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…
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48 results for “Molecular VAE”
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.
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.
New approach separates VAE and GP for better molecular optimisation.
problem Optimizing complex structured domains like molecular spaces using VAEs.
method Decouples VAE for structure generation and GP for predictive modelling, combining them with a Bayesian update rule.
result Improves identification of high-potential candidates in molecular optimisation.
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.
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…
We present RL-VAE, a graph-to-graph variational autoencoder that uses reinforcement learning to decode molecular graphs from latent embeddings. Methods have been described previously for graph-to-graph autoencoding, but these approaches require sophisticated decoders that increase the complexity of training and evaluat…
Deep generative models are attracting great attention as a new promising approach for molecular design. All models reported so far are based on either variational autoencoder (VAE) or generative adversarial network (GAN). Here we propose a new type model based on an adversarially regularized autoencoder (ARAE). It basi…
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.
DD-VAE uses deterministic decoding for better latent code utilization in discrete data.
problem Inflexible decoders in VAEs lead to poor utilization of latent codes in discrete data.
method Proposed DD-VAE with deterministic decoding and new proposal distributions.
result DD-VAE improves latent code utilization and structure of learned manifold.
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively.
PS-VAE extracts multi-parameter MRI biomarkers with uncertainty quantification.
problem Uncertainty in inverse problems limits clinical acceptance of quantitative MRI methods.
method Physics-Structured Variational Autoencoder (PS-VAE) integrating physics simulator and self-supervised learning.
result PS-VAE provides full covariance of inter-parameter correlations and accelerates multi-parametric MRI quantification.
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.
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.
A new diffusion model improves cryo-EM structure sampling.
problem Gaussian prior in VAE fails to match approximate posterior in cryo-EM data.
method Train a diffusion model as an expressive, learnable prior in cryoDRGN framework.
result Samples accurately follow the data distribution, not the VAE prior.
With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…
In this paper, we integrate VAEs and flow-based generative models successfully and get f-VAEs. Compared with VAEs, f-VAEs generate more vivid images, solved the blurred-image problem of VAEs. Compared with flow-based models such as Glow, f-VAE is more lightweight and converges faster, achieving the same performance und…
Framework designs antiviral drugs using deep learning and RL.
problem Designing effective antiviral drugs for SARS-CoV-2.
method Deep learning framework with conditional molecular generator and RL.
result Framework generates more antiviral ligands than a VAE baseline.
Interpretable Embeddings From Molecular Simulations Using Gaussian Mixture Variational Autoencodersphysics.chem-ph
Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic …
Evaluating, explaining, and visualizing high-level concepts in generative models, such as variational autoencoders (VAEs), is challenging in part due to a lack of known prediction classes that are required to generate saliency maps in supervised learning. While saliency maps may help identify relevant features (e.g., p…
This work tackles posterior collapse in conditional and hierarchical VAEs.
problem Posterior collapse in VAEs leads to poor latent variable representations.
method Theoretical analysis of linear conditional and hierarchical VAEs, empirical validation.
result Theoretical and empirical evidence of posterior collapse causes in conditional and hierarchical VAEs.
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.
BS-VAE separates decoder variance and beta to improve VAE performance.
problem Blurriness in VAE outputs and difficulty in analyzing model performance.
method Explicitly separates beta and decoder variance in Beta-Sigma VAE.
result Superior performance in natural image synthesis and controllable parameters.
A tutorial on VAEs explaining its derivation and applications.
problem Understanding the VAE model and its limitations.
method Explains VAE through probabilistic and information theoretic perspectives.
result Identifies two common misconceptions and their practical consequences.
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.
Molecular generative model based on conditional variational autoencoder for de novo molecular designcs.LG
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.
New system for i-vector speaker recognition based on variational autoencoder (VAE) is investigated. VAE is a promising approach for developing accurate deep nonlinear generative models of complex data. Experiments show that VAE provides speaker embedding and can be effectively trained in an unsupervised manner. LLR est…
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…
The paper provides convergence guarantees for VAEs using SGD and Adam.
problem Understanding theoretical convergence guarantees for VAEs.
method Derives non-asymptotic convergence rates for VAEs trained with SGD and Adam.
result Convergence rate of \(\mathcal{O}(\log n / \sqrt{n})\) with explicit hyperparameter dependencies.
Molecular Latent Space Simulatorsphysics.comp-ph
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.
VAEs help in learning latent variables for cryo-EM applications.
problem Learning latent variables for cryo-EM data.
method Used VAEs for latent variable learning, focusing on the encoder's role.
result The encoder of the VAE in cryo-EM applications resembles traditional latent variable representations.
PRI-VAE learns disentangled representations by optimizing principle-of-relevant-information.
problem Learning disentangled representations under VAE framework remains unknown.
method Proposes PRI-VAE, a novel learning objective to optimize disentanglement.
result Demonstrates effectiveness of PRI-VAE on four benchmark datasets.
CVAE learns disentangled and coupled representations without prior knowledge.
problem Learning disentangled and coupled representations in latent space.
method Introduces CVAE, a self-supervised VAE that factorizes posterior and uses Gaussian copula for dependencies.
result Demonstrates strong effect in enhancing disentangled representation learning.
Variational autoencoders (VAEs) have ushered in a new era of unsupervised learning methods for complex distributions. Although these techniques are elegant in their approach, they are typically not useful for representation learning. In this work, we propose a simple yet powerful class of VAEs that simultaneously resul…
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.
NE-VAE prevents posterior collapse in VAEs by embedding neighbors in latent space.
problem Posterior collapse in VAEs when strong decoders are used.
method Neighbor embedding in latent space to prevent collapse.
result NE-VAE produces qualitatively different latent representations with active latent dimensions.
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.
The variational autoencoder (VAE) framework remains a popular option for training unsupervised generative models, especially for discrete data where generative adversarial networks (GANs) require workaround to create gradient for the generator. In our work modeling US postal addresses, we show that our discrete VAE wit…
q-VAE extracts disentangled latent spaces for robot control and dynamic systems.
problem Disentangled representation learning for latent spaces in robotics.
method Proposes q-VAE based on Tsallis statistics, improving disentanglement and latent dynamics.
result Improves disentangled representation while maintaining data reconstruction accuracy.
Single training run learns optimal VAE parameters for various β values.
problem Training VAEs with varying β values for optimal trade-off between distortion and rate.
method Introduced Multi-Rate VAE (MR-VAE) using hypernetworks to map β to optimal parameters.
result MR-VAEs can construct the full rate-distortion curve without additional training.
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.
VAEs analyzed using harmonic analysis, showing how variance controls frequency content and robustness.
problem Understanding and optimizing VAEs for robustness and frequency control.
method Viewing VAE latent space as Gaussian space, deriving results on variance and frequency content, and demonstrating soft Lipschitz constraints.
result Increasing encoder variance reduces high frequency content and improves adversarial robustness.
SKR-VAE improves VAEs for ICA with reduced computational cost.
problem Efficiently performing ICA in VAEs with large datasets.
method Structured kernel functions to avoid costly GP kernel matrix inversion.
result SKR-VAE achieves greater computational efficiency and reduced resource consumption.
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.
Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamicsphysics.chem-ph
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.
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.