DOI: 10.5281/zenodo.17657635
title: Data and code for article "Graph Neural Network Prediction of Infrared Spectra of Interstellar Polycyclic Aromatic Hydrocarbons"

description: Data and code for article "Graph Neural Network Prediction of Infrared Spectra of Interstellar Polycyclic Aromatic Hydrocarbons"

USAGE INSTRUCTIONS:

--------------------------- Conda env configuration---------------------------aiohappyeyeballs          2.6.1                    aiohttp                   3.12.15                  aiosignal                 1.4.0                    async-timeout             5.0.1                    attrs                     25.3.0                   bzip2                     1.0.8ca-certificates           2025.7.14cloudpickle               3.1.1                    colorama                  0.4.6                    contourpy                 1.3.0                    cycler                    0.12.1                   deepchem                  2.8.1.dev20250723140145          dgl                       1.1.2                    dgllife                   0.3.2                    filelock                  3.18.0                   fonttools                 4.59.0                   frozenlist                1.7.0                    fsspec                    2025.7.0                 future                    1.0.0                    git                       2.49.0huggingface-hub           0.33.4                   hyperopt                  0.2.7                    importlib-resources       6.5.2                    jinja2                    3.1.6                    kiwisolver                1.4.7                    libexpat                  2.7.1libffi                    3.4.6liblzma                   5.8.1libsqlite                 3.50.3libzlib                   1.3.1matplotlib                3.9.4                    mpmath                    1.3.0                    multidict                 6.6.4                    networkx                  3.2.1                    openssl                   3.5.1pandas                    2.3.1                    pillow                    11.3.0                   pip                       25.1.1propcache                 0.3.2                    psutil                    7.0.0                    py4j                      0.10.9.9                 pyparsing                 3.2.3                    python                    3.9.23python-dateutil           2.9.0.post0              pytz                      2025.2                   pyyaml                    6.0.2                    rdkit                     2025.3.3                 regex                     2024.11.6                safetensors               0.5.3                    setuptools                80.9.0sympy                     1.14.0                   threadpoolctl             3.6.0                    tk                        8.6.13tokenizers                0.21.2                   torch                     2.1.2+cu121              torch-cluster             1.6.3+pt21cu121          torch-geometric           2.6.1                    torch-scatter             2.1.2+pt21cu121          torch-sparse              0.6.18+pt21cu121          torch-spline-conv         1.2.2+pt21cu121          torchdata                 0.7.1                    torchvision               0.16.2+cu121             tqdm                      4.67.1                   transformers              4.53.3                   tzdata                    2025.2                  ucrt                      10.0.22621.0         vc                        14.3                vc14_runtime              14.44.35208         wheel                     0.45.1          yarl                      1.20.1

---------------------------           Code---------------------------Model Code:This file contains four graph neural network-based models (AFP, GCN, GAT, MPNN) and the MFP model based on traditional molecular fingerprinting for predicting infrared spectral data, along with AFP models using different training loss functions.AFP model using EMD as training loss function: PAH_EMD_AFP.pyGAT model using EMD as training loss function: PAH_EMD_GAT.pyGCN model using EMD as training loss function: PAH_EMD_GCN.pyMFP model using EMD as training loss function: PAH_EMD_MFP.pyBased on MPNN using EMD as training loss function: PAH_EMD_MPNN.pyBased on HD as training loss function for AFP model: PAH_HD_AFP.pyBased on JSD as training loss function for AFP model: PAH_HD_JSD.pyAFP model using SIS as training loss function: PAH_HD_SIS.pyAFP model using TVD as training loss function: PAH_HD_TVD.pyTesting generalization capability of JSD-based AFP model: PAH_JSD_TEST_AFP.py

---------------------------           DATA---------------------------Data Aspects:Includes processed SMILES string representations of 1,570 high- and low-frequency molecules from the NASA 3.2 PAH database, along with their corresponding spectral data. Also includes processed SMILES string representations of 997 high- and low-frequency molecules (with carbon atom counts between 50-100) from the NASA 4.0 PAH database, along with their corresponding spectral data, used to test model generalization capability.High-frequency data: 3.2_CH_Cleaner ALL_High_PAHs Dataset.pickle, 4.0_CH_Cleaner 50_100_ALL_High_PAHs Dataset.pickleLow-frequency data: 3.2_CH_Cleaner PAHs Dataset.pickle, 4.0_CH_Cleaner 50_100_PAHs Dataset.pickle---------------------------            Run---------------------------Code Execution: After installing the above environment configurations, ensure all data files and code files reside in the same directory before running. Prediction outputs will be saved in the Fold_Predictions directory. The Best_model file within this directory contains the trained AFP model using JSD as the training loss function. This file is utilized when running PAH_JSD_TEST_AFP.py.

---------------------------        Limitations---------------------------The model is currently trained only on neutral PAHs and does not support charged molecules or isotopologues. Predictions for molecules that significantly differ from the training dataset may have increased uncertainty.