├── .github └── workflows │ └── tests.yaml ├── .gitignore ├── LICENSE ├── README.md ├── configs ├── augment │ ├── ir │ │ ├── combined.yaml │ │ ├── horizontal.yaml │ │ ├── pseudo.yaml │ │ ├── smiles.yaml │ │ └── smooth.yaml │ └── no_augment.yaml ├── config_predict.yaml ├── config_train.yaml ├── data │ ├── ir │ │ ├── patches.yaml │ │ ├── patches_mixture_percentage.yaml │ │ ├── patches_mixture_text_percentage.yaml │ │ └── patches_mixture_text_percentage_align.yaml │ ├── multimodal │ │ ├── carbon.yaml │ │ ├── hnmr.yaml │ │ ├── ir.yaml │ │ └── multimodal.yaml │ └── phosphor │ │ ├── formula_num.yaml │ │ ├── formula_txt.yaml │ │ └── num.yaml ├── hydra │ └── default.yaml ├── mixture │ └── ir │ │ ├── binary.yaml │ │ ├── binary_1_9.yaml │ │ ├── binary_3_7.yaml │ │ ├── binary_4_6.yaml │ │ ├── binary_real_data_mixed.yaml │ │ ├── multitask.yaml │ │ ├── multitask_extended.yaml │ │ └── ternary.yaml └── model │ ├── bart_medium.yaml │ ├── custom_hf_bart.yaml │ ├── custom_model.yaml │ ├── custom_model_align.yaml │ ├── custom_model_base.yaml │ ├── custom_model_large.yaml │ ├── hf_bart_medium.yaml │ └── t5_small.yaml ├── docs ├── index.html └── static │ ├── ir_mixture.png │ ├── ir_nmr_dataset.png │ ├── ir_v1.png │ ├── ir_v2.png │ ├── mm_dataset.png │ ├── multimodal.png │ ├── nmr_paper.png │ └── phosphor.png ├── paper_replication ├── figures │ ├── ir.png │ ├── mixture.png │ ├── multimodal.png │ └── phosphor.png ├── ir │ ├── README.md │ └── scripts │ │ ├── download_process_data.sh │ │ ├── filter_nist.py │ │ ├── finetuning.sh │ │ ├── process_data.py │ │ ├── replicate_table_1.sh │ │ ├── replicate_table_2.sh │ │ └── replicate_table_3.sh ├── mixture │ ├── README.md │ └── scripts │ │ ├── download_process_data.sh │ │ ├── replicate_table_1.sh │ │ ├── replicate_table_2_and_10.sh │ │ ├── replicate_table_3.sh │ │ ├── replicate_table_4.sh │ │ ├── replicate_table_5.sh │ │ ├── replicate_table_6.sh │ │ ├── replicate_table_7.sh │ │ └── replicate_table_8.sh ├── multimodal │ ├── README.md │ └── scripts │ │ ├── download_data.sh │ │ ├── finetuning.sh │ │ ├── multitask_model.sh │ │ └── singletask_models.sh ├── phosphor │ ├── README.md │ └── scripts │ │ ├── download_process_data.sh │ │ ├── phosphor_finetuning.sh │ │ ├── phosphor_from_scratch.sh │ │ ├── phosphor_pretraining.sh │ │ └── process_hack_data.py └── scripts_ir_nmr_multimodal_comp_spectra_dataset │ ├── README.md │ ├── figures │ ├── ir_spectra_id_0.png │ └── plot_autocorr_dipole_id_0.png │ ├── requirements.txt │ ├── sample_data │ ├── IR-data_dipole_id_0_auto_damped.csv │ ├── autocorr_damp_dipole_id_0.txt │ ├── autocorr_orig_dipole_id_0.txt │ └── dipole_id_0.npy │ ├── scripts │ ├── make_input_cpmd_from_xyz.py │ ├── make_input_cpmd_with_vdW_from_xyz.py │ └── make_xyz_file_from_smiles.py │ ├── scripts_dipole_true_pred_error_fig6_and_fig7 │ ├── README.md │ ├── collect_y_pred_y_true.py │ ├── collect_y_pred_y_true_Only_plot_selected.py │ ├── figure6.png │ ├── figure7_selected-ex-22447-and-11726.png │ ├── plot_figure6.py │ └── plot_figure7.py │ ├── scripts_ir_spectra │ ├── README.md │ ├── compute_ir_spectra_from_dipole_dipole_autocorrelation.py │ ├── make_IR_plot_from_parquet.py │ └── plot_IR_spectra_from_parquet.ipynb │ └── scripts_nmr_fig_9 │ ├── README.md │ ├── plot_H_NMR_C_NMR_selected_ids.ipynb │ ├── plot_H_NMR_C_NMR_selected_ids.py │ ├── plot_H_NMR_C_NMR_selected_ids.py.txt │ └── sample_exp_data.json ├── pyproject.toml ├── requirements.txt ├── scripts ├── test_model.sh ├── train_model.sh └── train_model_interactive.sh ├── src └── analytical_fm │ ├── __init__.py │ ├── cli │ ├── __init__.py │ ├── predict.py │ ├── training.py │ └── utils.py │ ├── configuration.py │ ├── data │ ├── __init__.py │ ├── augmentations.py │ ├── data_utils.py │ ├── datamodules.py │ ├── datasets.py │ ├── preprocessing │ │ ├── __init__.py │ │ ├── carbon.py │ │ ├── functional_group.py │ │ ├── msms_number.py │ │ ├── msms_text.py │ │ ├── multiplets.py │ │ ├── normalization.py │ │ ├── onehot.py │ │ ├── patches.py │ │ └── text_spectrum.py │ ├── preprocessors.py │ └── tokenizer.py │ ├── generation │ ├── __init__.py │ └── logit_processors.py │ ├── modeling │ ├── __init__.py │ ├── custom_bart_modeling.py │ ├── custom_modeling.py │ ├── utils.py │ └── wrapper.py │ ├── py.typed │ ├── resources │ └── test_data │ │ └── scoring │ │ └── test_data.pkl │ ├── trainer │ ├── __init__.py │ └── trainer.py │ └── utils.py ├── tests ├── __init__.py ├── test_data │ └── ir_dataset │ │ └── ir_data.parquet ├── test_run.py └── test_scoring.py └── uv.lock /.github/workflows/tests.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rxn4chemistry/MultimodalAnalytical/HEAD/.github/workflows/tests.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rxn4chemistry/MultimodalAnalytical/HEAD/.gitignore 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