Optimal distance query reconstruction for graphs without long induced cycles

Let $G=(V,E)$ be an $n$-vertex connected graph of maximum degree $\Delta$. Given access to $V$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? We give a simple deterministic algorithm to reconstruct trees using $\Delta n\log_\Delta n+(\Delta+2)n$ distance queries and show that even randomised algorithms need to use at least $\frac1{100} \Delta n\log_\Delta n$ queries in expectation. The best previous lower bound was an information-theoretic lower bound of $\Omega(n\log n/\log \log n)$. Our lower bound also extends to related query models including distance queries for phylogenetic trees, membership queries for learning partitions and path queries in directed trees. We extend our deterministic algorithm to reconstruct graphs without induced cycles of length at least $k$ using $O_{\Delta,k}(n\log n)$ queries, which includes various graph classes of interest such as chordal graphs, permutation graphs and AT-free graphs. Since the previously best known randomised algorithm for chordal graphs uses $O_{\Delta}(n\log^2 n)$ queries in expectation, we both get rid off the randomness and get the optimal dependency in $n$ for chordal graphs and various other graph classes. Finally, we build on an algorithm of Kannan, Mathieu, and Zhou [ICALP, 2015] to give a randomised algorithm for reconstructing graphs of treelength $k$ using $O_{\Delta,k}(n\log^2n)$ queries in expectation.Comment: 35 page

Exact antichain saturation numbers via a generalisation of a result of Lehman-Ron

For given positive integers $k$ and $n$, a family $\mathcal{F}$ of subsets of $\{1,\dots,n\}$ is $k$-antichain saturated if it does not contain an antichain of size $k$, but adding any set to $\mathcal{F}$ creates an antichain of size $k$. We use sat$^*(n, k)$ to denote the smallest size of such a family. For all $k$ and sufficiently large $n$, we determine the exact value of sat$^*(n, k)$. Our result implies that sat$^*(n, k)=n(k-1)-\Theta(k\log k)$, which confirms several conjectures on antichain saturation. Previously, exact values for sat$^*(n,k)$ were only known for $k$ up to $6$. We also prove a generalisation of a result of Lehman-Ron which may be of independent interest. We show that given $m$ disjoint chains in the Boolean lattice, we can create $m$ disjoint skipless chains that cover the same elements (where we call a chain skipless if any two consecutive elements differ in size by exactly one).Comment: 29 pages, 3 figure

Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees

Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To incorporate such uncertainty, we present a scalable Bayesian inference framework under a general Gaussian trait evolution model that exploits Hamiltonian Monte Carlo (HMC). HMC enables efficient sampling of the constrained model parameters and takes advantage of the tree structure for fast likelihood and gradient computations, yielding algorithmic complexity linear in the number of observations. This approach encompasses a wide family of stochastic processes, including the general Ornstein-Uhlenbeck (OU) process, with possible missing data and measurement errors. We implement inference tools for a biologically relevant subset of all these models into the BEAST phylogenetic software package and develop model comparison through marginal likelihood estimation. We apply our approach to study the morphological evolution in the superfamilly of Musteloidea (including weasels and allies) as well as the heritability of HIV virulence. This second problem furnishes a new measure of evolutionary heritability that demonstrates its utility through a targeted simulation study

Paneth cell - rich regions separated by a cluster of Lgr5+ cells initiate crypt fission in the intestinal stem cell niche

The crypts of the intestinal epithelium house the stem cells that ensure the continual renewal of the epithelial cells that line the intestinal tract. Crypt number increases by a process called crypt fission, the division of a single crypt into two daughter crypts. Fission drives normal tissue growth and maintenance. Correspondingly, it becomes less frequent in adulthood. Importantly, fission is reactivated to drive adenoma growth. The mechanisms governing fission are poorly understood. However, only by knowing how normal fission operates can cancer-associated changes be elucidated. We studied normal fission in tissue in three dimensions using high-resolution imaging and used intestinal organoids to identify underlying mechanisms. We discovered that both the number and relative position of Paneth cells and Lgr5+ cells are important for fission. Furthermore, the higher stiffness and increased adhesion of Paneth cells are involved in determining the site of fission. Formation of a cluster of Lgr5+ cells between at least two Paneth-cell-rich domains establishes the site for the upward invagination that initiates fission