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.
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48 results for “molecular optimization”
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.
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…
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.
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…
Improved CG force-field learning from all-atom data.
problem Training accurate coarse-grained models from all-atom simulations is challenging.
method Optimized force mapping to improve statistical efficiency of force-field learning.
result Substantially improved CG force-fields can be learned from the same simulation data.
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learningphysics.chem-ph
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.
The study addresses biases in evaluating molecular optimization methods and proposes methods to reduce these biases.
problem Biases in in silico evaluation of molecular optimization methods.
method Discussion and empirical investigation of bias reduction methods for predictor misspecification and sample reuse.
result Empirical investigation of bias reduction methods for predictor misspecification and sample reuse.
RAMBO optimizes multi-regime problems by discovering and modeling distinct energy basins.
problem Multi-regime problems in molecular conformation and drug discovery.
method Dirichlet Process Mixture of Gaussian Processes with adaptive hyperparameters and concentration parameters.
result Consistent improvements over state-of-the-art on multi-regime objectives.
EHVI outperforms scalarized EI in MOBO for molecule design.
problem Benchmarking MOBO strategies for molecule design.
method Compared EHVI against fixed-weight scalarized EI in MOBO.
result EHVI consistently outperforms scalarized EI in molecular optimization tasks.
Molecular optimization aims to discover novel molecules with desirable properties. Two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecu…
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.
This work improves molecular design by efficiently selecting diverse candidate molecules.
problem Designing molecules that satisfy multiple conflicting objectives.
method A modular 'generate-then-optimize' framework using generative models and a novel acquisition function.
result Significant improvements in sample efficiency across synthetic and application-driven tasks.
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 …
Improving in-context learning for latent space Bayesian optimization by adapting pretraining on molecular latent space.
problem Improving in-context learning for latent space Bayesian optimization.
method Adapting pretraining on molecular latent space.
result Achieving strong performance on held-out molecular optimization benchmarks.
Automates feature selection and weighting in molecular systems.
problem Optimal feature selection and alignment in molecular systems.
method Differentiable Information Imbalance (DII) method for automated feature ranking and scaling.
result Automated feature selection and scaling that preserves information content and interpretability.
Gradient GA uses gradient information to improve molecular design.
problem Random walk exploration limits genetic algorithms' quality and speed in molecular design.
method Gradient GA incorporates gradient information from the objective function into genetic algorithms, using a differentiable neural network and Discrete Langevin Proposal.
result Significantly improves convergence speed and solution quality over traditional genetic algorithms.
Hierarchical Graph-to-Graph Translation for Moleculesphysics.chem-ph
The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize …
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.
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoderscs.LG
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.
In the majority of molecular optimization tasks, predictive machine learning (ML) models are limited due to the unavailability and cost of generating big experimental datasets on the specific task. To circumvent this limitation, ML models are trained on big theoretical datasets or experimental indicators of molecular s…
In applications such as molecule design or drug discovery, it is desirable to have an algorithm which recommends new candidate molecules based on the results of past tests. These molecules first need to be synthesized and then tested for objective properties. We describe ChemBO, a Bayesian optimization framework for ge…
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.
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.
A new algorithm optimizes multiple molecular properties efficiently.
problem Designing molecules with conflicting objectives and costly evaluations.
method Multi-objective Bayesian optimization with GFlowNets.
result HN-GFN samples diverse molecules from an approximate Pareto front.
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.
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.
TALBO optimizes latent spaces for evolving design objectives.
problem Temporal drift in design objectives.
method GP-prior variational autoencoder for time-varying latent space.
result Consistently outperforms LSBO baselines across varying drift speeds and objectives.
Develops active learning for scale-bridging simulations.
problem Quantitative predictions in nanoporous media and inertial confinement fusion.
method Active learning approach to optimize fine-scale simulations for coarse-scale hydrodynamics.
result Optimizes use of fine-scale simulations for coarse-scale predictions.
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…
GEGL uses genetic experts to improve deep learning for molecular design.
problem Designing molecules with desired properties using deep learning.
method Genetic expert-guided learning (GEGL) framework for training DNN.
result Significantly improves molecular design, achieving high scores on benchmarks.
Gaussian Moments as Physically Inspired Molecular Descriptors for Accurate and Scalable Machine Learning Potentialsphysics.comp-ph
New method uses geometric moments for accurate machine learning potentials.
problem Creating high-dimensional potential energy surfaces efficiently.
method Feed-forward neural networks with invariant local molecular descriptors based on geometric moments.
result Accuracy comparable to established models, high efficiency.
Reliable identification of molecular biomarkers is essential for accurate patient stratification. While state-of-the-art machine learning approaches for sample classification continue to push boundaries in terms of performance, most of these methods are not able to integrate different data types and lack generalization…
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.
Chirality Effects in Molecular Chainmailcond-mat.soft
Chirality affects the curvature of molecular networks, influencing their shape and stability.
problem Understanding how chirality influences the curvature of molecular networks.
method Langevin dynamics simulations and constrained gradient optimization of square lattice networks.
result Linking chirality dictates the sign of Gaussian curvature in molecular chainmail networks.
Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep …
Generating point clouds, e.g., molecular structures, in arbitrary rotations, translations, and enumerations remains a challenging task. Meanwhile, neural networks utilizing symmetry invariant layers have been shown to be able to optimize their training objective in a data-efficient way. In this spirit, we present an ar…
Discriminator guidance improves autoregressive diffusion models for generating molecular graphs.
problem Improving the accuracy of autoregressive diffusion models for generating molecular graphs.
method Deriving ways to use a discriminator with a pretrained generative model in the discrete case, including optimal and sub-optimal scenarios.
result Using a discriminator can correct pretrained models and improve exact sampling from the data distribution.
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…
Active-GRPO improves molecular optimization by actively deciding when to imitate or self-improve.
problem Training robust and efficient molecular optimization models with large language models.
method Active-GRPO combines imitation and reinforcement learning, upgrading references and policies dynamically.
result Improves molecular optimization performance, achieving statistically significant gains.
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.
Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a particular scaffold as a substructure. On this account, our present work proposes a scaff…
Variational autoencoders (VAEs) defined over SMILES string and graph-based representations of molecules promise to improve the optimization of molecular properties, thereby revolutionizing the pharmaceuticals and materials industries. However, these VAEs are hindered by the non-unique nature of SMILES strings and the c…
New algorithm improves model generalization in structured biomedical domains.
problem Improving model generalization in structured biomedical domains.
method Proposes a new regret minimization (RGM) algorithm and its structured extension for better performance in diverse environments.
result Significantly outperforms previous state-of-the-art baselines on molecular property prediction, protein homology, and stability prediction.
DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentialsphysics.chem-ph
New dataset DFT 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 DFT containing energies, forces, and molecular properties for drug-like molecules.
result First dataset with relaxation trajectories for drug-like molecules.
Markov state models (MSMs) and Master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variationa…
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.
This paper proposes a new method to generate protein structures using deep learning.
problem Weak correlation between current scoring functions and protein molecular activity.
method Graph-generative models to sample novel tertiary protein structures.
result Generative models can reveal latent space and highlight structural factors.