Sarah Lutteropp
Sarah Lutteropp
At least run the searches from different start networks in parallel... It is just a few lines of code to add, and will make the experiments much faster already
How does the number of partitions influence the number of inferred reticulations? It is obvious that with LikelihoodType.BEST, network inference on an unpartitioned MSA will always lead to a tree....
Because of problems that emerged with the "small_network" experiments (NetRAX inferring a 0-reticulation network that has better loglikelihood than the "true" simulated network on the simulated MSA data), I have...
The entire data (including the plots) is in here: https://drive.google.com/drive/folders/1l6lOPbiyjDKi9bgTqGwD6zXzjvny_pCZ?usp=sharing The experiments were done on my own laptop (LG Gram 17, 2019 model) using this commit version: https://github.com/lutteropp/NetRAX/commit/e2cf9eb072714633cea0b495ef8eec09862041ea. I decided...
In this likelihood model, we only use the loglikelihood of a single displayed tree in the network, made smaller by multiplying it by the probability of that displayed tree. This...
The entire data (including the plots) is in here: https://drive.google.com/drive/folders/1odlBZo2LkJC9QitJMNJdxcVTgHIyDay1?usp=sharing The experiments were done on my own laptop (LG Gram 17, 2019 model) using this commit version: https://github.com/lutteropp/NetRAX/commit/7bdd404edf5af335d5f0e441ec66c9ebcdae5913. I decided...
I did a profiling run with NetRAX, on a 1000 sites MSA (belonging to a simulated 8 taxon-tree), with 1 random and 1 parsimony starting tree. Turns out that trying...
Now that the columns in the results CSV are fixed (see https://github.com/lutteropp/NetRAX/issues/14), let's list which plots we need. Here are some that I believe make sense to have: - Use...
The current results CSV header consists of: name | n_taxa | n_trees | n_reticulations | msa_size | sampling_type | simulation_type | likelihood_type | timeout | n_random_start_networks | n_parsimony_start_networks | start_from_raxml...
RAxML-NG gives: `WARNING: Best ML tree contains 2 near-zero branches! ` The sequences were simulated with Seq-Gen using `cmd = 'seq-gen -mHKY -t3.0 -f0.3,0.2,0.2,0.3 -l' + str(dataset.msa_size)+'-p' + str(dataset.n_trees)+' <...