ChemCrow enhances LLMs for chemistry tasks, automating complex chemical processes.
problem Limited access to computational chemistry tools for large-language models.
method Integrating 18 expert-designed chemistry tools into an LLM (ChemCrow).
result ChemCrow autonomously plans and executes chemical syntheses and discoveries.
Optimized DMD for fast atmospheric chemistry forecasting.
problem Forecasting global atmospheric chemistry dynamics efficiently.
method Optimized Dynamic Mode Decomposition (DMD) for reduced order modeling.
result Significant improvement in computational speed and interpretability.
ML4Chem offers a user-friendly platform for developing and deploying machine learning models in chemistry.
problem Developing and deploying machine learning models in chemistry and materials science.
method User-experience design, six core building blocks: data, featurization, models, model optimization, inference, and visualization.
result Ease of use and functionality of the atomistic module for neural networks and kernel ridge regression.
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.
The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the la…
A new method for joint noise removal and trend estimation from sparse signals.
problem Jointly removing noise and estimating trends from sparse signals.
method PENDANTSS combines SOOT/SPOQ penalties with BEADS algorithm in a Trust-Region block alternating variable metric forward-backward approach.
result Outperforms comparable methods in deconvolving analytical chemistry signals.
Neural network (NN) model chemistries (MCs) promise to facilitate the accurate exploration of chemical space and simulation of large reactive systems. One important path to improving these models is to add layers of physical detail, especially long-range forces. At short range, however, these models are data driven and…
Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural netwo…
Deep QMC methods use neural networks to solve quantum chemistry problems.
problem Solving the electronic Schrödinger equation from first principles.
method Quantum Monte Carlo with neural network wavefunctions.
result Highly accurate solutions at reduced computational cost.
Study examines how taxes affect wealth inequality in economic models.
problem Reducing economic inequality in models of economic activity.
method Examined Artificial Chemistry models and various tax measures.
result Effective tax measures can reduce economic inequality.
Derives symmetric and antisymmetric kernels for quantum physics and chemistry applications.
problem Efficiently handling symmetries and antisymmetries in machine learning for quantum physics and chemistry.
method Symmetrizing and antisymmetrizing conventional kernels, analyzing feature space dimensions, proving kernel properties, proposing Slater determinant representation.
result Efficient evaluation of antisymmetric Gaussian kernels even in high-dimensional state spaces, significant reduction in training data size.
Machine learning advances chemistry and materials science by enabling large-scale exploration of chemical space based on quantum chemical calculations. While these models supply fast and accurate predictions of atomistic chemical properties, they do not explicitly capture the electronic degrees of freedom of a molecule…
Graphs predict reaction conditions for organic chemistry.
problem Predicting specific reaction conditions in organic chemistry.
method Graph Neural Networks (GNNs) for modeling reaction graphs.
result GNNs can identify specific graph features affecting reaction conditions.
BoFire optimizes chemistry experiments using Bayesian Optimization.
problem Effective deployment of Bayesian Optimization in the chemical industry.
method Combines Bayesian Optimization with DoE strategies, providing a rich feature-set.
result BoFire enables seamless integration into RESTful APIs for real-world use.
This work improves chemistry modeling by jointly learning reaction progress variables and look-up models.
problem Jointly modeling turbulent combustion requires solving both chemistry and flow systems simultaneously, which is computationally expensive.
method Developed a deep neural network architecture that jointly learns reaction progress variables and look-up models, improving accuracy.
result Joint learning yields more accurate results in chemistry modeling.
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
Review of automation's role in chemical discoveries.
problem Improving autonomous discovery in chemistry.
method Classification of discovery types, assessment of autonomy, case studies.
result Rapid advancements in automation and machine learning are transforming experimentation and modeling.
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.
GGFPS improves model performance by sampling molecules more efficiently.
problem Improving model performance and reducing data costs in chemistry problems.
method Gradient-Guided Furthest Point Sampling (GGFPS) that leverages molecular force norms.
result GGFPS leads to superior data efficiency and model robustness compared to other sampling methods.
We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy…
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…
Olympus benchmarks optimization algorithms for noisy experiments.
problem Benchmarking optimization algorithms on realistic experimental scenarios is challenging.
method Introduces Olympus, a software package for benchmarking optimization algorithms on synthetic experiments.
result Mitigates barriers in benchmarking optimization algorithms on realistic experimental scenarios.
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of individual (artificial) molecules, subject of reversible, but otherwise determinist…
Kernelized PCovR reveals structure-property relations in chemistry and materials.
problem Understanding structure-property relations in complex systems.
method Kernel Principal Covariates Regression (kernel PCovR) with sparsification.
result Kernelized PCovR effectively reveals and predicts structure-property relations.
Deep neural network predicts molecular wave functions in minimal basis.
problem Improving accuracy and efficiency in quantum chemistry calculations.
method Adapted SchNet for Orbitals (SchNOrb) model in quasi-atomic minimal basis.
result Model accurately predicts molecular orbital energies and wavefunctions for large molecules.
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…
Accelerated RPCholesky speeds up kernel matrix approximations.
problem Efficiently approximating large kernel matrices.
method Accelerated randomly pivoted Cholesky (RPCholesky) with block matrix computations and rejection sampling.
result Approximates kernel matrices up to 40 times faster.
Machine learning aids excited-state molecular dynamics studies.
problem Challenges in studying electronically excited states of molecules.
method Employing machine learning techniques for excited-state molecular dynamics.
result Highlight successes and challenges in machine learning for excited-state processes.
Retro* uses neural networks to efficiently find high-quality synthetic routes in organic chemistry.
problem Finding efficient synthetic routes in organic chemistry is challenging due to the vast search space.
method Retro* is a neural-based A*-like algorithm that learns a neural search bias to guide efficient best-first search.
result Retro* outperforms existing methods in both success rate and solution quality while being more efficient.
A novel clustering method uses torque balance to group objects.
problem Grouping similar objects in various scientific fields.
method Inspired by gravitational interactions, a parameter-free clustering algorithm based on mass and distance.
result The algorithm effectively clusters objects regardless of their shape, size, or density.
Deep learning improves OFDFT for molecular systems.
problem Limited accuracy of OFDFT for non-periodic molecular systems.
method M-OFDFT using deep learning to approximate kinetic energy density.
result Achieves comparable accuracy to Kohn-Sham DFT on large molecules.
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…
ChemGrapher uses deep learning to automatically convert chemical compound images into accurate graphs.
problem Automatically converting chemical compound images into accurate graphs with correct bond multiplicity and stereochemical information.
method Developed a deep neural network model for optical compound recognition, including segmentation and classification models.
result Significant error reductions in bond multiplicity and stereochemical information compared to existing tools.
Steerable E(3) Graph Neural Networks incorporate geometric and physical covariant information.
problem Incorporating covariant information like position, force, velocity, or spin in graph neural networks.
method Steerable E(3) Equivariant Graph Neural Networks (SEGNNs) that use steerable MLPs to incorporate geometric and physical covariant information.
result SEGNNs improve upon classic linear point convolutions and recent equivariant graph networks that send invariant messages.
In the last few years, we have seen the transformative impact of deep learning in many applications, particularly in speech recognition and computer vision. Inspired by Google's Inception-ResNet deep convolutional neural network (CNN) for image classification, we have developed "Chemception", a deep CNN for the predict…
We present a framework, which we call Molecule Deep Q-Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double Q-learning and randomized value functions). We directly define modifications on molecules, thereby ensuring 100…
New model accurately predicts chemical bond breaking.
problem Challenges in describing bond breaking in quantum chemistry.
method Pretrained deep neural network wavefunction model Orbformer.
result Consistently converges to chemical accuracy (1 kcal/mol).
Zipper logic is a graph rewrite system, consisting in only local rewrites on a class of zipper graphs. Connections with the chemlambda artificial chemistry and with knot diagrammatics based computation are explored in the article.
ML predicts alloy properties considering chemistry, processing, and data transformations.
problem Designing and predicting alloy properties in high-dimensional design space.
method Physics-informed machine learning with engineered features from chemistry and heat treatment.
result ML models accurately predict alloy properties, including hysteresis in shape memory alloys.
Paper introduces untangling number to quantify 3-periodic tangle complexity.
problem Quantifying the complexity of 3-periodic tangles in biological, chemical, and physical systems.
method Introduces untangling number, a measure of minimum distance to ground state through diagrammatic operations.
result For infinite open curves, generic ground states are crystallographic rod packings.
There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction pred…
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.
New algorithm efficiently trains machine learning models to atomic forces data.
problem Efficiently training machine learning models to large amounts of force data.
method Developed an efficient algorithm for training machine learning models to all available force data.
result Training to all available force data is only a few times more expensive than training to energies alone.
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from both chemistry and computer science communities. Most existing approaches rely o…
Serial crystallography is the field of science that studies the structure and properties of crystals via diffraction patterns. In this paper, we introduce a new serial crystallography dataset comprised of real and synthetic images; the synthetic images are generated through the use of a simulator that is both scalable …
Physics-informed machine learning models improve biomolecular system simulations.
problem Modeling unresolved interactions beyond classical force fields.
method Physics-informed neural networks and operator learning.
result Accurate, mechanistic, generalizable models for long-timescale kinetics.
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.
A new training method improves MLIPs for faster, lighter simulations.
problem High computational and memory costs of complex MLIPs for large-scale MD simulations.
method Teacher-student training framework using latent atomic energy knowledge.
result Lightweight student MLIPs achieve faster MD speeds and comparable accuracy to teachers.