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Researcher profile

Shijia Wang

Shijia Wang contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
ComputationMethodologyMachine LearningQuantitative Methods

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Published work

3 published item(s)

preprint2026arXiv

Accelerating Bayesian Phylogenetic Inference via Delayed Acceptance Sequential Monte Carlo with Random Forest Surrogates

In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data, repeated evaluation of the likelihood function incurs a high computational cost. In this article, we propose a machine-learning algorithm with over 35 topological and branch-length features to predict the changes in the likelihood function caused by tree moves (\eg,~eSPR, stNNI) used in standard MCMC approaches. This algorithm is then used to design a delayed acceptance MCMC kernel, which utilized the predicted surrogate function for preliminary rejection, to accelerate tree space searches. Furthermore, we integrate our proposed MCMC kernel into the sequential Monte Carlo sampler framework. We validate the proposed delayed-acceptance sequential Monte Carlo approach (DA-SMC) on simulation and real data sets. Our delayed acceptance kernel can maintain robust estimation while reduces the number of likelihood evaluations significantly, yielding substantial computational time savings. We develop a Python package that is available at https://github.com/wentYu/DAphyloSMC.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Poisson Hyperplane Processes with Rectified Linear Units

Neural networks have shown state-of-the-art performances in various classification and regression tasks. Rectified linear units (ReLU) are often used as activation functions for the hidden layers in a neural network model. In this article, we establish the connection between the Poisson hyperplane processes (PHP) and two-layer ReLU neural networks. We show that the PHP with a Gaussian prior is an alternative probabilistic representation to a two-layer ReLU neural network. In addition, we show that a two-layer neural network constructed by PHP is scalable to large-scale problems via the decomposition propositions. Finally, we propose an annealed sequential Monte Carlo algorithm for Bayesian inference. Our numerical experiments demonstrate that our proposed method outperforms the classic two-layer ReLU neural network. The implementation of our proposed model is available at https://github.com/ShufeiGe/Pois_Relu.git.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Particle Gibbs Sampling for Bayesian Phylogenetic inference

The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain Monte Carlo (MCMC) for Bayesian phylogenetic tree inference using biological sequences. It is appealing to combine the CSMC and MCMC in the framework of the particle Gibbs (PG) sampler to jointly estimate the phylogenetic trees and evolutionary parameters. However, the Markov chain of the particle Gibbs may mix poorly if the underlying SMC suffers from the path degeneracy issue. Some remedies, including the particle Gibbs with ancestor sampling and the interacting particle MCMC, have been proposed to improve the PG. But they either cannot be applied to or remain inefficient for the combinatorial tree space. We introduce a novel CSMC method by proposing a more efficient proposal distribution. It also can be combined into the particle Gibbs sampler framework to infer parameters in the evolutionary model. The new algorithm can be easily parallelized by allocating samples over different computing cores. We validate that the developed CSMC can sample trees more efficiently in various particle Gibbs samplers via numerical experiments. Our implementation is available at https://github.com/liangliangwangsfu/phyloPMCMC

0 citations0 reviewsNo code linkedOpen access