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RESEARCH PAPER · Digital Discovery · 2022

Reaction classification and yield prediction using the differential reaction fingerprint DRFP

Daniel Probst, Philippe Schwaller, Jean‐Louis Reymond

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Reaction classification and yield prediction using the differential reaction fingerprint DRFPOriginalUnified Deep Learning Model for Multitask Reaction Predictions with Explanation129An Ensemble Structure and Physicochemical (SPOC) Descriptor for Machine‐Learning Prediction of Chemical Reaction and Molecular Properties35Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction26Machine Learning Yield Prediction from NiCOlit, a Small-Size Literature Data Set of Nickel Catalyzed C–O Couplings87Reaxtica: A knowledge-guided machine learning platform for fast and accurate reaction selectivity and yield prediction0Reaxtica: A knowledge-guided machine learning platform for fast and accurate reaction selectivity and yield prediction1Physics-based representations for machine learning properties of chemical reactions33Data-driven Reaction Template Fingerprints1Growing pains: Reacting to negative impacts of deep learning on machine learning for chemistry4AI-driven hypergraph network of organic chemistry: network statistics and applications in reaction classification20Bayesian optimisation for additive screening and yieldimprovements in chemical reactions – beyond one-hot encodings2Molecular Similarity for Drug Discovery, Target Prediction and Chemical Space Visualization13Alchemical analysis of FDA approved drugs14Multistep retrosynthesis combining a disconnection aware triple transformer loop with a route penalty score guided tree search27On the use of real-world datasets for reaction yield prediction141Prediction of product distribution using machine learning techniques1The challenge of balancing model sensitivity and robustness in predicting yields: a benchmarking study of amide coupling reactions39Machine Learning C–N Couplings: Obstacles for a General-Purpose Reaction Yield Prediction48Interpretable Machine Learning Enabled Inorganic Reaction Classification and Synthesis Condition Prediction41Explainable prediction of catalysing enzymes from reactions using multilayer perceptrons5Molecular Machine Learning for Chemical Catalysis: Prospects and Challenges88Global reactivity models are impactful in industrial synthesis applications15The Societal and Scientific Importance of Inclusivity, Diversity, and Equity in Machine Learning for Chemistry4Alchemical Analysis of FDA Approved Drugs0Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios27A Machine Learning Approach to Model Interaction Effects: Development and Application to Alcohol Deoxyfluorination23Multistep retrosynthesis combining a disconnection aware triple transformer loop with a route penalty score guided tree search2LinChemIn: SynGraph—a data model and a toolkit to analyze and compare synthetic routes12MetaRF: attention-based random forest for reaction yield prediction with a few trails30Learning Hierarchical Representations for Explainable Chemical Reaction Prediction2Bayesian optimisation for additive screening and yieldimprovements in chemical reactions – beyond one-hot encoding0Probing the origin of higher efficiency of terphenyl phosphine over the biaryl framework in Pd-catalyzed C-N coupling: A combined DFT and machine learning study6RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking10Reaction performance prediction with an extrapolative and interpretable graph model based on chemical knowledge73Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning184Open-Source Machine Learning in Computational Chemistry59Combining Molecular Quantum Mechanical Modeling and Machine Learning for Accelerated Reaction Screening and Discovery19A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data46Predicting solvents with the help of Artificial Intelligence3ORDerly: Datasets and benchmarks for chemical reaction data0Recent Applications of Machine Learning in Molecular Property and Chemical Reaction Outcome Predictions51Comment on ‘Physics-based representations for machine learning properties of chemical reactions’10Bayesian optimisation for additive screening and yield improvements – beyond one-hot encoding28Machine learning approach for predicting the yield of pyrroles and dipyrromethanes condensation reactions with aldehydes13SynCluster: Reaction Type Clustering and Recommendation Framework for Synthesis Planning11An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification13Bridging the gap between chemical reaction pretraining and conditional molecule generation with a unified model27Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR397Recent developments in the total synthesis of natural products using the Ugi multicomponent reactions as the key strategy20Enhancing Generic Reaction Yield Prediction through Reaction Condition-Based Contrastive Learning173DReact: Geometric Deep Learning for Chemical Reactions3Mining Large-Scale Knowledge Graphs for Chemical Reaction Fingerprints0Automatic orbital pair selection for multi-level local coupled-cluster based on orbital maps0When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges64Benchmarking machine-readable vectors of chemical reactions on computed activation barriers9Discrete and mixed-variable experimental design with surrogate-based approach8Generating a skeleton reaction network for reactions of large-scale ReaxFF MD pyrolysis simulations based on a machine learning predicted reaction class11Investigating the reliability and interpretability of machine learning frameworks for chemical retrosynthesis15Regio-MPNN: predicting regioselectivity for general metal-catalyzed cross-coupling reactions using a chemical knowledge informed message passing neural network8Repurposing quantum chemical descriptor datasets for on-the-fly generation of informative reaction representations: application to hydrogen atom transfer reactions18Leveraging large language models for predictive chemistry367Prediction of chemical reaction yields with large-scale multi-view pre-training30Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph19AutoTemplate: Enhancing Chemical Reaction Datasets forMachine Learning Applications in Organic Chemistry1Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective26Reaction Rebalancing: A Novel Approach to Curating Reaction Databases2Machine Learning-Based Yield Prediction for First-Row Transition Metal Catalyzed Cross-Coupling Reactions0A general model for predicting enzyme functions based on enzymatic reactions28Reaction Rebalancing: A Novel Approach to Curating Reaction Databases0ORDerly: Data Sets and Benchmarks for Chemical Reaction Data34Artificial intelligence-based parametrization of Michaelis–Menten maximal velocity: Toward in silico New Approach Methodologies (NAMs)0REME: an integrated platform for reaction enzyme mining and evaluation18Leveraging Language Model Multitasking To Predict C–H Borylation Selectivity7POxload: Machine Learning Estimates Drug Loadings of Polymeric Micelles25Completion of partial chemical equations3Deep Kernel learning for reaction outcome prediction and optimization19Machine Learning Algorithm Guides Catalyst Choices for Magnesium‐Catalyzed Asymmetric Reactions7Machine Learning Algorithm Guides Catalyst Choices for Magnesium‐Catalyzed Asymmetric Reactions32AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry25Molecular set representation learning403DReact: Geometric Deep Learning for Chemical Reactions24Reaction rebalancing: a novel approach to curating reaction databases6Path Toward High-Throughput Synthesis Planning via Performance Benchmarking0EnzChemRED, a rich enzyme chemistry relation extraction dataset11Machine learning-guided strategies for reaction conditions design and optimization49High-throughput experimentation and machine learning-promoted synthesis of α-phosphoryloxy ketones via Ru-catalyzed P(O)O-H insertion reactions of sulfoxonium ylides14Automatic Orbital Pair Selection for Multilevel Local Coupled-Cluster Based on Orbital Maps1Challenges with Literature-Derived Data in Machine Learning for Yield Prediction: A Case Study on Pd-Catalyzed Carbonylation Reactions6Machine learning applications for thermochemical and kinetic property prediction19Recent Advancements in the Application of Artificial Intelligence in Drug Molecular Generation and Synthesis Planning2Machine learning-based yield prediction for transition metal-catalyzed cross-coupling reactions4Revolutionizing Enzyme Turnover Predictions with Non-Binary Reaction Fingerprints and AI0Language Models for Predicting Organic Synthesis Procedures6EnzymeCAGE: A Geometric Foundation Model for Enzyme Retrieval with Evolutionary Insights6AI-driven parametrization of Michaelis–Menten maximal velocity: Advancing in silico new approach methodologies (NAMs)3BatGPT-Chem: A Foundation Large Model for Chemical Engineering19Commit: Reaction classification and yield prediction using the differential reaction fingerprint DRFP0SymChemAI: A Symbolically Informed Neural Network for Physicochemical Modeling of Reaction Systems0The physics-AI dialogue in drug design11CLAIRE: a contrastive learning-based predictor for EC number of chemical reactions16Application of Transformers to Chemical Synthesis4Improving the Reliability of, and Confidence in, DFT Functional Benchmarking through Active Learning10HiRXN: Hierarchical Attention-Based Representation Learning for Chemical Reaction5An active representation learning method for reaction yield prediction with small-scale data8Multi‐modal Homogeneous Chemical Reaction Performance Prediction with Graph and Chemical Language Information7SynTemp : Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases8YieldFCP: Enhancing Reaction Yield Prediction via Fine-grained Cross-modal Pre-training6Machine Learning Accelerated Analysis of Chemical Reaction Networks for Gas-Phase Reaction Systems2Discovery, design, and engineering of enzymes based on molecular retrobiosynthesis10Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop0Local reaction condition optimization via machine learning1DeepMolecules: a web server for predicting enzyme and transporter–small molecule interactions17Exploring BERT for Reaction Yield Prediction: Evaluating the Impact of Tokenization, Molecular Representation, and Pretraining Data Augmentation9Bridging chemistry and artificial intelligence by a reaction description language12Towards global reaction feasibility and robustness prediction with high throughput data and bayesian deep learning18Applying Active Learning toward Building a Generalizable Model for Ni-Photoredox Cross-Electrophile Coupling of Aryl and Alkyl Bromides18Developing Pharmaceutically Relevant Pd-Catalyzed C–N Coupling Reactivity Models Leveraging High-Throughput Experimentation23Interpretation of chemical reaction yields with graph neural additive network1A Mamba-based foundation model for materials11General Chemically Intuitive Atom- and Bond-Level DFT Descriptors for Machine Learning Approaches to Reaction Condition Prediction7Construction of Training Datasets for Chemical Reactivity Prediction Through Computational Means0Predicting Reactivity with Machine Learning1HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model0The converging moment of chemistry and artificial intelligence: a review and outlook0An open-source family of large encoder-decoder foundation models for chemistry19log-RRIM: Yield Prediction via Local-to-Global Reaction Representation Learning and Interaction Modeling1Agnostic Tools for Life Detection: A Multiscale Approach to Biological and Chemical Reaction Networks0Optimizing Model Learning Performance on a Challenging Heck Reaction Yield Data Set2Designing Buchwald–Hartwig Reaction Graph for Yield Prediction2MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis12Graph Neural Networks in Modern AI-Aided Drug Discovery87Mechanism-Aware Deep Learning for Polar Reaction Prediction6Metal-catalyzed homogeneous catalytic transfer hydrogenation: A data-driven approach0SynCat: molecule-level attention graph neural network for precise reaction classification2Efficient Machine Learning for Yield Prediction in Transition Metal-Catalyzed meta -C(sp 2 )–H Bond Activation and Other Reactions2A virtual platform for automated hybrid organic-enzymatic synthesis planning3Design and Experimental Validation of a Photocatalyst Recommender Based on a Large Language Model0Design and Experimental Validation of a Photocatalyst Recommender Based on a Large Language Model6Catalyst-Free C–N Coupling under Ambient Conditions via High-Throughput Microdroplet Reactions1ChemOrigins: a community-curated database for origins-of-life chemistry2Data augmentation in a triple transformer loop retrosynthesis model2EnzFinder: a sustainable alternative to chemical synthesis0Protocol-guided evaluation of reaction yield prediction under predictable distribution shifts: a review0Understanding key NOx/hydrocarbon interactions via Ṙ + HNO = RH + NO for alkyl, alkenyl and alkynyl radicals: ab initio kinetics and ML-based rate coefficient prediction0Enhancing kcat prediction through residue-aware attention mechanism and pre-trained representations2Enzyformer: a two-stage pretrained model for enzymatic retrosynthesis1A geometric foundation model for enzyme retrieval with evolutionary insights15EnzFinder: a sustainable alternative to chemical synthesis0ChemTorch: A Deep Learning Framework for Benchmarking and Developing Chemical Reaction Property Prediction Models6ReMol: A Chemical Reaction Knowledge-Guided Self-Supervised Molecular Image Representation Learning Framework0

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