Djork-Arné Clevert

54 papers A* 6Journal 39Unranked 8

Year	Rank	Type	Title / Venue / Authors
2025	—	`ed.`	AI in Drug Discovery - First International Workshop, AIDD 2024, Held in Conjunction with ICANN 2024, Lugano, Switzerland, September 19, 2024, Proceedings AIDD@ICANN Djork-Arné Clevert, Michael Wand, Kristína Malinovská, Jürgen Schmidhuber, Igor V. Tetko
2025	J	`jnl`	Accelerating the inference of string generation-based chemical reaction models for industrial applications. J. Cheminformatics Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
2025	J	`jnl`	Advanced machine learning for innovative drug discovery. J. Cheminformatics Igor V. Tetko, Djork-Arné Clevert
2025	J	`jnl`	Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstration. CoRR Alan Kai Hassen, Andrius Bernatavicius, Antonius P. A. Janssen, Mike Preuss, Gerard J. P. van Westen, Djork-Arné Clevert
2025	J	`jnl`	Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning. J. Cheminformatics Tuan Le, Julian Cremer, Djork-Arné Clevert, Kristof T. Schütt
2025	J	`jnl`	Exact Solutions to the Quantum Schrödinger Bridge Problem. CoRR Mykola Bordyuh, Djork-Arné Clevert, Marco Bertolini
2025	J	`jnl`	FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction. CoRR Julian Cremer, Tuan Le, Mohammad M. Ghahremanpour, Emilia Slugocka, Filipe Menezes, Djork-Arné Clevert
2025	J	`jnl`	FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation. CoRR Julian Cremer, Ross Irwin, Alessandro Tibo, Jon Paul Janet, Simon Olsson, Djork-Arné Clevert
2025	J	`jnl`	Fast and scalable retrosynthetic planning with a transformer neural network and speculative beam search. CoRR Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
2025	J	`jnl`	Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design. J. Cheminformatics Alan Kai Hassen, Martin Sícho, 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
2025	J	`jnl`	Generative Modeling on Lie Groups via Euclidean Generalized Score Matching. CoRR Marco Bertolini, Tuan Le, Djork-Arné Clevert
2025	A*	`conf`	KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA. ICLR Xiaorui Su, Yibo Wang, Shanghua Gao, Xiaolong Liu, Valentina Giunchiglia, Djork-Arné Clevert, Marinka Zitnik
2025	J	`jnl`	Practically Significant Method Comparison Protocols for Machine Learning in Small Molecule Drug Discovery. J. Chem. Inf. Model. Jeremy R. Ash, Cas Wognum, Raquel Rodríguez-Pérez, Matteo Aldeghi, Alan C. Cheng, Djork-Arné Clevert, Ola Engkvist, Cheng Fang, Daniel J. Price, Jacqueline M. Hughes-Oliver, W. Patrick Walters
2024	J	`jnl`	A call for an industry-led initiative to critically assess machine learning for real-world drug discovery. Nat. Mac. Intell. Cas Wognum, Jeremy R. Ash, Matteo Aldeghi, Raquel Rodríguez-Pérez, Cheng Fang, Alan C. Cheng, Daniel J. Price, Djork-Arné Clevert, Ola Engkvist, W. Patrick Walters
2024	J	`jnl`	A fast machine learning dataloader for epigenetic tracks from BigWig files. Bioinform. Joren Sebastian Retel, Andreas Poehlmann, Josh Chiou, Andreas Steffen, Djork-Arné Clevert
2024	J	`jnl`	Accelerating the inference of string generation-based chemical reaction models for industrial applications. CoRR Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
2024	—	`conf`	Curating Reagents in Chemical Reaction Data with an Interactive Reagent Space Map. AIDD@ICANN Mikhail Andronov, Natalia Andronova, Michael Wand, Jürgen Schmidhuber, Djork-Arné Clevert
2024	—	`conf`	Enhancing Interpretability in Molecular Property Prediction with Contextual Explanations of Molecular Graphical Depictions. AIDD@ICANN Marco Bertolini, Linlin Zhao, Floriane Montanari, Djork-Arné Clevert
2024	J	`jnl`	Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine. CoRR Xiaorui Su, Yibo Wang, Shanghua Gao, Xiaolong Liu, Valentina Giunchiglia, Djork-Arné Clevert, Marinka Zitnik
2024	—	`conf`	Latent-Conditioned Equivariant Diffusion for Structure-Based De Novo Ligand Generation. AIDD@ICANN Julian Cremer, Tuan Le, Djork-Arné Clevert, Kristof T. Schütt
2024	J	`jnl`	MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information. J. Chem. Inf. Model. Wouter Heyndrickx, Lewis H. Mervin, Tobias Morawietz, Noé Sturm, Lukas Friedrich, Adam Zalewski, Anastasia Pentina, Lina Humbeck, Martijn Oldenhof, Ritsuya Niwayama, Peter Schmidtke, Nikolas Fechner, Jaak Simm, Adam Arany, Nicolas Drizard, Rama Jabal, Arina Afanasyeva, Regis Loeb, Shlok Verma, Simon Harnqvist, Matthew Holmes, Balazs Pejo, Maria Telenczuk, Nicholas Holway, Arne Dieckmann, Nicola Rieke, Friederike Zumsande, Djork-Arné Clevert, Michael Krug, Christopher N. Luscombe, Darren V. S. Green, Peter Ertl, Peter Antal, David Marcus, Nicolas Do Huu, Hideyoshi Fuji, Stephen D. Pickett, Gergely Ács, Eric Boniface, Bernd Beck, Yax Sun, Arnaud Gohier, Friedrich Rippmann, Ola Engkvist, Andreas H. Göller, Yves Moreau, Mathieu N. Galtier, Ansgar Schuffenhauer, Hugo Ceulemans
2024	A*	`conf`	Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation. ICLR Tuan Le, Julian Cremer, Frank Noé, Djork-Arné Clevert, Kristof T. Schütt
2024	J	`jnl`	PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling. CoRR Julian Cremer, Tuan Le, Frank Noé, Djork-Arné Clevert, Kristof T. Schütt
2023	—	`conf`	Benchmarking deep learning models and classical de novo sequencing tools for immunopeptidomics. BCB Liang Xue, Mykola Bordyuh, Djork-Arné Clevert, Robert Stanton
2023	—	`conf`	Explaining, Evaluating and Enhancing Neural Networks' Learned Representations. ICANN (5) Marco Bertolini, Djork-Arné Clevert, Floriane Montanari
2023	J	`jnl`	From slides (through tiles) to pixels: an explainability framework for weakly supervised models in pre-clinical pathology. CoRR Marco Bertolini, Van-Khoa Le, Jake Pencharz, Andreas Poehlmann, Djork-Arné Clevert, Santiago Villalba, Floriane Montanari
2023	J	`jnl`	Models Matter: The Impact of Single-Step Retrosynthesis on Synthesis Planning. CoRR Paula Torren-Peraire, Alan Kai Hassen, Samuel Genheden, Jonas Verhoeven, Djork-Arné Clevert, Mike Preuss, Igor V. Tetko
2023	J	`jnl`	Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation. CoRR Tuan Le, Julian Cremer, Frank Noé, Djork-Arné Clevert, Kristof Schütt
2022	J	`jnl`	Equivariant Graph Attention Networks for Molecular Property Prediction. CoRR Tuan Le, Frank Noé, Djork-Arné Clevert
2022	J	`jnl`	Explaining, Evaluating and Enhancing Neural Networks' Learned Representations. CoRR Marco Bertolini, Djork-Arné Clevert, Floriane Montanari
2022	—	`conf`	Representation Learning on Biomolecular Structures Using Equivariant Graph Attention. LoG Tuan Le, Frank Noé, Djork-Arné Clevert
2022	A*	`conf`	Unsupervised Learning of Group Invariant and Equivariant Representations. NeurIPS Robin Winter, Marco Bertolini, Tuan Le, Frank Noé, Djork-Arné Clevert
2022	J	`jnl`	Unsupervised Learning of Group Invariant and Equivariant Representations. CoRR Robin Winter, Marco Bertolini, Tuan Le, Frank Noé, Djork-Arné Clevert
2021	J	`jnl`	Auto-Encoding Molecular Conformations. CoRR Robin Winter, Frank Noé, Djork-Arné Clevert
2021	A*	`conf`	Improving Molecular Graph Neural Network Explainability with Orthonormalization and Induced Sparsity. ICML Ryan Henderson, Djork-Arné Clevert, Floriane Montanari
2021	J	`jnl`	Improving Molecular Graph Neural Network Explainability with Orthonormalization and Induced Sparsity. CoRR Ryan Henderson, Djork-Arné Clevert, Floriane Montanari
2021	—	`conf`	Parameterized Hypercomplex Graph Neural Networks for Graph Classification. ICANN (3) Tuan Le, Marco Bertolini, Frank Noé, Djork-Arné Clevert
2021	J	`jnl`	Parameterized Hypercomplex Graph Neural Networks for Graph Classification. CoRR Tuan Le, Marco Bertolini, Frank Noé, Djork-Arné Clevert
2021	A*	`conf`	Permutation-Invariant Variational Autoencoder for Graph-Level Representation Learning. NeurIPS Robin Winter, Frank Noé, Djork-Arné Clevert
2021	J	`jnl`	Permutation-Invariant Variational Autoencoder for Graph-Level Representation Learning. CoRR Robin Winter, Frank Noé, Djork-Arné Clevert
2021	J	`jnl`	Self-supervised feature extraction from image time series in plant phenotyping using triplet networks. Bioinform. Paula A. Marin Zapata, Sina Roth, Dirk Schmutzler, Thomas Wolf, Erica Manesso, Djork-Arné Clevert
2021	J	`jnl`	pKPDB: a protein data bank extension database of pKa and pI theoretical values. Bioinform. Pedro B. P. S. Reis, Djork-Arné Clevert, Miguel Machuqueiro
2020	J	`jnl`	Gini in a Bottleneck: Gotta Train Me the Right Way. CoRR Ryan Henderson, Djork-Arné Clevert, Floriane Montanari
2020	J	`jnl`	grünifai: interactive multiparameter optimization of molecules in a continuous vector space. Bioinform. Robin Winter, Joren Sebastian Retel, Frank Noé, Djork-Arné Clevert, Andreas Steffen
2019	J	`jnl`	Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks. J. Chem. Inf. Model. Markus Hofmarcher, Elisabeth Rumetshofer, Djork-Arné Clevert, Sepp Hochreiter, Günter Klambauer
2019	J	`jnl`	PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. Bioinform. Moritz Schaefer, Djork-Arné Clevert, Bertram Weiss, Andreas Steffen
2017	J	`jnl`	IVE-GAN: Invariant Encoding Generative Adversarial Networks. CoRR Robin Winter, Djork-Arné Clevert
2017	J	`jnl`	Rectified factor networks for biclustering of omics data. Bioinform. Djork-Arné Clevert, Thomas Unterthiner, Gundula Povysil, Sepp Hochreiter
2016	A*	`conf`	Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs). ICLR (Poster) Djork-Arné Clevert, Thomas Unterthiner, Sepp Hochreiter
2015	—	`conf`	Rectified Factor Networks. NIPS Djork-Arné Clevert, Andreas Mayr, Thomas Unterthiner, Sepp Hochreiter
2015	J	`jnl`	Rectified Factor Networks. CoRR Djork-Arné Clevert, Thomas Unterthiner, Andreas Mayr, Hubert Ramsauer, Sepp Hochreiter
2010	J	`jnl`	FABIA: factor analysis for bicluster acquisition. Bioinform. Sepp Hochreiter, Ulrich Bodenhofer, Martin Heusel, Andreas Mayr, Andreas Mitterecker, Adetayo Kasim, Tatsiana Khamiakova, Suzy Van Sanden, Dan Lin, Willem Talloen, Luc Bijnens, Hinrich W. H. Göhlmann, Ziv Shkedy, Djork-Arné Clevert
2007	J	`jnl`	I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. Bioinform. Willem Talloen, Djork-Arné Clevert, Sepp Hochreiter, Dhammika Amaratunga, Luc Bijnens, Stefan Kass, Hinrich W. H. Göhlmann
2006	J	`jnl`	A new summarization method for affymetrix probe level data. Bioinform. Sepp Hochreiter, Djork-Arné Clevert, Klaus Obermayer