diff --git a/.gitignore b/.gitignore index ab906f7..08518d5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ # Custom /data +/seq /env /wandb .DS_Store diff --git a/README.md b/README.md index ba61fb7..b1dcfee 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Check out the accompanying paper ['Multi-State RNA Design with Geometric Multi-G > >[PDF](https://arxiv.org/pdf/2305.14749.pdf) | [Thread](https://twitter.com/chaitjo/status/1662118334412800001) -❗️**Note:** gRNAde is under active development. +❗️**Note:** gRNAde is under active development; the `main` branch contains the most recent version of the code and models, but the manuscript may not be updated with the latest results. Please check the ['Releases'](https://github.com/chaitjo/geometric-rna-design/releases) tab to reproduce our results. ## Directory Structure and Usage diff --git a/configs/default.yaml b/configs/default.yaml index e188027..31c4db7 100644 --- a/configs/default.yaml +++ b/configs/default.yaml @@ -37,18 +37,18 @@ num_conformers: # Splitting configurations eval_size: - value: 200 + value: 100 desc: Number of samples in val/test sets split: - value: 'rmsd' - desc: Type of data split (random/rmsd/struct/seq_identity) + value: 'seqid_rmsd' + desc: Type of data split (rmsd/struct) # Model configurations model: - value: 'MultiGVPGNN' - desc: Model architecture + value: 'NAR' + desc: Model architecture (AR/NAR) node_in_dim: - value: [1, 4] + value: [64, 4] desc: Input dimensions for node features (scalar channels, vector channels) node_h_dim: value: [128, 16] @@ -60,7 +60,7 @@ edge_h_dim: value: [32, 1] desc: Hidden dimensions for edge features (scalar channels, vector channels) num_layers: - value: 3 + value: 4 desc: Number of layers for encoder/decoder drop_rate: value: 0.1