Related papers: Statistical study of asymmetry in cell lineage dat…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute…
Exploratory data analysis is crucial for developing and understanding classification models from high-dimensional datasets. We explore the utility of a new unsupervised tree ensemble called uncharted forest for visualizing class…
Branching processes model the evolution of populations of agents that randomly generate offsprings. These processes, more patently Galton-Watson processes, are widely used to model biological, social, cognitive, and technological phenomena,…
Network models provide a powerful framework for analysing single-cell count data, facilitating the characterisation of cellular identities, disease mechanisms, and developmental trajectories. However, uncertainty modeling in unsupervised…
Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though methods incorporating symmetries often require prior knowledge. While recent advancements have been made…
Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…
Recently, there has been interest in extending long-known results about the multispecies coalescent tree to other models of gene trees. Results about the gene duplication and loss (GDL) tree have mathematical proofs, including species tree…
Integrative analysis of datasets generated by multiple cohorts is a widely-used approach for increasing sample size, precision of population estimators, and generalizability of analysis results in epidemiological studies. However, often…
Single-cell data analysis seeks to characterize cellular heterogeneity based on high-dimensional gene expression profiles. Conventional approaches represent each cell as a vector in Euclidean space, which limits their ability to capture…
Segregation of different cell types is a crucial process for the pattern formation in tissues, in particular during embryogenesis. Since the involved cell interactions are complex and difficult to measure individually in experiments,…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
Trajectory inference is a critical problem in single-cell transcriptomics, which aims to reconstruct the dynamic process underlying a population of cells from sequencing data. Of particular interest is the reconstruction of differentiation…
This paper presents a model of asymmetric bifurcating autoregressive process with random coefficients. We couple this model with a Galton Watson tree to take into account possibly missing observations. We propose least-squares estimators…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
This article introduces a novel nonparametric methodology for Generalized Linear Models which combines the strengths of the binary regression and latent variable formulations for categorical data, while overcoming their disadvantages.…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
Graph alignment - identifying node correspondences between two graphs - is a fundamental problem with applications in network analysis, biology, and privacy research. While substantial progress has been made in aligning correlated…
The question of testing for equality in distribution between two linear models, each consisting of sums of distinct discrete independent random variables with unequal numbers of observations, has emerged from the biological research. In…
Growth-fragmentation processes model systems of cells that grow continuously over time and then fragment into smaller pieces. Typically, on average, the number of cells in the system exhibits asynchronous exponential growth and, upon…