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.
SMILES Transformer learns molecular fingerprints for drug discovery.
problem Poor performance of rule-based molecular fingerprints in shallow prediction models or small datasets.
method Unsupervised pre-training of a sequence-to-sequence language model on a corpus of SMILES.
result SMILES Transformer outperformed existing methods in small-data settings.
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.
Model learns molecular structures from graphs without explicit rules.
problem Learning molecular structures from graphs without explicit rules.
method Adapted Transformer model for undirected molecular graphs.
result Transformer model can learn complex molecular structures.
Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built…
A2I Transformer predicts atom energies from coordinates, avoiding heavy featurization.
problem Efficiently predicting atom energies from molecular coordinates with minimal featurization.
method End-to-end model using self-attention, permutation-equivariant.
result Stable predictions with significantly smaller errors than molecular dynamics simulations.
G2Gs transforms target molecules into reactants without templates, improving accuracy.
problem Predicting retrosynthesis from target molecules efficiently and accurately.
method Transforming target molecular graphs into reactant graphs via variational graph translation.
result G2Gs achieves top-1 accuracy close to state-of-the-art template-based methods.
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.
MAT uses attention mechanism for molecule property prediction.
problem Designing a competitive neural network for molecule property prediction.
method Augmented attention mechanism using inter-atomic distances and molecular graph structure.
result MAT achieves state-of-the-art performance on diverse molecular prediction tasks.
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.
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…
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.
We introduce multiscale invariant dictionaries to estimate quantum chemical energies of organic molecules, from training databases. Molecular energies are invariant to isometric atomic displacements, and are Lipschitz continuous to molecular deformations. Similarly to density functional theory (DFT), the molecule is re…
Graph Polish optimizes molecular structures by minimizing changes and maximizing preservation.
problem Error-prone traditional molecular optimization methods.
method Graph Polish transforms optimization into a polishing task, focusing on optimization centers and minimizing changes.
result Significant advantage over state-of-the-art methods on multiple optimization tasks.
We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over hierarchical terms. These terms are generated from a neural network--a composit…
BERT learns molecular substructures for chemistry problems.
problem Predicting chemical properties and synthesizing molecules.
method Transformer-based BERT model on molecule string representations, attention visualization.
result BERT learns to represent functional groups and atoms for various chemical properties.
Graph Neural Networks (GNNs) achieve an impressive performance on structured graphs by recursively updating the representation vector of each node based on its neighbors, during which parameterized transformation matrices should be learned for the node feature updating. However, existing propagation schemes are far fro…
Transferable Boltzmann Generators learn to sample unseen molecules efficiently.
problem Generating equilibrium samples of molecular systems.
method Boltzmann Generators using normalizing flows to learn transformations.
result Transferable Boltzmann Generators can predict zero-shot Boltzmann distributions for unseen molecules.
Generalizes CNNs for Lie group equivariance across various data types.
problem Equivariance to transformations like rotations for non-image data.
method Constructs equivariant convolutional layers for Lie groups.
result Models conserve linear and angular momentum in Hamiltonian systems.
New model predicts chemical reactions without human input.
problem Automating retrosynthetic planning in chemistry.
method Combined Molecular Transformer and hyper-graph exploration.
result Improved accuracy in predicting reactants, reagents, solvents, and catalysts.
We present an approach to make molecular optimization more efficient. We infer a hypergraph replacement grammar from the ChEMBL database, count the frequencies of particular rules being used to expand particular nonterminals in other rules, and use these as conditional priors for the policy model. Simulating random mol…
PARD generates graphs efficiently and invariantly to node ordering.
problem Graph generation sensitivity to node ordering.
method Integrates autoregressive and diffusion models with a partial order for nodes and edges.
result PARD achieves state-of-the-art performance on molecular and non-molecular datasets.
CSLVAE generates large chemical libraries efficiently.
problem Navigating ultra-large combinatorial synthesis libraries.
method Hierarchically-organized database with molecular encoder and decoder.
result Generates valid molecular graphs without autoregression.
CW Networks leverage cell complexes to enhance GNNs, achieving state-of-the-art results on molecular datasets.
problem Graph Neural Networks struggle with long-range interactions and lack principled ways to model higher-order structures.
method CW Networks use cell complexes to decouple computational and input graph structures, enabling flexible hierarchical message passing.
result CW Networks achieve state-of-the-art results on molecular datasets.
Smooth flows for physical systems with smooth energies and forces.
problem Smooth energies for physical simulations and force computation.
method Smooth mixture transformations on compact intervals and hypertori, using root-finding and the inverse function theorem.
result Smooth flows allow training by force matching and use as molecular dynamics potentials.
Equivariant diffusion model generates 3D molecules efficiently.
problem Generating high-quality 3D molecules efficiently.
method Equivariant Diffusion Model (EDM) that operates on atom coordinates and types.
result Significantly outperforms previous methods in molecule quality and training efficiency.
Normalizing flows model atomic solids without needing ground-truth samples.
problem Modeling atomic solids without ground-truth samples.
method Normalizing flows to transform a base distribution into the target solid.
result Excellent agreement between model estimates and literature values for Helmholtz free energy.
New model learns symmetry transformations from complex data.
problem Learning symmetry transformations in complex domains like chemical space.
method Two latent subspaces, deep information bottleneck, continuous mutual information regularizer.
result Model outperforms state-of-the-art methods on artificial and molecular datasets.
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.
New model learns graph neural networks equivariant to various transformations.
problem Learning equivariant graph neural networks for complex transformations.
method E(n)-Equivariant Graph Neural Networks (EGNNs) that are computationally efficient and scalable.
result Achieves competitive or better performance without higher-order representations.
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.
Simple linear models outperform complex BO methods in high dimensions.
problem Overcoming the curse of dimensionality in Bayesian optimization.
method Bayesian linear regression with linear kernels, applied to high-dimensional search spaces.
result Simple linear models match or outperform state-of-the-art BO methods in high-dimensional tasks.
We developed OmicsMapNet approach to take advantage of existing deep leaning frameworks to analyze high-dimensional omics data as 2-dimensional images. The omics data of individual samples were first rearranged into 2D images in which molecular features related in functions, ontologies, or other relationships were orga…
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…
Novel RL approach for molecular design using quantum mechanics.
problem Existing RL methods for molecular design are limited in scope and reward function.
method Formulation in Cartesian coordinates, direct use of quantum mechanics for reward function, translation and rotation invariant state-action space.
result Agent efficiently learns to solve molecular design tasks from scratch.
GraphDETR detects subgraphs in large graphs using deep learning.
problem Detecting subgraphs in large graphs efficiently and accurately.
method Formulates subgraph detection as a set prediction problem using GraphDETR, a deep learning framework.
result GraphDETR can detect diverse patterns in large graphs, achieving strong performance on molecular functional group detection.
DimeNet uses directional message passing to improve molecular predictions.
problem Lack of directional information in graph neural networks for molecules.
method Directional message passing, rotationally equivariant embeddings, spherical functions.
result DimeNet outperforms previous GNNs by 76% on MD17 and 31% on QM9.
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…
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.
Generative model learns molecular geometry from graph representations.
problem Generating equilibrium states for molecular systems is computationally expensive.
method Probabilistic model based on Euclidean distance geometry.
result Generative model achieves state-of-the-art accuracy in molecular conformation generation.
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.
BBRT improves molecular properties through iterative translation.
problem Optimizing molecular structures for improved biochemical properties.
method Iterative translation of molecules using a black box approach.
result Improvement in molecular properties with each iteration of the translator.
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.
New model predicts molecular wavefunctions and densities with unprecedented accuracy.
problem Challenging task of predicting wavefunctions due to molecular rotations.
method Introduces SE(3)-equivariant operations for deep learning.
result Achieves speedups and error reductions over ab initio methods.
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.
New RL method designs 3D molecules with improved symmetry.
problem Lack of 3D information in molecular design.
method Symmetry-aware actor-critic architecture using spherical harmonics.
result Improves generalization and molecule quality.
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.