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ASKCOS: an open source software suite for synthesis planning

Tu, Zhengkai, Choure, Sourabh J., Fong, Mun Hong, Roh, Jihye, Levin, Itai, Yu, Kevin, Joung, Joonyoung F., Morgan, Nathan, Li, Shih-Cheng, Sun, Xiaoqi, Lin, Huiqian, Murnin, Mark, Liles, Jordan P., Struble, Thomas J., Fortunato, Michael E., Liu, Mengjie, Green, William H., Jensen, Klavs F., Coley, Connor W.

arXiv.org Artificial Intelligence

The advancement of machine learning and the availability of large-scale reaction datasets have accelerated the development of data-driven models for computer-aided synthesis planning (CASP) in the past decade. Here, we detail the newest version of ASKCOS, an open source software suite for synthesis planning that makes available several research advances in a freely available, practical tool. Four one-step retrosynthesis models form the basis of both interactive planning and automatic planning modes. Retrosynthetic planning is complemented by other modules for feasibility assessment and pathway evaluation, including reaction condition recommendation, reaction outcome prediction, and auxiliary capabilities such as solubility prediction and quantum mechanical descriptor prediction. ASKCOS has assisted hundreds of medicinal, synthetic, and process chemists in their day-to-day tasks, complementing expert decision making. It is our belief that CASP tools like ASKCOS are an important part of modern chemistry research, and that they offer ever-increasing utility and accessibility.


Yield-predicting AI needs chemists to stop ignoring failed experiments

#artificialintelligence

Machine-learning algorithms that can predict reaction yields have remained elusive because chemists tend to bury low-yielding reactions in their lab notebooks instead of publishing them, researchers say. 'We have this image that failed experiments are bad experiments,' says Felix Strieth-Kalthoff. 'But they contain knowledge, they contain valuable information both for humans and for an AI.' Strieth-Kalthoff from the University of Toronto, Canada, and a team around Frank Glorius from Germany's University of Münster are asking chemists to start including not only their best but also their worst results in their papers. This, as well as unbiased reagent selection and reporting experimental procedures in a standardised format, will allow researchers to finally create yield-prediction algorithms. Retrosynthesis is already using machine-learning models to create shorter, cheaper or non-proprietary synthetic routes. But there have been few attempts at creating programs that predict yields.


Retrosynthetic Planning with Experience-Guided Monte Carlo Tree Search

Hong, Siqi, Zhuo, Hankz Hankui, Jin, Kebing, Zhou, Zhanwen

arXiv.org Artificial Intelligence

Retrosynthetic planning problem is to analyze a complex molecule and give a synthetic route using simple building blocks. The huge number of chemical reactions leads to a combinatorial explosion of possibilities, and even the experienced chemists could not select the most promising transformations. The current approaches rely on human-defined or machine-trained score functions which have limited chemical knowledge or use expensive estimation methods such as rollout to guide the search. In this paper, we propose {\tt MCTS}, a novel MCTS-based retrosynthetic planning approach, to deal with retrosynthetic planning problem. Instead of exploiting rollout, we build an Experience Guidance Network to learn knowledge from synthetic experiences during the search. Experiments on benchmark USPTO datasets show that, our {\tt MCTS} gains significant improvement over state-of-the-art approaches both in efficiency and effectiveness.


Using computational tools for molecule discovery

#artificialintelligence

Discovering a drug, material, or anything new requires finding and understanding molecules. It's a time- and labor-intensive process, which can be helped along by a chemist's expertise, but it can only go so quickly, be so efficient, and there's no guarantee for success. Connor Coley is looking to change that dynamic. The Henri Slezynger (1957) Career Development Assistant Professor in the MIT Department of Chemical Engineering is developing computational tools that would be able to predict molecular behavior and learn from the successes and mistakes. It's an intuitive approach and one that still has obstacles, but Coley says that this autonomous platform holds enormous potential for remaking the discovery process.


AI translates chemistry to predict reaction outcomes

@machinelearnbot

IBM researchers have developed a program that can predict the products of organic chemistry reactions.1 Modelled on the latest language translation systems – like Google's artificial neural network – the AI picked the right product 80% of the time despite not having been taught any organic chemistry rules. 'What this tool is trying to do is imitate a top pro chemist in more or less the entire domain of organic chemistry,' says Teodoro Laino, one of the researchers involved in the study at IBM in Zurich, Switzerland. His ambitious goal is shared by other chemists who have been attempting to create a functioning AI chemist since the 1970s, when organic chemist E J Corey kick-started the field by creating a chemical knowledge database. However, making a tool based on chemistry knowledge can be time-consuming; Bartosz Grzybowski's team took 10 years to encode their Chematica retrosynthesis program with 20,000 chemical rules. Moreover, a knowledge-based AI has difficulty tackling reactions that lie outside of its rule set. 'There's a way to learn organic chemistry that's not memorising chemical rules, by just trying to find out the underlying patterns in reactions and trying to rationalise them,' Laino says, explaining the approach that his team took.


The Cognitive Bias President Trump Understands Better Than You

WIRED

Americans born in the United States are more murderous than undocumented immigrants. After all, that's just what the numbers say. Still, be honest: you wouldn't linger over a story with that headline. Instead, you'll see two dozen reporters flock to a single burning trash can during an Inauguration protest. The aberrant occurrence is the story you'll read and the picture you'll see.