Deep learning finds convergent melanocytic morphology despite noisy archival slides
Tada M et al., Cell Rep Methods 2025 |
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Cell-type-directed network-correcting combination therapy for Alzheimer’s disease
Li Y et al., Cell 2025 |
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Mendeley |
The polypharmacology of psychedelics reveals multiple targets for potential therapeutics
Jain MK et al., Neuron 2025 |
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Mendeley |
Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results
Shub L et al., J Chem Inf Model 2025 |
autoparty |
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MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures
Shub L et al., Nat Commun 2025 |
MIC |
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Zenodo |
Evolutionary-scale enzymology enables exploration of a rugged catalytic landscape
Muir DF et al., Science 2025 |
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Zenodo |
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation
Nogueira VHR et al., J Chem Inf Model 2025 |
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ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
Gunsalus LM et al., PLoS Comput Biol 2025 |
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Deep phenotypic profiling of neuroactive drugs in larval zebrafish
Gendelev L et al., Nat Commun 2024 |
deepfish |
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Zenodo |
Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds
Hall BW et al., J Chem Inf Model 2024 |
RAD |
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Learning chemical sensitivity reveals mechanisms of cellular response
Connell W et al., Commun Biol 2024 |
chemprobe |
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Zenodo |
Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks
Gale-Day ZJ et al., J Chem Inf Model 2024 |
torch_pgn |
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Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations
Ghandian S et al., bioRxiv 2024 |
tangle-tracer |
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BioStudies |
Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles
Vizcarra JC et al., Acta Neuropathol Commun 2023 |
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Google Drive |
Autoregressive fragment-based diffusion for pocket-aware ligand design
Ghorbani M et al., arXiv - NeurIPS GenBio 2023 |
autofragdiff |
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In silico discovery of repetitive elements as key sequence determinants of 3D genome folding
Gunsalus LM et al., Cell Genom 2023 |
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Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels
Wong DR et al., Commun Biol 2023 |
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OSF |
A single-cell gene expression language model
Connell W et al., arXiv - NeurIPS LMRL 2022 |
exceiver |
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Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
Fassio AV et al., J Chem Inf Model 2022 |
LUNA |
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Simultaneous analysis of neuroactive compounds in zebrafish
Myers-Turnbull D et al., bioRxiv 2022 |
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OSF |
Trans-channel fluorescence learning improves high-content screening for Alzheimer’s disease therapeutics
Wong DR et al., Nat Mach Intell 2022 |
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OSF |
Deep learning from multiple experts improves identification of amyloid neuropathologies
Wong DR et al., Acta Neuropathol Commun 2022 |
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OSF |
Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction
Caceres EL et al., J Chem Inf Model 2020 |
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Predicting Cellular Drug Sensitivity using Conditional Modulation of Gene Expression
Connell W et al., bioRxiv - NeurIPS LMRL 2020 |
film-gex |
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Robust Semantic Interpretability: Revisiting Concept Activation Vectors
Pfau J et al., arXiv - ICML - WHI 2020 |
RCAV |
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Zenodo |
Validation of machine learning models to detect amyloid pathologies across institutions
Vizcarra JC et al., Acta Neuropathol Commun 2020 |
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Emory |
Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation
McCarroll MN et al., Nat Commun 2019 |
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Zenodo |
Interpretable classification of Alzheimer’s disease pathologies with a convolutional neural network pipeline
Tang Z et al., Nat Commun 2019 |
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Zenodo |
Comment on "Predicting reaction performance in C-N cross-coupling using machine learning"
Chuang KV et al., Science 2018 |
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Predicted Biological Activity of Purchasable Chemical Space
Irwin JJ et al., J Chem Inf Model 2018 |
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ZINC15
files.docking.org |
A Simple Representation of Three-Dimensional Molecular Structure
Axen SD et al., J Med Chem 2017 |
E3FP |
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| [Project] Keras implementation of Neural Graph Fingerprints (Duvenaud et al., arXiv:1509.09292, 2015) |
keras-neural-graph-fingerprint |
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