Lecture

Molecular Synthesis Planning: Transformer Models and Atom Mapping

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In course

PHYS-754: Lecture series on scientific machine learning

This lecture presents ongoing work on how scientific questions can be tackled using machine learning. Machine learning enables extracting knowledge from data computationally and in an automatized way. We will learn on examples how this is influencing the v ...

Description

This lecture covers the use of Molecular Transformer models for multi-step synthesis planning, including retro and forward steps, path scoring, and hyper-graph exploration strategies. It also delves into the application of self-supervised training, attention weights visualization, atom-mapping discovery, and benchmarking studies. The lecture further explores the role of AI in synthesis planning, focusing on template-based and graph neural network approaches, as well as SMILES-to-SMILES methods. It concludes with insights on applying language methods to chemistry, data-driven reaction fingerprints, and the transformative impact of Transformers in capturing the grammar of chemical reactions.

Instructors (10)

Paolo De Los Rios

Paolo De Los Rios earned his master in Electronic Engineering at the Turin Institute of Technology (Politecnico di Torino) in May 1993. In November 1993 he moved to Trieste, Italy, to enter the PhD program in Theoretical Condensed Matter Theory at the International School for Advanced Studies (SISSA/ISAS) where he obtained the PhD degree in October 1996 for his work on the statistical physics of disordered systems. After a one year postdoc at the Max-Planck Institute for the Physics of Complex Systems in Dresden, Germany, in November 1997 he moved to the University of Fribourg, Switzerland, to join the group of Prof. Yi-Cheng Zhang. There he has worked on various applications of statistical physics to complex systems. In September 2000 he has been appointed Assistant Professor in Statistical Physics of Living Matter and Complex Systems at the Institute of Theoretical Physics of the University of Lausanne, Switzerland. Since April 2010 he is Associate Professor at the Institute of Theoretical Physics of the Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland.

Anne-Clémence Corminboeuf

Teaching & PhD PhD Students Liam Oliver Marsh, Pratham Pushparaj Deshmukh, Roel Christiaan M Raike, Thanapat Worakul, Osvaldo Hernandez Cuellar, Juliette Veronique Schleicher, Yannick Calvino Alonso, Sara Bassetta, Yuri Cho, Kelian Dietmar Marc Gaedecke, Guoyuan Liu Past EPFL PhD Students Fabrice Avaltroni, Daniel Filipe Jana, Stephan Niklaus Steinmann, Jérôme Florian Gonthier, Riccardo Petraglia, Antonio Prlj, Laurent Alexis Clément Vannay, Alberto Fabrizio, Kun-Han Lin, Boodsarin Sawatlon, Raimon Fabreg

Philippe Schwaller

Michele Ceriotti

Michele Ceriotti received his Ph.D. in Physics from ETH Zürich in 2010. He spent three years in Oxford as a Junior Research Fellow at Merton College. Since 2013 he leads the laboratory for Computational Science and Modeling in the Institute of Materials at EPFL. His research revolves around the atomic-scale modelling of materials, based on the sampling of quantum and thermal fluctuations and on the use of machine learning to predict and rationalize structure-property relations. He has been awarded the IBM Research Forschungspreis in 2010, the Volker Heine Young Investigator Award in 2013, an ERC Starting Grant in 2016, and the IUPAP C10 Young Scientist Prize in 2018.

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Related concepts (32)

Speech synthesis

Speech synthesis is the artificial production of human speech. A computer system used for this purpose is called a speech synthesizer, and can be implemented in software or hardware products. A text-to-speech (TTS) system converts normal language text into speech; other systems render symbolic linguistic representations like phonetic transcriptions into speech. The reverse process is speech recognition. Synthesized speech can be created by concatenating pieces of recorded speech that are stored in a database.

Recurrent neural network

A recurrent neural network (RNN) is one of the two broad types of artificial neural network, characterized by direction of the flow of information between its layers. In contrast to uni-directional feedforward neural network, it is a bi-directional artificial neural network, meaning that it allows the output from some nodes to affect subsequent input to the same nodes. Their ability to use internal state (memory) to process arbitrary sequences of inputs makes them applicable to tasks such as unsegmented, connected handwriting recognition or speech recognition.

Self-supervised learning

Self-supervised learning (SSL) is a paradigm in machine learning for processing data of lower quality, rather than improving ultimate outcomes. Self-supervised learning more closely imitates the way humans learn to classify objects. The typical SSL method is based on an artificial neural network or other model such as a decision list. The model learns in two steps. First, the task is solved based on an auxiliary or pretext classification task using pseudo-labels which help to initialize the model parameters.

Transformer (machine learning model)

A transformer is a deep learning architecture that relies on the parallel multi-head attention mechanism. The modern transformer was proposed in the 2017 paper titled 'Attention Is All You Need' by Ashish Vaswani et al., Google Brain team. It is notable for requiring less training time than previous recurrent neural architectures, such as long short-term memory (LSTM), and its later variation has been prevalently adopted for training large language models on large (language) datasets, such as the Wikipedia corpus and Common Crawl, by virtue of the parallelized processing of input sequence.

Artificial neural network

Artificial neural networks (ANNs, also shortened to neural networks (NNs) or neural nets) are a branch of machine learning models that are built using principles of neuronal organization discovered by connectionism in the biological neural networks constituting animal brains. An ANN is based on a collection of connected units or nodes called artificial neurons, which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit a signal to other neurons.

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