# Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions

arXiv: https://arxiv.org/abs/2408.05058 · HTML: https://mlsanity.com/paper/2408.05058/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 30 of its 56 references that are in the map.
- First posted on arXiv 9 Aug 2024.

## Builds on (most cited first, 30 of 30)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [Density estimation using Real NVP](https://mlsanity.com/paper/1605.08803/) (2016)
- [Variational Inference: A Review for Statisticians](https://mlsanity.com/paper/1601.00670/) (2016)
- [Normalizing Flows for Probabilistic Modeling and Inference](https://mlsanity.com/paper/1912.02762/) (2019)
- [Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs)](https://mlsanity.com/paper/1511.07289/) (2015)
- [Improving Variational Inference with Inverse Autoregressive Flow](https://mlsanity.com/paper/1606.04934/) (2016)
- [Importance Weighted Autoencoders](https://mlsanity.com/paper/1509.00519/) (2015)
- [Sliced Score Matching: A Scalable Approach to Density and Score Estimation](https://mlsanity.com/paper/1905.07088/) (2019)
- [Black Box Variational Inference](https://mlsanity.com/paper/1401.0118/) (2013)
- [Inference Suboptimality in Variational Autoencoders](https://mlsanity.com/paper/1801.03558/) (2018)
- [Adversarial Variational Bayes: Unifying Variational Autoencoders and Generative Adversarial Networks](https://mlsanity.com/paper/1701.04722/) (2017)
- [Variational inference for Monte Carlo objectives](https://mlsanity.com/paper/1602.06725/) (2016)
- [Tighter Variational Bounds are Not Necessarily Better](https://mlsanity.com/paper/1802.04537/) (2018)
- [Reweighted Wake-Sleep](https://mlsanity.com/paper/1406.2751/) (2014)
- [Semi-Implicit Variational Inference](https://mlsanity.com/paper/1805.11183/) (2018)
- [Variational Inference using Implicit Distributions](https://mlsanity.com/paper/1702.08235/) (2017)
- [Unbiased Implicit Variational Inference](https://mlsanity.com/paper/1808.02078/) (2018)
- [PhyloGFN: Phylogenetic inference with generative flow networks](https://mlsanity.com/paper/2310.08774/) (2023)
- [Importance Weighted Hierarchical Variational Inference](https://mlsanity.com/paper/1905.03290/) (2019)
- [Improved Variational Bayesian Phylogenetic Inference with Normalizing Flows](https://mlsanity.com/paper/2012.00459/) (2020)
- [Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks](https://mlsanity.com/paper/2302.08840/) (2023)
- [GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies](https://mlsanity.com/paper/2307.03675/) (2023)
- [VaiPhy: a Variational Inference Based Algorithm for Phylogeny](https://mlsanity.com/paper/2203.01121/) (2022)
- [A Variational Approach to Bayesian Phylogenetic Inference](https://mlsanity.com/paper/2204.07747/) (2022)
- [ARTree: A Deep Autoregressive Model for Phylogenetic Inference](https://mlsanity.com/paper/2310.09553/) (2023)
- [Improved Variational Bayesian Phylogenetic Inference using Mixtures](https://mlsanity.com/paper/2310.00941/) (2023)

## Built on by (most cited first, 1 of 1)

- [Variational phylogenetic inference with products over bipartitions](https://mlsanity.com/paper/2502.15110/) (2025)

## Abstract (arXiv)

Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the complicated space of phylogenetic trees, especially when the number of sequences is large. An alternative approach is variational Bayesian phylogenetic inference (VBPI) which transforms the inference problem into an optimization problem. While effective, the default diagonal lognormal approximation for the branch lengths of the tree used in VBPI is often insufficient to capture the complexity of the exact posterior. In this work, we propose a more flexible family of branch length variational posteriors based on semi-implicit hierarchical distributions using graph neural networks. We show that this semi-implicit construction emits straightforward permutation equivariant distributions, and therefore can handle the non-Euclidean branch length space across different tree topologies with ease. To deal with the intractable marginal probability of semi-implicit variational distributions, we develop several alternative lower bounds for stochastic optimization. We demonstrate the effectiveness of our proposed method over baseline methods on benchmark data examples, in terms of both marginal likelihood estimation and branch length posterior approximation.