arXiv subjects

Sebastien Roch

Publications and source records attributed to Sebastien Roch.

At least 19 recordsLinked to original sources

arXiv2025

Sample Complexity of Branch-length Estimation by Maximum Likelihood

We consider the branch-length estimation problem on a bifurcating tree: a character evolves along the edges of a binary tree according to a two-state symmetric Markov process, and we seek to recover the edge transition probabilities from repeated observations at the leaves. This problem arises in phylogenetics, and is related to latent tree graphical model inference. In general, the log-likelihood function is non-concave and may admit many critical points. Nevertheless, simple coordinate maximization has been known to perform well in practice, defying the complexity of the likelihood landscape. In this work, we provide the first theoretical guarantee as to why this might be the case. We show that deep inside the Kesten-Stigum reconstruction regime, provided with polynomially many $m$ samples (assuming the tree is balanced), there exists a universal parameter regime (independent of the size of the tree) where the log-likelihood function is strongly concave and smooth with high probability. On this high-probability likelihood landscape event, we show that the standard coordinate maximization algorithm converges exponentially fast to the maximum likelihood estimator, which is within $O(1/\sqrt{m})$ from the true parameter, provided a sufficiently close initial point.

stat.CO↗

arXiv2025

Likelihood landscape of binary latent model on a tree

We investigate the optimization landscape of maximum likelihood estimation (MLE) for the Cavender-Farris-Neyman (CFN) model, a two-state latent tree model fundamental to statistical phylogenetics and the ferromagnetic Ising model. Although the log-likelihood function is non-concave and may admit many critical points, simple coordinate maximization algorithms are remarkably effective in practice. We provide the first theoretical justification for this success. We prove that sufficiently deep inside the reconstruction regime, the population log-likelihood is strongly concave and smooth within a box around the true parameter, whose size is independent of tree topology and number of leaves. This fundamental result implies that the empirical landscape shares these regularity properties with high probability given polynomial sample complexity and also that coordinate maximization converges exponentially fast to an $O(1/\sqrt{m})$-consistent MLE. Our analysis centers on a novel decay property of the population Hessian: diagonal entries remain large while off-diagonal entries decay exponentially with graph distance. These results provide rigorous theoretical evidence for the efficacy of likelihood-based tree inference and suggest broader principles for latent variable models.

math.ST↗

arXiv2025

Likelihood-Based Root State Reconstruction on a Tree: Sensitivity to Parameters and Applications

We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state with edge-dependent probabilities. The goal of the reconstruction problem is to infer the root state given the observations at the leaves only. Specifically, we study the sensitivity of maximum likelihood estimation (MLE) to uncertainty in the edge parameters under this model, which is also known as the Cavender-Farris-Neyman (CFN) model. Our main result shows that when the true flip probabilities are sufficiently small, the posterior root mean (or magnetization of the root) under estimated parameters (within a constant factor) agrees with the root spin with high probability and deviates significantly from it with negligible probability. This provides theoretical justification for the practical use of MLE in ancestral sequence reconstruction in phylogenetics, where branch lengths (i.e., the edge parameters) must be estimated. As a separate application, we derive an approximation for the gradient of the population log-likelihood of the leaf states under the CFN model, with implications for branch length estimation via coordinate maximization.

math.PR↗

arXiv2024

Understanding Of Size And Scale And Order-Of-Magnitude Reasoning In Secondary Science: A Teaching Experiment With Worked Examples As Educational Scaffold

Understanding size and scale (USS) and order-of-magnitude reasoning (OMR) are critical for scientific literacy. This study examines an educational approach to enhance these skills in high school science, considering the cognitive prerequisites and challenges. It explores worked examples (WEs) as an effective method to teach USS and OMR, comparing their impact on students' knowledge and transfer abilities with conventional tasks in a quasi-experimental study. The results indicate significant improvements in procedural and conceptual knowledge, effective for diverse learners regardless of prior knowledge.

physics.ed-ph↗

arXiv2022

Expanding the class of global objective functions for dissimilarity-based hierarchical clustering

Recent work on dissimilarity-based hierarchical clustering has led to the introduction of global objective functions for this classical problem. Several standard approaches, such as average linkage, as well as some new heuristics have been shown to provide approximation guarantees. Here we introduce a broad new class of objective functions which satisfy desirable properties studied in prior work. Many common agglomerative and divisive clustering methods are shown to be greedy algorithms for these objectives, which are inspired by related concepts in phylogenetics.

cs.LG↗

arXiv2022

Pairwise sequence alignment at arbitrarily large evolutionary distance

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many biological applications, it has played a key role in elucidating the statistical performance of phylogeny estimation methods. Here we establish a formal connection to another important bioinformatics problem, multiple sequence alignment, where one attempts to best align a collection of molecular sequences under some mismatch penalty score by inserting gaps. Our result is counter-intuitive: we show that perfect pairwise sequence alignment with high probability is possible in principle at arbitrary large evolutionary distances - provided the phylogeny is known and dense enough. We use techniques from ancestral sequence reconstruction in the taxon-rich setting together with the probabilistic analysis of sequence evolution models involving insertions and deletions.

q-bio.PE↗

arXiv2021

Estimating Graph Dimension with Cross-validated Eigenvalues

In applied multivariate statistics, estimating the number of latent dimensions or the number of clusters, $k$, is a fundamental and recurring problem. We study a sequence of statistics called "cross-validated eigenvalues." Under a large class of random graph models, including both Poisson and Bernoulli edges, without parametric assumptions, we provide a $p$-value for each cross-validated eigenvalue. It tests the null hypothesis that the sample eigenvector is orthogonal to (i.e., uncorrelated with) the true latent dimensions. This approach naturally adapts to problems where some dimensions are not statistically detectable. In scenarios where all $k$ dimensions can be estimated, we show that our procedure consistently estimates $k$. In simulations and data example, the proposed estimator compares favorably to alternative approaches in both computational and statistical performance.

stat.ME↗

arXiv2020

Impossibility of phylogeny reconstruction from $k$-mer counts

We consider phylogeny estimation under a two-state model of sequence evolution by site substitution on a tree. In the asymptotic regime where the sequence lengths tend to infinity, we show that for any fixed $k$ no statistically consistent phylogeny estimation is possible from $k$-mer counts over the full leaf sequences alone. Formally, we establish that the joint distribution of $k$-mer counts over the entire leaf sequences on two distinct trees have total variation distance bounded away from $1$ as the sequence length tends to infinity. Our impossibility result implies that statistical consistency requires more sophisticated use of $k$-mer count information, such as block techniques developed in previous theoretical work.

math.PR↗

arXiv2020

Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods

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 process). Through a probabilistic analysis of the model, we derive sample complexity bounds for widely used quartet-based inference methods that highlight the effect of the duplication and loss rates in both subcritical and supercritical regimes.

math.PR↗

arXiv2020

Impossibility of consistent distance estimation from sequence lengths under the TKF91 model

We consider the problem of distance estimation under the TKF91 model of sequence evolution by insertions, deletions and substitutions on a phylogeny. In an asymptotic regime where the expected sequence lengths tend to infinity, we show that no consistent distance estimation is possible from sequence lengths alone. More formally, we establish that the distributions of pairs of sequence lengths at different distances cannot be distinguished with probability going to one.

math.PR↗

arXiv2018

On the variance of internode distance under the multispecies coalescent

We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of reconstruction methods in this setting is based on internode distances, i.e. the average graph distance between pairs of species across gene trees. While statistical consistency in the limit of large numbers of loci has been established in some cases, little is known about the sample complexity of such methods. Here we make progress on this question by deriving a lower bound on the worst-case variance of internode distance which depends linearly on the corresponding graph distance in the species tree. We also discuss some algorithmic implications.

q-bio.PE↗

arXiv2018

Reducing Seed Bias in Respondent-Driven Sampling by Estimating Block Transition Probabilities

Respondent-driven sampling (RDS) is a popular approach to study marginalized or hard-to-reach populations. It collects samples from a networked population by incentivizing participants to refer their friends into the study. One major challenge in analyzing RDS samples is seed bias. Seed bias refers to the fact that when the social network is divided into multiple communities (or blocks), the RDS sample might not provide a balanced representation of the different communities in the population, and such unbalance is correlated with the initial participant (or the seed). In this case, the distributions of estimators are typically non-trivial mixtures, which are determined (1) by the seed and (2) by how the referrals transition from one block to another. This paper shows that (1) block-transition probabilities are easy to estimate with high accuracy, and (2) we can use these estimated block-transition probabilities to estimate the stationary distribution over blocks and thus, an estimate of the block proportions. This stationary distribution on blocks has previously been used in the RDS literature to evaluate whether the sampling process has appeared to `mix'. We use these estimated block proportions in a simple post-stratified (PS) estimator that greatly diminishes seed bias. By aggregating over the blocks/strata in this way, we prove that the PS estimator is $\sqrt{n}$-consistent under a Markov model, even when other estimators are not. Simulations show that the PS estimator has smaller Root Mean Square Error (RMSE) compared to the state-of-the-art estimators.

math.ST↗

arXiv2018

Asymptotic Seed Bias in Respondent-driven Sampling

Respondent-driven sampling (RDS) collects a sample of individuals in a networked population by incentivizing the sampled individuals to refer their contacts into the sample. This iterative process is initialized from some seed node(s). Sometimes, this selection creates a large amount of seed bias. Other times, the seed bias is small. This paper gains a deeper understanding of this bias by characterizing its effect on the limiting distribution of various RDS estimators. Using classical tools and results from multi-type branching processes (Kesten and Stigum, 1966), we show that the seed bias is negligible for the Generalized Least Squares (GLS) estimator and non-negligible for both the inverse probability weighted and Volz-Heckathorn (VH) estimators. In particular, we show that (i) above a critical threshold, VH converge to a non-trivial mixture distribution, where the mixture component depends on the seed node, and the mixture distribution is possibly multi-modal. Moreover, (ii) GLS converges to a Gaussian distribution independent of the seed node, under a certain condition on the Markov process. Numerical experiments with both simulated data and empirical social networks suggest that these results appear to hold beyond the Markov conditions of the theorems.

math.ST↗

arXiv2018

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods

With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when different genomic regions can evolve differently, is a common phenomenon in multi-locus datasets, and reduces the accuracy of standard methods for species tree estimation that do not take this heterogeneity into account. New methods have been developed for species tree estimation that specifically address gene tree heterogeneity, and that have been proven to converge to the true species tree when the number of loci and number of sites per locus both increase (i.e., the methods are said to be "statistically consistent"). Yet, little is known about the biologically realistic condition where the number of sites per locus is bounded. We show that when the sequence length of each locus is bounded (by any arbitrarily chosen value), the most common approaches to species tree estimation that take heterogeneity into account (i.e., traditional fully partitioned concatenated maximum likelihood and newer approaches, called summary methods, that estimate the species tree by combining gene trees) are not statistically consistent, even when the heterogeneity is extremely constrained. The main challenge is the presence of conditions such as long branch attraction that create biased tree estimation when the number of sites is restricted. Hence, our study uncovers a fundamental challenge to species tree estimation using both traditional and new methods.

q-bio.PE↗

arXiv2017

Geometry of the sample frequency spectrum and the perils of demographic inference

The sample frequency spectrum (SFS), which describes the distribution of mutant alleles in a sample of DNA sequences, is a widely used summary statistic in population genetics. The expected SFS has a strong dependence on the historical population demography and this property is exploited by popular statistical methods to infer complex demographic histories from DNA sequence data. Most, if not all, of these inference methods exhibit pathological behavior, however. Specifically, they often display runaway behavior in optimization, where the inferred population sizes and epoch durations can degenerate to 0 or diverge to infinity, and show undesirable sensitivity of the inferred demography to perturbations in the data. The goal of this paper is to provide theoretical insights into why such problems arise. To this end, we characterize the geometry of the expected SFS for piecewise-constant demographic histories and use our results to show that the aforementioned pathological behavior of popular inference methods is intrinsic to the geometry of the expected SFS. We provide explicit descriptions and visualizations for a toy model with sample size 4, and generalize our intuition to arbitrary sample sizes n using tools from convex and algebraic geometry. We also develop a universal characterization result which shows that the expected SFS of a sample of size n under an arbitrary population history can be recapitulated by a piecewise-constant demography with only k(n) epochs, where k(n) is between n/2 and 2n-1. The set of expected SFS for piecewise-constant demographies with fewer than k(n) epochs is open and non-convex, which causes the above phenomena for inference from data.

q-bio.PE↗

arXiv2017

Generalized least squares can overcome the critical threshold in respondent-driven sampling

In order to sample marginalized and/or hard-to-reach populations, respondent-driven sampling (RDS) and similar techniques reach their participants via peer referral. Under a Markov model for RDS, previous research has shown that if the typical participant refers too many contacts, then the variance of common estimators does not decay like $O(n^{-1})$, where $n$ is the sample size. This implies that confidence intervals will be far wider than under a typical sampling design. Here we show that generalized least squares (GLS) can effectively reduce the variance of RDS estimates. In particular, a theoretical analysis indicates that the variance of the GLS estimator is $O(n^{-1})$. We then derive two classes of feasible GLS estimators. The first class is based upon a Degree Corrected Stochastic Blockmodel for the underlying social network. The second class is based upon a rank-two model. It might be of independent interest that in both model classes, the theoretical results show that it is possible to estimate the spectral properties of the population network from the sampled observations. Simulations on empirical social networks show that the feasible GLS (fGLS) estimators can have drastically smaller error and rarely increase the error. A diagnostic plot helps to identify where fGLS will aid estimation. The fGLS estimators continue to outperform standard estimators even when they are built from a misspecified model and when there is preferential recruitment.

math.ST↗

arXiv2017

Sufficient condition for root reconstruction by parsimony on binary trees with general weights

We consider the problem of inferring an ancestral state from observations at the leaves of a tree, assuming the state evolves along the tree according to a two-state symmetric Markov process. We establish a general branching rate condition under which maximum parsimony, a common reconstruction method requiring only the knowledge of the tree, succeeds better than random guessing uniformly in the depth of the tree. We thereby generalize previous results of (Zhang et al., 2010) and (Gascuel and Steel, 2010). Our results apply to both deterministic and i.i.d. edge weights.

math.PR↗

arXiv2017

Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees

We establish necessary and sufficient conditions for consistent root reconstruction in continuous-time Markov models with countable state space on bounded-height trees. Here a root state estimator is said to be consistent if the probability that it returns to the true root state converges to 1 as the number of leaves tends to infinity. We also derive quantitative bounds on the error of reconstruction. Our results answer a question of Gascuel and Steel and have implications for ancestral sequence reconstruction in a classical evolutionary model of nucleotide insertion and deletion.

math.PR↗