bert-loves-chemistry
bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
File Explorer
Download Latest Version (.zip)- FUNDING.yml
- config.json
- vocab.txt
- test_attention.py
- __init__.py
- file_utils.py
- modeling_bert.py
- modeling_gpt2.py
- modeling_openai.py
- modeling_roberta.py
- modeling_transfo_xl.py
- modeling_transfo_xl_utilities.py
- modeling_utils.py
- modeling_xlm.py
- modeling_xlnet.py
- tokenization_bert.py
- tokenization_gpt2.py
- tokenization_openai.py
- tokenization_roberta.py
- tokenization_transfo_xl.py
- tokenization_utils.py
- tokenization_xlm.py
- tokenization_xlnet.py
- __init__.py
- head_view.js
- head_view.py
- model_view.js
- model_view.py
- neuron_view.js
- neuron_view.py
- util.py
- head_thumbnail_left.png
- head_thumbnail_right.gif
- model_thumbnail.jpg
- neuron_thumbnail.png
- head_view_albert.ipynb
- head_view_bert.ipynb
- head_view_distilbert.ipynb
- head_view_gpt2.ipynb
- head_view_roberta.ipynb
- head_view_xlm.ipynb
- head_view_xlnet.ipynb
- model_view_albert.ipynb
- model_view_bert.ipynb
- model_view_distilbert.ipynb
- model_view_gpt2.ipynb
- model_view_roberta.ipynb
- model_view_xlm.ipynb
- model_view_xlnet.ipynb
- neuron_view_bert.ipynb
- neuron_view_gpt2.ipynb
- neuron_view_roberta.ipynb
- .gitignore
- atom_weight_visualization.ipynb
- AttentiveFP_Aromaticity_pre_trained.pth
- head_view_chemberta.ipynb
- LICENSE
- model_view_chenberta.ipynb
- README.md
- requirements.txt
- tox21_dglgraph.bin
- vocab.txt
- 100k_rndm_zinc_drugs_clean.txt
- 250k_rndm_zinc_drugs_clean_sorted copy.txt
- csv_to_txt.sh
- pubchem_1k_smiles.txt
- pubchem_descriptors_sample_1k_clean.csv
- pubchem_descriptors_sample_1k_normalization_values_199.json
- pubchem_descriptors_sample_1k_normalization_values_207.json
- tox21_balanced_revised_no_id.csv
- eval_all_finetune_over_time.ipynb
- eval_scaling_effects.ipynb
- 22_Transfer_Learning_With_ChemBERTa_Transformers.ipynb
- 23_Transfer_Learning_With_ChemBERTa_Transformers_Pt_2.ipynb
- ZINC100k_Transfer_Learning_With_HuggingFace_tox21.ipynb
- ZINC250K_Transfer_Learning_With_HuggingFace_tox21.ipynb
- __init__.py
- aggregate_metrics.py
- finetune.py
- finetune_multiple_with_freeze.py
- finetune_with_freeze.py
- README.md
- utils.py
- SMILES_Tokenizer_PubChem10M.ipynb
- smiles_tokenizer_pubchem10m.py
- HuggingFace_RoBERTa_pretrained.ipynb
- huggingface_roberta_upload.ipynb
- MLM_ZINC_250k_ROBERTA.ipynb
- train_roberta_mlm.py
- train_roberta_regression.py
- train_roberta_sequenceclass.py
- finetune.ipynb
- hf_molnet_finetuning.ipynb
- molnet_finetune.py
- benchmarking_data_loaders.ipynb
- HuggingFace_ZINC_ROBERTA.ipynb
- flags.py
- test_mlm.sh
- test_mtr.sh
- test_mtr_lazy.sh
- train_roberta.py
- train_roberta_with_hp_tune.py
- utils.py
- __init__.py
- cloud.py
- compute_norms.py
- data_collators.py
- molnet_dataloader.ipynb
- molnet_dataloader.py
- raw_text_dataset.py
- roberta_regression.py
- ChemBERTA_dimensionaliy_reduction_BBBP.ipynb
- viz_utils.py
- __init__.py
- .gitignore
- .pre-commit-config.yaml
- atom_weight_visualization.ipynb
- DeepChemDev.ipynb
- environment.yml
- LICENSE
- README.md
- setup.py
# Installation Guide
1. Get the code
git clone https://github.com/seyonechithrananda/bert-loves-chemistry
Downloads the entire project code from GitHub to your computer.
cd bert-loves-chemistry
Moves into the project folder you just downloaded.
2. Python
Easy RecommendedPrerequisites
pip install -r chemberta/bertviz_clone/requirements.txt
Installs the Python libraries listed in requirements.txt (or similar).
jupyter notebook
Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.
If it runs without errors and prints output in the terminal, it worked.
// repository documentation
Was this content helpful?
(0 ratings)