazyteleporting MCMC simulations from the root to a particular terminal state, i.e., the probability of node i reaching terminalstate j as the number of times cell i is visited along a successful path (i.e., terminalstate j is reached) divided by the number of times cell i is visited along all of the simulations. In contrast to other trajectory reconstruction methods which compute the shortest paths between root and terminal node^{1,2}, the lazyteleporting MCMC simulations in VIA offer a probabilistic view of pathways under relaxed conditions that are not only restricted to the randomwalk along a treelike graph, but can also be generalizable to other types of topologies, such as cyclic or connected/disconnected paths. In the same vein, we avoid confining the graph to an absorbing Markov chain^{18,51} (AMC) as this places prematurely strict/potentially inaccurate constraints on nodetonode mobility and can impede sensitivity to cell fates (as demonstrated by VIA’s superior cell fate detection across numerous datasets (Supplementary Fig. 1).
Downstream visualization and analysis
VIA generates a visualization that combines the network topology and singlecell level pseudotime/lineage probability properties onto an embedding based on UMAP or PHATE. Generalized additive models (GAMs) are used to draw edges found in the highdimensional graph onto the lower dimensional visualization (Fig. 1). An unsupervised downstream analysis of cell features (e.g., marker gene expression, protein expression or image phenotype) along pseudotime for each lineage is performed (Fig. 1). Specifically, VIA plots the expression of features across pseudotime for each lineage by using the lineage likelihood properties to weight the GAMs. A clusterlevel lineage pathway is automatically produced by VIA to visualize feature heat maps at the clusterlevel along a lineagepath to see the regulation of genes. VIA provides the option of gene imputation before plotting the lineage specific gene trends. The imputation is fast as it relies on the singlecell KNN (scKNN) graph computed in Step 1. Using an affinitybased imputation method^{52}, this step computes a “diffused” transition matrix on the scKNN graph used to impute and denoise the original gene expressions.
Simulated data
We employed the DynToy^{5} (https://github.com/dynverse/dyntoy) package, which generates synthetic singlecell gene expression data (~1000 cells × 1000 “genes”), to simulate different complex trajectory models. Using these datasets, we tested that VIA consistently and more accurately captures both tree and nontree like structures compared to other methods (Fig. 2). The types of topologies span multifurcating, cyclic, connected (hybrid of cyclic and multifurcating) and disconnected (hybrid of the first three). All methods are subject to the same data preprocessing steps, PCA dimension reduction, and rootcell to initialize the path.
The composite accuracy metric assesses multiple layers of the inferred trajectory, taking into account the topological similarity between the reference model and the inferred topology, the correlation between the real and “pseudo” times, and the prediction accuracy of the terminal cell fates (lineages). Absolute measurements of similarities are converted into a percentage scale before taking the arithmetic mean (of the 5 metrics, see below) which gives the composite accuracy. Since PAGA does not predict lineages, the composite score is simply the average of the first 4 metrics for PAGA. A detailed explanation of the 5 metrics can be referred to Supplementary Note 3. The 5 metrics are:
Ipsen–Mikhailov (IM)
is used to measure the similarity of global graph topology. The IM ranges from 0 to 1 and equals the difference in spectral densities of two graphs.
Graph edit distance (GED)
is the cost of converting \({G}_{TI}\) to \({G}_{REF}\) with the least possible number of operations. Each operation has a cost of one and includes insertion/deletion of edges and nodes.
F1branch score
We compute the harmonic mean of recall and precision for the local branch accuracy relative to the reference model. A False Negative edge in the inferred model is when there is an edge in the reference model between cell types that is absent in the inferred trajectory. A False Positive edge in the inferred model is an edge that is not actually present in the reference model.
Temporal correlation
Pearson correlation coefficient is used as a measure of how closely the inferred pseudotime follows the true sampling times.
F1cell fate score
Similar to the F1branch score, we use the harmonic mean of recall and precision to quantify the prediction accuracy of terminal states.
Benchmarked methods
The methods were mainly chosen based on their superior performance in a recent largescale benchmarking study^{5}, including a select few recent methods claiming to supersede those in the study. Specifically, recent and popular methods exhibiting reasonable scalability, and automated cell fate prediction in multilineage trajectories, not limited to treetopologies, were favored as candidates for benchmarking (see Supplementary Table 1 for the key characteristics of methods). Performance stresstests in terms of lineage detection of each biological dataset, automated gene trend prediction along lineages, and pseudotime correlation were conducted over a range of key input parameters (e.g., numbers of knearest neighbors, highly variable genes (HVGs), PCs) and preprocessing protocols (see Supplementary Fig. 1). Methods that focus exclusively on a single data modality or on topology without predicting cell fates and their lineage pathways (e.g., TinGa^{53}, Tempora^{54}) were generally not included in the benchmarking as they would require manual selection of cell fates and differentiation pathways. All comparisons were run on a computer with an Intel(R) Xeon (R) W2123 central processing unit (3.60 GHz, 8 cores) and 126 GB RAM.
Details of parameter settings for each of the benchmarked methods can be found in Supplementary Tables 4, 5, with an emphasis on the rationale for changes deviating from default parameters.
Quantifying terminal state prediction accuracy for parameter tests was done using the F1score, defined as the harmonic mean of recall and precision and calculated as:
Where tp is a truepositive: the identification of a terminal cluster that is in fact a final differentiated cell fate; fp is a false positive identification of a cluster as terminal when in fact it represents an intermediate state; and fn is a false negative where a known cell fate fails to be identified.
Downstream analysis enabled by the automated lineage prediction capabilities of each method is key to facilitating the exploration of biological data. The unsupervised genetrend analysis inferred by VIA is compared to the lineage genetrends predicted by other methods both quantitatively and qualitatively. We follow an approach used by Chen et al.^{3} where pseudotime is correlated against expression of a marker gene known to monotonically increase along the lineage. The geneexpression of such markers can be considered a surrogate for the correct sampling time and thus the resulting correlation is an indication of the accuracy of cell ordering by pseudotime. We also provide a sidebyside comparison of the predicted topology and genetrends generated by each method to visually assess how well separated the predicted lineages are (e.g., if multiple lineages that represent distinct cell fates exhibit significant crosstalk in the plotted trends or uniquely express the genes most relevant to their lineages). The Pearson correlation coefficient is given by \({\rho }_{x,y}\), where \({\sigma }_{X}\) is the standard deviation and \({\mu }_{X}\) is the mean of X
Builtin functions for genetrend plotting (wherever available), and in other cases manually selection of branches/clusters or extension of a method by adding GAMs to general genetrend curves was required to facilitate comparison (e.g., PAGA and STREAM). Additionally, when methods cannot automatically detect all the relevant lineages, we either chose the most relevant lineage (e.g., for the megakaryocyte lineage, we plotted its CD41 marker gene along the detected erythroid lineage which often absorbed the smaller megakaryocytic cell line), or we noted that the lineage was missed, (e.g., in the small delta cell population in the endocrine dataset) when the lost lineage was not an obvious part of another lineage. Given that these nuances are not necessarily captured by the correlation coefficient,the outputs of the genetrend plots inferred by each method are shown for three datasets which have multiple lineages of different abundances, and well known lineage markers (scRNAseq and scATACseq hematopoiesis, and endocrine genesis in Supplementary Figs. 9, 11, 15).
PAGA^{55}
It uses a clustergraph representation to capture the underlying topology. PAGA computes a unified pseudotime by averaging the singlecell level diffusion pseudotime computed by DPT, but requires manual specification of terminal cell fates and clusters that contribute to lineages of interest in order to compare gene expression trends across lineages.
Palantir^{2}
It uses diffusionmap^{56}. components to represent the underlying trajectory. Pseudotimes are computed as the shortest path along a KNNgraph constructed in a lowdimensional diffusion component space, with edges weighted such that the distance between nodes corresponds to the diffusion pseudotime^{57} (DPT). Terminal states are identified as extrema of the diffusion maps that are also outliers of the stationary distribution. The lineagelikelihood probabilities are computed using Absorbing Markov Chains (constructed by removing outgoing edges of terminal states, and thresholding reverse edges).
Slingshot^{1}
It is designed to process lowdimensional embeddings of the singlecell data. By default Slingshot runs clustering based on Gaussian mixture modeling and recommends using the first few PCs as input. Slingshot connects the clusters using a minimum spanning tree and then fits principle curves for each detected branch. It uses the orthogonal projection against each principal curve to fit a separate pseudotime for each lineage, and hence the gene expressions cannot be compared across lineages. Also, the runtimes are prohibitively long for large datasets or high input dimensions.
CellRank^{13}
This method combines the information of RNA velocity (computed using scVelo^{58}) and geneexpression to infer trajectories. Given it is mainly suited for the scRNAseq data, with the RNAvelocity computation limiting the overall runtime for larger dataset, we limit our comparison to the pancreatic dataset which the authors of CellRank used to highlight its performance.
Monocle3^{4}
The workflow consists of three steps: the first is to project the data to two or three dimensions using UMAP (this is a strict requirement), followed by Louvain clustering on a KNearest Neighbor graph constructed in the lowdimensional UMAP space. A clustergraph is then created and partitioned to deduce disconnected trajectories. Subsequently, it learns a principal graph in the lowdimensional space along which it calculates pseudotimes as the geodesic distance from root to cell.
STREAM^{3}
After selecting the desired number of PCs, STREAM projects the cells to a lower dimensional PCA space using a nonlinear dimensionality reduction method (such as Modified Locally Linear Embedding, Spectral Embedding or UMAP). In the embedded space, STREAM constructs a treemodel trajectory using an Elastic Principal Graph implementation called ElPiGraph. The results are visualized as a branching structure or reorganized as a subway plot relative to a userdesignated starting branch.
Biological data
The preprocessing steps described below for each dataset are not included in the reported runtimes as these steps are typically very fast, (typically <1–10% of the total runtime depending on the method. E.g., only a few minutes for preprocessing 100,000 s of cells) and only need to be performed once as they remain the same for all subsequent analyses. It should also be noted that visualization (e.g., UMAP, tSNE) are not included in the runtimes. VIA provides a subsampling option at the visualization stage to accelerate this process for large datasets without impacting the previous computational steps. However, to ensure fair comparisons between TI methods (e.g., other methods do not have an option to compute the embedding on a subsampled input and transfer the results between the full trajectory and the sampled visualization, or rely on a slow version of tSNE), we simply provide each TI method with a precomputed visualization embedding on which the computed results are projected.
ScRNAseq of mouse preB cells
This dataset^{21} models the preBI cell (Hardy fraction C′) process during which cells progress to the preBII stage and B cell progenitors undergo growth arrest and differentiation. Measurements were obtained at 0, 2, 6, 12, 18, and 24 h (h) for a total of 313 cells × 9075 genes. We follow a standard Scanpy preprocessing recipe^{59} that filters cells with low counts, and genes that occur in <3 cells. The filtered cells are normalized by library size and log transformed. The top 5000 HVG are retained. Cells are renormalized by library count and scaled to unit variance and zero mean. VIA identifies the terminal state at 18–24 h and accurately recapitulates the gene expression trends^{21} along inferred pseudotime of IgII1, Slc7a5, Fox01, Myc, Ldha, and Lig4. (Supplementary Fig. 6a). We show the results generalize across a range of PCs for two values of K of the graph with higher accuracy in locating the later cell fates than Slingshot and Palantir (Supplementary Fig. 6b).
ScRNAseq of human CD34+ bone marrow cells
This is a scRNAseq dataset of 5800 cells representing human hematopoiesis^{2}. We used the filtered, normalized and logtransformed count matrix provided by Setty et al.^{2} with PCA performed on all the remaining (~14,000) genes. The cells were annotated using SingleR^{60}. which automatically labeled cells based on the hematopoietic reference dataset Novershtern Hematopoietic Cell Data—GSE24759^{61}. The annotations are in agreement with the labels inferred by Setty et al. for the seven clusters, including the root HSCs cluster that differentiates into six different lineages: monocytes, erythrocytes, and B cells, as well as the less populous megakaryocytes, cDCs, and pDCs. VIA consistently identifies these lineages across a wider range of input parameters and data dimensions (e.g., the number of K and PCs provided as input to the algorithms see Fig. 2p, and Supplementary Figs. 7–9). Notably, the upregulated gene expression trends of the small populations can be recovered in VIA, i.e., pDC and cDC show elevated CD123 and CSF1R levels relative to other lineages, and the upregulated CD41 expression in megakaryocytes (Supplementary Figs. 7–9).
ScRNAseq of human embryoid body
This is a midsized scRNAseq dataset of 16,825 human cells in embryoid bodies (EBs)^{17}. We followed the same preprocessing steps as Moon et al. to filter out dead cells and those with too high or low library count. Cells are normalized by library count followed by square root transform. Finally the transformed counts are scaled to unit variance and zero mean. The filtered data contained 16,825 cells × 17,580 genes. PCA is performed on the processed data before running each TI method. VIA identifies six cell fates, which, based on the upregulation of marker genes as cells proceed towards respective lineages, are in accord with the annotations given by Moon et al. (see the gene heatmap and changes in gene expression along respective lineage trajectories in Supplementary Fig. 13). Note that Palantir and Slingshot do not capture the cardiac cell fate, and Slingshot also misses the neural crest (see the F1scores summary for terminal state detection Supplementary Fig. 13).
ScRNAseq of mouse organogenesis cell atlas
This is a large and complex scRNAseq dataset of mouse organogenesis cell atlas (MOCA) consisting of 1.3 million cells^{4}. The dataset contains cells from 61 embryos spanning 5 developmental stages from early organogenesis (E9.5–E10.5) to organogenesis (E13.5). Of the 2 million cells profiled, 1.3 million are “highquality” cells that are analysed by VIA. The runtime is ~40 min which is in stark contrast to the next fastest tool Palantir which takes 4 h (excluding visualization). The authors of MOCA manually annotated 38 celltypes based on the differentially expressed genes of the clusters. In general, each cell type exclusively falls under one of 10 major and disjoint trajectories inferred by applying Monocle3 to the UMAP of MOCA. The authors attributed the disconnected nature of the ten trajectories to the paucity of earlier stage common predecessor cells. We followed the same steps as Cao et al.^{4} to retain highquality cells (i.e., remove cells with less than 400 mRNA, and remove doublet cells and cells from doubled derived subclusters). PCA was applied to the top 2000 HVGs with the top 30 PCs selected for analysis. VIA analyzed the data in the highdimensional PC space. We bypass the step in Monocle3^{4} which applies UMAP on the PCs prior to TI as this incurs an additional bias from choice of manifoldlearning parameters and a further loss in neighborhood information. As a result, VIA produces a more connected structure with linkages between some of the major cell types that become segregated in UMAP (and hence Monocle3), and favors a biologically relevant interpretation (Fig. 2, Supplementary Fig. 11). A detailed explanation of these connections (graphedges) extending between certain major groups using references to literature on organogenesis is presented in Supplementary Note 3.
ScRNAseq of murine endocrine development^{23}
This is an scRNAseq dataset of E15.5 murine pancreatic cells spanning all developmental stages from an initial endocrine progenitorprecursor (EP) state (low level of Ngn3, or Ngn3^{low}), to the intermediate EP (high level of Ngn3, or Ngn3^{high}) and Fev^{+} states, to the terminal states of hormoneproducing alpha, beta, epsilon, and delta cells^{23}. Following steps by Lange et al.^{18} we preprocessed the data using scVelo to filter genes, normalize each cell by total counts over all genes, keep the top most variable genes, and take the logtransform. PCA was applied to the processed gene matrix. We assessed the performance of VIA and other TI methods (CellRank, Palantir, Slingshot) across a range of number of retained HVGs and input PCs (Fig. 2m, Supplementary Figs. 16, 16, 18, 29).
ScATACseq of human bone marrow cells
This scATACseq data profiles 3072 cells isolated from human bone marrow using FL activated cell sorting (FACS), yielding 9 populations^{20}: HSC, MPP, CMP, CLP, LMPP, GMP, MEP, mono, and plasmacytoid DCs (Fig. 3a and Supplementary Figs. 10, 11). We examined TI results for two different preprocessing pipelines to gauge how robust VIA is on the scATACseq analysis which is known to be challenging for its extreme intrinsic sparsity. We used the preprocessed data consisting of PCA applied to the zscores of the transcription factor (TF) motifs used by Buenrostro et a^{20}. Their approach corrects for batch effects in select populations and weighting of PCs based on reference populations and hence involves manual curation. We also employed a more general approach used by Chen et al.^{22} which employs ChromVAR to compute kmer accessibility zscores across cells. VIA infers the correct trajectories and the terminal cell fates for both of these inputs, again across a wide range of input parameters (Fig. 3d and Supplementary Figs. 11–13).
ScRNAseq and scATACseq of Isl1+ cardiac progenitor cells
This timeseries dataset captures murine Isl1+ cardiac progenitor cells (CPCs) from E7.5 to E9.5 characterized by scRNAseq (197 cells) and scATACseq (695 cells)^{26}. The Isl1+ CPCs are known to undergo multipotent differentiation to cardiomyocytes or endothelial cells. For the scRNAseq data, the quality filtered genes and the sizefactor normalized expression values are provided by Jia et al.^{26} as a “Single Cell Expression Set” object in R. Similarly, the cells in the scATACseq experiment were provided in a “SingleCellExperiment” object with low quality cells excluded from further analysis. The accessibility of peaks was transformed to a binary representation as input for TFIDF (term frequencyinverse document frequency) weighting prior to singular value decomposition (SVD). The highlighted TF motifs in the heatmap (Fig. 2j) correspond to those highlighted by Jia et al. We tested the performance when varying the number of SVDs used. We also considered the outcome when merging the scATACseq and scRNAseq data using Seurat3^{62}. Despite the relatively low cell count of both datasets, and the relatively underrepresented scRNAseq cell count, the two datasets overlapped reasonably well and allowed us to infer the expected lineages in an unsupervised manner (Fig. 2d and Supplementary Fig. 8. In contrast, Jia et al. performed a supervised TI by manually selecting cells relevant to the different lineages (for the scATACseq cells) and choosing the two diffusion components that best characterize the developmental trajectories in low dimension^{26}.
Mass cytometry data of mouse embryonic stem cells (mESC)
This is a mass cytometry (or CyTOF) dataset, consisting of 90,000 cells and 28 antibodies (corresponding to ~7000 cells each from Day 0–11 measurements), that represents differentiation of mESC to mesoderm cells^{36}. An arcsinh transform with a scaling factor of five was applied on all features—a standard procedure for CyTOF datasets, followed by normalization to unit variance and zero mean. All 28 antibodies are used by the TI methods (with the exception of Slingshot which requires PCA followed by subsetting of the first 5 PCs in order to computationally handle the high cell count) (Supplementary Fig. 9). To improve Palantir performance we used 5000 waypoints (instead of default 1200) but this takes almost 20 min to complete (excluding time taken for embedding the visualization). VIA runs in ~3 min and produces results consistent with the known ordering and identifies regions of Day 10–11 cells.
Singlecell biophysical phenotypes derived from imaging flow cytometry
This is the inhouse dataset of singlecell biophysical phenotypes of two different human breast cancer types (MDAMB231 and MCF7). Following our recent imagebased biophysical phenotyping strategy^{63,64} we defined the spatiallyresolved biophysical features of a cell in a hierarchical manner based on both brightfield and QPI captured by the FACED imaging flow cytometer (i.e., from the bulk features to the subcellular textures)^{65}. At the bulk level, we extracted the cell size, dry mass density, and cell shape. At the subcellular texture level, we parameterized the global and local textural characteristics of optical density and mass density at both the coarse and fine scales (e.g., local variation of mass density, its higherorder statistics, phase entropy radial distribution etc.). This hierarchical phenotyping approach^{63,64} allowed us to establish a singlecell biophysical profile of 38 features, which were normalized based on the zscore (see Supplementary Tables 4, 5). All these features, without any PCA, are used as input to VIA. In order to weigh the features, we use a mutual information classifier to rank the features, based on the integrated FL intensity of the FL FACED images of the cells (which serve as the ground truth of the cellcycle stages). Following normalization, the top three features (which relate to cell size) are weighted (using a factor between 3 and 10).
Imaging flow cytometry experiment
FACED imaging flow cytometer setup
A multimodal FACED IFC platform was used to obtain the quantitative phase and FL images of single cells in microfluidic flow at an imaging throughput of ~70,000 cells/s. The light source consisted of an Nd:YVO picosecond laser (center wavelength = 1064 nm, TimeBandwidth) and a periodicallypoled lithium niobate (PPLN) crystal (Covesion) for second harmonic generation of a green pulsed beam (center wavelength = 532 nm) with a repetition rate of 20 MHz. The beam was then directed to the FACED module, which mainly consists of a pair of almostparallel plane mirrors. This module generated a linear array of 50 beamlets (foci) which were projected by an objective lens (40X, 0.6NA, MRH08430, Nikon) on the flowing cells in the microfluidic channel for imaging. Each beamlet was designed to have a time delay of 1 ns with the neighboring beamlet in order to minimize the FL crosstalk due to the FL decay. Detailed configuration of the FACED module can be referred to Wu et al.^{13}. The epifluorescence image signal was collected by the same objective lens and directed through a bandpass dichroic beamsplitter (center: 575 nm, bandwidth: 15 nm). The filtered orange FL signal was collected by the photomultiplier tube (PMT) (rise time: 0.57 ns, Hamamatsu). On the other hand, the transmitted light through the cell was collected by another objective lens (40X, 0.8NA, MRD07420, Nikon). The light was then split equally by the 50:50 beamsplitter into two paths, each of which encodes different phasegradient image contrasts of the same cell (a concept similar to Scherlien photography^{66}). The two beams are combined, timeinterleaved, and directed to the photodetector (PD) (bandwidth: >10 GHz, Alphalas) for detection. The signals obtained from both PMT and PD were then passed to a realtime highbandwidth digitizer (20 GHz, 80 GS/s, Lecroy) for data recording.
Cell culture and preparation
MDAMB231 (ATCC) and MCF7 (ATCC), which are two different breast cancer cell lines, were used for the cell cycle study. The culture medium for MDAMB231was ATCC modified RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% antibioticantimycotic (AntiAnti) (Gibco), while that for MCF7 was DMEM supplemented with 10% FBS (Gibco) and 1% AntiAnti (Gibco). The cells were cultured inside an incubator under 5% CO_{2} and 37 °C, and subcultured twice a week. 1e6 cells were pipetted out from each cell line and stained with Vybrant DyeCycle orange stain (Invitrogen).
Reporting summary
Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Data availability
The Pancreatic data used in this study are available in the Gene Expression Omnibus (GEO) database under accession code GSE132188. The Cardiac progenitor data used in this study are available in the ENA repository under the accession code PRJEB23303 or from [https://github.com/loosolab/cardiacprogenitors]. The Bcell data used in this study are available in the STATegraData GitHub repository. [https://github.com/STATegraData/STATegraData] and under the GEO database under accession code GSE75417. The Mass cytometry mesoderm data used in this study are available in the Cytobank database [https://community.cytobank.org/cytobank/experiments/71953]. The scRNAseq Human Hematopoiesis data used in this study are available in the Human Cell Atlas data portal database [https://data.humancellatlas.org/explore/projects/091cf39b01bc42e59437f419a66c8a45]. The Embryoid Body data used in this study are available in the Mendeley Data database at [https://doi.org/10.17632/v6n743h5ng.1]. The Mouse organogenesis data used in this study are available in the NCBI Gene Expression Omnibus database under accession code GSE119945. The FACED cell cycle data used in this study are available at https://github.com/ShobiStassen/VIA and on FigShare database [https://doi.org/10.6084/m9.figshare.13601405.v1]. The scATACseq Hematopoiesis data used in this study are available in the GEO database under accession code GSE96772. Processed scATACseq data, which include PC values and TF scores per cell can be found in Data S1. [https://doi.org/10.1016/j.cell.2018.03.074]. The Toy Data used in the study is available in [https://zenodo.org/record/5205377] https://doi.org/10.5281/zenodo.5205377 [https://github.com/ShobiStassen/VIA].
Code availability
VIA is available as a pip installable python library “pyVIA” with tutorials and sample data available on https://github.com/ShobiStassen/VIA, https://pypi.org/project/pyVIA/ and https://zenodo.org/record/5205377^{67}.
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Acknowledgements
This work was funded by the Research Grants Council of the Hong Kong Special Administrative Region of China (grant nos. 17208918, 17209017, 17259316, RFS20217S06, and C704716G).
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K.K.T., J.W.K.H. and S.V.S. conceived the project. S.V.S developed the algorithm and software to analyze the data. S.V.S. G.G.K.Y. and K.K.Y.W. designed and performed the FACED experiments. K.K.T. and S.V.S. wrote the paper. All authors commented on and edited the text.
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Stassen, S.V., Yip, G.G.K., Wong, K.K.Y. et al. Generalized and scalable trajectory inference in singlecell omics data with VIA. Nat Commun 12, 5528 (2021). https://doi.org/10.1038/s41467021257733
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DOI: https://doi.org/10.1038/s41467021257733
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