Skip to content

Minor formatting updates to README #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
chrisyeh96 wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Minor formatting updates to README #5

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 2 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -284,10 +284,10 @@ MLDE predictions are made using the execute_mlde.py script. This script should b
### Inputs for execute_mlde.py
| Argument | Type | Description |
|:---------|-----------|-------------|
| training_data | Required Argument | A csv file containing the sequence-function information for sampled combinations. More information on this file can be found [below](#trainingdata.csv). |
| training_data | Required Argument | A csv file containing the sequence-function information for sampled combinations. More information on this file can be found [below](#trainingdatacsv). |
| encoding_data | Required Argument | A numpy array containing the embedding information for the full combinatorial space. Encoding arrays generated by generate_encoding.py can be passed directly in here. Custom encodings can be passed in here too, the details of which are discussed [below](#custom-encodings). |
| combo_to_ind_dict | Required Argument | A pickle file containing a dictionary that links a combination to its index. The ComboToIndex.pkl file output by generate_encoding.py can be passed in directly here. |
| model_params | Optional Argument | A csv file dictating which inbuilt MLDE models to use as well as how many rounds of hyperparameter optimization to perform. The makeup of this file is discussed [below](#mldeparameters.csv). |
| model_params | Optional Argument | A csv file dictating which inbuilt MLDE models to use as well as how many rounds of hyperparameter optimization to perform. The makeup of this file is discussed [below](#mldeparameterscsv). |
| output | Optional Argument | The location to save the results. Default is the current working directory. |
| n_averaged | Optional Argument | The number of top-performing models to average to get final prediction results. Default is 3. |
| n_cv | Optional Argument | The number of rounds of cross validation to perform during training. Default is 5. |
Expand Down Expand Up @@ -435,7 +435,6 @@ MLDE requires the dependencies given below. Instructions on the [tape-neurips](h
- torchaudio
- cudatoolkit
- transformers

- evcouplings

Any specific versions listed were those used during the development of MLDE. There should be some leeway if users use different versions, though if running in a new environment, it is strongly recommended to perform the [pytest validation](#Installation-Validation) first.
Expand Down