Publications – LEARNING MATTER

Year of Publication:
2023
- Simon Axelrod
- Rafael Gómez-Bombarelli
Molecular machine learning with conformer ensembles

Machine Learning: Science and Technology
,

2023
Year of Publication:
2023
Graph theory-based structural analysis on density anomaly of silica glass

Computational Materials Science
,

vol.
225
,

pp.
112190
,

2023
Year of Publication:
2023
Learning Pair Potentials using Differentiable Simulations

The Journal of Chemical Physics
,

vol.
158
,

pp.
044113
,

2023
Year of Publication:
2023
- Winter, Gavin
- Rafael Gómez-Bombarelli
Simulations with machine learning potentials identify the ion conduction mechanism mediating non-Arrhenius behavior in LGPS

Journal of Physics Energy
,

2023
Year of Publication:
2023
Differentiable Simulations for Enhanced Sampling of Rare Events

arXiv:2301.03480
,

2023
Year of Publication:
2023
Chemistry-Informed Machine Learning for Polymer Electrolyte Discovery

ACS Central Science
,

2023
Year of Publication:
2023
Representations of Materials for Machine Learning

Annual Review of Materials Research
,

vol.
53
,

2023
Year of Publication:
2023
Thermal Half-Lives of Azobenzene Derivatives: Virtual Screening Based on Intersystem Crossing Using a Machine Learning Potential

ACS Central Science
,

2023
Year of Publication:
2023
Mapping the space of photoswitchable ligands and photodruggable proteins with computational modeling

J. Chem. Inf. Model.
,

2023
Year of Publication:
2023
- Yang, Soojung
- Rafael Gómez-Bombarelli
Chemically Transferable Generative Backmapping of Coarse-Grained Proteins

arXiv:2303.01569
,

2023
Year of Publication:
2023
Automated patent extraction powers generative modeling in focused chemical spaces

Digital Discovery
,

2023
Year of Publication:
2023
- Daniel Schwalbe-Koda
- Rafael Gómez-Bombarelli
Generating, Managing, and Mining Big Data in Zeolite Simulations

AI‐Guided Design and Property Prediction for Zeolites and Nanoporous Materials
,

pp.
81-111
,

2023
Year of Publication:
2023
Autonomous, multiproperty-driven molecular discovery: from predictions to measurements and back

Science
,

vol.
382(6677)
,

pp.
eadi1407
,

2023
Year of Publication:
2023
Data-Driven, Physics-Informed Descriptors of Cation Ordering in Multicomponent Oxides

arXiv:2305.01806
,

2023
Year of Publication:
2023
Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles

arXiv:2305.01754
,

2023
Year of Publication:
2023
A Model Ensemble Approach Enables Data-Driven Property Prediction for Chemically Deconstructable Thermosets in the Low Data Regime

ChemRxiv
,

2023
Year of Publication:
2023
Entropy and Energy Profiles of Chemical Reactions

arXiv:2304.10676
,

2023
Year of Publication:
2023
Machine-learning-accelerated simulations enable heuristic-free surface reconstruction

arXiv:2305.07251
,

2023
Year of Publication:
2023
Lamellar ionenes with highly dissociative, anionic channels provide lower barriers for cation transport

J. Am. Chem. Soc.
,

2023
Year of Publication:
2023
Approaching enzymatic catalysis with zeolites or how to select one reaction mechanism competing with others

Nature Communications
,

vol.
14
,

pp.
2878
,

2023
Year of Publication:
2023
Effect of framework composition and NH3 on the diffusion of Cu+ in Cu-CHA catalysts predicted by machine-learning accelerated molecular dynamics

arXiv:2305.12896
,

2023
Year of Publication:
2023
Unsupervised machine learning leads to an abiotic picomolar peptide ligand

ChemRxiv
,

2023
Year of Publication:
2023
Expanding the Extrapolation Limits of Neural Network Force Fields using Physics-Based Data Augmentation

Workshop on “Machine Learning for Materials” at ICLR
,

2023
Year of Publication:
2023
Atom-by-atom design of metal oxide catalysts for the oxygen evolution reaction with machine learning

arXiv:2305.19930
,

2023
Year of Publication:
2023
Learning a reactive potential for silica-water through uncertainty attribution

arXiv:2307.01705
,

2023
Year of Publication:
2023
Regularized indirect learning improves phage display ligand discovery

ChemRxiv
,

2023
Year of Publication:
2022
- Simon Axelrod
- Rafael Gómez-Bombarelli
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation

Scientific Data
,

vol.
9
,

pp.
185
,

2022
Year of Publication:
2022
Chemistry-informed Macromolecule Graph Representation for Similarity Computation, Unsupervised and Supervised Learning

Machine Learning: Science and Technology
,

2022
Year of Publication:
2022
Multi-fidelity prediction of molecular optical peaks with deep learning

Chemical Science
,

vol.
13(4)
,

pp.
1152 – 1162
,

2022
Year of Publication:
2022
Sampling Lattices in Semi-Grand Canonical Ensemble with Autoregressive Machine Learning

npj Computational Materials
,

vol.
8
,

pp.
61
,

2022
Year of Publication:
2022
Bottlebrush polymers with flexible enantiomeric side chains display differential biological properties

Nature Chemistry
,

vol.
14
,

pp.
85-93
,

2022
Year of Publication:
2022
Suppression of Rayleigh Scattering in Silica Glass by Codoping Boron and Fluorine: Molecular Dynamics Simulations with Force-Matching and Neural Network Potentials

The Journal of Physical Chemistry C
,

vol.
126(4)
,

pp.
2264–2275
,

2022
Year of Publication:
2022
Generative Coarse-Graining of Molecular Conformations

arXiv:2201.12176
,

2022
Year of Publication:
2022
Learning Matter: Materials Design with Machine Learning and Atomistic Simulations

Accounts of Materials Research
,

2022
Year of Publication:
2022
Tunable CHA/AEI Zeolite Intergrowths with A Priori Biselective Organic Structure-Directing Agents: Controlling Enrichment and Implications for Selective Catalytic Reduction of NOx

Angewandte Chemie International Edition
,

2022
Year of Publication:
2022
From Free-Energy Profiles to Activation Free Energies

The Journal of Chemical Physics
,

vol.
157
,

pp.
084113
,

2022
Year of Publication:
2022
Repurposing Templates for Zeolite Synthesis from Simulations and Data Mining

Chemistry of Materials
,

2022
Year of Publication:
2022
Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential

Nature Communications
,

vol.
13
,

pp.
3440
,

2022
Year of Publication:
2022
Neural Scaling of Deep Chemical Models

ChemRxiv
,

2022
Year of Publication:
2022
Examining graph neural networks for crystal structures: limitation on capturing periodicity

arXiv:2208.05039
,

2022
Year of Publication:
2022
Human- and machine-centred designs of molecules and materials for sustainability and decarbonization

Nature Reviews Materials
,

2022
Year of Publication:
2022
Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations

arXiv:2210.07237
,

2022
Year of Publication:
2022
Machine Learning and High Throughput Synthesis Acceleration of the Discovery of Alkaline Electrolyte Oxygen Evolution Reaction Electrocatalysts

ECS Meeting Abstracts
,

2022
Year of Publication:
2021
- Daniel Schwalbe-Koda
- Rafael Gómez-Bombarelli
Supramolecular Recognition in Crystalline Nanocavities Through Monte Carlo and Voronoi Network Algorithms

The Journal of Physical Chemistry C
,

vol.
125 (5)
,

pp.
3009-3017
,

2021
Year of Publication:
2021
Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks

Nature Communications
,

vol.
12
,

pp.
5104
,

2021
Year of Publication:
2021
- Daniel Schwalbe-Koda
- Rafael Gómez-Bombarelli
Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

The Journal of Chemical Physics
,

vol.
154
,

pp.
174109
,

2021
Year of Publication:
2021
Deep learning to design nuclear-targeting abiotic miniproteins

Nature Chemistry
,

2021
Year of Publication:
2021
A priori control of zeolite phase competition and intergrowth with high-throughput simulations

Science
,

pp.
eabh3350
,

2021
Year of Publication:
2021
Data-Driven Design of Biselective Templates for Intergrowth Zeolites

The Journal of Physical Chemistry Letters
,

vol.
12
,

pp.
10689-10694
,

2021
Year of Publication:
2021
An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming

International Conference on Machine Learning
,

2021
Year of Publication:
2021
Accelerating the screening of amorphous polymer electrolytes by learning to reduce random and systematic errors in molecular dynamics simulations

arXiv:2101.05339
,

2021
Year of Publication:
2021
Discovering relationships between OSDAs and zeolites through data mining and generative neural networks

ACS Central Science
,

vol.
7
,

pp.
858–867
,

2021
Year of Publication:
2021
Synthetic Glycomacromolecules of Defined Valency, Absolute Configuration, and Topology Distinguish between Human Lectins

JACS Au
,

vol.
1(10)
,

pp.
1621–1630
,

2021
Year of Publication:
2021
Deep Learning Enables Discovery of a Short Nuclear Targeting Peptide for Efficient Delivery of Antisense Oligomers

JACS Au
,

vol.
1(11)
,

pp.
2009–2020
,

2021
Year of Publication:
2021
Machine Learning Guides Peptide Nucleic Acid Flow Synthesis and Sequence Design

Advanced Science
,

pp.
2201988
,

2021
Year of Publication:
2021
Crystal graph convolutional neural networks for per-site property prediction

Fourth Workshop on Machine Learning and the Physical Sciences at NeurIPS
,

2021
Year of Publication:
2020
Differentiable Molecular Simulations for Control and Learning

arXiv:2003.00868
,

2020
Year of Publication:
2020
Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

Chem
,

vol.
7(3)
,

pp.
738-51
,

2020
Year of Publication:
2020
Generative Models for Automatic Chemical Design

Machine Learning Meets Quantum Physics
,

pp.
445 – 467
,

2020
Year of Publication:
2020
Quantitative Mapping of Molecular Substituents to Macroscopic Properties Enables Predictive Design of Oligoethyleneglycol-Based Lithium Electrolytes

ACS Central Science
,

2020
Year of Publication:
2020
Active Learning and Neural Network Potentials Accelerate Molecular Screening of Ether-based Solvate Ionic Liquids

Chemical Communications
,

2020
Year of Publication:
2020
Temperature-transferable coarse-graining of ionic liquids with dual graph convolutional neural networks

The Journal of Chemical Physics
,

vol.
153
,

pp.
164501
,

2020
Year of Publication:
2020
Reusability report: Designing organic photoelectronic molecules with descriptor conditional recurrent neural networks

Nature Machine Intelligence
,

vol.
2
,

pp.
749–752
,

2020
Year of Publication:
2020
- Rafael Gómez-Bombarelli
- Alán Aspuru-Guzik
Machine learning and big-data in computational chemistry

Handbook of Materials Modeling: Methods: Theory and Modeling
,

pp.
1939–1962
,

2020
Year of Publication:
2020
Deep learning for prediction and optimization of fast-flow peptide synthesis

ACS Central Science
,

vol.
6
,

pp.
2277–2286
,

2020
Year of Publication:
2019
Mapping the frontiers of quinone stability in aqueous media: implications for organic aqueous redox flow batteries

J. Mater. Chem. A
,

vol.
7
,

pp.
12833-12841
,

2019
Year of Publication:
2019
Graph similarity drives zeolite diffusionless transformations and intergrowth

Nature Materials
,

vol.
18
,

pp.
1177 – 1179
,

2019
Year of Publication:
2019
- Wang, Wujie
- Rafael Gómez-Bombarelli
Coarse-graining auto-encoders for molecular dynamics

npj Computational Materials
,

vol.
5
,

pp.
125
,

2019
Year of Publication:
2019
The Materials Research Platform: Defining the Requirements from User Stories

Matter
,

vol.
1
,

pp.
1433 – 1438
,

2019
Year of Publication:
2019
- Rafael Gómez-Bombarelli
- Alán Aspuru-Guzik
Computational discovery of organic LED materials

Comput. Mater. Disc
,

pp.
423–446
,

2019
Year of Publication:
2019
Complex algorithms for data-driven model learning in science and engineering

2019
Year of Publication:
2019
Data-driven modeling and learning in science and engineering

Comptes Rendus Mécanique
,

vol.
347
,

pp.
845–855
,

2019
Year of Publication:
2018

Rafael Gómez-Bombarelli

Reaction: The Near Future of Artificial Intelligence in Materials Discovery

Chem
,

vol.
4
,

pp.
1189 – 1190
,

2018
Year of Publication:
2018
Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

ACS Central Science
,

vol.
4
,

pp.
268 – 276
,

2018
Year of Publication:
2017
An Alternative Host Material for Long-Lifespan Blue Organic Light-Emitting Diodes Using Thermally Activated Delayed Fluorescence

Advanced Science
,

vol.
4
,

2017
Year of Publication:
2017
Anthraquinone Derivatives in Aqueous Flow Batteries

Advanced Energy Materials
,

vol.
7
,

2017
Year of Publication:
2017
UV-Vis spectrophotometry of quinone flow battery electrolyte for: In situ monitoring and improved electrochemical modeling of potential and quinhydrone formation

Physical Chemistry Chemical Physics
,

vol.
19
,

2017
Year of Publication:
2016
Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach

Nature Materials
,

vol.
15
,

2016
Year of Publication:
2016
Turbocharged molecular discovery of OLED emitters: From high-throughput quantum simulation to highly efficient TADF devices

Proceedings of SPIE – The International Society for Optical Engineering
,

vol.
9941
,

2016
Year of Publication:
2016
A redox-flow battery with an alloxazine-based organic electrolyte

Nature Energy
,

vol.
1
,

2016
Year of Publication:
2016
Comparative study of singlet oxygen production by photosensitiser dyes encapsulated in silicone: Towards rational design of anti-microbial surfaces

Physical Chemistry Chemical Physics
,

vol.
18
,

2016
Year of Publication:
2016
Photocell optimization using dark state protection

Physical Review Letters
,

vol.
117
,

2016
Year of Publication:
2015
Synthesis and investigation of donor-porphyrin-acceptor triads with long-lived photo-induced charge-separate states

Chemical Science
,

vol.
6
,

2015
Year of Publication:
2015
Convolutional networks on graphs for learning molecular fingerprints

Advances in Neural Information Processing Systems
,

vol.
2015-Janua
,

2015
Year of Publication:
2015
Combinatorial design of OLED-emitting materials

Digest of Technical Papers – SID International Symposium
,

vol.
46
,

2015
Year of Publication:
2015
What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery

Annual Review of Materials Research
,

vol.
45
,

2015
Year of Publication:
2014
Interference by nitrous acid decomposition in the kinetic study of nitrosation reactions

International Journal of Chemical Kinetics
,

vol.
46
,

2014
Year of Publication:
2014
Alkylating potential of styrene oxide: Reactions and factors involved in the alkylation process

Chemical Research in Toxicology
,

vol.
27
,

2014
Year of Publication:
2014
Vibration-assisted resonance in photosynthetic excitation-energy transfer

Physical Review A – Atomic, Molecular, and Optical Physics
,

vol.
90
,

2014
Year of Publication:
2013
Mechanisms of lactone hydrolysis in acidic conditions

Journal of Organic Chemistry
,

vol.
78
,

2013
Year of Publication:
2013
Mechanisms of lactone hydrolysis in neutral and alkaline conditions

Journal of Organic Chemistry
,

vol.
78
,

2013
Year of Publication:
2012
Taurine-nitrite interaction as a precursor of alkylation mechanisms

Food Chemistry
,

vol.
134
,

2012
Year of Publication:
2012
Connecting the chemical and biological reactivity of epoxides

Chemical Research in Toxicology
,

vol.
25
,

2012
Year of Publication:
2012
Genotoxic halofuranones in water: Isomerization and acidity of mucohalic acids

Journal of Physical Organic Chemistry
,

vol.
25
,

2012
Year of Publication:
2012
DNA damage by genotoxic hydroxyhalofuranones: An in silico approach to MX

Environmental Science and Technology
,

vol.
46
,

2012
Year of Publication:
2012
Erratum: Potential of the NBP method for the study of alkylation mechanisms: NBP as a DNA-model (Chemical Research in Toxicology (2012) 25:6 (1176-1191) DOI: 10.1021/tx300065v)

Chemical Research in Toxicology
,

vol.
25
,

2012
Year of Publication:
2012
Potential of the NBP method for the study of alkylation mechanisms: NBP as a DNA-model

Chemical Research in Toxicology
,

vol.
25
,

2012
Year of Publication:
2012
Biocatalytic oxidation of phenolic compounds by bovine methemoglobin in the presence of H\textlessinf\textgreater2\textless/inf\textgreaterO\textlessinf\textgreater2\textless/inf\textgreater: Quantitative structure-activity relationships

Journal of Hazardous Materials
,

vol.
241-242
,

2012
Year of Publication:
2011
Reactivity of p-nitrostyrene oxide as an alkylating agent. A kinetic approach to biomimetic conditions

Organic and Biomolecular Chemistry
,

vol.
9
,

2011
Year of Publication:
2011
DNA-damaging disinfection byproducts: Alkylation mechanism of mutagenic mucohalic acids

Environmental Science and Technology
,

vol.
45
,

2011