On-line Lectures / paper club
Alan Kai Hassen gave a talk based on the article "Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design" (23.10.2024).
Igor Tetko gave a lecture "Advanced Machine Learning in Drug Discovery" at KU Leuven. (03.09.2024)
Dr. Iris Köhler and Dr. Sarah de Carvalho Hartmann of The Scientist Coach delivered workshops on "Competency Profiles" and "Job Applications" for the ESRs (18.06.24 and 24.06.24).
Vincenzo Palmacci gave a talk titled "Statistical approach enabling technology-specific assay interference prediction from large screening data sets". (30.04.2024)
Mikhail Andronov gave a talk based on his recently uploaded pre-print, titled "A reagent-driven visual method for analyzing chemical reaction data" (21.02.24)
Julian Cremer gave an online lecture titled "Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation" (12.12.23)
Arslan Masood gave an online lecture titled "Dissecting Drug-Induced-Liver-Injury" (28.11.23)
Rosa Friesacher gave an online lecture, titled "Understanding Model Uncertainty and Enhancing Probability Calibration in Neural Networks" (25.10.23)
Varvara Voinarovska gave an online lecture titled “When yield prediction does not yield prediction: an overview of the current challenges” (19.09.23)
Mariia Radaeva gave lecture "Targeting Androgen Receptor with CADD" (19.07.23)
On-line presentation "Science is fun but not only: career perspectives for young talented researchers in a modern society" with focus on opportunities in European Union and Germany by Igor Tetko (11.07.23)
"Success stories of structure-based drug discovery" by Ana Messias (22.06.23)
"FSL-CP: Few-shot Prediction of small molecule activity using cell microscopy images" by Son Ha (17.05 .23)
"Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction" by Paula Torren (5.04.23)
"Extending 3D generative modeling of molecules with quantum-mechanical properties" by Alessio Fallani (8.03.23)
"Reagent prediction with a transformer and its benefits for reaction product prediction" by Mikhail Andronov (1.02.23)
"Equivariant Graph Neural Networks for Toxicity Prediction" by Julian Cremer (1.02.23)
A tour through molecular representations in AI-driven drug discovery by Laurianne David (13.07.22)
AIDD Codebase: a Framework for Model Integration, Collaboration and Sharing by Emma Svensson and Peter Hartog (22.06.22)
Contrastive Learning of Image and Structure-Based Representations in Drug Discovery by Ana Sanchez-Fernandez (08.06.22)
Development of a CCR5 antagonist for HIV therapy by Tiago Rodrigues (27.04.22)
Hands-on: Data preparation and interactive visualization of chemical structures in KNIME Analytics Platform by Daria Goldmann (21.04.2022), meeting recording password: fv+.$@3M
A Survey on Human-in-the-loop Machine Learning by Yasmine Hahal (16.03)
3D structure refinement by Filipe Miguel Cardoso Micu Menezes (23.02.2022) see also additional files (174MB)
Coarse graining molecular dynamics with graph neural networks (paper club) by Andrey Mossyayev (27.01.2022)
AiZynthFinder: how it works and why by Samuel Genheden (20.12.2021) - meeting recording 
Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction by Mikhail Andronov (8.12.2021)
Final School (Berlin, March 4 - 12, 2024)
Monday 4th March 10:45 - 11:45, PI Intros (Tetko slides, Haese slides, Clevert).
Monday 4th March 12:00 - 13:00, PI Intros (Kabeshov slides, Varnek slides, Roncaglioni slides)
Monday 4th March 15:00 - 16:00, Lecture by John O'Donnell (Bayer) Integrated Structural Biology: everything but the kitchen sink
Monday 4th March 16:00 - 17:00, Lecture by Thomas Löhr (AstraZeneca) Navigating the Maize: Computational chemistry workflows with cycles and conditions
Tuesday 5th March 10:45 - 11:30, Lecture by Anna Montebaur (Bayer) Introduction to CRISPR.
Tuesday 5th March 11:30 - 12:15, Lecture by Verena Ziegler and Sandra Berndt (Bayer) Introduction to Tox.
Tuesday 5th March 13:30 - 14:15, Lecture by Felix Oden (Bayer) Intro to targeted radiotherapies.
Tuesday 5th March 14:15 - 15:00, Lecture by Hans Briem (Bayer) Introduction to Computer-Aided Drug Design.
Wednesday 6th March 09:30 - 11:45 (short break between 10:30 and 10:45), Workshop by Gilles Marcou (UNISTRA) Intro to KNIME and Standardization of Molecules in KNIME. Materials and instructions https://filesender.renater.fr/?s=download&token=68637050-0446-4319-aef5-732b7f53a8f8 For Window and Linux use the latest version of KNIME (5.2). For Mac users, use the version 4.5 from the official KNIME web site
Wednesday 6th March 12:00 - 15:00 (break between 13:00 and 14:00), Workshop by Alex Tropsha (UNC Eshelman School of Pharmacy) Rigor and reproducibility of Chemoinformatics models: from data curation to experimental validation
Wednesday 6th March 15:30 - 17:00 Practical Session by David Winkler (La Trobe University), Choosing an algorithm, descriptors and approach for diverse applications of AI and ML
Thursday 7th March 09:30 - 10:30, Lecture by Alessandra Roncaglioni (IRFMN), Machine Learning Models to Address Cardiotoxicity within an AOP Framework
Thursday 7th March 10:45 - 11:45, Lecture by Alexandre Tkatchenko (ULUX), Navigating Chemical Compound Space Directly and Inversely
Thursday 7th March 12:00 - 13:00, Lecture by Aixia Yan (Beijing University of Chemical Technology), Application of Machine Learning Methods for Prediction of Compound Activities and SAR Analysis
Thursday 7th March 14:00 - 15:00, Lecture by Robin Winter (Pfizer), Multi-Objective Optimization in Continuous Latent Spaces
Monday 11th March 09:30 - 13:00 (two breaks 10:30 - 10:45 and 11:30 - 11:45), GPU Programming Workshop by NVIDIA
Monday 11th March 14:00 - 18:00 (with break from 15:00 until 15:30), Project Management Workshop by Alexander Egeling
Tuesday 12th March 09:30 - 10:30, Lecture by Geemi Wellawatte (EPFL), XAI for Chemistry
Tuesday 12th March 11:10 - 12:10, Lecture by Mike Preuss (ULEI) Monte Carlo tree search and multi-objective variants
Tuesday 12th March 14:00 - 17:00, AIDD Presentations, Peter Hartog slides, Son Ha slides, Ana Sanchez Fernandez slides, Yasmine Nahal slides, Vincenzo Palmacci slides
See also AiChemist School lectures (13-15 March)
Fifth School (Gothenburg, July 3-7, 2023)
AI from a MedChem perspective, Werngard Czechtizky
Predicting reaction selectivity, Per-Ola Norrby
Overcoming safety liabilities with machine learning - An industry perspective, Vignesh Subramanian
Journey of Developing AI solutions for Digital Pathology Data, Feng Gu
The promise of graphs & graph-based learning in drug discovery, Ufuk Kirik
Data-driven enhanced sampling of conformational changes in membrane proteins, Lucie Delemotte
Knowledge graphs, Michaël Ughetto
The new journey on AI modelling after REINVENT, Hongming Chen
REINVENT+CAZP workshop (interactive)
Introduction to iLab, Tove Slagbrand
LLM, Chemistry, and the Future of AI, Mike Preuss
Introduction AI Sweden, Emma Ytterström
Privacy preserving ML at AI Sweden, Johan Östman
Fourth School (Aalto, March 20-23)
Collaborative modelling, design and decision making with AI, Samuel Kaski
Predicting drug combination responses in cancer, Juho Rousu
Deep latent variable models for longitudinal biomedical data, Harri Lähdesmäki
AI assistance for drug design tutorial, Elena Shaw, Sebastiaan de Peuter, Alex Hämäläinen
Efficient uncertainty estimation with node-based BNNs, Trung Trinh
Neural network potentials and beyond, Kristof Schutt
Qptuna: easy, automated QSAR model building, Lewis Mervin
Priors in Bayesian Deep Learning, Tianyu Cui
Treatment effect estimation with neural network-based models, Manuel Hausmann
Hybrid physics and AI methods for pKa predictions in proteins, Pedro Reis
Hamiltonian Monte Carlo, Aki Vehtari
Overview of the EUOS/SLAS Compound Solubility Kaggle Challenge, Wenyu Wang
OCHEM EUOS/SLAS Solubility Challenge solubility models, Igor Tetko
The Kaggle EUOS/SLAS Solubility Challenge: Visualizing and Understanding The Data Helps in Modelling, Bernhard Rohde
Third School (Leuven, October 17-26, 2022)
Use of Sampling Methods in Bayesian Inference, Christel Faes
Variational inference: from basics to modern applications, Ádám Arany
Time-to-event modelling: approaches and pitfalls, Jaak Simm
Causality-inspired ML: what can causality do for ML? The domain adaptation case, Sara Maglicane
Artificial intelligence and big data in synthetic chemistry, Timur Madzhidov (Reaxys)
Neural networks and kernel machines: the best of both worlds, Johan Suykens
Melloddy, Wouter Heyndrickx
High Content Imaging in drug discovery, Seong Joo Koo
JUMP-Cell Painting: A new public dataset to advance image-based drug discovery, Steffen Jaensch
Bidirectional Graphormer for Reactivity Understanding Neural Network Trained to Reaction Atom-to-Atom Mapping Task, Ramil Nugmanov
Multivalent interactions, Bence Bruncsics
Bayesian Deep Learning, Günter Klambauer
Molecule property prediction, federated learning and uncertainty quantification, Lewis Mervin
Materials Informatics: The Marriage of Materials and Data Sciences, Hanoch Senderowitz
Unlocking new training data sources for Drug Discovery Machine Learning, Hugo Ceulemans
Responsible Conduct of Research, how to do it, Marcel van der Heyden
The intersection of Optical Chemical Structure Recognition (OCSR) and object detection, Martijn Oldenhof
Inferring missing data with auto-associators, Mark Embrechts
Second School (Lugano, May 8-18, 2022)
Sequential decision making, RL and MDPs by (lecture_1, lecture_2) Oleg Szehr
Synthesis planning strategies by Philippe Schwaller
SELFIES: self-referencing embedded strings by Florian Häse
HPC for drug discovery by Silvano Coletti and Carmine Talaric
Artificial curiosity by Jürgen Schmidhuber
Constructing accurate machine learning force fields for flexible molecules by Leonardo Medrano
Few and zero-shot learning in drug discovery by Günter Klambauer
Experimental computational work by Mike Preuss
Magic rings: navigation in the ring chemical space guided by the bioactive ring by Peter Ertl
Geometric Deep Learning by Silvio Giancola
Artificial intelligence and the chemical space by Jean-Louis Reymond
Comparing and clustering synthetic route prediction by Samuel Genheden
Explainable AIU: interpreting, explaining and visualising deep learning (lecture 1 - contact Alessandro Facchini, lecture 2) by Alessandro Antonucci and Alessandro Facchini
Graph neural networks at the service of molecular simulations by Vittorio Limongelli
Structure based drug discovery (contact Michael Sattler) by Michael Sattler
AI formula generator by Guillaume Godin
Conformal prediction for the design problem by Clara Wong-Fannjiang
Gaussian processes and sequential design of experiments by Dario Azzimonti
Bayesian inference by Adam Arany
Cell painting assay, data analysis and reporting, and its application for identifying biological activity in new chemical matter by Axel Pahl
Overview of toxicity prediction methods by Emilio Benfenati
Explainability for molecular neural networks by Floriane Montanari
Equivariant (G)NNs by Marco Bertolini
Presentation of the "VIRTUOUS" project (contact Dario Piga) by Dario Piga and Gianvito Grasso
First School (Helmholtz Munich, October 18-29) see also Newsletter
RDkit: basics by Gregory Landram The github repo with the notebook is: https://github.com/greglandrum/AIDD_RDKit_Tutorial_2021
Workshop on PyTorch by Thomas Viehmann
Reinforcement Learning by Philipp Renz
Recurrent Neural Networks by Michael Widrich also available on https://github.com/widmi/aidd-school-2021-rnn-lstm-mhn
SMILES based modelling by Esben Jannik Bjerrum
Introduction to modeling chem reactions with ML by Marvin Segler
High Performance Computing by Martijn Oldenhof
Generative models and optimization for molecules by Rocio Mercado
Public Posters/Lectures by Fellows
2022
Towards the inverse design of molecules with targeted quantum-mechanical properties at APS March Meeting 2022, by Alessio Fallani