molfm-molt5.json

{
    "model": "MolFM-MolT5",
    "data": {
        "mol": {
            "modality": ["structure", "text"],
            "featurizer": {
                "structure": {
                    "name": "MultiScale",
                    "scales": ["SMILES", "graph"],
                    "SMILES": {
                        "name": "transformer",
                        "transformer_type": "t5",
                        "model_name_or_path": "./ckpts/text_ckpts/MolT5-base",
                        "max_length": 512
                    },
                    "graph": {
                        "name": "BaseGNN"
                    }
                },
                "text": {
                    "name": "TransformerTokenizer",
                    "transformer_type": "t5",
                    "max_length": 512,
                    "model_name_or_path": "./ckpts/text_ckpts/MolT5-base"
                }
            }
        }
    },
    "network": {
        "graph": {
            "name": "molfm",
            "gin_hidden_dim": 300,
            "gin_num_layers": 5,
            "drop_ratio": 0.0,
            "bert_config_path": "./configs/encoders/multimodal/molfm_bert_config.json",
            "max_n_nodes": 256,
            "projection_dim": 256,
            "kge": {
                "n_ents": 49111,
                "n_rels": 16,
                "norm": 1,
                "hidden_size": 256,
                "margin": 1.0
            },
            "output_dim": 300,
            "init_checkpoint": "./ckpts/fusion_ckpts/molfm.pth",
            "param_key": "model",
            "stop_grad": false
        },
        "text": {
            "model_name_or_path": "./ckpts/text_ckpts/MolT5-base",
            "stop_grad": false
        }
    }
}