From 279d22d965236fe278362542a882105715c409c4 Mon Sep 17 00:00:00 2001 From: Sean <28655920+seanrjohnson@users.noreply.github.com> Date: Tue, 2 Feb 2021 15:03:24 -0500 Subject: [PATCH] fixed links --- src/tasks/evaluation/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/tasks/evaluation/README.md b/src/tasks/evaluation/README.md index e7ff504..d909521 100644 --- a/src/tasks/evaluation/README.md +++ b/src/tasks/evaluation/README.md @@ -1,20 +1,20 @@ # Evaluation ## HMM scores -Calculated in this notebook (first half): [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb]{https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb} +Calculated in this notebook (first half): [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb](https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb) ## First and Second Order sequence statistics -Calculated in this notebook (second half): [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb]{https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb} +Calculated in this notebook (second half): [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb](https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/sequence_stats.ipynb) ## Alignment to training data There is a notebook "Align to training data" that contains all of the logic for the -corresponding section of the report. [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/Align%20to%20training%data.ipynb]{https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/Align%20to%20training%20data.ipynb} +corresponding section of the report. [https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/Align%20to%20training%data.ipynb](https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/Align%20to%20training%20data.ipynb) ## GB1 Evaluation The notebook "GB1_fitness.ipynb" was used to generate the analysis of the ability to generate GB1 scores. The notebook is configured to run using the ESM34 model by default. This model can be changed in the notebook to explore other pre-trained models. -[https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/GB1_fitness.ipynb]{https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/GB1_fitness.ipynb} +[https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/GB1_fitness.ipynb](https://github.com/seanrjohnson/protein_gibbs_sampler/blob/main/src/tasks/evaluation/GB1_fitness.ipynb)