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RESEARCH PAPER · Journal of Chemical Information and Modeling · 2022

Unified Deep Learning Model for Multitask Reaction Predictions with Explanation

Jieyu Lü, Yingkai Zhang

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Unified Deep Learning Model for Multitask Reaction Predictions with ExplanationOriginalTranslation between Molecules and Natural Language165Regression Transformer enables concurrent sequence regression and generation for molecular language modelling6Roadmap to Pharmaceutically Relevant Reactivity Models Leveraging High-Throughput Experimentation17Predictive chemistry: machine learning for reaction deployment, reaction development, and reaction discovery138Human brain-inspired chemical artificial intelligence tools for the analysis and prediction of the anion-sensing characteristics of an imidazole-based luminescent Os( ii )-bipyridine complex7Reagent prediction with a molecular transformer improves reaction data quality36Interpretable Machine Learning Enabled Inorganic Reaction Classification and Synthesis Condition Prediction41Harnessing Deep Neural Networks to Analyze Multi‐Channel Anion Sensing Characteristics of a Ru(II)‐Pyrazolyl‐Bis(Benzimidazole) Complex3Regression Transformer enables concurrent sequence regression and generation for molecular language modelling141Learning Chemical Rules of Retrosynthesis with Pre-training12Machine Learning Methods for Small Data Challenges in Molecular Science499A Unified View of Deep Learning for Reaction and Retrosynthesis Prediction: Current Status and Future Challenges8Doubly Stochastic Graph-based Non-autoregressive Reaction Prediction6Pretrained transformer models for predicting the withdrawal of drugs from the market15In silico ADME/tox comes of age: twenty years later26Deep learning for metabolic pathway design26pADR: Towards Personalized Adverse Drug Reaction Prediction by Modeling Multi-sourced Data1Integrated Molecular Modeling and Machine Learning for Drug Design70SynCluster: Reaction Type Clustering and Recommendation Framework for Synthesis Planning11PolyNC: a natural and chemical language model for the prediction of unified polymer properties68Generative LLMs in Organic Chemistry: Transforming Esterification Reactions into Natural Language Procedures5CatScore: evaluating asymmetric catalyst design at high efficiency2Every atom counts: predicting sites of reaction based on chemistry within two bonds0Language Models in Molecular Discovery19Collider.py: A Framework to Simulate Molecular Collisions1Reaction Space Charting as a Tool in Organic Chemistry Research and Development11De novo Molecular Design using Deep Learning4Advances in machine learning with chemical language models in molecular property and reaction outcome predictions29Large language models for science and medicine54Prediction of chemical reaction yields with large-scale multi-view pre-training30Leveraging Language Model Multitasking To Predict C–H Borylation Selectivity7Emerging opportunities of using large language models for translation between drug molecules and indications24Feedback-aligned Mixed LLMs for Machine Language-Molecule Translation0Completion of partial chemical equations3Data-Efficient, Chemistry-Aware Machine Learning Predictions of Diels–Alder Reaction Outcomes34Transformer technology in molecular science65Fabrication of molecular-scale logic devices and implication of artificial neural networks for analysis of anion-responsive behaviors of luminescent ruthenium-terpyridine complex2Reproducing Reaction Mechanisms with Machine‐Learning Models Trained on a Large‐Scale Mechanistic Dataset13Reproducing Reaction Mechanisms with Machine‐Learning Models Trained on a Large‐Scale Mechanistic Dataset4User-friendly and industry-integrated AI for medicinal chemists and pharmaceuticals55Intermediate Knowledge Enhanced the Performance of N-Acylation Yield Prediction Model0Specialising and analysing instruction-tuned and byte-level language models for organic reaction prediction2Chemical reaction enhanced graph learning for molecule representation5Chemical Graph-Based Transformer Models for Yield Prediction of High-Throughput Cross-Coupling Reaction Datasets10Reinforcement Learning for Improving Chemical Reaction Performance15Machine learning-guided strategies for reaction conditions design and optimization49Applying machine learning and genetic algorithms accelerated for optimizing ethanol production11Computer-aided drug discovery: From traditional simulation methods to language models and quantum computing35Precision Adverse Drug Reactions Prediction with Heterogeneous Graph Neural Network38Analog Accessibility Score (AAscore) for Rational Compound Selection3A review of large language models and autonomous agents in chemistry269Language Models for Predicting Organic Synthesis Procedures6A Survey of Large Language Model for Drug Research and Development16Computational tools for the prediction of site- and regioselectivity of organic reactions33Cross-disciplinary perspectives on the potential for artificial intelligence across chemistry51Data-driven recommendation of agents, temperature, and equivalence ratios for organic synthesis9Improving reaction prediction through chemically aware transfer learning7Intermediate knowledge enhanced the performance of the amide coupling yield prediction model14Molecular Machine Learning Approach to Enantioselective C–H Bond Activation Reactions: From Generative AI to Experimental Validation5Application of Transformers to Chemical Synthesis4Knowledge-guided large language model for material science16Impact of Membership Functions on the Performance of AI‐Assisted Neuro‐Fuzzy System for Analysis of Anion‐Responsive Behaviours of Polypyridyl‐Imidazole Based Ru(II) Receptors1AI-enabled language models (LMs) to large language models (LLMs) and multimodal large language models (MLLMs) in drug discovery and development40Bidirectional Chemical Intelligent Net: A unified deep learning–based framework for predicting chemical reaction3YieldFCP: Enhancing Reaction Yield Prediction via Fine-grained Cross-modal Pre-training6Influence of helmet positioning on uncertainty of blunt impact absorption performance tests0Precise mitigation strategies for urban heat island effect in Hong Kong's new towns using automated machine learning17Integrating a multitask graph neural network with DFT calculations for site-selectivity prediction of arenes and mechanistic knowledge generation19Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem6Enhancing Transthyretin Binding Affinity Prediction with a Consensus Model: Insights from the Tox24 Challenge8Exploring BERT for Reaction Yield Prediction: Evaluating the Impact of Tokenization, Molecular Representation, and Pretraining Data Augmentation9Language models for materials discovery and sustainability: Progress, challenges, and opportunities26Bridging 3D Molecular Structures and Artificial Intelligence by a Conformation Description Language0Empowering Generalist Material Intelligence with Large Language Models29Bridging chemistry and artificial intelligence by a reaction description language12Machine learning predictions for regioselectivity of hydroformylation reactions: leveraging limited data for high-precision results0Developing Pharmaceutically Relevant Pd-Catalyzed C–N Coupling Reactivity Models Leveraging High-Throughput Experimentation23A self-feedback knowledge elicitation approach for chemical reaction predictions1CSGL: chemical synthesis graph learning for molecule representation6Q‐GEM: Quantum Chemistry Knowledge Fusion Geometry‐Enhanced Molecular Representation for Property Prediction3HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model0Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge and Reasoning Capability of Large Language Models23log-RRIM: Yield Prediction via Local-to-Global Reaction Representation Learning and Interaction Modeling1CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions0A Method‐Oriented Review of Explainable Artificial Intelligence for Neurological Medical Imaging18A unified pre-trained deep learning framework for cross-task reaction performance prediction and synthesis planning14ReactionT5: a pre-trained transformer model for accurate chemical reaction prediction with limited data15Revolutionizing pharmacology: AI-powered approaches in molecular modeling and ADMET prediction44Explainable Artificial Intelligence in Drug Discovery: Bridging Predictive Power and Mechanistic Insight49Deep learning in chemical synthesis and retrosynthesis0Progress of AI-Driven Drug–Target Interaction Prediction and Lead Optimization23Large Language Models Meet Molecules: A Systematic Review of Advances and Challenges in AI-Driven Cheminformatics7Mechanism-Aware Deep Learning for Polar Reaction Prediction6Measuring Chemical LLM robustness to molecular representations: a SMILES variation-based framework6Bond-editing driven electron flow mapping for reaction mechanism modeling0Towards Few-shot Chemical Reaction Outcome Prediction3SFMMoE: A Semi-Empirical Descriptor-Augmented Multi-Expert Graph Neural Network for Accurate Prediction of Singlet Fission Properties3Opportunities of Large Language Models in the Development of Organic Electrosynthesis1Efficient Machine Learning for Yield Prediction in Transition Metal-Catalyzed meta -C(sp 2 )–H Bond Activation and Other Reactions2Chemistry-informed deep learning model for predicting stereoselectivity and absolute configuration in asymmetric hydrogenation10An overview of reaction outcome prediction with physics-based and data-driven methods2Designing less noble yet high-performing multimetallic catalysts for catalytic converters using a high-throughput approach0Large Language Models in Drug Discovery0Machine learning models for catalytic asymmetric reactions of simple alkenes: from enantioselectivity predictions to chemical insights4Transfer learning for reaction optimisation: overview of its applications and limits0Transformer0EnzRetro: Enzymatic Retrosynthetic Planning With Site‐Specific Reaction Edits Based on Sequence Generative Architecture0Explainable AI methods for drug discovery: A survey of interpretability, metrics and mechanistic insight13From graphs to tokens: Substructure-aware molecular representation for large language models0SynRXN: An Open Benchmark and Curated Dataset for Computational Reaction Modeling2A general-purpose framework for chemical reaction representation with atomic correspondence and flexible condition adaptation1Unifying p K a and Protonation Prediction with Sequence-Based Deep Learning0Capturing stereochemical information with AI: Driving stereoselectivity prediction and rational design in asymmetric catalysis0Bridging three-dimensional molecular structures and artificial intelligence with a conformation description language2Benchmarking molecular representations and machine learning algorithms for asymmetric catalysis: a palladium-catalysed decarboxylative asymmetric allylic alkylation case study0AI‐Driven Synthesis in Medicinal Chemistry: Integrating Large Language Models, Robotic Automation, and Sustainability Metrics to Accelerate Drug Discovery0Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms1From in silico screening to mechanism: computational advances in developing anti-allergic agents for food allergy0ChemRANG: Building AI-ready datasets via mechanism-informed curation to learn reaction feasibility boundaries0Machine Learning-Empowered Electromagnetic Wave Absorbing Materials: From Forward Prediction to Generative Inverse Design4Chemical Language Model Applications in Medicinal Chemistry0Driving Reaction Trajectories via Latent Flow Matching0Dual-Attention Multimodal Framework for Molecular Property Prediction0AI-driven drug discovery and personalized medicine: integrating quantum computing and next-generation technologies0Prediction of sugar reactions in high-temperature water using natural language processing0EZSolver: Template-Free Prediction of Polar Enzymatic Mechanisms via Bidirectional Flow Matching and Search0Explainable artificial intelligence (XAI) in schizophrenia: enhancing transparency in clinical decision-making0Advancing chemical reaction prediction in data-scarce drug discovery with active and geometric deep learning1

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