maremita

-fork-awesome-normalizing-flows

Awesome resources on normalizing flows.

-fork-beer

Bayesian enrichment estimation in R

-fork-benchmark_VAE

Unifying Generative Autoencoder implementations in Python

-fork-ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

-fork-PhIPSeq_external

-fork-physher

Phylogenetic analysis of genetic data

-fork-PyTorch-VAE

A Collection of Variational Autoencoders (VAE) in PyTorch.

-fork-vbpi-nf

Code for improved variational Bayesian phylogenetic inference with normalizing flows

-fork-vbsky

Variational Bayesian skyline infers evolutionary models from large amounts of phylogenetic data.

evoVGM

Evolutionary-based Variational Generative Model using Multiple Sequence Alignments

evoVGM_Exp

nnTreeVB

nnTreeVB: a Neural Network-based Variational Bayesian Framework for Phylogenetic Parameter Estimation

phd_projects

Thesis projects

-fork-amortized-optimization-tutorial

Tutorial on amortized optimization for learning to optimize over continuous domains

-fork-BDA_course_Aalto

Bayesian Data Analysis course at Aalto

-fork-beer_manuscript

-fork-bito

Python-interface C++ library for Bayesian phylogenetics via optimization

-fork-Dolphyn

-fork-genslm

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

-fork-gp-benchmark-1

-fork-HaROLD-1

Haplotype Reconstruction of Longitudinal Deep sequencing data

-fork-just-the-class

A modern, highly customizable, responsive Jekyll template for course websites.

-fork-llama

Inference code for LLaMA models

-fork-PhyloNet

-fork-torchtree

A probabilistic framework in PyTorch for phylogenetic models

-fork-vbpi-gnn

Code for learnable topological features for phylogenetic inference via graph neural networks

dna_bayes_clf

Probabilistic framework for DNA classification

mlr_kgenomvir

evaluation of Multinomial Logistic Regression for Kmer-based GENOMe VIRus classification

nnTreeVB_Exp

A repository for the evaluation experiments of nnTreeVB

pytorch_mlr

A modern implementation of Multinomial Logistic Regression with SGD training