Improved molecular property prediction using WL embedding in GNNs.
problem Limited performance of GNNs in predicting molecular properties.
method Explored Weisfeiler-Lehman (WL) embedding to replace GNN layers, enhancing representability and performance.
result WL embedding consistently improves GNN performance across multiple datasets.
A new drug embedding method using hierarchical drug relations and chemical structures.
problem Learning accurate drug representations from chemical structures and hierarchies.
method Semi-supervised drug embedding using VAE in hyperbolic space.
result The method accurately places drugs in a hierarchy and predicts side-effects.
MBE combined with NNs reduces computational cost and improves accuracy.
problem Expensive computational cost of MBE for large systems.
method MBE combined with NNs, using NNs to reduce computational overhead.
result MBE and NNs complement each other, providing accurate predictions.
Graph neural network predicts protonation energies of oxygen atoms in bio-oil molecules.
problem Predicting protonation energies of oxygen atoms in bio-oil molecules for chemical upgrading.
method Site-specific graph neural network approach using iterative local nonlinear embedding.
result Effective prediction of protonation energies of individual oxygen atoms in bio-oil molecules.
New neural networks explain quantum chemistry predictions atomically.
problem Need for interpretable quantum chemical models.
method Atomistic neural networks and aggregation of atom-wise contributions.
result Atom-wise explanations reveal chemical insights.
MoFlow generates chemically valid molecular graphs from latent representations.
problem Generating chemically valid molecular graphs from latent representations is challenging.
method MoFlow uses a flow-based approach with Glow for bond generation and a novel graph conditional flow for atom generation, ensuring chemical validity and efficiency.
result MoFlow achieves state-of-the-art performance in molecular graph generation and optimization.
Automates molecule design with a novel variational autoencoder.
problem Designing molecules based on specific chemical properties.
method Junction tree variational autoencoder generating tree-structured scaffolds and combining them into molecules.
result Significantly outperforms previous models on molecular generation and optimization tasks.
ChemBoost predicts protein-ligand binding affinity using SMILES syntax.
problem Predicting high affinity drug-target interactions from sequence similarity alone.
method ChemBoost uses SMILES syntax to represent ligands as documents and proteins as sequences or ligand-centric features. It learns chemical word embeddings and predicts affinities using eXtreme Gradient Boosting.
result ChemBoost outperforms state-of-the-art systems in predicting protein-ligand affinities.
Framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative importance.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
A framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative contributions.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
DeepVARMA predicts chemical industry index trends using LSTM and VARMAX models.
problem Forecasting the chemical industry index for economic analysis.
method Combines LSTM and VARMAX models to predict nonstationary series.
result DeepVARMA achieves best prediction accuracy and adaptability.
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
A new method for inferring latent states in Markov jump processes.
problem Intractable exact inference for Markov jump processes.
method Entropic matching within expectation propagation.
result Superior performance in approximating the mean of the posterior process.
The paper develops a Gaussian process model for predicting chemical efficacy.
problem Statistical methodologies for analyzing chemical databases are limited.
method Conditional Gaussian process models with Tanimoto distance and a scaling parameter.
result Predictive performance improves when accounting for chemical space correlation.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
problem Inaccurate drug-target interaction prediction due to insufficient chemical information extraction.
method Hierarchical graph representation learning to extract chemical information from atoms, motifs, and molecules.
result HiGraphDTI outperforms state-of-the-art methods in DTI prediction and interaction interpretation.
Neural networks predict substructures from mass spectra to identify chemical threats.
problem Identifying unknown chemical threats from mass spectra and formulas.
method Data-driven approach using neural networks to rank and match substructures.
result Substructure classifiers achieve over 90% micro F1-score and correctly identify structures in 88-71% of cases.
This review discusses challenges and solutions for AI in chemical engineering.
problem Challenges in applying classical machine learning to chemical engineering data.
method Identifying four data characteristics and discussing their applications and solutions.
result Current research extends data science and machine learning to handle chemical engineering data challenges.
SMILES2Vec learns chemical properties from SMILES strings without feature engineering.
problem Predicting chemical properties from SMILES strings without manual feature engineering.
method Deep RNN (SMILES2Vec) learns features from SMILES strings, optimized using Bayesian optimization.
result Optimized SMILES2Vec outperforms MLP neural networks and achieves 88% accuracy in predicting solubility.
GraphAF generates chemically valid molecules efficiently and accurately.
problem Generating chemically valid molecular structures while optimizing chemical properties.
method Flow-based autoregressive model combining autoregressive and flow-based approaches.
result GraphAF generates 68% chemically valid molecules without chemical knowledge rules and 100% with rules, achieving state-of-the-art performance.
AI models struggle to generate diverse natural chemical structures.
problem Generating diverse chemical structures for drug discovery.
method Quantified internal chemical diversity; challenge with two models.
result AI models fail to reproduce natural chemical diversity.
Machine learning recreates the periodic table from element properties.
problem Recreating the periodic table using machine learning.
method Unsupervised machine learning with GTM for feature embedding.
result PTG autonomously generates various periodic table layouts.
Analyzes Indian chemical industry post-Covid.
problem Global uncertainty impacts chemical industry performance.
method Fundamental analysis of key players and trends.
result Various geopolitical and macroeconomic trends shape industry performance.
Paper defines untangling number to measure entanglement complexity in 3-periodic networks.
problem Measuring the complexity of entanglement in 3-periodic networks.
method Defining ground states through knot-theoretic crossing diagrams and measuring untangling number.
result Introduced untangling number as a measure of entanglement complexity.
MEGAN models chemical reactions as graph edits, improving synthesis planning.
problem Generating and predicting chemical reactions under constraints.
method End-to-end encoder-decoder neural model inspired by arrow pushing formalism.
result State-of-the-art accuracy in standard benchmarks for retrosynthesis prediction.
CRNN discovers chemical reaction pathways from data.
problem Challenging to infer reaction pathways for complex systems.
method Neural network approach that satisfies fundamental physics laws.
result CRNN autonomously discovers reaction pathways from species concentration data.
Neural network speeds up atmospheric chemistry modeling 4250x.
problem Computational expense of simulating atmospheric chemistry.
method Created a neural network to emulate a complex chemical mechanism.
result Achieved a 250x computational speedup.
New method explains complex fuel compound classifications.
problem Understanding complex quantitative structure-activity relationship models.
method Locally Interpretable Machine-Agnostic Explanations (LIME) applied to 2-D chemical structures.
result Replicates chemical intuition, allowing direct acceptance/rejection of decisions.
Chemical networks outperform spiking neural networks in classification tasks.
problem Learning tasks with spiking neural networks require hidden layers, which are computationally expensive.
method Used deterministic mass-action kinetics to prove chemical reaction networks without hidden layers can solve tasks previously solved by spiking neural networks.
result A chemical reaction network without hidden layers outperforms a spiking neural network with hidden layers in a handwritten digit classification task.
AI system synthesizes chemical plant operation procedures for efficiency and stability.
problem Developing efficient and stable operation procedures for complex chemical plants.
method Integrates automated reasoning, deep reinforcement learning, and dynamic simulation with external knowledge.
result Synthesized procedure achieves faster recovery from malfunctions compared to standard PID control.
Researchers derive the chemical potential equation for ideal agent systems.
problem Missing equation of state for chemical potential in ideal agent systems.
method Derived from econophysical model assumptions of ideal agent systems.
result Equation of state for chemical potential derived for ideal agent systems.
Machine learning speeds up chemical equilibrium calculations in reactive transport simulations.
problem High computational cost of chemical equilibrium calculations in reactive transport models.
method Machine learning method to quickly estimate new equilibrium states based on previous calculations.
result Achieved almost two orders of magnitude speedup in equilibrium calculations.
Heteroencoders improve chemical latent space diversity and molecular generation.
problem Improving chemical latent space properties and diversity in autoencoders.
method Employing SMILES enumeration for encoder or decoder, training RNNs with LSTM, and using QSAR models.
result Heteroencoders yield more diverse latent spaces and better molecular generation.
MatGAN uses GAN to efficiently generate new inorganic materials.
problem Efficiently searching the vast chemical design space for new materials.
method Generative adversarial network (GAN) trained on ICSD materials database.
result 92.53% novelty and 84.5% chemically valid samples generated.
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
ChemNet uses rule-based labels for weakly supervised learning to predict chemical properties.
problem Lack of labeled data in chemistry.
method Rule-based knowledge for training ChemNet, a deep neural network, on large unlabeled chemical databases.
result ChemNet outperforms DNN models trained with conventional supervised learning on smaller datasets.
Combines PCA and message passing for better graph node embeddings.
problem Challenges of learning long-range dependencies in graph data.
method PCAPass: PCA + message passing for unsupervised node embeddings.
result Empirically shows competitive performance on node classification benchmarks.
AI model identifies chemical agents in MCI with high accuracy.
problem Identifying chemical agents in mass casualty incidents.
method Reverse engineered signs/symptoms, trained using ANN, BDT, and WISER.
result WISER outperformed ANN and BDT in identifying chemical agents.
Neural networks learn molecule and material representations.
problem Learning efficient representations for molecules and materials.
method Continuous-filter convolutional network SchNet.
result SchNet accurately predicts chemical properties across various datasets.
TeaNet uses GCNs to model complex atomic interactions inspired by electronic relaxation.
problem Creating a universal interatomic potential for all elements.
method Tensor-embedded atom network (TeaNet) using graph convolutional neural networks (GCNs).
result TeaNet achieves good performance (19 meV/atom) for structures and reactions involving elements from H to Ar.
Hyperbolic volume correlates with chemical properties of fullerenes.
problem Understanding the relationship between fullerene structure and chemical properties.
method Calculated hyperbolic volumes of fullerenes and correlated them with topological indices.
result Hyperbolic volume correlates with Wiener index and other topological indices of fullerenes.
Deep RL finds efficient pathways for sugar to chemicals.
problem Finding efficient pathways from sugar to value-added chemicals.
method Markov decision process with deep reinforcement learning.
result Promising preliminary results in efficient biomass conversion.
A new method uses active learning to improve chemical simulation efficiency.
problem Efficiently estimating equilibrium-based chemical simulations.
method Sequential data-driven approach using Gaussian process uncertainty.
result Significantly reduced number of function evaluations.
NLP techniques improve drug discovery by analyzing chemical and protein text.
problem Improving drug discovery through better analysis of chemical and protein text.
method Natural language processing techniques applied to biochemical entities.
result Enhanced prediction of molecular properties and design of novel molecules.
Graph neural networks improve molecular property prediction.
problem Efficiently predicting molecular properties with high accuracy and scalability.
method Gated Graph Recursive Neural Networks (GGNN) with skip connections.
result GGNN achieves state-of-the-art performance on molecular property prediction benchmarks.
ChemGrapher uses deep learning to automatically convert chemical compound images into accurate graphs.
problem Automatically converting chemical compound images into accurate graphs with correct bond multiplicity and stereochemical information.
method Developed a deep neural network model for optical compound recognition, including segmentation and classification models.
result Significant error reductions in bond multiplicity and stereochemical information compared to existing tools.
Time-lagged autoencoders improve molecular dynamics data analysis.
problem Analyzing slow collective variables in molecular kinetics.
method Modified autoencoder neural network for dimension reduction.
result Time-lagged autoencoders reliably capture slow dynamics.
This review introduces methods for modeling and inferring stochastic biochemical kinetics.
problem Challenges in modeling and inferring stochastic biochemical kinetics due to complex dynamics and computational limitations.
method Introduction to modelling concepts, simulation, exact solution methods, approximation methods, and inference methods.
result Efficient approximation and inference methods have been developed to handle the complexity of stochastic biochemical kinetics.
Unified CNN identifies chemical species from Raman spectra.
problem Challenges in identifying chemical species from Raman spectra due to preprocessing requirements.
method A deep convolutional neural network trained to automatically identify substances from Raman spectra.
result Superior classification performance compared to other machine learning methods.