Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex chemical properties. In this work, we develop SMILES2vec, a deep RNN that automat…
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.
With access to large datasets, deep neural networks (DNN) have achieved human-level accuracy in image and speech recognition tasks. However, in chemistry, data is inherently small and fragmented. In this work, we develop an approach of using rule-based knowledge for training ChemNet, a transferable and generalizable de…
Proposes a new model to predict polymer properties by integrating various data types.
problem Inaccurate polymer property prediction due to separate modeling of different data types.
method Multi-modal cascade feature transfer using GCN for chemical structure and molecular descriptors.
result Empirically evaluated model shows higher predictive performance than single-feature approaches.
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.
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.
We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two deep neural networks - generative and predictive - that are trained separately b…
New method predicts activity coefficients for binary mixtures without using physical descriptors.
problem Predicting activity coefficients for unexplored binary mixtures.
method Probabilistic matrix factorization model.
result Method outperforms state-of-the-art models requiring less training effort.
Unified machine learning predicts molecular wavefunctions efficiently.
problem Lack of explicit electronic structure in machine learning models for chemistry.
method Deep neural network for quantum mechanical wavefunction prediction.
result Efficient prediction of molecular wavefunctions with full electronic structure access.
Improved chemical predictions through compressed atomic species representations.
problem Intractable chemical space of molecules and materials.
method Introducing elemental modes for compressed representation of atomic species.
result Elemental modes enable improvements in machine learning tasks for chemical predictions.
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.
Improved atomistic model predicts molecular properties using weighted skip-connections.
problem Understanding the relative importance of interactions in molecular property prediction.
method Extended SchNet architecture with weighted skip-connections to analyze molecule properties.
result Relative weighting of interaction blocks depends on molecule's chemical composition and configurational degrees of freedom.
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.
Deep featurization improves ADMET prediction accuracy.
problem Predicting ADMET properties to reduce clinical trial failures.
method Learning features from explicit molecular graphs using graph convolutions.
result Achieved unprecedented accuracy in ADMET property prediction.
Graph Convolutional Neural Networks identify molecular functional groups.
problem Automatic discovery of molecular functional groups to reduce lab experiments.
method Graph Convolutional Neural Networks (GCNNs) trained on relational graphs of molecules.
result Grad-CAM method identified the most specific and relevant molecular substructures.
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.
BayesGrad explains graph convolutional network predictions.
problem Uncertainty in chemical property predictions due to small sample size and label imbalance.
method Bayesian predictive distribution with dropout technique to define node importance.
result BayesGrad successfully visualizes substructures responsible for predictions in small sample size scenarios.
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.
Bayesian neural networks quantify uncertainties in molecular property predictions.
problem Poor predictions in molecular property predictions due to unreliable training data.
method Bayesian neural networks to estimate model-driven and data-driven uncertainties.
result Uncertainty quantification is necessary for reliable molecular applications.
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.
The meteoric rise of deep learning models in computer vision research, having achieved human-level accuracy in image recognition tasks is firm evidence of the impact of representation learning of deep neural networks. In the chemistry domain, recent advances have also led to the development of similar CNN models, such …
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.
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.
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.
Improved molecular property prediction using multitask learning.
problem Predicting molecular properties from chemical data is challenging.
method Multitask learning applied to graph neural networks.
result Multitask learning significantly improves model performance and reduces variance.
Novel ML model predicts solvation free energies from atom interactions.
problem Predicting solvation free energies from atomistic interactions.
method Two encoding functions extract atomic feature vectors, interactions calculated by inner product.
result Outstanding performance and transferability on 6,493 experimental measurements.
For quantitative structure-property relationship (QSPR) studies in chemoinformatics, it is important to get interpretable relationship between chemical properties and chemical features. However, the predictive power and interpretability of QSPR models are usually two different objectives that are difficult to achieve s…
CASTER predicts drug interactions using chemical substructures.
problem Identifying potential drug-drug interactions during drug design.
method CASTER uses sequential pattern mining, auto-encoding, and dictionary learning to predict DDIs.
result CASTER outperformed state-of-the-art models and provided interpretable predictions.
Rank-based Bayesian Optimization improves molecule selection in chemical systems.
problem Optimizing chemical compounds using traditional regression models.
method Introducing Rank-based Bayesian Optimization (RBO) using ranking models.
result RBO outperforms regression-based BO, especially for rough landscapes and activity cliffs.
A new graph model HMG and neural network HMGNN improve molecule property predictions.
problem Predicting quantum mechanical properties of molecules with limited consideration of many-body interactions.
method Introducing heterogeneous molecular graphs (HMG) and building HMGNN on neural message passing scheme.
result HMGNN achieves state-of-the-art performance in 9 out of 12 tasks on the QM9 dataset.
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.
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.
CRYSPNet predicts crystal structures from chemical compositions.
problem Predicting crystal structures of solids is challenging and computationally expensive.
method CRYSPNet uses a neural network to predict crystal properties from chemical composition.
result CRYSPNet outperforms alternative methods and is robustly validated.
Graph neural networks outperform fixed molecular descriptors in property prediction.
problem Comparing graph neural networks to fixed molecular descriptors for property prediction.
method Benchmarked graph convolutional neural networks on public and proprietary datasets.
result Graph convolutional model consistently matches or outperforms existing models on both public and proprietary datasets.
Study evaluates uncertainty quantification for atomistic neural networks, revealing complex relationships between error and uncertainty.
problem Uncertainty quantification for predictions of atomistic neural networks.
method Modified PhysNet NN architecture, evaluated with various metrics, analyzed QM9 and tautomerization reaction databases.
result Error and uncertainty are not linearly related; redundancy and noise complicate predictions, especially for small changes.
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.
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.
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.
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.
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical accuracy is still prohibitively expensive for ab-initio MBE to compete with force fi…
Machine learning predicts liquid water properties from cluster data.
problem Accuracy of bulk properties from machine-learned potentials is limited by training data.
method Local, atom-centred descriptors enable prediction of bulk properties from cluster data.
result Excellent agreement with experimental and theoretical counterparts of liquid water properties.
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.
A new model designs molecules with desired properties.
problem Finding molecules with optimal chemical or biological properties.
method A latent prompt Transformer model with three components: latent vector, molecule generation, and property prediction.
result The model achieves state-of-the-art performance on molecule design tasks.
MoleculeSTM learns from molecule structures and texts for better drug design.
problem Lack of integration between chemical structures and textual knowledge in AI drug discovery.
method Jointly learns chemical structures and texts via contrastive learning, using a large dataset.
result MoleculeSTM achieves state-of-the-art performance in zero-shot tasks like structure-text retrieval and molecule editing.
Nuclear magnetic resonance (NMR) spectroscopy exploits the magnetic properties of atomic nuclei to discover the structure, reaction state and chemical environment of molecules. We propose a probabilistic generative model and inference procedures for NMR spectroscopy. Specifically, we use a weighted sum of trigonometric…
Deep neural networks improve chemical reactor control using MPC.
problem Improving control of chemical reactors with neural networks.
method Training neural networks on model predictive control (MPC) for reactor control.
result Neural network can mimic MPC control inputs while maintaining constraints.
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.