Advanced machine learning for Innovative Drug Discovery

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Software for retrosynthesis

Publicly available source code for chemical retrosynthesis

First newsletter

Publication of the first newsletter

ML toolbox for QM property prediction

Open source Machine Learning (ML) toolbox for Quantum Mechanics (QM) property prediction

One Chemistry model

"Source code of the ""One Chemistry"" that combines individual developments of others ESRs"

Modular AI systems

Methodology and source code for robust training of modular AI systems

Software for phenotypic screening

Open source software for phenotypic screening predictions with confidence estimation

Use of human knowledge for models development

Methodology to improve machine learning models in drug discovery with human knowledge

SS2 school report
Recruitment meeting

Minutes of the recruitment meeting

Minutes of the kick-off meeting
SS3 school report
Communication and public engagement activities

Overview of communication and public engagement activities

Final conference

Final conference report

SS1 school report

Web site

The web site and web application system is established

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Publicaciones

Equivariant Graph Neural Networks for Toxicity Prediction

Autores: Julian Cremer, Leonardo Medrano Sandonas, Alexandre Tkatchenko, Djork-Arné Clevert, Gianni De Fabritiis
Publicado en: Chemical Research in Toxicology, 2023, ISSN 0893-228X
Editor: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00032

Developing novel Lin28 inhibitors by computer aided drug design

Autores: 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
Publicado en: Cell Death Discovery, 2025, ISSN 2058-7716
Editor: 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

Autores: Andrea Hunklinger, Peter Hartog, Martin Šícho, Guillaume Godin, Igor V. Tetko
Publicado en: SLAS Discovery, Edición 29, 2024, Página(s) 100144, ISSN 2472-5552
Editor: Elsevier BV
DOI: 10.1016/j.slasd.2024.01.005

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

Autores: Emma Svensson, Pieter-Jan Hoedt, Sepp Hochreiter, Günter Klambauer
Publicado en: Journal of Chemical Information and Modeling, Edición 64, 2024, Página(s) 2539-2553, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/acs.jcim.3c01417

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

Autores: Peter B. R. Hartog, Fabian Krüger, Samuel Genheden, Igor V. Tetko
Publicado en: Journal of Cheminformatics, 2024, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.26434/chemrxiv-2024-kdx3g

Modeling noncovalent interatomic interactions on a photonic quantum computer

Autores: Matthieu Sarkis, Alessio Fallani, Alexandre Tkatchenko
Publicado en: Physical Review Research, Edición 5, 2023, ISSN 2643-1564
Editor: American Physical Society (APS)
DOI: 10.1103/physrevresearch.5.043072

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

Autores: Alessio Fallani, Ramil Nugmanov, Jose Arjona-Medina, Jörg Kurt Wegner, Alexandre Tkatchenko, Kostiantyn Chernichenko
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-00970-0

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

Autores: Andrius Bernatavicius, Martin Šícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuss, Gerard J. P. van Westen
Publicado en: Journal of Chemical Information and Modeling, Edición 64, 2024, Página(s) 8113-8122, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/acs.jcim.4c00309

Investigations into the efficiency of computer-aided synthesis planning

Autores: Peter B.R. Hartog, Annie M. Westerlund, Igor V. Tetko, Samuel Genheden
Publicado en: Journal of Chemical Information and Modeling, 2024, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.26434/chemrxiv-2024-q2v87

Unsupervised Representation Learning for Proteochemometric Modeling

Autores: Kim, PT., Winter, R., Clevert, DA.
Publicado en: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)

Improving route development using convergent retrosynthesis planning

Autores: Paula Torren-Peraire, Jonas Verhoeven, Dorota Herman, Hugo Ceulemans, Igor V. Tetko, Jörg K. Wegner
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: 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

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

Img2Mol – accurate SMILES recognition from molecular graphical depictions

Autores: Clevert, DA., Le, T., Winter, R., Montanari, F.
Publicado en: CHEMICAL SCIENCE, 2021, ISSN 2041-6520
Editor: 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

Autores: 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
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-024-00910-4

Be aware of overfitting by hyperparameter optimization!

Autores: Igor V. Tetko, Ruud van Deursen, Guillaume Godin
Publicado en: Journal of Cheminformatics, Edición 16, 2024, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-024-00934-w

The Promise of AI for DILI Prediction

Autores: Vall, A., Sabnis, Y., Shi, J., Class, R., Hochreiter, S., Klambauer, G.
Publicado en: Front. Artif. Intell., 2021, ISSN 0922-6389
Editor: IOS Press
DOI: 10.3389/frai.2021.638410

Expanding the chemical space using a chemical reaction knowledge graph

Autores: Emma Rydholm, Tomas Bastys, Emma Svensson, Christos Kannas, Ola Engkvist, Thierry Kogej
Publicado en: Digital Discovery, Edición 3, 2024, Página(s) 1378-1388, ISSN 2635-098X
Editor: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00230f

Tackling assay interference associated with small molecules

Autores: Lu Tan, Steffen Hirte, Vincenzo Palmacci, Conrad Stork, Johannes Kirchmair
Publicado en: Nature Reviews Chemistry, Edición 8, 2024, Página(s) 319-339, ISSN 2397-3358
Editor: 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

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

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

Autores: Ana Sanchez-Fernandez, Elisabeth Rumetshofer, Sepp Hochreiter, Günter Klambauer
Publicado en: Nature Communications, Edición 14, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-42328-w

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

Autores: Vincenzo Palmacci, Steffen Hirte, Jorge Enrique Hernández González, Floriane Montanari, Johannes Kirchmair
Publicado en: Artificial Intelligence in the Life Sciences, Edición 5, 2024, Página(s) 100099, ISSN 2667-3185
Editor: Elsevier BV
DOI: 10.1016/j.ailsci.2024.100099

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

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

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

Autores: Emma Svensson, Emma Granqvist, Tomas Bastys, Christos Kannas, Mikhail Kabeshov, Samuel Genheden, Ola Engkvist, Thierry Kogej
Publicado en: Molecular Informatics, Edición 44, 2025, ISSN 1868-1743
Editor: 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

Autores: Muhammad Arslan Masood, Samuel Kaski, Tianyu Cui
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-00986-6

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

Autores: 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
Publicado en: Scientific Data, Edición 11, 2024, ISSN 2052-4463
Editor: 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

Autores: Alessio Fallani, Leonardo Medrano Sandonas, Alexandre Tkatchenko
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-024-50401-1

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

Autores: Roland, T., Bock, C., Tschoellitsch, T., Maletzky, A., Hochreiter, S., Meier, J., Klambauer, G.
Publicado en: JOURNAL OF MEDICAL SYSTEMS, 2022, ISSN 0148-5598
Editor: Kluwer Academic/Plenum Publishers
DOI: 10.1007/s10916-022-01807-1

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

Autores: Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arné Clevert, Mike Preuss, Igor V. Tetko
Publicado en: Digital Discovery, Edición 3, 2024, Página(s) 558-572, ISSN 2635-098X
Editor: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00252g

Decoding phenotypic screening: A comparative analysis of image representations

Autores: Adriana Borowa, Dawid Rymarczyk, Marek Żyła, Maciej Kańduła, Ana Sánchez-Fernández, Krzysztof Rataj, Łukasz Struski, Jacek Tabor, Bartosz Zieliński
Publicado en: Computational and Structural Biotechnology Journal, Edición 23, 2025, Página(s) 1181-1188, ISSN 2001-0370
Editor: 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

Autores: Kratzert, F., Klotz, D., Hochreiter, S., Nearing, GS.
Publicado en: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2021, ISSN 1027-5606
Editor: European Geophysical Society
DOI: 10.5194/hess-25-2685-2021

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

Autores: Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-00974-w

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

Autores: Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko
Publicado en: Journal of Chemical Information and Modeling, Edición 64, 2024, Página(s) 42-56, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/acs.jcim.3c01524

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

Autores: Janosch Menke, Yasmine Nahal, Esben Jannik Bjerrum, Mikhail Kabeshov, Samuel Kaski, Ola Engkvist
Publicado en: Journal of Cheminformatics, Edición 16, 2024, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-024-00892-3

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

Autores: Tuan Le, Julian Cremer, Djork-Arné Clevert, Kristof T. Schütt
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-01028-x

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

Autores: Son V. Ha, Steffen Jaensch, Lorena G. A. Freitas, Dorota Herman, Paul Czodrowski, Hugo Ceulemans
Publicado en: Scientific Reports, 2024, ISSN 2045-2322
Editor: 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

Autores: Hannah Rosa Friesacher, Emma Svensson, Susanne Winiwarter, Lewis Mervin, Adam Arany, Ola Engkvist
Publicado en: Artificial Intelligence in the Life Sciences, Edición 8, 2025, Página(s) 100132, ISSN 2667-3185
Editor: Elsevier BV
DOI: 10.1016/j.ailsci.2025.100132

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

Autores: Gauch, M., Kratzert, F., Klotz, D., Nearing, G., Lin, J., Hochreiter, S.
Publicado en: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2021, ISSN 1027-5606
Editor: European Geophysical Society
DOI: 10.5194/hess-25-2045-2021

Reagent Prediction with a Molecular Transformer Improves Reaction Data Quality

Autores: Andronov, M., Voinarovska, V., Andronova, N., Wand, M., Clevert, D.-A., Schmidhuber, J.
Publicado en: Chemical Science, 2023, ISSN 2573-2293
Editor: Royal Society of Chemistry
DOI: 10.1039/d2sc06798f

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

Autores: Son V. Ha, Lucas Leuschner, Paul Czodrowski
Publicado en: Digital Discovery, Edición 3, 2024, Página(s) 719-727, ISSN 2635-098X
Editor: Royal Society of Chemistry (RSC)
DOI: 10.1039/d3dd00205e

Enhancing uncertainty quantification in drug discovery with censored regression labels

Autores: Emma Svensson, Hannah Rosa Friesacher, Susanne Winiwarter, Lewis Mervin, Adam Arany, Ola Engkvist
Publicado en: Artificial Intelligence in the Life Sciences, Edición 7, 2025, Página(s) 100128, ISSN 2667-3185
Editor: 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

Autores: Hannah Rosa Friesacher, Ola Engkvist, Lewis Mervin, Yves Moreau, Adam Arany
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-00964-y

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

Autores: Vincenzo Palmacci, Yasmine Nahal, Matthias Welsch, Ola Engkvist, Samuel Kaski, Johannes Kirchmair
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-01014-3

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

Autores: Lakshidaa Saigiridharan, Alan Kai Hassen, Helen Lai, Paula Torren-Peraire, Ola Engkvist, Samuel Genheden
Publicado en: Journal of Cheminformatics, Edición 16, 2024, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-024-00860-x

Uncertainty estimation with deep learning for rainfall-runoff modeling

Autores: Klotz, D., Kratzert, F., Gauch, M., Sampson, AK., Brandstetter, J., Klambauer, G., Hochreiter, S., Nearing, G.
Publicado en: HYDROLOGY AND EARTH SYSTEM SCIENCES, 2022, ISSN 1027-5606
Editor: 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

Autores: Mariia Radaeva, Fuqiang Ban, Fan Zhang, Eric LeBlanc, Nada Lallous, Paul S. Rennie, Martin E. Gleave, Artem Cherkasov
Publicado en: International Journal of Molecular Sciences, Edición 22, 2025, Página(s) 2493, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22052493

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

Autores: Yasmine Nahal, Janosch Menke, Julien Martinelli, Markus Heinonen, Mikhail Kabeshov, Jon Paul Janet, Eva Nittinger, Ola Engkvist, Samuel Kaski
Publicado en: Journal of Cheminformatics, Edición 16, 2024, ISSN 1758-2946
Editor: 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

Autores: Son V. Ha, Steffen Jaensch, Maciej M. Kańduła, Dorota Herman, Paul Czodrowski, Hugo Ceulemans
Publicado en: Scientific Reports, Edición 15, 2025, ISSN 2045-2322
Editor: 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

Autores: Julian Cremer, Tuan Le, Frank Noé, Djork-Arné Clevert, Kristof T. Schütt
Publicado en: Chemical Science, Edición 15, 2024, Página(s) 14954-14967, ISSN 2041-6520
Editor: Royal Society of Chemistry
DOI: 10.1039/d4sc03523b

Synergies between Quantum Mechanics and Machine Learning for Advancing Pharmaceutical Research

Autores: Alessio Fallani
Publicado en: PhD dissertation, 2024
Editor: 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

Autores: Mariia Radaeva
Publicado en: Doctoral Thesis, 2024
Editor: 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

Autores: Peter Bart Rudolf Hartog
Publicado en: Doctoral thesis, 2025
Editor: TUM School of Life Sciences

Prediction of yields of chemical reactions

Autores: Varvara Voinarovska
Publicado en: Doctoral thesis, 2024
Editor: TUM School of Natural Sciences

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

Autores: Julian Cremer
Publicado en: PhD dissertation, 2024, Página(s) 147
Editor: Universitat Pompeu Fabra

Computer-aided synthesis planning for real-world applications

Autores: Paula Torren Peraire
Publicado en: Doctoral thesis, 2025
Editor: TUM School of Natural Sciences

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

Autores: Alan Kai Hassen, Paula Torren-Peraire, Samuel Genheden, Jonas Verhoeven, Mike Preuss, Igor V. Tetko
Publicado en: NeurIPS 2022 Workshop AI4Science, 2022
Editor: OpenReview.net

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

Autores: Svensson, E., Hoedt, P.-J., Hochreiter, S., Klambauer, G.
Publicado en: 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Editor: NeurIPS 2022
DOI: 10.5281/zenodo.8138500

Atom-Level Optical Chemical Structure Recognition with Limited Supervision

Autores: Martijn Oldenhof, Edward De Brouwer, Adam Arany, Yves Moreau
Publicado en: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024, Página(s) 17669-17678
Editor: IEEE
DOI: 10.1109/cvpr52733.2024.01673

Multi-Modal Representation learning for molecules

Autores: Muhammad Arslan Masood, Markus Heinonen, Samuel Kaski
Publicado en: ICLR 2025 Workshop LMRL, 2025
Editor: OpenReview.net
DOI: 10.5281/zenodo.15484224

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

Autores: Julien Martinelli, Yasmine Nahal, Duong Lê, Ola Engkvist, Samuel Kaski
Publicado en: NeurIPS 2023 AI for Drug Discovery and Development (AI4D3) workshop, 2023, Página(s) 1-16
Editor: NeurIPS

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

Autores: Tuan Le, Julian Cremer, Frank Noé, Djork-Arné Clevert, Kristof Schütt
Publicado en: ICLR 2024, 2024
Editor: arXiv
DOI: 10.48550/arxiv.2309.17296

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

Autores: Sanchez-Fernandez, A., Rumetshofer, E., Hochreiter, S., Klambauer, G.
Publicado en: International Conference on Learning Representations, 2022
Editor: MLDD workshop, ICLR 2022
DOI: 10.5281/zenodo.8137823

MC-LSTM: Mass-Conserving LSTM

Autores: Hoedt, PJ., Kratzert, F., Klotz, D., Halmich, C., Holzleitner, M., Nearing, G., Hochreiter, S., Klambauer, G.
Publicado en: INTERNATIONAL CONFERENCE ON MACHINE LEARNING, 2021, ISSN 2640-3498
Editor: Cambridge MA: JMLR
DOI: 10.5281/zenodo.8138359

Expressive Graph Informer Networks

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

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

Autores: Alan Kai Hassen, Helen Lai, Samuel Genheden, Mike Preuss, Djork-Arné Clevert
Publicado en: ChemRxiv Preprint, 2025
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2025-js7dt

A reagent-driven visual method for analyzing chemical reaction data

Autores: Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Publicado en: arXiv preprint, 2024
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2024-q9tc4

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

Autores: Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
Publicado en: arXiv preprint, 2025
Editor: arXiv
DOI: 10.48550/arxiv.2508.01459

Modeling Non-Covalent Interatomic Interactions on a Photonic Quantum Computer

Autores: Sarkis, M., Fallani, A.,Tkatchenko, A.
Publicado en: 2023
Editor: arXiv
DOI: 10.48550/arxiv.2306.08544

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

Autores: Stephanie A. Eytcheson, Igor V. Tetko
Publicado en: 2025
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2025-7k7x3

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

Autores: Thierry Kogej, Emma Svensson, Emma Rydholm, Tomas Bastys, Christos Kannas, Mikhail Kabeshov, Samuel Genheden, Ola Engkvist
Publicado en: Chemrxiv, Edición Chemrxiv, 2024
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2024-h4qlt

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

Autores: Kopp, A., Hartog, P., Šícho, M., Godin, G., Tetko, I.V.
Publicado en: 2023
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2023-p8qcv

Equivariant Graph Neural Networks for Toxicity Prediction

Autores: Cremer, J., Medrano Sandonas, L., Tkatchenko, A., Clevert, D.A., De Fabritiis, G.
Publicado en: 2023, ISSN 2573-2293
Editor: ChemRxiv
DOI: 10.26434/chemrxiv-2023-9kb55

Temporal Evaluation of Probability Calibration with Experimental Errors

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

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

Autores: Julian Cremer, Tuan Le, Djork-Arné Clevert, Kristof T. Schütt
Publicado en: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Página(s) 36-46
Editor: 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

Autores: Alessio Fallani, José Arjona-Medina, Konstantin Chernichenko, Ramil Nugmanov, Jörg Kurt Wegner, Alexandre Tkatchenko
Publicado en: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Página(s) 71-81
Editor: 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

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

Balancing Imbalanced Toxicity Models: Using MolBERT with Focal Loss

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

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

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

Temporal Evaluation of Uncertainty Quantification Under Distribution Shift

Autores: Emma Svensson, Hannah Rosa Friesacher, Adam Arany, Lewis Mervin, Ola Engkvist
Publicado en: Lecture Notes in Computer Science, AI in Drug Discovery, 2024, Página(s) 132-148
Editor: 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

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

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

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

Deep Bayesian Experimental Design for Drug Discovery

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

Introduction to the Special Issue: AI Meets Toxicology

Autores: Günter Klambauer, Djork-Arné Clevert, Imran Shah, Emilio Benfenati, Igor V. Tetko
Publicado en: Chemical Research in Toxicology, Edición 36, 2023, Página(s) 1163-1167, ISSN 0893-228X
Editor: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00217

Tox24 Challenge

Autores: Igor V. Tetko
Publicado en: Chemical Research in Toxicology, Edición 37, 2024, Página(s) 825-826, ISSN 0893-228X
Editor: 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

Autores: Stephanie A. Eytcheson, Igor V. Tetko
Publicado en: Chemical Research in Toxicology, 2025, ISSN 0893-228X
Editor: American Chemical Society
DOI: 10.1021/acs.chemrestox.5c00273

Advanced machine learning for innovative drug discovery

Autores: Igor V. Tetko, Djork-Arné Clevert
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-01061-w

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

Autores: I.V. Tetko
Publicado en: Toxicology Letters, Edición 368, 2022, Página(s) S25-S26, ISSN 0378-4274
Editor: Elsevier BV
DOI: 10.1016/j.toxlet.2022.07.085

S02-04 Computational Toxicology in Drug Safety

Autores: I. Tetko
Publicado en: Toxicology Letters, Edición 399, 2024, Página(s) S14, ISSN 0378-4274
Editor: Elsevier BV
DOI: 10.1016/j.toxlet.2024.07.047

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