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1. Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited

   https://doi.org/10.1093/bioinformatics/btab263  

   Wang, Wei; Hejasebazzi, Ahmad; Zheng, Julia; Liu, Kevin J (July 2021, Bioinformatics)

   null (Ed.)

   Abstract Motivation The standard bootstrap method is used throughout science and engineering to perform general-purpose non-parametric resampling and re-estimation. Among the most widely cited and widely used such applications is the phylogenetic bootstrap method, which Felsenstein proposed in 1985 as a means to place statistical confidence intervals on an estimated phylogeny (or estimate ‘phylogenetic support’). A key simplifying assumption of the bootstrap method is that input data are independent and identically distributed (i.i.d.). However, the i.i.d. assumption is an over-simplification for biomolecular sequence analysis, as Felsenstein noted. Results In this study, we introduce a new sequence-aware non-parametric resampling technique, which we refer to as RAWR (‘RAndom Walk Resampling’). RAWR consists of random walks that synthesize and extend the standard bootstrap method and the ‘mirrored inputs’ idea of Landan and Graur. We apply RAWR to the task of phylogenetic support estimation. RAWR’s performance is compared to the state-of-the-art using synthetic and empirical data that span a range of dataset sizes and evolutionary divergence. We show that RAWR support estimates offer comparable or typically superior type I and type II error compared to phylogenetic bootstrap support. We also conduct a re-analysis of large-scale genomic sequence data from a recent study of Darwin’s finches. Our findings clarify phylogenetic uncertainty in a charismatic clade that serves as an important model for complex adaptive evolution. Availability and implementation Data and software are publicly available under open-source software and open data licenses at: https://gitlab.msu.edu/liulab/RAWR-study-datasets-and-scripts. 

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2. Local Access to Random Walks , January 2022

   Biswas, A.S.; Pyne, E.; Rubinfeld, R. (January 2022, Innovations in Theoretical Computer Science (ITCS 2022))

   For a graph G on n vertices, naively sampling the position of a random walk of at time t requires work Ω(t). We desire local access algorithms supporting positionG(t) queries, which return the position of a random walk from some fixed start vertex s at time t, where the joint distribution of returned positions is 1/ poly(n) close to those of a uniformly random walk in ℓ1 distance. We first give an algorithm for local access to random walks on a given undirected d-regular graph with eO( 1 1−λ √ n) runtime per query, where λ is the second-largest eigenvalue of the random walk matrix of the graph in absolute value. Since random d-regular graphs G(n, d) are expanders with high probability, this gives an eO(√ n) algorithm for a graph drawn from G(n, d) whp, which improves on the naive method for small numbers of queries. We then prove that no algorithm with subconstant error given probe access to an input d-regular graph can have runtime better than Ω(√ n/ log(n)) per query in expectation when the input graph is drawn from G(n, d), obtaining a nearly matching lower bound. We further show an Ω(n1/4) runtime per query lower bound even with an oblivious adversary (i.e. when the query sequence is fixed in advance). We then show that for families of graphs with additional group theoretic structure, dramatically better results can be achieved. We give local access to walks on small-degree abelian Cayley graphs, including cycles and hypercubes, with runtime polylog(n) per query. This also allows for efficient local access to walks on polylog degree expanders. We show that our techniques apply to graphs with high degree by extending or results to graphs constructed using the tensor product (giving fast local access to walks on degree nϵ graphs for any ϵ ∈ (0, 1]) and Cartesian product. 

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3. Non-Markovian Monte Carlo on Directed Graphs

   https://doi.org/10.1145/3322205.3311086  

   Lee, Chul-Ho; Kang, Min; Eun, Do Young (June 2019, ACM SIGMETRICS performance evaluation review)

   Markov Chain Monte Carlo (MCMC) has been the de facto technique for sampling and inference of large graphs such as online social networks. At the heart of MCMC lies the ability to construct an ergodic Markov chain that attains any given stationary distribution \pi, often in the form of random walks or crawling agents on the graph. Most of the works around MCMC, however, presume that the graph is undirected or has reciprocal edges, and become inapplicable when the graph is directed and non-reciprocal. Here we develop a similar framework for directed graphs called Non- Markovian Monte Carlo (NMMC) by establishing a mapping to convert \pi into the quasi-stationary distribution of a carefully constructed transient Markov chain on an extended state space. As applications, we demonstrate how to achieve any given distribution \pi on a directed graph and estimate the eigenvector centrality using a set of non-Markovian, history-dependent random walks on the same graph in a distributed manner.We also provide numerical results on various real-world directed graphs to confirm our theoretical findings, and present several practical enhancements to make our NMMC method ready for practical use inmost directed graphs. To the best of our knowledge, the proposed NMMC framework for directed graphs is the first of its kind, unlocking all the limitations set by the standard MCMC methods for undirected graphs. 

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4. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

   https://doi.org/10.1371/journal.pcbi.1010422  

   Guo, Fangfang; Carbone, Ignazio; Rasmussen, David A. (August 2022, PLOS Computational Biology)

   Schiffels, Stephan (Ed.)

   Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome. 

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5. From Sampling to Optimization on Discrete Domains with Applications to Determinant Maximization

   Anari, Nima; Vuong, Thuy-Duong (July 2022, Proceedings of Thirty Fifth Conference on Learning Theory)

   Loh, Po-Ling; Raginsky, Maxim (Ed.)

   We establish a connection between sampling and optimization on discrete domains. For a family of distributions $$\mu$$ defined on size $$k$$ subsets of a ground set of elements, that is closed under external fields, we show that rapid mixing of natural local random walks implies the existence of simple approximation algorithms to find $$\max \mu(\cdot)$$. More precisely, we show that if $$t$$-step down-up random walks have spectral gap at least inverse polynomially large, then $$t$$-step local search finds $$\max \mu(\cdot)$$ within a factor of $$k^{O(k)}$$. As the main application of our result, we show that $$2$$-step local search achieves a nearly-optimal $$k^{O(k)}$$-factor approximation for MAP inference on nonsymmetric $$k$$-DPPs. This is the first nontrivial multiplicative approximation algorithm for this problem. In our main technical result, we show that an exchange inequality, a concept rooted in discrete convex analysis, can be derived from fast mixing of local random walks. We further advance the state of the art on the mixing of random walks for nonsymmetric DPPs and more generally sector-stable distributions, by obtaining the tightest possible bound on the step size needed for polynomial-time mixing of random walks. We bring the step size down by a factor of $$2$$ compared to prior works, and consequently get a quadratic improvement on the runtime of local search steps; this improvement is potentially of independent interest in sampling applications. 

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