Comparing Machine Learning Models for Aromatase (P450 19A1)

Integrated Transfer Learning and Multitask Learning Strategies to Construct Graph Neural Network Models for Predicting Bioaccumulation Parameters of Chemicals

Accurate prediction of parameters related to the environmental exposure of chemicals is crucial for the sound management of chemicals. However, the lack of large data sets for training models may result in poor prediction accuracy and robustness. Herein, integrated transfer learning (TL) and multitask learning (MTL) was proposed for constructing a graph neural network (GNN) model (abbreviated as TL-MTL-GNN model) using n-octanol/water partition coefficients as a source domain. The TL-MTL-GNN model was trained to predict three bioaccumulation parameters based on enlarged data sets that cover 2496 compounds with at least one bioaccumulation parameter. Results show that the TL-MTL-GNN model outperformed single-task GNN models with and without the TL, as well as conventional machine learning models trained with molecular descriptors or fingerprints. Applicability domains were characterized by a state-of-the-art structure-activity landscape-based (abbreviated as ADSAL) methodology. The TL-MTL-GNN model coupled with the optimal ADSAL was employed to predict bioaccumulation parameters for around 60,000 chemicals, with more than 13,000 compounds identified as bioaccumulative chemicals. The high predictive accuracy and robustness of the TL-MTL-GNN model demonstrate the feasibility of integrating the TL and MTL strategy in modeling small-sized data sets. The strategy holds significant potential for addressing small data challenges in modeling environmental chemicals.

Toward a comprehensive understanding of alicyclic compounds: Bio-effects perspective and deep learning approach

The escalating use of alicyclic compounds in modern industrial production has led to a rapid increase of these substances in the environment, posing significant health hazards. Addressing this challenge necessitates a comprehensive understanding of these compounds, which can be achieved through the deep learning approach. Graph neural networks (GNN) known for its' extraordinary ability to process graph data with rich relationships, have been employed in various molecular prediction tasks. In this study, alicyclic molecules screened from PCBA, Toxcast and Tox21 are made as general bioactivity and biological targets' activity prediction datasets. GNN-based models are trained on the two datasets, while the Attentive FP and PAGTN achieve best performance individually. In addition, alicyclic carbon atoms make the greatest contribution to biological activity, which indicate that the alicycle structures have significant impact on the carbon atoms' contribution. Moreover, there are terrific number of active molecules in other public datasets, indicates that alicyclic compounds deserve more attention in POPs control. This study uncovered deeper structural-activity relationships within these compounds, offering new perspectives and methodologies for academic research in the field.

Applied Machine Learning for Prediction of CO2 Adsorption on Biomass Waste-Derived Porous Carbons

Biomass waste-derived porous carbons (BWDPCs) are a class of complex materials that are widely used in sustainable waste management and carbon capture. However, their diverse textural properties, the presence of various functional groups, and the varied temperatures and pressures to which they are subjected during CO₂ adsorption make it challenging to understand the underlying mechanism of CO₂ adsorption. Here, we compiled a data set including 527 data points collected from peer-reviewed publications and applied machine learning to systematically map CO₂ adsorption as a function of the textural and compositional properties of BWDPCs and adsorption parameters. Various tree-based models were devised, where the gradient boosting decision trees (GBDTs) had the best predictive performance with R² of 0.98 and 0.84 on the training and test data, respectively. Further, the BWDPCs in the compiled data set were classified into regular porous carbons (RPCs) and heteroatom-doped porous carbons (HDPCs), where again the GBDT model had R² of 0.99 and 0.98 on the training and 0.86 and 0.79 on the test data for the RPCs and HDPCs, respectively. Feature importance revealed the significance of adsorption parameters, textural properties, and compositional properties in the order of precedence for BWDPC-based CO₂ adsorption, effectively guiding the synthesis of porous carbons for CO₂ adsorption applications.