Polynomial invariants classify molecular chains based on their contact arrangements.
problem No established invariants for molecular chains with both hard and soft contacts.
method Developed polynomial invariants for circuit topology of molecular chains.
result Polynomial invariants efficiently classify chains with various contact types.
GeoPhy uses geometric gradients to efficiently infer phylogenetic trees from molecular data.
problem Challenges in accurately inferring species relationships from molecular data due to combinatorially vast tree topologies.
method Introduces a novel, fully differentiable formulation of phylogenetic inference using geometric spaces and variational Bayesian methods.
result Significantly outperforms other approximate Bayesian methods in inferring phylogenetic trees.
Enhanced coloring invariant distinguishes folded molecular chain topologies.
problem Apparent indistinguishability of folded chain topologies using current coloring invariants.
method Introduced Boltzmann weights to improve the resolving power of quandle colorings.
result Improved resolution in distinguishing folded chain topologies.
New method uses cohomology to quantify molecular similarity.
problem Quantifying structural dissimilarity in molecular data.
method Gromov-Hausdorff ultrametric based on simplicial complexes and cohomology.
result Demonstrates effectiveness in clustering organic-inorganic halide perovskite structures.
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes in molecular structure. A zero-th order analysis is achieved by viewing a compu…
Develops a braid-theoretic framework to analyze chirality in molecular knots.
problem Analyzing chirality in molecular knots constructed using circuit topology.
method Translated circuit topology approach to knot engineering into braid-theoretic framework, calculating Jones polynomial for binary combinations.
result Jones polynomial provides a powerful tool for analyzing chirality of molecular knots.
Persistent homology provides a new, efficient molecular descriptor for protein dynamics.
problem Designing effective molecular descriptors for high-dimensional MD trajectories.
method Introduced masked Flood complex, a protein-tailored modification of simplicial complexes, for persistent homology.
result Persistent homology-based descriptors are competitive across protein dynamics tasks, including frame-level observable regression and MSM estimation.
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.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
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.
Machine learning reveals hidden features in knot classification.
problem Classifying the topology of closed curves.
method Investigating shortcut methods used by ML for knot classification.
result Developed a dataset and code to remove non-topological features.
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the vector to handle the spatial information from molecular topology. The 3DGCN model ex…
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.
Lecture notes on crystallography and discrete surfaces.
problem Mathematical modeling of crystal structures.
method Variational principle and discrete surface theory.
result Most symmetric crystal structures identified.
Knot theory applied to proteins, distinguishing folded linear chains.
problem Classifying proteins as unknots when intra-chain interactions are ignored.
method Developing knot theory for folded linear molecular chains, considering self-bonding, and using Gauss codes and quandles.
result Extended knot theory to distinguish topologies of proteins with intra-chain bonds.
The symmetries of complex molecular structures can be modeled by the {\em topological symmetry group} of the underlying embedded graph. It is therefore important to understand which topological symmetry groups can be realized by particular abstract graphs. This question has been answered for complete graphs; it is natu…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular s…
Framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative importance.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
A framework separates chemical and structural contributions to aqueous solubility.
problem Merging chemical and structural information in solubility models obscures their relative contributions.
method Additive MLP-GNN framework with separate chemical and structural branches.
result Framework reveals distinct roles of chemical and structural information in solubility.
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.
Introduces P-tensors for generalized higher-order message passing in graph neural networks.
problem Expanding the expressive power of graph neural networks through higher-order structures.
method Introduces P-tensors to define the most general form of permutation equivariant message passing.
result Achieves state-of-the-art performance on 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.
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.
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 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.
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.
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.
Novel graph network learns hierarchical network structure.
problem Lack of information in hierarchical network topology.
method Hierarchical clustering for multiscale decomposition, graph convolutional layers.
result Competitive performance on citation network benchmark.
We compute Khovanov homology for tangles using TQFT.
problem Khovanov homology for tangles is not well studied or computed.
method Topological Quantum Field Theory (TQFT) construction.
result A comprehensive method for computing Khovanov homology of tangles.
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.
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.
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.
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.
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.
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…
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.
Timewarp accelerates molecular dynamics by learning to simulate long timescales.
problem Efficiently simulating long timescales in molecular dynamics.
method Uses a normalizing flow to learn large time steps in Markov chain Monte Carlo.
result Generalizes to unseen small peptides, accelerating sampling.
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…
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.
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.
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…
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.