Commit 32795d96 authored by Ngan Thi Dong's avatar Ngan Thi Dong

update readme

parent 979c0acf
......@@ -33,6 +33,22 @@ other configurable parameters include:
- _use_seq_sim_: whether to use seq sim or not
- _randseed_: the random seed used to generate train/test split
3. For **EPMDA** since the features took a lot of time to run, we provide all calculated features in epmda/data folder
Please run `` with the corresponding arguments for evaluating EPMDA with the balance set up
and `` with corresponding arguments for the original evaluation set up
For feature calculation, please refer to the *.py files in epmda folder.
4. To run all the model with the **NEW** dataset, the following files are needed:
m-d.csv: store the association matrix where rows are miRNAs and columns are diseases
miRNA-disease.txt: store miRNA-disease association list
miRNA_seq.csv: the miRNAs sequence similarity matrix
disease_sim.csv: the disease semantic similarity.
disease_sim2.csv: the disease semantic + phenotype similarity
disease_not_found_list.txt: list of ids of diseases that are not found in MESH
To calculate disease semantic similarity from MESH ontology, disease GIP or miRNA sequence/functiona/GIP kernel similarity, please use the code provided in data/preparation folder.
If you use the code in your work, please cite the following paper:
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