Reconstructing complex lineage trees from scRNA-seq data using MERLoT

Advances in single-cell transcriptomics techniques are revolutionizing studies of cellular differentiation and heterogeneity. It has become possible to track the trajectory of thousands of genes across the cellular lineage trees that represent the temporal emergence of cell types during dynamic processes. However, reconstruction of cellular lineage trees with more than a few cell fates has proved challenging. We present MERLoT (https://github.com/soedinglab/merlot), a flexible and user-friendly tool to reconstruct complex lineage trees from single-cell transcriptomics data. It can impute temporal gene expression profiles along the reconstructed tree. We show MERLoT’s capabilities on various real cases and hundreds of simulated datasets

Active dendrites enhance neuronal dynamic range

Since the first experimental evidences of active conductances in dendrites, most neurons have been shown to exhibit dendritic excitability through the expression of a variety of voltage-gated ion channels. However, despite experimental and theoretical efforts undertaken in the last decades, the role of this excitability for some kind of dendritic computation has remained elusive. Here we show that, owing to very general properties of excitable media, the average output of a model of active dendritic trees is a highly non-linear function of their afferent rate, attaining extremely large dynamic ranges (above 50 dB). Moreover, the model yields double-sigmoid response functions as experimentally observed in retinal ganglion cells. We claim that enhancement of dynamic range is the primary functional role of active dendritic conductances. We predict that neurons with larger dendritic trees should have larger dynamic range and that blocking of active conductances should lead to a decrease of dynamic range.Comment: 20 pages, 6 figure

The number and degree distribution of spanning trees in the Tower of Hanoi graph

The number of spanning trees of a graph is an important invariant related to topological and dynamic properties of the graph, such as its reliability, communication aspects, synchronization, and so on. However, the practical enumeration of spanning trees and the study of their properties remain a challenge, particularly for large networks. In this paper, we study the number and degree distribution of the spanning trees in the Hanoi graph. We first establish recursion relations between the number of spanning trees and other spanning subgraphs of the Hanoi graph, from which we find an exact analytical expression for the number of spanning trees of the n-disc Hanoi graph. This result allows the calculation of the spanning tree entropy which is then compared with those for other graphs with the same average degree. Then, we introduce a vertex labeling which allows to find, for each vertex of the graph, its degree distribution among all possible spanning trees.Postprint (author's final draft

Distributed Maintenance of Anytime Available Spanning Trees in Dynamic Networks

We address the problem of building and maintaining distributed spanning trees in highly dynamic networks, in which topological events can occur at any time and any rate, and no stable periods can be assumed. In these harsh environments, we strive to preserve some properties such as cycle-freeness or the existence of a root in each tree, in order to make it possible to keep using the trees uninterruptedly (to a possible extent). Our algorithm operates at a coarse-grain level, using atomic pairwise interactions in a way akin to recent population protocol models. The algorithm relies on a perpetual alternation of \emph{topology-induced splittings} and \emph{computation-induced mergings} of a forest of spanning trees. Each tree in the forest hosts exactly one token (also called root) that performs a random walk {\em inside} the tree, switching parent-child relationships as it crosses edges. When two tokens are located on both sides of a same edge, their trees are merged upon this edge and one token disappears. Whenever an edge that belongs to a tree disappears, its child endpoint regenerates a new token instantly. The main features of this approach is that both \emph{merging} and \emph{splitting} are purely localized phenomenons. In this paper, we present and motivate the algorithm, and we prove its correctness in arbitrary dynamic networks. Then we discuss several implementation choices around this general principle. Preliminary results regarding its analysis are also discussed, in particular an analytical expression of the expected merging time for two given trees in a static context.Comment: Distributed Maintenance of Anytime Available Spanning Trees in Dynamic Networks, Poland (2013

Compositional synthesis of temporal fault trees from state machines

Dependability analysis of a dynamic system which is embedded with several complex interrelated components raises two main problems. First, it is difficult to represent in a single coherent and complete picture how the system and its constituent parts behave in conditions of failure. Second, the analysis can be unmanageable due to a considerable number of failure events, which increases with the number of components involved. To remedy this problem, in this paper we outline an analysis approach that converts failure behavioural models (state machines) to temporal fault trees (TFTs), which can then be analysed using Pandora -- a recent technique for introducing temporal logic to fault trees. The approach is compositional and potentially more scalable, as it relies on the synthesis of large system TFTs from smaller component TFTs. We show, by using a Generic Triple Redundant (GTR) system, how the approach enables a more accurate and full analysis of an increasingly complex system

Parameterized Approximation Schemes using Graph Widths

Combining the techniques of approximation algorithms and parameterized complexity has long been considered a promising research area, but relatively few results are currently known. In this paper we study the parameterized approximability of a number of problems which are known to be hard to solve exactly when parameterized by treewidth or clique-width. Our main contribution is to present a natural randomized rounding technique that extends well-known ideas and can be used for both of these widths. Applying this very generic technique we obtain approximation schemes for a number of problems, evading both polynomial-time inapproximability and parameterized intractability bounds