Generative model creates drug-like molecules with multiple properties.
problem Designing molecules with multiple desired properties.
method Conditional Variational Autoencoder (VAE) in latent space control.
result Can generate drug-like molecules with five target properties.
A new framework optimizes molecules using deep reinforcement learning.
problem Optimizing molecules while maintaining chemical validity and drug-likeness.
method Combining deep reinforcement learning with domain knowledge of chemistry, MolDQN directly modifies molecules.
result MolDQN achieves optimization of molecules without bias from pre-training datasets.
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
problem Designing efficient drugs for novel viral proteins.
method End-to-end framework combining VAE, controlled sampling, and predictors.
result Highly selective and affinity molecules for SARS-CoV-2 targets.
New dataset abla2DFT for drug-like molecules benchmarks neural network potentials.
problem Lack of large, diverse datasets for training neural network potentials in quantum chemistry.
method Developed a new dataset abla2DFT containing energies, forces, and molecular properties for drug-like molecules. result First dataset with relaxation trajectories for drug-like molecules.
A new RL framework optimizes drug-like molecules synthetically.
problem Optimizing drug-like molecules for specific criteria.
method Deep Reinforcement Learning framework for chemical space optimization.
result Outperforms existing methods in pharmacological optimization.
Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently. In this paper, we present a conditional molecular design method that facilitates generating new molecules with desired properties. The p…
New molecular design model outperforms existing methods.
problem Designing valid, unique, and novel molecules.
method Adversarially Regularized Autoencoder (ARAE) combining latent variables from VAE and adversarial training from GAN.
result ARAE outperforms conventional models in validity, uniqueness, and novelty.
Paper proposes a method to design molecules with specific properties.
problem Designing molecules with desired chemical and biological properties.
method Energy-based model in latent space, SGDS algorithm for gradual distribution shifting.
result Method achieves strong performances on various molecule design tasks.
Mol-CycleGAN generates optimized molecules with similar structure.
problem Designing molecules with desired properties is challenging.
method CycleGAN-based model that generates optimized compounds with high structural similarity.
result Significantly outperforms previous results in optimizing penalized logP of drug-like molecules.
CORE optimizes molecules by copying or generating substructures, improving accuracy.
problem Inaccurate substructure prediction in molecule optimization.
method Copy & Refine (CORE) strategy combining scaffolding tree generation and adversarial training.
result Significant improvement in various molecule optimization metrics.
COLD optimizes samples by projecting them into a latent space, ensuring they are distinct from training data.
problem Optimizing discrete data for specific characteristics using gradient-based methods often leads to dissimilar samples.
method Constrained Optimisation with Latent Distributions (COLD) to find optimal samples similar to but distinct from training data.
result COLD generates diverse, high-quality samples with similar properties to training data.
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …
MolecularRNN generates realistic molecules with desired properties.
problem Designing new molecules with specific properties.
method Graph recurrent generative model with likelihood pretraining and policy gradient tuning.
result Significant distribution shift to desired ranges for lipophilicity, drug-likeness, and melting point.
GCPN uses reinforcement learning to generate molecules optimizing desired properties.
problem Generating novel molecules with desired properties while obeying physical laws.
method Graph Convolutional Policy Network (GCPN) trained with reinforcement learning.
result GCPN achieves significant improvements in molecule optimization tasks.
Benchmark proposes to assess molecule docking efficiency.
problem Lack of realistic benchmarks for measuring progress in drug design.
method Proposes a docking-based benchmark using SMINA software.
result Graph-based generative models fail to generate high-scoring molecules.
Generative models encode and decode 3D crystal structures from a large dataset.
problem Challenges in encoding and decoding 3D crystal structures from large datasets.
method Training two neural networks on a dataset of over 120,000 crystal structures to encode and decode 3D atom positions.
result Ability to generate compressed, continuous latent space representations and decode molecules accurately.
HLTF generates chemically valid 3D molecules with improved topology control.
problem Generating chemically valid 3D molecules is challenging due to bond topology errors.
method HLTF uses a latent multi-scale plan for global context and a constraint-aware sampler to suppress topology-driven failures.
result HLTF achieves high validity and uniqueness on QM9 and GEOM-DRUGS datasets.
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.
Sparse molecular representations improve interpretability in graph neural networks.
problem Difficulty in understanding which molecular graph aspects drive deep learning predictions.
method Constrain weights in a graph convolutional neural network using the Gini index to maximize representation inequality.
result The Gini-constrained approach does not degrade evaluation metrics and allows for interpretable representation combination.
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.
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
DECAF optimizes molecular graphs for ensemble properties, improving drug design accuracy.
problem Designing molecules with ensemble properties rather than single conformations.
method DECAF uses Boltzmann-expected design with decoupled annealing flows to optimize molecular graphs.
result DECAF optimizes molecular graphs to shift ensemble properties towards targets, improving accuracy over single-conformer methods.
Optimizes latent space of VAEs using decoder uncertainty to generate valid objects.
problem Lack of robustness in optimizing VAE latent space for black-box properties.
method Importance sampling-based estimator of decoder epistemic uncertainty to guide optimization.
result Improves trade-off between black-box objective and validity of generated samples.
Generative model predicts synthesizable molecules from reactants.
problem Generating molecules with desirable properties doesn't guarantee synthesis feasibility.
method Proposes a realistic synthesis process model with reactant selection and reaction prediction.
result Model generates diverse, valid, and unique synthesizable molecules.
BOAT optimizes multiple antibody properties efficiently.
problem Balancing multiple drug-like properties in antibody design.
method Bayesian optimization framework coupling surrogate modeling and genetic algorithm.
result Competitive performance with state-of-the-art multi-objective protein optimization methods.
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.
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language process…
SILVR generates new molecules fitting protein binding sites.
problem Generating novel small molecule compounds for drug design.
method Selective Iterative Latent Variable Refinement (SILVR) for diffusion-based molecule generation.
result SILVR can generate new molecules similar in shape to original fragments without protein knowledge.
GCDM generates valid large 3D molecules and optimizes existing molecules.
problem Lack of geometric properties in 3D molecule generation models.
method Introduces Geometry-Complete Diffusion Model (GCDM) using equivariant GNNs.
result Significantly outperforms existing models in 3D molecule generation and optimization.
Modof-pipe optimizes molecules by modifying a single site, outperforming state-of-the-art methods.
problem Improving drug candidates' properties through chemical modification.
method Deep generative model Modof over molecular graphs for molecule optimization.
result Modof-pipe achieves significant improvements in octanol-water partition coefficient and molecule similarity constraints.
Improved RL model for fragment-based molecule generation.
problem Generating molecules with high docking scores.
method Thorough reproduction, scrutiny, and improvement of the FREED model.
result The improved model produces molecules with superior docking scores.
Generative model creates new molecules retaining a scaffold with certainty.
problem Designing new molecules with a specific scaffold.
method Generative model that extends scaffold graph by adding vertices and edges.
result Model can generate novel molecules with high validity, uniqueness, and novelty.
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…
A new method improves molecule generation accuracy and efficiency.
problem Posterior collapse in VAEs for molecule sequence generation.
method Re-balancing reconstruction loss to avoid posterior collapse.
result Our method achieves state-of-the-art reconstruction accuracy and competitive validity.
Generative model learns to create molecules with multiple properties using interpretable substructures.
problem Creating molecules with multiple chemical properties is challenging.
method Compose molecules from substructures identified as responsible for each property, using graph generative models.
result Significant improvements in accuracy, diversity, and novelty of generated compounds over state-of-the-art baselines.
A new deep model generates molecules by fragments, improving validity and uniqueness.
problem Generating valid and unique molecules using deep learning.
method Develops a language model for molecular fragments, using frequency-based masking.
result Significantly outperforms other language model-based competitors in molecule generation.
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which can be of medical and biological importance. Graphs are are useful in this prob…
MHG-VAE achieves 100% valid molecules with simpler architecture.
problem Generating valid molecules and evaluating properties efficiently.
method MHG-VAE uses molecular hypergraph grammar to guide a single VAE.
result 100% validity achieved with simpler architecture.
Generative neural network designs novel 3D molecules with specified properties.
problem Designing molecules with desired properties in chemistry.
method Conditional generative neural network for 3D molecular structures.
result Demonstrated utility in generating novel molecules with specified motifs or composition.
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.
ALMGIG uses adversarial learning to generate and infer novel molecules efficiently.
problem Efficiently generating and inferring novel molecules using graph representations.
method Adversarial learning framework that avoids explicit graph isomorphism, using cycle-consistency loss and multi-graph Graph Isomorphism Network.
result ALMGIG more accurately learns the distribution over the space of molecules and efficiently searches the molecular space.
SELFIES solves molecular string representation weaknesses for material design.
problem Weaknesses in SMILES for representing valid molecules in material design.
method Introducing SELFIES, a 100% robust string-based molecular representation.
result SELFIES strings correspond to valid molecules, allowing arbitrary machine learning applications.
Two-step process generates molecules from latent vectors.
problem Generating valid molecules from latent representations.
method Two-step decoding: first formula, then bonds.
result Highest reconstruction rate of 90.5%.
Bayesian optimization improves molecule design by addressing three pitfalls.
problem Bayesian optimization pitfalls cause poor performance in molecule design.
method Identified and addressed three pitfalls: incorrect prior width, over-smoothing, and inadequate acquisition function maximization.
result Basic BO setup achieves highest performance on PMO benchmark.
Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required…
New model generates larger molecules more effectively.
problem Previous graph generation techniques struggle with larger molecules.
method Hierarchical graph encoder-decoder using structural motifs.
result Model significantly outperforms previous baselines on molecule generation tasks.
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.
Machine learning predicts atomization energies accurately from low-fidelity calculations.
problem Predicting accurate atomization energies of organic molecules efficiently.
method Machine learning models trained on low-fidelity B3LYP energies to predict high-fidelity G4MP2 energies.
result Predicted G4MP2 atomization energies within 0.012 eV for molecules with 10-14 heavy atoms.