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Machine Learning Methods for Property Prediction in Chemoinformatics:Quo Vadis?

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Collaborative Filtering on a Family of Biological Targets
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Robust QSAR Models Using Bayesian Regularized Neural Networks
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Multitask Learning
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MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: A comparative 3D QSAR study in a series of steroids
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Linear Programming Boosting via Column Generation
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Construction of Neural-Network Structure–Condition–Property Relationships: Modeling of Physicochemical Properties of Hydrocarbons
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Bagging Predictors
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Statistical Asymptotic Theory of Active Learning
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Artificial neural network and fragmental approach in prediction of physicochemical properties of organic compounds
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Support Vector Data Description
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Chemoinformatics Approaches to Virtual Screening
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Neural networks as a method for elucidating structure–property relationships for organic compounds
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Statistical Learning Theory
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An approach to the interpretation of backpropagation neural network models in QSAR studies
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Support Vector Training of Protein Alignment Models
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A Dictionary of Statistics
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Protein homology detection using string alignment kernels
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Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor
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Multitask Machine Learning for Classifying Highly and Weakly Potent Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acsomega.9b00595openalex-snapshot
Integrating the Structure–Activity Relationship Matrix Method with Molecular Grid Maps and Activity Landscape Models for Medicinal Chemistry Applications
inferred← citeshttps://doi.org/10.1021/acsomega.9b02470openalex-snapshot
Large-Scale Comparison of Alternative Similarity Search Strategies with Varying Chemical Information Contents
inferred← citeshttps://doi.org/10.1021/ci400737sopenalex-snapshot
QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem
inferred← citeshttps://doi.org/10.1021/ci500410gopenalex-snapshot
Introduction of a Methodology for Visualization and Graphical Interpretation of Bayesian Classification Models
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Boosting Computational Catalysis and Chemical Reactivity with Artificial Intelligence
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Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology
inferred← citeshttps://doi.org/10.1038/s41467-023-37570-1openalex-snapshot
Predicting compound activity from phenotypic profiles and chemical structures
inferred← citeshttps://doi.org/10.1038/s41524-018-0128-1openalex-snapshot
Deep-learning-based inverse design model for intelligent discovery of organic molecules
inferred← citeshttps://doi.org/10.1038/s41524-023-01099-0openalex-snapshot
Molecular design with automated quantum computing-based deep learning and optimization
inferred← citeshttps://doi.org/10.1038/s41597-024-03933-6openalex-snapshot
QM9star, two Million DFT-computed Equilibrium Structures for Ions and Radicals with Atomic Information
inferred← citeshttps://doi.org/10.1038/s41597-024-04190-3openalex-snapshot
A comprehensive dataset on cytotoxicity of ionic liquids
inferred← citeshttps://doi.org/10.1038/s41598-021-93771-yopenalex-snapshot
Feature importance correlation from machine learning indicates functional relationships between proteins and similar compound binding characteristics
inferred← citeshttps://doi.org/10.1038/s41598-023-46930-2openalex-snapshot
Calculation of exact Shapley values for explaining support vector machine models using the radial basis function kernel
inferred← citeshttps://doi.org/10.1038/s41598-024-57135-6openalex-snapshot
Relationship between prediction accuracy and uncertainty in compound potency prediction using deep neural networks and control models
inferred← citeshttps://doi.org/10.1039/9781788018982-00231openalex-snapshot
Machine Learning in Drug Design
inferred← citeshttps://doi.org/10.1039/c5tx00406copenalex-snapshot
Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data
inferred← citeshttps://doi.org/10.1039/c7sc02664aopenalex-snapshot
MoleculeNet: a benchmark for molecular machine learning
inferred← citeshttps://doi.org/10.1039/d2dd00136eopenalex-snapshot
Generating structural alerts from toxicology datasets using the local interpretable model-agnostic explanations method
inferred← citeshttps://doi.org/10.1039/d2dd00146bopenalex-snapshot
Calibration and generalizability of probabilistic models on low-data chemical datasets with DIONYSUS
inferred← citeshttps://doi.org/10.1039/d3ma00535fopenalex-snapshot
Machine learning-based q-RASPR predictions of detonation heat for nitrogen-containing compounds
inferred← citeshttps://doi.org/10.1039/d4ya00215fopenalex-snapshot
Predicting the performance and stability parameters of energetic materials (EMs) using a machine learning-based q-RASPR approach
inferred← citeshttps://doi.org/10.1063/1.5054968openalex-snapshot
Machine learning model for non-equilibrium structures and energies of simple molecules
inferred← citeshttps://doi.org/10.1063/5.0123091openalex-snapshot
Artificial intelligence: Evolving role in drug design
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Representing molecular and materials data for unsupervised machine learning
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Using machine learning to classify the immunosuppressive activity of per- and polyfluoroalkyl substances
inferred← citeshttps://doi.org/10.1080/17425255.2023.2298827openalex-snapshot
Where developmental toxicity meets explainable artificial intelligence: state-of-the-art and perspectives
inferred← citeshttps://doi.org/10.1080/17435390.2023.2186280openalex-snapshot
Efficient predictions of cytotoxicity of TiO2-based multi-component nanoparticles using a machine learning-based q-RASAR approach
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A renaissance of neural networks in drug discovery
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Is one-shot learning a viable option in drug discovery?
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The power of deep learning to ligand-based novel drug discovery
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Practical constraints with machine learning in drug discovery
inferred← citeshttps://doi.org/10.1088/1361-6528/aa82e5openalex-snapshot
Machine learning and genetic algorithm prediction of energy differences between electronic calculations of graphene nanoflakes
inferred← citeshttps://doi.org/10.1093/bib/bbv037openalex-snapshot
Building a virtual ligand screening pipeline using free software: a survey
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac112openalex-snapshot
Advanced graph and sequence neural networks for molecular property prediction and drug discovery
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Quantum evolution kernel: Machine learning on graphs with programmable arrays of qubits
inferred← citeshttps://doi.org/10.1109/bibm47256.2019.8982989openalex-snapshot
Interpretable Prediction of Protein-Ligand Interaction by Convolutional Neural Network
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CurrMG: A Curriculum Learning Approach for Graph Based Molecular Property Prediction
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Recent advances for handling imbalancement and uncertainty in labelling in medicinal chemistry data analysis
inferred← citeshttps://doi.org/10.1111/cbdd.12294openalex-snapshot
Modeling of Compound Profiling Experiments Using Support Vector Machines
inferred← citeshttps://doi.org/10.1111/cbdd.14057openalex-snapshot
Machine learning approaches and their applications in drug discovery and design
inferred← citeshttps://doi.org/10.1145/3511808.3557085openalex-snapshot
Graph Neural Networks Pretraining Through Inherent Supervision for Molecular Property Prediction
inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-122120-124216openalex-snapshot
Machine Learning in Chemoinformatics and Medicinal Chemistry
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Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates
inferred← citeshttps://doi.org/10.1177/11779322221090349openalex-snapshot
Applied Machine Learning Toward Drug Discovery Enhancement: Leishmaniases as a Case Study
inferred← citeshttps://doi.org/10.1177/24725552211017520openalex-snapshot
Validating ADME QSAR Models Using Marketed Drugs
inferred← citeshttps://doi.org/10.1186/1758-2946-6-21openalex-snapshot
Self organising hypothesis networks: a new approach for representing and structuring SAR knowledge
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Convolutional architectures for virtual screening
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BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics
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Computational methods for prediction of in vitro effects of new chemical structures
inferred← citeshttps://doi.org/10.1186/s13321-017-0215-1openalex-snapshot
ChemSAR: an online pipelining platform for molecular SAR modeling
inferred← citeshttps://doi.org/10.1186/s13321-017-0256-5openalex-snapshot
An automated framework for QSAR model building
inferred← citeshttps://doi.org/10.1186/s13321-018-0270-2openalex-snapshot
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
inferred← citeshttps://doi.org/10.1186/s13321-018-0300-0openalex-snapshot
Exploring non-linear distance metrics in the structure–activity space: QSAR models for human estrogen receptor
inferred← citeshttps://doi.org/10.1186/s13321-019-0356-5openalex-snapshot
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity
inferred← citeshttps://doi.org/10.1186/s13321-019-0396-xopenalex-snapshot
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation
inferred← citeshttps://doi.org/10.1186/s13321-020-00426-7openalex-snapshot
Predicting liver cytosol stability of small molecules
inferred← citeshttps://doi.org/10.1186/s13321-021-00510-6openalex-snapshot
Multi-PLI: interpretable multi‐task deep learning model for unifying protein–ligand interaction datasets
inferred← citeshttps://doi.org/10.1186/s13321-025-00989-3openalex-snapshot
Enhancing molecular property prediction with quantized GNN models
inferred← citeshttps://doi.org/10.13005/ojc/420110openalex-snapshot
Prediction of new ESIPT Molecules by Machine Learning and Quantum Modelling
inferred← citeshttps://doi.org/10.1371/journal.pone.0073587openalex-snapshot
In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases
inferred← citeshttps://doi.org/10.1371/journal.pone.0119301openalex-snapshot
Systematic Artifacts in Support Vector Regression-Based Compound Potency Prediction Revealed by Statistical and Activity Landscape Analysis
inferred← citeshttps://doi.org/10.1371/journal.pone.0282924openalex-snapshot
Guidance for good practice in the application of machine learning in development of toxicological quantitative structure-activity relationships (QSARs)
inferred← citeshttps://doi.org/10.1515/jib-2018-0065openalex-snapshot
Deep Convolutional Neural Networks for the Prediction of Molecular Properties: Challenges and Opportunities Connected to the Data
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Prediction of modes of action of components of traditional medicinal preparations
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Use of machine learning approaches for novel drug discovery
inferred← citeshttps://doi.org/10.17863/cam.36962openalex-snapshot
INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY
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