Lectures and Seminars | AiChemist MSCA-DN

2025

Third AiChemist School + AIChemist CECAM Flagship School 23rd April - 2nd May 2025 (lecture recordings coming to https://alpha.lhumos.org/spaces/cecam very soon!)

2nd May

Teaching Language Models to Speak Chemistry, Philippe Schwaller, EPFL
Encoding and Decoding Chemistry with Language Models, Kevin Jablonka, University of Jena + Helmholtz Berlin
Transformers for Chemistry and Materials Science, Kevin Jablonka, University of Jena + Helmholtz Berlin

1st May

Integrated machine-learning models for atomic-scale simulations, Michele Ceriotti, EPFL
Machine Learning Potentials for Excited States, Julia Maria Westermayr, Universität Leipzig
Consensus modelling of reaction pathways: interactive prediction and visualisation of millions of pathways using a Java-enabled platform and Javascript, Luc Patiny, EPFL and Igor Tetko, HMGU

30th April

Introduction to (Bio)Molecular Simulations with ML Force Fields, Adil Kabylda, University of Luxembourg
Exploring chemical reactivity in aqueous solutions and at interfaces with deep potential molecular simulations, Damien Laage, ENS-PSL
Concepts in Synthesis Planning and Generative Molecular Design, Marwin Segler, Microsoft
Navigating the Future of Reaction Informatics: issues solved and challenges ahead, Timur Madzhidov, Reaxys
Deep Learning for Protein and Protein-Ligand Structure Prediction, Janani Durairaj, University of Basel
Tutorial on Multi-Task Learning: Compound profiling using QSAR modeling, Gilles Marcou, UNISTRA

29th April

How to select your molecular features?, Guillaume Godin, Osmo Labs
A Mental Toolbox for Chemical Synthesis: Insights into Representation, Algorithms, and Their Constraints, Amol Thakkar, former IBM
How (not) to produce data and code for reaction machine learning, Esther Heid, TU Wien
Improving Route Development Using Convergent Retrosynthesis Planning, Paula Torren-Peraire, former JnJ, currently Novartis
Monte Carlo Tree Search: From Single-objective To Multi-objective, Mike Preuss, ULEI
Hands-on tutorial: Retrosynthesis with AiZynthFinder, Samuel Genheden, AstraZeneca

28th April

Expanding chemical reaction space for synthesizing the GDB, Jean-Louis Reymond, University of Bern
Leveraging experimental data in machine learning and screening to get from computational model to real world materials fast, Heather Kulik, MIT
Chemography approach to (ultra)big chemical space analysis, Alexandre Varnek, UNISTRA
Modelling Chemical Reactions in Solution with Machine Learning Potentials – Balancing Efficiency and Accuracy, Fernanda Duarte, University of Oxford
Computational Chemistry Joins Forces with Artificial Intelligence in the Design of Biomimetic (Metallo)Enzymes, Ursula Roethlisberger, EPFL
Capturing homology in protein language models, Anne-Florence Bitbol, EPFL

25th April

AI enabled winning strategies for CACHE, Artem Cherkasov, University of British Columbia. Video
Overview of the Tox24 Challenge, Igor Tetko, HMGU
Diffusion Models and Geometric Deep Learning, Julian Cremer, Pfizer
DC Presentations DC1 DC2 DC3 DC4 DC5 DC6 DC7 DC9 DC10 DC11 DC14

24th April

NAMS for Liver- and Cardio-toxicity prediction, Dongying Li, U.S. FDA
Using sLLMs to build autonomous agents, Hyun-Kil Shin, KIT/UST. Videos
Scientific Writing for PhDs, Ann Bless https://www.annbless.com

23rd April

Atom-centred representations for atomistic ML, Davide Tisi, EPFL. Video
Structure-based Drug Design using 3D Equivariant Generative Models, Tuan Le, Pfizer
Blender for scientific figures and graphics, Edvin Fako, EPFL. Video

2024

09.12.2024 Fabian Krüger (DC1) gave a lecture "Can Publishing Neural Networks Expose Confidential Training Data? Risks in Drug Discovery" for the final AiChemist seminar of the year.

24.10.2024 Make Science Pop! - an online workshop on effective science communication co-organised by Chelonia Applied Science, the AiChemist and AVITHRAPID projects took place, attracting 60 participants from Europe and the US, including the AiChemist fellows. The workshop was hosted by Dr. James Beacham, physicist at the LHC at CERN, and featured talks by Dr. Andrea "Annie" Kritcher of the Lawrence Livermore National Laboratory, Ryan Mandelbaum of IBM Quantum and Dr. Michelle Roberts, Digital Health Editor at the BBC.

Second AiChemist School - Strasbourg Summer School in Chemoinformatics (June 24th - 27th, 2024, Strasbourg)

Thursday 27th June

Integration of Deep Docking into Virtual Screening Workflow: The CACHE-1 Study Case, Artem Cherkasov, University of British Columbia. Abstract, video.
Ab initio chemical reaction design and discovery through automated pathway exploration, Satoshi Maeda, Hokkaido University. Abstract, video.
Target IA and structural analysis protocol contribution to in silico drug design, Anne-Claude Camproux, Paris City University. Abstract.
Ultra-large virtual screens using fuzzy similarity, QSAR, docking, and molecular dynamics for multi-target anti-Alzheimer’s agents, Guilherme Martins Silva, Harvard BIDMC. Abstract.
Targeting the Todalam site on α-Tubulin: toward novel protein immobilization systems, Stefano Pieraccini, University of Milan. Abstract.
Essential Steps in Protein-Ligand Preparation with Conserved Waters and Water Networks in Drug Design, Marko Jukic, University of Maribor, Slovenia. Abstract.
Artificial Intelligence (AI) Solutions for Computational Chemistry and Organic Chemistry Tasks, Olexandr Isayev, Carnegie Mellon University. Abstract, video.
Multi-instance learning as a response to the complexity of molecular entities, Pavel Polishchuk, Palacky University, Czech Republic. Abstract, video.
Structure-based organic chemistry-driven ligand design from ultra-large chemical spaces, Didier Rognan, University of Strasbourg. Abstract, video.
Materials Informatics for green energy harvesting and storage, Hanoch Senderowitz, Bar Ilan University, Israel. Abstract, video.

Wednesday 26th June

Next Generation Pharmacophore Modeling: Tools and Applications, Thierry Langer, University of Vienna. Abstract, video.
Balancing the design of molecular structures with the design of their syntheses, Connor Coley, MIT. Abstract, video.
Chemical space of food chemicals and natural products from Latin America, Jose L. Medina-Franco, National Autonomous University of Mexico. Abstract, video.
The use of QSAR in hazard assessment and (eco)toxicity for regulatory applications, Alessandra Roncaglioni, IRFMN, Milan. Abstract, video.
From chemical space visualization to strategic planning: leveraging chemography in drug discovery at Eli Lilly, Yuliana Zabolotna, Eli Lilly, Madrid. Abstract.
Detection of Cryptic Pockets for Drug Discovery, Mireille Krier, OpenEye, Cologne. Abstract.
How Pharma Saves Tons Money: On-Demand Hits from Docking Ultralarge Spaces, Marcus Gastreich, BioSolvIT GmbH, St. Augustin. Abstract.
Protein structure prediction with AlphaFold2 for drug discovery, Esther Kellenberger and Luca Chiesa, University of Strasbourg. Abstract.

Tuesday 25th June

De Novo Molecular Design with Machine Intelligence, Gisbert Schneider, ETH Zurich. Abstract.
Language Models for Drug Design, Jürgen Bajorath, University of Bonn. Abstract, video.
The Potential of Progress Informatics, Kimito Funatsu, NAIST Japan. Abstract, video.
News from the Outer Rim of Chemical Space, Matthias Rarey, University of Hamburg. Abstract, video.
AI tools for chemical synthesis and chemistry automation, Mikhail Kabeshov, AstraZeneca, Sweden. Abstract.
Exploring molecular heteroencoders with latent space arithmetic: atomic descriptors and molecular operators, Joao Aires-de-Sousa, New University of Lisbon. Abstract.
Construction of order-independent molecular fragments space with vector quantised graph autoencoder, Tagir Akhmetshin, University of Strasbourg. Abstract.
Zooming Chemical Space with Generative Topographic Mapping, Gilles Marcou, University of Strasbourg. Abstract.

Monday 24th June

Reminiscing about the future: New trends in QSAR Modelling in the age of big data, generative AI, and large language models. Alexander Tropsha, University of North Carolina. Abstract, video.

23.10.2024 Alan Kai Hassen delivered a talk "Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design" at the October AiChemist/AIDD seminar

18.06.2024 Yves Moreau gave a 3-part lecture on "Ethics of Big Data" lecture 1, lecture 2, lecture 3.

30.04.2024 Vincenzo Palmacci delivered a talk "Statistical approach enabling technology-specific assay interference prediction from large screening data sets” at a joint AiChemist/AIDD online seminar.

22.03.2024 Andreas Poehlmann (Pfizer) delivered an online workshop "Intro to Git" to the AiChemist DCs.

First AiChemist School (March 4 - 15, 2024, Berlin)

The first AiChemist School took place in Berlin, from the 4th to the 15th of March, with most of the lectures and workshops running in hybrid mode and open to the general public.

Friday 15th March