Advanced machine learning for Innovative Drug Discovery

Equivariant Graph Neural Networks for Toxicity Prediction

Author(s): Julian Cremer, Leonardo Medrano Sandonas, Alexandre Tkatchenko, Djork-Arné Clevert, Gianni De Fabritiis
Published in: Chemical Research in Toxicology, 2023, ISSN 0893-228X
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00032

Developing novel Lin28 inhibitors by computer aided drug design

Author(s): Xuesen Dong, Victor Barrios, Mariia Radaeva, Graciella Rosellinny, Qiongqiong Jia, Ning Xie, Jason Smith, Martin Gleave, Nada Lallous, Artem Cherkasov, Hanadi Ibrahim, Monica Villanueva, Suzana Straus
Published in: Cell Death Discovery, 2025, ISSN 2058-7716
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-4644460/v1

The openOCHEM consensus model is the best-performing open-source predictive model in the First EUOS/SLAS joint compound solubility challenge

Author(s): Andrea Hunklinger, Peter Hartog, Martin Šícho, Guillaume Godin, Igor V. Tetko
Published in: SLAS Discovery, Issue 29, 2024, Page(s) 100144, ISSN 2472-5552
Publisher: Elsevier BV
DOI: 10.1016/j.slasd.2024.01.005

HyperPCM: Robust Task-Conditioned Modeling of Drug–Target Interactions

Author(s): Emma Svensson, Pieter-Jan Hoedt, Sepp Hochreiter, Günter Klambauer
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 2539-2553, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c01417

Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition

Author(s): Peter B. R. Hartog, Fabian Krüger, Samuel Genheden, Igor V. Tetko
Published in: Journal of Cheminformatics, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.26434/chemrxiv-2024-kdx3g

Modeling noncovalent interatomic interactions on a photonic quantum computer

Author(s): Matthieu Sarkis, Alessio Fallani, Alexandre Tkatchenko
Published in: Physical Review Research, Issue 5, 2023, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/physrevresearch.5.043072

Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling

Author(s): Alessio Fallani, Ramil Nugmanov, Jose Arjona-Medina, Jörg Kurt Wegner, Alexandre Tkatchenko, Kostiantyn Chernichenko
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-00970-0

AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models

Author(s): Andrius Bernatavicius, Martin Šícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuss, Gerard J. P. van Westen
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 8113-8122, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.4c00309

Investigations into the efficiency of computer-aided synthesis planning

Author(s): Peter B.R. Hartog, Annie M. Westerlund, Igor V. Tetko, Samuel Genheden
Published in: Journal of Chemical Information and Modeling, 2024, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.26434/chemrxiv-2024-q2v87

Unsupervised Representation Learning for Proteochemometric Modeling

Author(s): Kim, PT., Winter, R., Clevert, DA.
Published in: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)

Improving route development using convergent retrosynthesis planning

Author(s): Paula Torren-Peraire, Jonas Verhoeven, Dorota Herman, Hugo Ceulemans, Igor V. Tetko, Jörg K. Wegner
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-00953-1

Development of Novel Inhibitors Targeting the D-Box of the DNA Binding Domain of Androgen Receptor

Author(s): Radaeva, M., Ban, F., Zhang, F., LeBlanc, E., Lallous, N., Rennie, P.S., Gleave, M.E., Cherkasov, A.
Published in: Int. J. Mol. Sci., 2021, Page(s) 2493, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22052493

Img2Mol – accurate SMILES recognition from molecular graphical depictions

Author(s): Clevert, DA., Le, T., Winter, R., Montanari, F.
Published in: CHEMICAL SCIENCE, 2021, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1sc01839f

Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design

Author(s): Alan Kai Hassen, Martin Šícho, Yorick J. van Aalst, Mirjam C. W. Huizenga, Darcy N. R. Reynolds, Sohvi Luukkonen, Andrius Bernatavicius, Djork-Arné Clevert, Antonius P. A. Janssen, Gerard J. P. van Westen, Mike Preuss
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00910-4

Be aware of overfitting by hyperparameter optimization!

Author(s): Igor V. Tetko, Ruud van Deursen, Guillaume Godin
Published in: Journal of Cheminformatics, Issue 16, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00934-w

The Promise of AI for DILI Prediction

Author(s): Vall, A., Sabnis, Y., Shi, J., Class, R., Hochreiter, S., Klambauer, G.
Published in: Front. Artif. Intell., 2021, ISSN 0922-6389
Publisher: IOS Press
DOI: 10.3389/frai.2021.638410

Expanding the chemical space using a chemical reaction knowledge graph

Author(s): Emma Rydholm, Tomas Bastys, Emma Svensson, Christos Kannas, Ola Engkvist, Thierry Kogej
Published in: Digital Discovery, Issue 3, 2024, Page(s) 1378-1388, ISSN 2635-098X
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00230f

Tackling assay interference associated with small molecules

Author(s): Lu Tan, Steffen Hirte, Vincenzo Palmacci, Conrad Stork, Johannes Kirchmair
Published in: Nature Reviews Chemistry, Issue 8, 2024, Page(s) 319-339, ISSN 2397-3358
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41570-024-00593-3

Online OCHEM multi-task model for solubility and lipophilicity prediction of platinum complexes

Author(s): Nesma Mousa, Hristo P. Varbanov, Vidya Kaipanchery, Elisabetta Gabano, Mauro Ravera, Andrey A. Toropov, Larisa Charochkina, Filipe Menezes, Guillaume Godin, Igor V. Tetko
Published in: Journal of Inorganic Biochemistry, Issue 269, 2025, Page(s) 112890, ISSN 0162-0134
Publisher: Elsevier BV
DOI: 10.1016/j.jinorgbio.2025.112890

CLOOME: contrastive learning unlocks bioimaging databases for queries with chemical structures

Author(s): Ana Sanchez-Fernandez, Elisabeth Rumetshofer, Sepp Hochreiter, Günter Klambauer
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42328-w

Statistical approaches enabling technology-specific assay interference prediction from large screening data sets

Author(s): Vincenzo Palmacci, Steffen Hirte, Jorge Enrique Hernández González, Floriane Montanari, Johannes Kirchmair
Published in: Artificial Intelligence in the Life Sciences, Issue 5, 2024, Page(s) 100099, ISSN 2667-3185
Publisher: Elsevier BV
DOI: 10.1016/j.ailsci.2024.100099

Multi-objective synthesis planning by means of Monte Carlo Tree search

Author(s): Helen Lai, Christos Kannas, Alan Kai Hassen, Emma Granqvist, Annie M. Westerlund, Djork-Arné Clevert, Mike Preuss, Samuel Genheden
Published in: Artificial Intelligence in the Life Sciences, Issue 7, 2025, Page(s) 100130, ISSN 2667-3185
Publisher: Elsevier BV
DOI: 10.1016/j.ailsci.2025.100130

Network Analysis of the Organic Chemistry in Patents, Literature, and Pharmaceutical Industry

Author(s): Emma Svensson, Emma Granqvist, Tomas Bastys, Christos Kannas, Mikhail Kabeshov, Samuel Genheden, Ola Engkvist, Thierry Kogej
Published in: Molecular Informatics, Issue 44, 2025, ISSN 1868-1743
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/minf.202500011

Molecular property prediction using pretrained-BERT and Bayesian active learning: a data-efficient approach to drug design

Author(s): Muhammad Arslan Masood, Samuel Kaski, Tianyu Cui
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-00986-6

Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules

Author(s): Leonardo Medrano Sandonas, Dries Van Rompaey, Alessio Fallani, Mathias Hilfiker, David Hahn, Laura Perez-Benito, Jonas Verhoeven, Gary Tresadern, Joerg Kurt Wegner, Hugo Ceulemans, Alexandre Tkatchenko
Published in: Scientific Data, Issue 11, 2024, ISSN 2052-4463
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41597-024-03521-8

Inverse mapping of quantum properties to structures for chemical space of small organic molecules

Author(s): Alessio Fallani, Leonardo Medrano Sandonas, Alexandre Tkatchenko
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-50401-1

Domain Shifts in Machine Learning Based Covid-19 Diagnosis From Blood Tests

Author(s): Roland, T., Bock, C., Tschoellitsch, T., Maletzky, A., Hochreiter, S., Meier, J., Klambauer, G.
Published in: JOURNAL OF MEDICAL SYSTEMS, 2022, ISSN 0148-5598
Publisher: Kluwer Academic/Plenum Publishers
DOI: 10.1007/s10916-022-01807-1

Models Matter: the impact of single-step retrosynthesis on synthesis planning

Author(s): Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arné Clevert, Mike Preuss, Igor V. Tetko
Published in: Digital Discovery, Issue 3, 2024, Page(s) 558-572, ISSN 2635-098X
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00252g

Decoding phenotypic screening: A comparative analysis of image representations

Author(s): Adriana Borowa, Dawid Rymarczyk, Marek Żyła, Maciej Kańduła, Ana Sánchez-Fernández, Krzysztof Rataj, Łukasz Struski, Jacek Tabor, Bartosz Zieliński
Published in: Computational and Structural Biotechnology Journal, Issue 23, 2025, Page(s) 1181-1188, ISSN 2001-0370
Publisher: Elsevier BV
DOI: 10.1016/j.csbj.2024.02.022

A note on leveraging synergy in multiple meteorological data sets with deep learning for rainfall-runoff modeling

Author(s): Kratzert, F., Klotz, D., Hochreiter, S., Nearing, GS.
Published in: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2021, ISSN 1027-5606
Publisher: European Geophysical Society
DOI: 10.5194/hess-25-2685-2021

Accelerating the inference of string generation-based chemical reaction models for industrial applications

Author(s): Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-00974-w

When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges

Author(s): Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 42-56, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c01524

Metis: a python-based user interface to collect expert feedback for generative chemistry models

Author(s): Janosch Menke, Yasmine Nahal, Esben Jannik Bjerrum, Mikhail Kabeshov, Samuel Kaski, Ola Engkvist
Published in: Journal of Cheminformatics, Issue 16, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00892-3

Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning

Author(s): Tuan Le, Julian Cremer, Djork-Arné Clevert, Kristof T. Schütt
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-01028-x

Low Concentration Cell Painting Images Enable the Identification of Highly Potent Compounds

Author(s): Son V. Ha, Steffen Jaensch, Lorena G. A. Freitas, Dorota Herman, Paul Czodrowski, Hugo Ceulemans
Published in: Scientific Reports, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-4466969/v1

Temporal distribution shift in real-world pharmaceutical data: Implications for uncertainty quantification in QSAR models

Author(s): Hannah Rosa Friesacher, Emma Svensson, Susanne Winiwarter, Lewis Mervin, Adam Arany, Ola Engkvist
Published in: Artificial Intelligence in the Life Sciences, Issue 8, 2025, Page(s) 100132, ISSN 2667-3185
Publisher: Elsevier BV
DOI: 10.1016/j.ailsci.2025.100132

Rainfall-runoff prediction at multiple timescales with a single Long Short-Term Memory network

Author(s): Gauch, M., Kratzert, F., Klotz, D., Nearing, G., Lin, J., Hochreiter, S.
Published in: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2021, ISSN 1027-5606
Publisher: European Geophysical Society
DOI: 10.5194/hess-25-2045-2021

Reagent Prediction with a Molecular Transformer Improves Reaction Data Quality

Author(s): Andronov, M., Voinarovska, V., Andronova, N., Wand, M., Clevert, D.-A., Schmidhuber, J.
Published in: Chemical Science, 2023, ISSN 2573-2293
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2sc06798f

FSL-CP: a benchmark for small molecule activity few-shot prediction using cell microscopy images

Author(s): Son V. Ha, Lucas Leuschner, Paul Czodrowski
Published in: Digital Discovery, Issue 3, 2024, Page(s) 719-727, ISSN 2635-098X
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00205e

Enhancing uncertainty quantification in drug discovery with censored regression labels

Author(s): Emma Svensson, Hannah Rosa Friesacher, Susanne Winiwarter, Lewis Mervin, Adam Arany, Ola Engkvist
Published in: Artificial Intelligence in the Life Sciences, Issue 7, 2025, Page(s) 100128, ISSN 2667-3185
Publisher: Elsevier BV
DOI: 10.1016/j.ailsci.2025.100128

Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models

Author(s): Hannah Rosa Friesacher, Ola Engkvist, Lewis Mervin, Yves Moreau, Adam Arany
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-00964-y

E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays

Author(s): Vincenzo Palmacci, Yasmine Nahal, Matthias Welsch, Ola Engkvist, Samuel Kaski, Johannes Kirchmair
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-01014-3

AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application

Author(s): Lakshidaa Saigiridharan, Alan Kai Hassen, Helen Lai, Paula Torren-Peraire, Ola Engkvist, Samuel Genheden
Published in: Journal of Cheminformatics, Issue 16, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00860-x

Uncertainty estimation with deep learning for rainfall-runoff modeling

Author(s): Klotz, D., Kratzert, F., Gauch, M., Sampson, AK., Brandstetter, J., Klambauer, G., Hochreiter, S., Nearing, G.
Published in: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2022, ISSN 1027-5606
Publisher: European Geophysical Society
DOI: 10.5194/hess-26-1673-2022

Development of Novel Inhibitors Targeting the D-Box of the DNA Binding Domain of Androgen Receptor

Author(s): Mariia Radaeva, Fuqiang Ban, Fan Zhang, Eric LeBlanc, Nada Lallous, Paul S. Rennie, Martin E. Gleave, Artem Cherkasov
Published in: International Journal of Molecular Sciences, Issue 22, 2025, Page(s) 2493, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22052493

Human-in-the-loop active learning for goal-oriented molecule generation

Author(s): Yasmine Nahal, Janosch Menke, Julien Martinelli, Markus Heinonen, Mikhail Kabeshov, Jon Paul Janet, Eva Nittinger, Ola Engkvist, Samuel Kaski
Published in: Journal of Cheminformatics, Issue 16, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00924-y

Cross modality learning of cell painting and transcriptomics data improves mechanism of action clustering and bioactivity modelling

Author(s): Son V. Ha, Steffen Jaensch, Maciej M. Kańduła, Dorota Herman, Paul Czodrowski, Hugo Ceulemans
Published in: Scientific Reports, Issue 15, 2025, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-025-05914-0

PILOT: equivariant diffusion for pocket-conditioned <i>de novo</i> ligand generation with multi-objective guidance <i>via</i> importance sampling

Author(s): Julian Cremer, Tuan Le, Frank Noé, Djork-Arné Clevert, Kristof T. Schütt
Published in: Chemical Science, Issue 15, 2024, Page(s) 14954-14967, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d4sc03523b

Synergies between Quantum Mechanics and Machine Learning for Advancing Pharmaceutical Research

Author(s): Alessio Fallani
Published in: PhD dissertation, 2024
Publisher: University of Luxembourg Open Repository and Bibliography

Development of small molecule inhibitors of protein nucleic acid interactions with the use of computer-aided drug discovery tools

Author(s): Mariia Radaeva
Published in: Doctoral Thesis, 2024
Publisher: University of British Columbia Library
DOI: 10.14288/1.0445334

Current Limitations of Text-based Molecular Representations for Machine Learning in Small Molecule Drug Discovery

Author(s): Peter Bart Rudolf Hartog
Published in: Doctoral thesis, 2025
Publisher: TUM School of Life Sciences

Prediction of yields of chemical reactions

Author(s): Varvara Voinarovska
Published in: Doctoral thesis, 2024
Publisher: TUM School of Natural Sciences

Equivariant graph neural networks in drug discover: from property prediction to molecule generation

Author(s): Julian Cremer
Published in: PhD dissertation, 2024, Page(s) 147
Publisher: Universitat Pompeu Fabra

Computer-aided synthesis planning for real-world applications

Author(s): Paula Torren Peraire
Published in: Doctoral thesis, 2025
Publisher: TUM School of Natural Sciences

Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction

Author(s): Alan Kai Hassen, Paula Torren-Peraire, Samuel Genheden, Jonas Verhoeven, Mike Preuss, Igor V. Tetko
Published in: NeurIPS 2022 Workshop AI4Science, 2022
Publisher: OpenReview.net

Robust Task-Specific Adaption of Models for Drug-Target Interaction Prediction

Author(s): Svensson, E., Hoedt, P.-J., Hochreiter, S., Klambauer, G.
Published in: 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Publisher: NeurIPS 2022
DOI: 10.5281/zenodo.8138500

Atom-Level Optical Chemical Structure Recognition with Limited Supervision

Author(s): Martijn Oldenhof, Edward De Brouwer, Adam Arany, Yves Moreau
Published in: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024, Page(s) 17669-17678
Publisher: IEEE
DOI: 10.1109/cvpr52733.2024.01673

Multi-Modal Representation learning for molecules

Author(s): Muhammad Arslan Masood, Markus Heinonen, Samuel Kaski
Published in: ICLR 2025 Workshop LMRL, 2025
Publisher: OpenReview.net
DOI: 10.5281/zenodo.15484224

Leveraging expert feedback to align proxy and ground truth rewards in goal-oriented molecular generation

Author(s): Julien Martinelli, Yasmine Nahal, Duong Lê, Ola Engkvist, Samuel Kaski
Published in: NeurIPS 2023 AI for Drug Discovery and Development (AI4D3) workshop, 2023, Page(s) 1-16
Publisher: NeurIPS

Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

Author(s): Tuan Le, Julian Cremer, Frank Noé, Djork-Arné Clevert, Kristof Schütt
Published in: ICLR 2024, 2024
Publisher: arXiv
DOI: 10.48550/arxiv.2309.17296

Contrastive Learning of Image- and Structure-Based Representations in Drug Discovery

Author(s): Sanchez-Fernandez, A., Rumetshofer, E., Hochreiter, S., Klambauer, G.
Published in: International Conference on Learning Representations, 2022
Publisher: MLDD workshop, ICLR 2022
DOI: 10.5281/zenodo.8137823

MC-LSTM: Mass-Conserving LSTM

Author(s): Hoedt, PJ., Kratzert, F., Klotz, D., Halmich, C., Holzleitner, M., Nearing, G., Hochreiter, S., Klambauer, G.
Published in: INTERNATIONAL CONFERENCE ON MACHINE LEARNING, 2021, ISSN 2640-3498
Publisher: Cambridge MA: JMLR
DOI: 10.5281/zenodo.8138359

Expressive Graph Informer Networks

Author(s): Simm, J., Arany, A., De Brouwer, E., Moreau, Y.
Published in: MACHINE LEARNING, OPTIMIZATION, AND DATA SCIENCE (LOD 2021), PT II, Book Series Title: Lecture Notes in Computer Science, 2022, ISSN 0302-9743
Publisher: Springer Verlag
DOI: 10.1007/978-3-030-95470-3_15

Synthesis Planning in Reaction Space: A Study on Success, Robustness and Diversity

Author(s): Alan Kai Hassen, Helen Lai, Samuel Genheden, Mike Preuss, Djork-Arné Clevert
Published in: ChemRxiv Preprint, 2025
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2025-js7dt

A reagent-driven visual method for analyzing chemical reaction data

Author(s): Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Published in: arXiv preprint, 2024
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2024-q9tc4

Fast and scalable retrosynthetic planning with a transformer neural network and speculative beam search

Author(s): Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Published in: arXiv preprint, 2025
Publisher: arXiv
DOI: 10.48550/arxiv.2508.01459

Modeling Non-Covalent Interatomic Interactions on a Photonic Quantum Computer

Author(s): Sarkis, M., Fallani, A.,Tkatchenko, A.
Published in: 2023
Publisher: arXiv
DOI: 10.48550/arxiv.2306.08544

Which modern AI methods provide accurate predictions of toxicological endpoints? Analysis of Tox24 challenge results.

Author(s): Stephanie A. Eytcheson, Igor V. Tetko
Published in: 2025
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2025-7k7x3

NETWORK ANALYSIS OF THE ORGANIC CHEMISTRY IN PATENTS, LITERATURE, AND PHARMACEUTICAL INDUSTRY

Author(s): Thierry Kogej, Emma Svensson, Emma Rydholm, Tomas Bastys, Christos Kannas, Mikhail Kabeshov, Samuel Genheden, Ola Engkvist
Published in: Chemrxiv, Issue Chemrxiv, 2024
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2024-h4qlt

openOCHEM consensus model wins Kaggle First EUOS/SLAS Joint Compound Solubility Challenge

Author(s): Kopp, A., Hartog, P., Šícho, M., Godin, G., Tetko, I.V.
Published in: 2023
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2023-p8qcv

Equivariant Graph Neural Networks for Toxicity Prediction

Author(s): Cremer, J., Medrano Sandonas, L., Tkatchenko, A., Clevert, D.A., De Fabritiis, G.
Published in: 2023, ISSN 2573-2293
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2023-9kb55

Temporal Evaluation of Probability Calibration with Experimental Errors

Author(s): Hannah Rosa Friesacher, Emma Svensson, Adam Arany, Lewis Mervin, Ola Engkvist
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 13-20
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_2

Latent-Conditioned Equivariant Diffusion for Structure-Based De Novo Ligand Generation

Author(s): Julian Cremer, Tuan Le, Djork-Arné Clevert, Kristof T. Schütt
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 36-46
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_4

Atom-Level Quantum Pretraining Enhances the Spectral Perception of Molecular Graphs in Graphormer

Author(s): Alessio Fallani, José Arjona-Medina, Konstantin Chernichenko, Ramil Nugmanov, Jörg Kurt Wegner, Alexandre Tkatchenko
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 71-81
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_7

Towards Interpretable Models of Chemist Preferences for Human-in-the-Loop Assisted Drug Discovery

Author(s): Yasmine Nahal, Markus Heinonen, Mikhail Kabeshov, Jon Paul Janet, Eva Nittinger, Ola Engkvist, Samuel Kaski
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 58-70
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_6

Balancing Imbalanced Toxicity Models: Using MolBERT with Focal Loss

Author(s): Muhammad Arslan Masood, Samuel Kaski, Hugo Ceulemans, Dorota Herman, Markus Heinonen
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 82-97
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_8

Curating Reagents in Chemical Reaction Data with an Interactive Reagent Space Map

Author(s): Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 21-35
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_3

Temporal Evaluation of Uncertainty Quantification Under Distribution Shift

Author(s): Emma Svensson, Hannah Rosa Friesacher, Adam Arany, Lewis Mervin, Ola Engkvist
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 132-148
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_11

Leveraging Quantum Mechanical Properties to Predict Solvent Effects on Large Drug-Like Molecules

Author(s): Mathias Hilfiker, Leonardo Medrano Sandonas, Marco Klähn, Ola Engkvist, Alexandre Tkatchenko
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 47-57
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_5

Registries in Machine Learning-Based Drug Discovery: A Shortcut to Code Reuse

Author(s): Peter B. R. Hartog, Emma Svensson, Lewis Mervin, Samuel Genheden, Ola Engkvist, Igor V. Tetko
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 98-115
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_9

Deep Bayesian Experimental Design for Drug Discovery

Author(s): Muhammad Arslan Masood, Tianyu Cui, Samuel Kaski
Published in: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Page(s) 149-159
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72381-0_12

Introduction to the Special Issue: AI Meets Toxicology

Author(s): Günter Klambauer, Djork-Arné Clevert, Imran Shah, Emilio Benfenati, Igor V. Tetko
Published in: Chemical Research in Toxicology, Issue 36, 2023, Page(s) 1163-1167, ISSN 0893-228X
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00217

Tox24 Challenge

Author(s): Igor V. Tetko
Published in: Chemical Research in Toxicology, Issue 37, 2024, Page(s) 825-826, ISSN 0893-228X
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrestox.4c00192

Which Modern AI Methods Provide Accurate Predictions of Toxicological End Points? Analysis of Tox24 Challenge Results

Author(s): Stephanie A. Eytcheson, Igor V. Tetko
Published in: Chemical Research in Toxicology, 2025, ISSN 0893-228X
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrestox.5c00273

Advanced machine learning for innovative drug discovery

Author(s): Igor V. Tetko, Djork-Arné Clevert
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-01061-w

S-07-03 A snapshot of AI in predictive toxicology: explainable AI

Author(s): I.V. Tetko
Published in: Toxicology Letters, Issue 368, 2022, Page(s) S25-S26, ISSN 0378-4274
Publisher: Elsevier BV
DOI: 10.1016/j.toxlet.2022.07.085

S02-04 Computational Toxicology in Drug Safety

Author(s): I. Tetko
Published in: Toxicology Letters, Issue 399, 2024, Page(s) S14, ISSN 0378-4274
Publisher: Elsevier BV
DOI: 10.1016/j.toxlet.2024.07.047

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