A new model designs molecular latent vectors for drug discovery.
problem Designing effective molecular descriptors from molecular structures.
method Proposes a denoising diffusion probabilistic model (DDPM) for variational autoencoding molecular graphs.
result Demonstrates superior prediction performance and robustness compared to existing approaches.
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.
Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tas…
Framework for training-free guidance in discrete diffusion models for molecular generation.
problem No equivalent training-free guidance methods for discrete diffusion models.
method Framework using guidance functions for discrete data.
result Demonstrated utility on molecular graph generation tasks.
We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules w…
LSS learns molecular trajectories from MD data.
problem Limited integration time steps in MD simulations.
method Three deep learning networks for slow collective variables, dynamics, and configuration reconstruction.
result Generates ultra-long synthetic folding trajectories.
Optimizes molecular generation for chemist preferences.
problem Models lack inherent preferences for chemist-desired structures.
method Fine-tuning with Direct Preference Optimization.
result Approach is simple, efficient, and highly effective.
AniDS improves molecular force field modeling by learning anisotropic noise.
problem Molecular force field modeling suffers from oversimplified assumptions about atomic motions.
method AniDS introduces anisotropic noise generation for better modeling of directional and structural variability.
result AniDS outperforms existing methods on benchmarks, achieving significant improvements in force prediction accuracy.
Machine learning models simulate molecular spectra and reactions in solvents.
problem Accurate simulation of molecular spectra and reactions in solvent environments.
method Introduced FieldSchNet, a deep neural network for modeling molecular interactions with external fields.
result Demonstrated significant lowering of Claisen rearrangement reaction activation barrier using FieldSchNet.
Researchers use active subspaces to quantify uncertainty in deep generative models for molecular design.
problem Uncertainty quantification in deep generative models for molecular design due to high parameter space.
method Leveraging active subspaces to approximate posterior distribution over low-dimensional parameters.
result The proposed UQ scheme effectively estimates epistemic uncertainty in high-dimensional parameter space without altering model architecture.
Model predicts stable molecules with AI and physics constraints.
problem Designing stable molecules with limited data.
method Graph Scattering Variational Autoencoder with physical constraints.
result Model generates stable molecules with desired properties.
Generative models accelerate molecular dynamics by four orders of magnitude.
problem Femtosecond time steps limit access to slow molecular processes.
method Deep generative modeling framework that accelerates sampling.
result Quantitative characterization of equilibrium ensembles and dynamical relaxation processes.
Framework learns surrogates for molecular dynamics across multiple time-scales.
problem Stable molecular dynamics simulations require small time-steps, but long-time-scale moments need repeated simulations.
method Implicit Transfer Operator Learning with denoising diffusion probabilistic models and SE(3) equivariant architecture.
result Models can generate self-consistent stochastic dynamics across multiple time-scales.
RC flow learns molecular kinetics in low dimensions.
problem Discovering interpretable low-dimensional models of molecular kinetics.
method Normalizing flow for coordinate transformation and Brownian dynamics for kinetics approximation.
result Tractable and trainable model of reduced kinetics in continuous time and space.
Paper proposes a self-training method to generate molecular targets.
problem Challenges in training generative models for complex molecular design.
method Iterative target augmentation using a property predictor and EM iterations.
result Significant gains in molecular design, outperforming previous methods.
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-d…
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a…
Great computational effort is invested in generating equilibrium states for molecular systems using, for example, Markov chain Monte Carlo. We present a probabilistic model that generates statistically independent samples for molecules from their graph representations. Our model learns a low-dimensional manifold that p…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory computations or the limited accuracy of classical empirical force fields. Machine l…
Study compares GNNs and classical molecular featurisations for molecular property and cliff prediction.
problem Comparing GNNs and classical featurisations for molecular property and cliff prediction.
method Systematic exploration and comparison of PDVs, ECFPs, and GNNs; introduction of substructure pooling.
result Sort & Slice outperforms hash-based folding in ECFP vectorization.
FlowMO uses Gaussian Processes for molecular property prediction with uncertainty.
problem Predicting molecular properties with uncertainty for small datasets.
method Gaussian Processes implemented in FlowMO, built on GPflow and RDKit.
result Comparable predictive performance to deep learning but superior uncertainty calibration.
We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings …
Advanced GNNs improve molecular generation models.
problem Generating complete graphs with multiple nodes and edges based on labels.
method Replaced standard GNNs with more expressive GNNs in autoregressive and one-shot generation models.
result Advanced GNNs can improve performance of graph generative models, but expressiveness is not a necessity.
MolHF generates complex molecules with hierarchical flow-based model.
problem Designing novel molecular structures with desired properties.
method MolHF is a hierarchical normalizing flow model that generates molecular graphs in a coarse-to-fine manner.
result MolHF achieves state-of-the-art performance in random generation and property optimization.
There is an increasing demand for computing the relevant structures, equilibria and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension red…
Machine learning algorithms for generating molecular structures offer a promising new approach to drug discovery. We cast molecular optimization as a translation problem, where the goal is to map an input compound to a target compound with improved biochemical properties. Remarkably, we observe that when generated mole…
This paper reviews deep learning and knowledge-based methods for molecular design.
problem Optimizing molecular properties for scientific advances and process performance.
method Survey of deep learning and knowledge-based methods for molecular design.
result Deep learning models show promise in overcoming computational challenges.
GAGA accelerates 3D molecular generation by replacing long trajectories with Gaussian approximations.
problem High computational cost of long generative trajectories in 3D molecular generation.
method GAGA identifies a characteristic step where molecular data becomes sufficiently Gaussian, replacing the trajectory with a Gaussian approximation.
result Significant improvement in both generation quality and computational efficiency.
In chemistry, deep neural network models have been increasingly utilized in a variety of applications such as molecular property predictions, novel molecule designs, and planning chemical reactions. Despite the rapid increase in the use of state-of-the-art models and algorithms, deep neural network models often produce…
Transformer-M learns molecular data in 2D or 3D formats.
problem Learning models for molecules are limited to specific data formats.
method Developed a Transformer-based model that can handle 2D and 3D molecular data.
result Transformer-M achieves strong performance on both 2D and 3D molecular tasks.
ASGN uses active semi-supervised learning to predict molecular properties efficiently.
problem Predicting molecular properties with scarce labeled data and high computational cost.
method ASGN combines a teacher-student framework with active learning to handle joint representation and property learning.
result ASGN achieves remarkable performance in property prediction on public datasets.
ConfFlow uses transformer networks to generate molecular conformations efficiently.
problem Efficient generation of valid conformations for large molecules.
method Flow-based model using transformer networks that directly samples in coordinate space.
result ConfFlow improves accuracy by up to 40% for large molecule conformations.
A new neural network model for molecular graphs that learns efficiently and accurately.
problem Learning on molecular graphs with cycles and complex structures.
method Hierarchical inter-message passing using raw graph and junction tree representations.
result The model outperforms classical GNNs in detecting cycles and is efficient to train.
Neural network learns from higher-order connections in molecules.
problem Graph neural networks fail to account for local and hidden structures in graphs.
method Developed a neural network that can pass messages and aggregate information across higher-order paths.
result The model improves molecular property prediction.
Paper improves molecular property prediction using denoising autoencoders.
problem Limited data for molecular property prediction from 3D structures.
method Pre-training via denoising for learning molecular force fields.
result Achieves new state-of-the-art performance on QM9 dataset.
Enhances molecular design models by fine-tuning uncertainty-guided VAEs.
problem Fine-tuning pre-trained generative models for specific molecular property optimization.
method Uncertainty-guided fine-tuning of variational autoencoders in an active learning setting.
result Uncertainty-guided fine-tuning improves model performance across multiple molecular properties.
Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that…
Tiered latent representations and latent spaces for molecular graphs provide a simple but effective way to explicitly represent and utilize groups (e.g., functional groups), which consist of the atom (node) tier, the group tier and the molecule (graph) tier. They can be learned using the tiered graph autoencoder archit…
We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph…
Molecular structure-property relationships are key to molecular engineering for materials and drug discovery. The rise of deep learning offers a new viable solution to elucidate the structure-property relationships directly from chemical data. Here we show that the performance of graph convolutional networks (GCNs) for…
Deep learning improves OFDFT for molecular systems.
problem Limited accuracy of OFDFT for non-periodic molecular systems.
method M-OFDFT using deep learning to approximate kinetic energy density.
result Achieves comparable accuracy to Kohn-Sham DFT on large molecules.
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.
Differentiable simulations control molecular Hamiltonians for desired outcomes.
problem Control and learning of molecular Hamiltonians for desired outcomes.
method Differentiable simulations to differentiate Hamiltonians with respect to target observables.
result Control and learning of molecular Hamiltonians for desired outcomes.
PG-EVIKAL refines molecular property predictions using neighbor fusion and evidential neural networks.
problem Improving molecular property predictions using test-time neighbor fusion.
method Adapting evidential neural networks to refine predictions by re-ranking structurally similar neighbors.
result PG-EVIKAL reduces RMSE on 14 out of 16 molecular datasets, improving calibration and sequential refinement.
We propose GraphNVP, the first invertible, normalizing flow-based molecular graph generation model. We decompose the generation of a graph into two steps: generation of (i) an adjacency tensor and (ii) node attributes. This decomposition yields the exact likelihood maximization on graph-structured data, combined with t…
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approa…
POEM predicts drug properties without tuning, outperforming other methods.
problem Predicting drug properties from molecular structures efficiently.
method POEM combines multiple molecular representations without hyperparameter tuning.
result POEM outperforms industry-standard methods across 17 tasks.
Machine learning generates coarse-grained force fields for molecular dynamics.
problem Creating thermodynamically consistent coarse-grained models for larger systems.
method Hybrid architecture using graph neural networks to learn molecular features.
result Framework reproduces thermodynamics for small biomolecular systems.