Accurate Phylogenetic Inference with Symmetry-Preserving Neural Networks

Last update: Feb 11, 2022

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Accurate Phylogenetic Inference with a Symmetry-preserving Neural Network Model

Claudia Solis-Lemus
Shengwen Yang
Leonardo Zepeda-Núñez

This repository contains the scripts, data, and plots for the paper:

@misc{solislemus2022accurate,
      title={Accurate Phylogenetic Inference with a Symmetry-preserving Neural Network Model}, 
      author={Claudia Solis-Lemus and Shengwen Yang and Leonardo Zepeda-Nunez},
      year={2022},
      eprint={2201.04663},
      archivePrefix={arXiv},
      primaryClass={q-bio.PE}
}

Folder structure

scripts contains the python scripts with the neural network implementations.
plotscontains the link to the Google Drive with the output files needed to reproduce the plots as well as the Rmd script with the R code for the plots.
simulations-realdata contains the scripts and code to do the simulations and real data analysis in the manuscript.
LICENSE: this repository is under the MIT license.

Issues and questions

Issues and questions are encouraged through the GitHub issue tracker. For bugs or errors, please make sure to provide enough details for us to reproduce the error on our end.

Accurate Phylogenetic Inference with Symmetry-Preserving Neural Networks

Related tags

Overview

Accurate Phylogenetic Inference with a Symmetry-preserving Neural Network Model

Folder structure

Issues and questions

Owner

Leonardo Zepeda-Núñez

The Python3 import playground

PyTorch implementation of our paper: Decoupling and Recoupling Spatiotemporal Representation for RGB-D-based Motion Recognition

Implementation of TransGanFormer, an all-attention GAN that combines the finding from the recent GanFormer and TransGan paper

Official PyTorch Implementation of Mask-aware IoU and maYOLACT Detector [BMVC2021]

PyTorch implementation of Densely Connected Time Delay Neural Network

Minimalistic PyTorch training loop

PaRT: Parallel Learning for Robust and Transparent AI

Implementation of the paper titled "Using Sampling to Estimate and Improve Performance of Automated Scoring Systems with Guarantees"

Manifold-Mixup implementation for fastai V2

Code for the Higgs Boson Machine Learning Challenge organised by CERN & EPFL

Python3 / PyTorch implementation of the following paper: Fine-grained Semantics-aware Representation Enhancement for Self-supervisedMonocular Depth Estimation. ICCV 2021 (oral)

Compact Bidirectional Transformer for Image Captioning

Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more

Multi-layer convolutional LSTM with Pytorch

code for paper "Not All Unlabeled Data are Equal: Learning to Weight Data in Semi-supervised Learning" by Zhongzheng Ren, Raymond A. Yeh, Alexander G. Schwing.

Implementation of ICCV 2021 oral paper -- A Novel Self-Supervised Learning for Gaussian Mixture Model

Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (CVAMD)

Official implementation of the Neurips 2021 paper Searching Parameterized AP Loss for Object Detection.

FairFuzz: AFL extension targeting rare branches

Accurate Phylogenetic Inference with Symmetry-Preserving Neural Networks

Related tags

Overview

Accurate Phylogenetic Inference with a Symmetry-preserving Neural Network Model

Folder structure

Issues and questions

Owner

Leonardo Zepeda-Núñez

The Python3 import playground

PyTorch implementation of our paper: Decoupling and Recoupling Spatiotemporal Representation for RGB-D-based Motion Recognition

Implementation of TransGanFormer, an all-attention GAN that combines the finding from the recent GanFormer and TransGan paper

Official PyTorch Implementation of Mask-aware IoU and maYOLACT Detector [BMVC2021]

PyTorch implementation of Densely Connected Time Delay Neural Network

Minimalistic PyTorch training loop

PaRT: Parallel Learning for Robust and Transparent AI

Implementation of the paper titled "Using Sampling to Estimate and Improve Performance of Automated Scoring Systems with Guarantees"

Manifold-Mixup implementation for fastai V2

Code for the Higgs Boson Machine Learning Challenge organised by CERN & EPFL

Python3 / PyTorch implementation of the following paper: Fine-grained Semantics-aware Representation Enhancement for Self-supervisedMonocular Depth Estimation. ICCV 2021 (oral)

Compact Bidirectional Transformer for Image Captioning

Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more

Multi-layer convolutional LSTM with Pytorch

code for paper "Not All Unlabeled Data are Equal: Learning to Weight Data in Semi-supervised Learning" by Zhongzheng Ren*, Raymond A. Yeh*, Alexander G. Schwing.

Implementation of ICCV 2021 oral paper -- A Novel Self-Supervised Learning for Gaussian Mixture Model

Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (CVAMD)

Official implementation of the Neurips 2021 paper Searching Parameterized AP Loss for Object Detection.

FairFuzz: AFL extension targeting rare branches

code for paper "Not All Unlabeled Data are Equal: Learning to Weight Data in Semi-supervised Learning" by Zhongzheng Ren, Raymond A. Yeh, Alexander G. Schwing.