Commit
·
3a19a3f
1
Parent(s):
f14c1f8
Clean re-commit using proper Git LFS
Browse files- classification/config.json +19 -0
- classification/configuration_bbb.py +22 -0
- classification/model.safetensors +3 -0
- classification/model_classification.pth +3 -0
- classification/modeling_bbb.py +99 -0
- classification/normalize_image.joblib +0 -0
- classification/normalize_tabular.joblib +0 -0
- classification/normalize_text.joblib +0 -0
- classification/tokenizer_bbb.py +133 -0
- classification/tokenizer_config.json +13 -0
- convert_weights.py +63 -0
- regression/config.json +19 -0
- regression/configuration_bbb.py +22 -0
- regression/model.safetensors +3 -0
- regression/model_regression.pth +3 -0
- regression/modeling_bbb.py +99 -0
- regression/normalize_image.joblib +0 -0
- regression/normalize_tabular.joblib +0 -0
- regression/normalize_text.joblib +0 -0
- regression/tokenizer_bbb.py +131 -0
- regression/tokenizer_config.json +13 -0
classification/config.json
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{
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"architectures": [
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"BBBModelForSequenceClassification"
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],
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"auto_map": {
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"AutoConfig": "configuration_bbb.BBBConfig",
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"AutoModelForSequenceClassification": "modeling_bbb.BBBModelForSequenceClassification"
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},
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"d_img": 2048,
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"d_tab": 384,
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"d_txt": 768,
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"dropout": 0.1,
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"dtype": "float32",
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"model_type": "bbb-model",
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"problem_type": "single_label_classification",
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"proj_dim": 2048,
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"task": "classification",
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"transformers_version": "4.57.3"
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}
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classification/configuration_bbb.py
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from transformers import PretrainedConfig
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class BBBConfig(PretrainedConfig):
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model_type = "bbb-model"
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def __init__(
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self,
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d_tab : int = 384,
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d_img: int = 2048,
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d_txt: int = 768,
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proj_dim: int = 2048,
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dropout: float = 0.1,
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task: str = 'classification',
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**kwargs):
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self.d_tab = d_tab
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self.d_img = d_img
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self.d_txt = d_txt
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self.proj_dim = proj_dim
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self.dropout = dropout
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self.task = task
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super().__init__(**kwargs)
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classification/model.safetensors
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version https://git-lfs.github.com/spec/v1
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oid sha256:aa5ab19333e753976e402ac0c8c70615fa65065ca2ed3f5e5b6fcb5f54564c58
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size 59853476
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classification/model_classification.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:580e8747c45b9db60ff2b9b38384a0089a29d3066d02a50a09c7ab3fab3d3253
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size 59859439
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classification/modeling_bbb.py
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import torch
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import torch.nn as nn
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import torch.nn.functional as F
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from transformers import PreTrainedModel
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from transformers.modeling_outputs import BaseModelOutputWithPooling, SequenceClassifierOutput
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from .configuration_bbb import BBBConfig
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class BBBModelForSequenceClassification(PreTrainedModel):
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config_class = BBBConfig
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def __init__(self, config: BBBConfig):
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super().__init__(config)
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self.config = config
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self.proj_tab = nn.Sequential(
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nn.LayerNorm(config.d_tab),
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nn.Linear(config.d_tab, config.proj_dim),
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nn.ReLU(),
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nn.Dropout(config.dropout)
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)
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self.proj_img = nn.Sequential(
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nn.LayerNorm(config.d_img),
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nn.Linear(config.d_img, config.proj_dim),
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nn.ReLU(),
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nn.Dropout(config.dropout)
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)
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self.proj_txt = nn.Sequential(
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nn.LayerNorm(config.d_txt),
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nn.Linear(config.d_txt, config.proj_dim),
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nn.ReLU(),
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nn.Dropout(config.dropout)
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)
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self.attention_pooling = nn.Sequential(
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nn.Linear(config.proj_dim, config.proj_dim),
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nn.Tanh(),
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nn.Linear(config.proj_dim, 1, bias=False)
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)
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self.classifier = nn.Sequential(
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nn.Linear(config.proj_dim, config.proj_dim),
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nn.ReLU(),
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nn.Dropout(config.dropout),
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nn.Linear(config.proj_dim, 1)
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)
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def _init_weights(self, module):
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if isinstance(module, nn.Linear):
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module.weight.data.normal_(mean=0.0, std=1.0)
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if module.bias is not None:
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module.bias.data.zero_()
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elif isinstance(module, nn.Embedding):
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module.weight.data.normal_(mean=0.0, std=1.0)
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if module.padding_idx is not None:
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module.weight.data[module.padding_idx].zero_()
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elif isinstance(module, nn.LayerNorm):
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module.bias.data.zero_()
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module.weight.data.fill_(1.0)
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def forward(self,
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tab: torch.Tensor = None,
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img: torch.Tensor = None,
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txt: torch.Tensor = None,
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labels: torch.Tensor = None):
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if tab is None or img is None or txt is None:
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raise ValueError('You have to specify tabular, image, and text features')
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h_tab = self.proj_tab(tab)
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h_img = self.proj_img(img)
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h_txt = self.proj_txt(txt)
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embeddings = torch.stack([h_tab, h_img, h_txt], dim=1)
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scores = self.attention_pooling(embeddings)
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weights = F.softmax(scores, dim=1)
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weighted_embeddings = embeddings * weights
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pooled_embeddings = torch.sum(weighted_embeddings, dim=1)
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logits = self.classifier(pooled_embeddings).squeeze(-1)
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loss = None
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if labels is not None:
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if self.config.task == "regression":
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loss_fct = nn.MSELoss()
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loss = loss_fct(logits.squeeze(-1), labels.squeeze(-1))
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elif self.config.task == "classification":
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loss_fct = nn.BCEWithLogitsLoss()
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loss = loss_fct(logits, labels.float().unsqueeze(-1))
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return SequenceClassifierOutput(
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loss=loss,
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logits=logits,
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hidden_states=pooled_embeddings,
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attentions=weights.squeeze(-1)
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)
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classification/normalize_image.joblib
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Binary file (49.8 kB). View file
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classification/normalize_tabular.joblib
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Binary file (9.83 kB). View file
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classification/normalize_text.joblib
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Binary file (19 kB). View file
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classification/tokenizer_bbb.py
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import torch
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import torch.nn as nn
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from transformers import PreTrainedTokenizer
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from transformers.tokenization_utils_base import BatchEncoding
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from transformers import AutoTokenizer, AutoModel
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from rdkit import Chem
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from rdkit.Chem import Descriptors, AllChem, MACCSkeys
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from rdkit.ML.Descriptors import MoleculeDescriptors
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from rdkit import RDLogger
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from rdkit.Chem import Draw
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| 11 |
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import joblib
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import numpy as np
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import os
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from huggingface_hub import snapshot_download
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import warnings
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| 16 |
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from sklearn.exceptions import InconsistentVersionWarning
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| 17 |
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from torchvision import models, transforms
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| 18 |
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from PIL import Image
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warnings.filterwarnings("ignore", category=InconsistentVersionWarning)
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RDLogger.DisableLog('rdApp.*')
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class BBBTokenizer(PreTrainedTokenizer):
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self.calc = MoleculeDescriptors.MolecularDescriptorCalculator([i[0] for i in Descriptors.descList])
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| 28 |
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self.tokenizer = AutoTokenizer.from_pretrained('DeepChem/ChemBERTa-100M-MLM')
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self.chemberta = AutoModel.from_pretrained('DeepChem/ChemBERTa-100M-MLM').eval()
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| 31 |
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self.resnet50_backbone = models.resnet50(weights="IMAGENET1K_V1")
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self.resnet = nn.Sequential(*list(self.resnet50_backbone.children())[:-1]).eval()
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self.img_preprocess = transforms.Compose([
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transforms.Resize((224, 224)),
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transforms.ToTensor(),
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transforms.Normalize(
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mean=[0.485, 0.456, 0.406],
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std=[0.229, 0.224, 0.225],
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)
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])
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model_dir = snapshot_download("SaeedLab/TITAN-BBB/classification", allow_patterns=["normalize"])
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transformer_tab_path = os.path.join(model_dir, "normalize_tabular.joblib")
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| 44 |
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transformer_img_path = os.path.join(model_dir, "normalize_image.joblib")
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| 45 |
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transformer_txt_path = os.path.join(model_dir, "normalize_text.joblib")
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| 47 |
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self.feature_transformer_tab = joblib.load(transformer_tab_path)
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self.feature_transformer_img = joblib.load(transformer_img_path)
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self.feature_transformer_txt = joblib.load(transformer_txt_path)
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def generate_tab_features(self, smiles):
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mol = Chem.MolFromSmiles(smiles)
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if mol is None:
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return torch.tensor(self.feature_transformer_tab.n_features_in_, dtype=torch.float32)
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rdkit_2d = np.array(self.calc.CalcDescriptors(mol))
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rdkit_2d[np.isinf(rdkit_2d)] = np.nan
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rdkit_2d = np.nan_to_num(rdkit_2d, nan=0.0, posinf=0.0, neginf=0.0)
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maccs = np.array(list(MACCSkeys.GenMACCSKeys(mol).ToBitString()), dtype=int)
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tab_input = np.concatenate([rdkit_2d, maccs])
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tab_input = self.feature_transformer_tab.transform(tab_input.reshape(1, -1))[0]
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return torch.tensor(tab_input, dtype=torch.float32)
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def generate_img_features(self, smiles):
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mol = Chem.MolFromSmiles(smiles)
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if mol is None:
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img = Image.new("RGB", (300,300), color=(0,0,0))
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else:
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img = Draw.MolToImage(mol, size=(300, 300))
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img = self.img_preprocess(img)
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with torch.no_grad():
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| 73 |
+
img_input = self.resnet(img.unsqueeze(0)).squeeze(-1).squeeze(-1)
|
| 74 |
+
img_input = self.feature_transformer_img.transform(img_input.reshape(1, -1))[0]
|
| 75 |
+
return torch.tensor(img_input, dtype=torch.float32)
|
| 76 |
+
|
| 77 |
+
def generate_txt_features(self, smiles):
|
| 78 |
+
encoded = self.tokenizer(smiles, return_tensors="pt")
|
| 79 |
+
with torch.no_grad():
|
| 80 |
+
outputs = self.chemberta(**encoded)
|
| 81 |
+
hidden_states = outputs.last_hidden_state[0].mean(axis=0).numpy()
|
| 82 |
+
txt_input = self.feature_transformer_txt.transform(hidden_states.reshape(1, -1))[0]
|
| 83 |
+
return torch.tensor(txt_input, dtype=torch.float32)
|
| 84 |
+
|
| 85 |
+
def _batch_encode_plus(
|
| 86 |
+
self,
|
| 87 |
+
batch_smiles: list[str],
|
| 88 |
+
return_tensors: str = "pt",
|
| 89 |
+
**kwargs
|
| 90 |
+
):
|
| 91 |
+
data_list = []
|
| 92 |
+
tab, img, txt = [], [], []
|
| 93 |
+
|
| 94 |
+
for smiles in batch_smiles:
|
| 95 |
+
tab.append(self.generate_tab_features(smiles))
|
| 96 |
+
img.append(self.generate_img_features(smiles))
|
| 97 |
+
txt.append(self.generate_txt_features(smiles))
|
| 98 |
+
|
| 99 |
+
tab = torch.stack(tab)
|
| 100 |
+
img = torch.stack(img)
|
| 101 |
+
txt = torch.stack(txt)
|
| 102 |
+
|
| 103 |
+
output = {}
|
| 104 |
+
output["tab"] = tab
|
| 105 |
+
output["img"] = img
|
| 106 |
+
output["txt"] = txt
|
| 107 |
+
|
| 108 |
+
return BatchEncoding(output, tensor_type=return_tensors)
|
| 109 |
+
|
| 110 |
+
def encode(self,
|
| 111 |
+
batch_smiles: list[str],
|
| 112 |
+
return_tensors: str = "pt",
|
| 113 |
+
**kwargs):
|
| 114 |
+
return self._batch_encode_plus(batch_smiles, return_tensors, **kwargs)
|
| 115 |
+
|
| 116 |
+
def __call__(self,
|
| 117 |
+
batch_smiles: list[str],
|
| 118 |
+
return_tensors: str = "pt",
|
| 119 |
+
**kwargs):
|
| 120 |
+
return self._batch_encode_plus(batch_smiles, return_tensors, **kwargs)
|
| 121 |
+
|
| 122 |
+
def _tokenize(self, text, **kwargs):
|
| 123 |
+
return []
|
| 124 |
+
|
| 125 |
+
def save_vocabulary(self, save_directory, filename_prefix=None):
|
| 126 |
+
return ()
|
| 127 |
+
|
| 128 |
+
def get_vocab(self):
|
| 129 |
+
return {"<pad>":0, "<bos>":1, "<eos>":2, "<unk>":3, "<mask>":4}
|
| 130 |
+
|
| 131 |
+
@property
|
| 132 |
+
def vocab_size(self):
|
| 133 |
+
return len(self.get_vocab())
|
classification/tokenizer_config.json
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"auto_map": {
|
| 3 |
+
"AutoTokenizer": ["tokenizer_bbb.BBBTokenizer", "tokenizer_bbb.BBBTokenizer"]
|
| 4 |
+
},
|
| 5 |
+
"clean_up_tokenization_spaces": true,
|
| 6 |
+
"cls_token": "<bos>",
|
| 7 |
+
"mask_token": "<mask>",
|
| 8 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 9 |
+
"pad_token": "<pad>",
|
| 10 |
+
"sep_token": "<eos>",
|
| 11 |
+
"tokenizer_class": "BBBTokenizer",
|
| 12 |
+
"unk_token": "<unk>"
|
| 13 |
+
}
|
convert_weights.py
ADDED
|
@@ -0,0 +1,63 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import torch
|
| 2 |
+
from configuration_bbb import BBBConfig
|
| 3 |
+
from modeling_bbb import BBBModelForSequenceClassification
|
| 4 |
+
import os
|
| 5 |
+
|
| 6 |
+
BASE_ARCH_PARAMS = {
|
| 7 |
+
"d_tab": 384,
|
| 8 |
+
"d_img": 2048,
|
| 9 |
+
"d_txt": 768,
|
| 10 |
+
"proj_dim": 2048
|
| 11 |
+
}
|
| 12 |
+
|
| 13 |
+
def convert_model(checkpoint_path: str, task_name: str, problem_type: str, dropout: float, save_directory: str):
|
| 14 |
+
config_params = BASE_ARCH_PARAMS.copy()
|
| 15 |
+
config_params["task"] = task_name
|
| 16 |
+
config_params["problem_type"] = problem_type
|
| 17 |
+
config_params["dropout"] = dropout
|
| 18 |
+
|
| 19 |
+
config = BBBConfig(**config_params)
|
| 20 |
+
|
| 21 |
+
hf_model = BBBModelForSequenceClassification(config)
|
| 22 |
+
hf_model.eval()
|
| 23 |
+
|
| 24 |
+
if not os.path.exists(checkpoint_path):
|
| 25 |
+
return
|
| 26 |
+
|
| 27 |
+
old_state_dict = torch.load(checkpoint_path, map_location="cpu")
|
| 28 |
+
|
| 29 |
+
new_state_dict = {}
|
| 30 |
+
for key, value in old_state_dict.items():
|
| 31 |
+
if key.startswith("proj") or key.startswith("attention_pooling"):
|
| 32 |
+
new_state_dict[key] = value
|
| 33 |
+
|
| 34 |
+
elif key.startswith("classifier."):
|
| 35 |
+
# The 'fc' layer is already in the correct place
|
| 36 |
+
new_state_dict[key] = value
|
| 37 |
+
|
| 38 |
+
else:
|
| 39 |
+
print(f"[Warning] Unmapped key found: {key}")
|
| 40 |
+
new_state_dict[key] = value
|
| 41 |
+
|
| 42 |
+
print("State dict key names adjusted.")
|
| 43 |
+
|
| 44 |
+
try:
|
| 45 |
+
hf_model.load_state_dict(new_state_dict, strict=True)
|
| 46 |
+
print("State dict loaded successfully into HF")
|
| 47 |
+
except RuntimeError as e:
|
| 48 |
+
print("\n--- ERROR LOADING STATE DICT ---")
|
| 49 |
+
print("Verify that the parameters in BASE_ARCH_PARAMS are correct.")
|
| 50 |
+
print(e)
|
| 51 |
+
return
|
| 52 |
+
|
| 53 |
+
print(f"Saving HF-formatted model to {save_directory}")
|
| 54 |
+
hf_model.save_pretrained(save_directory)
|
| 55 |
+
|
| 56 |
+
if __name__ == "__main__":
|
| 57 |
+
convert_model(
|
| 58 |
+
checkpoint_path="model_classification.pth",
|
| 59 |
+
task_name="classification",
|
| 60 |
+
dropout=0.1,
|
| 61 |
+
problem_type="single_label_classification",
|
| 62 |
+
save_directory="./classification"
|
| 63 |
+
)
|
regression/config.json
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architectures": [
|
| 3 |
+
"BBBModelForSequenceClassification"
|
| 4 |
+
],
|
| 5 |
+
"auto_map": {
|
| 6 |
+
"AutoConfig": "configuration_bbb.BBBConfig",
|
| 7 |
+
"AutoModelForSequenceClassification": "modeling_bbb.BBBModelForSequenceClassification"
|
| 8 |
+
},
|
| 9 |
+
"d_img": 2048,
|
| 10 |
+
"d_tab": 384,
|
| 11 |
+
"d_txt": 768,
|
| 12 |
+
"dropout": 0.3,
|
| 13 |
+
"dtype": "float32",
|
| 14 |
+
"model_type": "bbb-model",
|
| 15 |
+
"problem_type": "regression",
|
| 16 |
+
"proj_dim": 2048,
|
| 17 |
+
"task": "regression",
|
| 18 |
+
"transformers_version": "4.57.3"
|
| 19 |
+
}
|
regression/configuration_bbb.py
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from transformers import PretrainedConfig
|
| 2 |
+
|
| 3 |
+
class BBBConfig(PretrainedConfig):
|
| 4 |
+
model_type = "bbb-model"
|
| 5 |
+
|
| 6 |
+
def __init__(
|
| 7 |
+
self,
|
| 8 |
+
d_tab : int = 384,
|
| 9 |
+
d_img: int = 2048,
|
| 10 |
+
d_txt: int = 768,
|
| 11 |
+
proj_dim: int = 2048,
|
| 12 |
+
dropout: float = 0.1,
|
| 13 |
+
task: str = 'classification',
|
| 14 |
+
**kwargs):
|
| 15 |
+
|
| 16 |
+
self.d_tab = d_tab
|
| 17 |
+
self.d_img = d_img
|
| 18 |
+
self.d_txt = d_txt
|
| 19 |
+
self.proj_dim = proj_dim
|
| 20 |
+
self.dropout = dropout
|
| 21 |
+
self.task = task
|
| 22 |
+
super().__init__(**kwargs)
|
regression/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:1d281e439bcf72bcccf563020f14589d8388c5ae6c1cfd1ec03610458e8bef64
|
| 3 |
+
size 59853476
|
regression/model_regression.pth
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:093e549d68ce6137dd0ca89a4742f6717e9a628b97a0835210402d60b2a1266c
|
| 3 |
+
size 59859339
|
regression/modeling_bbb.py
ADDED
|
@@ -0,0 +1,99 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import torch
|
| 2 |
+
import torch.nn as nn
|
| 3 |
+
import torch.nn.functional as F
|
| 4 |
+
|
| 5 |
+
from transformers import PreTrainedModel
|
| 6 |
+
from transformers.modeling_outputs import BaseModelOutputWithPooling, SequenceClassifierOutput
|
| 7 |
+
|
| 8 |
+
from .configuration_bbb import BBBConfig
|
| 9 |
+
|
| 10 |
+
class BBBModelForSequenceClassification(PreTrainedModel):
|
| 11 |
+
config_class = BBBConfig
|
| 12 |
+
|
| 13 |
+
def __init__(self, config: BBBConfig):
|
| 14 |
+
super().__init__(config)
|
| 15 |
+
|
| 16 |
+
self.config = config
|
| 17 |
+
|
| 18 |
+
self.proj_tab = nn.Sequential(
|
| 19 |
+
nn.LayerNorm(config.d_tab),
|
| 20 |
+
nn.Linear(config.d_tab, config.proj_dim),
|
| 21 |
+
nn.ReLU(),
|
| 22 |
+
nn.Dropout(config.dropout)
|
| 23 |
+
)
|
| 24 |
+
|
| 25 |
+
self.proj_img = nn.Sequential(
|
| 26 |
+
nn.LayerNorm(config.d_img),
|
| 27 |
+
nn.Linear(config.d_img, config.proj_dim),
|
| 28 |
+
nn.ReLU(),
|
| 29 |
+
nn.Dropout(config.dropout)
|
| 30 |
+
)
|
| 31 |
+
|
| 32 |
+
self.proj_txt = nn.Sequential(
|
| 33 |
+
nn.LayerNorm(config.d_txt),
|
| 34 |
+
nn.Linear(config.d_txt, config.proj_dim),
|
| 35 |
+
nn.ReLU(),
|
| 36 |
+
nn.Dropout(config.dropout)
|
| 37 |
+
)
|
| 38 |
+
|
| 39 |
+
self.attention_pooling = nn.Sequential(
|
| 40 |
+
nn.Linear(config.proj_dim, config.proj_dim),
|
| 41 |
+
nn.Tanh(),
|
| 42 |
+
nn.Linear(config.proj_dim, 1, bias=False)
|
| 43 |
+
)
|
| 44 |
+
|
| 45 |
+
self.classifier = nn.Sequential(
|
| 46 |
+
nn.Linear(config.proj_dim, config.proj_dim),
|
| 47 |
+
nn.ReLU(),
|
| 48 |
+
nn.Dropout(config.dropout),
|
| 49 |
+
nn.Linear(config.proj_dim, 1)
|
| 50 |
+
)
|
| 51 |
+
|
| 52 |
+
def _init_weights(self, module):
|
| 53 |
+
if isinstance(module, nn.Linear):
|
| 54 |
+
module.weight.data.normal_(mean=0.0, std=1.0)
|
| 55 |
+
if module.bias is not None:
|
| 56 |
+
module.bias.data.zero_()
|
| 57 |
+
elif isinstance(module, nn.Embedding):
|
| 58 |
+
module.weight.data.normal_(mean=0.0, std=1.0)
|
| 59 |
+
if module.padding_idx is not None:
|
| 60 |
+
module.weight.data[module.padding_idx].zero_()
|
| 61 |
+
elif isinstance(module, nn.LayerNorm):
|
| 62 |
+
module.bias.data.zero_()
|
| 63 |
+
module.weight.data.fill_(1.0)
|
| 64 |
+
|
| 65 |
+
def forward(self,
|
| 66 |
+
tab: torch.Tensor = None,
|
| 67 |
+
img: torch.Tensor = None,
|
| 68 |
+
txt: torch.Tensor = None,
|
| 69 |
+
labels: torch.Tensor = None):
|
| 70 |
+
|
| 71 |
+
if tab is None or img is None or txt is None:
|
| 72 |
+
raise ValueError('You have to specify tabular, image, and text features')
|
| 73 |
+
|
| 74 |
+
h_tab = self.proj_tab(tab)
|
| 75 |
+
h_img = self.proj_img(img)
|
| 76 |
+
h_txt = self.proj_txt(txt)
|
| 77 |
+
|
| 78 |
+
embeddings = torch.stack([h_tab, h_img, h_txt], dim=1)
|
| 79 |
+
scores = self.attention_pooling(embeddings)
|
| 80 |
+
weights = F.softmax(scores, dim=1)
|
| 81 |
+
weighted_embeddings = embeddings * weights
|
| 82 |
+
pooled_embeddings = torch.sum(weighted_embeddings, dim=1)
|
| 83 |
+
logits = self.classifier(pooled_embeddings).squeeze(-1)
|
| 84 |
+
|
| 85 |
+
loss = None
|
| 86 |
+
if labels is not None:
|
| 87 |
+
if self.config.task == "regression":
|
| 88 |
+
loss_fct = nn.MSELoss()
|
| 89 |
+
loss = loss_fct(logits.squeeze(-1), labels.squeeze(-1))
|
| 90 |
+
elif self.config.task == "classification":
|
| 91 |
+
loss_fct = nn.BCEWithLogitsLoss()
|
| 92 |
+
loss = loss_fct(logits, labels.float().unsqueeze(-1))
|
| 93 |
+
|
| 94 |
+
return SequenceClassifierOutput(
|
| 95 |
+
loss=loss,
|
| 96 |
+
logits=logits,
|
| 97 |
+
hidden_states=pooled_embeddings,
|
| 98 |
+
attentions=weights.squeeze(-1)
|
| 99 |
+
)
|
regression/normalize_image.joblib
ADDED
|
Binary file (49.8 kB). View file
|
|
|
regression/normalize_tabular.joblib
ADDED
|
Binary file (9.83 kB). View file
|
|
|
regression/normalize_text.joblib
ADDED
|
Binary file (19 kB). View file
|
|
|
regression/tokenizer_bbb.py
ADDED
|
@@ -0,0 +1,131 @@
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|
|
| 1 |
+
import torch
|
| 2 |
+
import torch.nn as nn
|
| 3 |
+
from transformers import PreTrainedTokenizer
|
| 4 |
+
from transformers.tokenization_utils_base import BatchEncoding
|
| 5 |
+
from transformers import AutoTokenizer, AutoModel
|
| 6 |
+
from rdkit import Chem
|
| 7 |
+
from rdkit.Chem import Descriptors, AllChem, MACCSkeys
|
| 8 |
+
from rdkit.ML.Descriptors import MoleculeDescriptors
|
| 9 |
+
from rdkit import RDLogger
|
| 10 |
+
from rdkit.Chem import Draw
|
| 11 |
+
import joblib
|
| 12 |
+
import numpy as np
|
| 13 |
+
import os
|
| 14 |
+
from huggingface_hub import snapshot_download
|
| 15 |
+
import warnings
|
| 16 |
+
from sklearn.exceptions import InconsistentVersionWarning
|
| 17 |
+
from torchvision import models, transforms
|
| 18 |
+
from PIL import Image
|
| 19 |
+
warnings.filterwarnings("ignore", category=InconsistentVersionWarning)
|
| 20 |
+
RDLogger.DisableLog('rdApp.*')
|
| 21 |
+
|
| 22 |
+
class BBBTokenizer(PreTrainedTokenizer):
|
| 23 |
+
def __init__(self, **kwargs):
|
| 24 |
+
super().__init__(**kwargs)
|
| 25 |
+
|
| 26 |
+
self.calc = MoleculeDescriptors.MolecularDescriptorCalculator([i[0] for i in Descriptors.descList])
|
| 27 |
+
|
| 28 |
+
self.tokenizer = AutoTokenizer.from_pretrained('DeepChem/ChemBERTa-100M-MLM')
|
| 29 |
+
self.chemberta = AutoModel.from_pretrained('DeepChem/ChemBERTa-100M-MLM').eval()
|
| 30 |
+
|
| 31 |
+
self.resnet50_backbone = models.resnet50(weights="IMAGENET1K_V1")
|
| 32 |
+
self.resnet = nn.Sequential(*list(self.resnet50_backbone.children())[:-1]).eval()
|
| 33 |
+
self.img_preprocess = transforms.Compose([
|
| 34 |
+
transforms.Resize((224, 224)),
|
| 35 |
+
transforms.ToTensor(),
|
| 36 |
+
transforms.Normalize(
|
| 37 |
+
mean=[0.485, 0.456, 0.406],
|
| 38 |
+
std=[0.229, 0.224, 0.225],
|
| 39 |
+
)
|
| 40 |
+
])
|
| 41 |
+
|
| 42 |
+
#model_dir = snapshot_download("SaeedLab/BBBP-Classification", allow_patterns=["transformer.pkl"])
|
| 43 |
+
#transformer_path = os.path.join(model_dir, "transformer.pkl")
|
| 44 |
+
|
| 45 |
+
self.feature_transformer_tab = joblib.load('classification/normalize_tabular.joblib')
|
| 46 |
+
self.feature_transformer_img = joblib.load('classification/normalize_image.joblib')
|
| 47 |
+
self.feature_transformer_txt = joblib.load('classification/normalize_text.joblib')
|
| 48 |
+
|
| 49 |
+
def generate_tab_features(self, smiles):
|
| 50 |
+
mol = Chem.MolFromSmiles(smiles)
|
| 51 |
+
|
| 52 |
+
if mol is None:
|
| 53 |
+
return torch.tensor(self.feature_transformer_tab.n_features_in_, dtype=torch.float32)
|
| 54 |
+
|
| 55 |
+
rdkit_2d = np.array(self.calc.CalcDescriptors(mol))
|
| 56 |
+
rdkit_2d[np.isinf(rdkit_2d)] = np.nan
|
| 57 |
+
rdkit_2d = np.nan_to_num(rdkit_2d, nan=0.0, posinf=0.0, neginf=0.0)
|
| 58 |
+
maccs = np.array(list(MACCSkeys.GenMACCSKeys(mol).ToBitString()), dtype=int)
|
| 59 |
+
tab_input = np.concatenate([rdkit_2d, maccs])
|
| 60 |
+
tab_input = self.feature_transformer_tab.transform(tab_input.reshape(1, -1))[0]
|
| 61 |
+
return torch.tensor(tab_input, dtype=torch.float32)
|
| 62 |
+
|
| 63 |
+
def generate_img_features(self, smiles):
|
| 64 |
+
mol = Chem.MolFromSmiles(smiles)
|
| 65 |
+
if mol is None:
|
| 66 |
+
img = Image.new("RGB", (300,300), color=(0,0,0))
|
| 67 |
+
else:
|
| 68 |
+
img = Draw.MolToImage(mol, size=(300, 300))
|
| 69 |
+
img = self.img_preprocess(img)
|
| 70 |
+
with torch.no_grad():
|
| 71 |
+
img_input = self.resnet(img.unsqueeze(0)).squeeze(-1).squeeze(-1)
|
| 72 |
+
img_input = self.feature_transformer_img.transform(img_input.reshape(1, -1))[0]
|
| 73 |
+
return torch.tensor(img_input, dtype=torch.float32)
|
| 74 |
+
|
| 75 |
+
def generate_txt_features(self, smiles):
|
| 76 |
+
encoded = self.tokenizer(smiles, return_tensors="pt")
|
| 77 |
+
with torch.no_grad():
|
| 78 |
+
outputs = self.chemberta(**encoded)
|
| 79 |
+
hidden_states = outputs.last_hidden_state[0].mean(axis=0).numpy()
|
| 80 |
+
txt_input = self.feature_transformer_txt.transform(hidden_states.reshape(1, -1))[0]
|
| 81 |
+
return torch.tensor(txt_input, dtype=torch.float32)
|
| 82 |
+
|
| 83 |
+
def _batch_encode_plus(
|
| 84 |
+
self,
|
| 85 |
+
batch_smiles: list[str],
|
| 86 |
+
return_tensors: str = "pt",
|
| 87 |
+
**kwargs
|
| 88 |
+
):
|
| 89 |
+
data_list = []
|
| 90 |
+
tab, img, txt = [], [], []
|
| 91 |
+
|
| 92 |
+
for smiles in batch_smiles:
|
| 93 |
+
tab.append(self.generate_tab_features(smiles))
|
| 94 |
+
img.append(self.generate_img_features(smiles))
|
| 95 |
+
txt.append(self.generate_txt_features(smiles))
|
| 96 |
+
|
| 97 |
+
tab = torch.stack(tab)
|
| 98 |
+
img = torch.stack(img)
|
| 99 |
+
txt = torch.stack(txt)
|
| 100 |
+
|
| 101 |
+
output = {}
|
| 102 |
+
output["tab"] = tab
|
| 103 |
+
output["img"] = img
|
| 104 |
+
output["txt"] = txt
|
| 105 |
+
|
| 106 |
+
return BatchEncoding(output, tensor_type=return_tensors)
|
| 107 |
+
|
| 108 |
+
def encode(self,
|
| 109 |
+
batch_smiles: list[str],
|
| 110 |
+
return_tensors: str = "pt",
|
| 111 |
+
**kwargs):
|
| 112 |
+
return self._batch_encode_plus(batch_smiles, return_tensors, **kwargs)
|
| 113 |
+
|
| 114 |
+
def __call__(self,
|
| 115 |
+
batch_smiles: list[str],
|
| 116 |
+
return_tensors: str = "pt",
|
| 117 |
+
**kwargs):
|
| 118 |
+
return self._batch_encode_plus(batch_smiles, return_tensors, **kwargs)
|
| 119 |
+
|
| 120 |
+
def _tokenize(self, text, **kwargs):
|
| 121 |
+
return []
|
| 122 |
+
|
| 123 |
+
def save_vocabulary(self, save_directory, filename_prefix=None):
|
| 124 |
+
return ()
|
| 125 |
+
|
| 126 |
+
def get_vocab(self):
|
| 127 |
+
return {"<pad>":0, "<bos>":1, "<eos>":2, "<unk>":3, "<mask>":4}
|
| 128 |
+
|
| 129 |
+
@property
|
| 130 |
+
def vocab_size(self):
|
| 131 |
+
return len(self.get_vocab())
|
regression/tokenizer_config.json
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"auto_map": {
|
| 3 |
+
"AutoTokenizer": ["tokenizer_bbb.BBBTokenizer", "tokenizer_bbb.BBBTokenizer"]
|
| 4 |
+
},
|
| 5 |
+
"clean_up_tokenization_spaces": true,
|
| 6 |
+
"cls_token": "<bos>",
|
| 7 |
+
"mask_token": "<mask>",
|
| 8 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 9 |
+
"pad_token": "<pad>",
|
| 10 |
+
"sep_token": "<eos>",
|
| 11 |
+
"tokenizer_class": "BBBTokenizer",
|
| 12 |
+
"unk_token": "<unk>"
|
| 13 |
+
}
|