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Award Abstract # 1734082
D3SC and EAGER: Using Deep Learning to Find Algorithms for Optimizing Chemical Reactions

NSF Org: CHE
Division Of Chemistry
Recipient: THE LELAND STANFORD JUNIOR UNIVERSITY
Initial Amendment Date: June 9, 2017
Latest Amendment Date: June 9, 2017
Award Number: 1734082
Award Instrument: Standard Grant
Program Manager: Tingyu Li
tli@nsf.gov
 (703)292-4949
CHE
 Division Of Chemistry
MPS
 Directorate for Mathematical and Physical Sciences
Start Date: September 1, 2017
End Date: August 31, 2020 (Estimated)
Total Intended Award Amount: $209,734.00
Total Awarded Amount to Date: $209,734.00
Funds Obligated to Date: FY 2017 = $209,734.00
History of Investigator:
  • Richard Zare (Principal Investigator)
    zare@stanford.edu
Recipient Sponsored Research Office: Stanford University
450 JANE STANFORD WAY
STANFORD
CA  US  94305-2004
(650)723-2300
Sponsor Congressional District: 16
Primary Place of Performance: Stanford University
333 Campus Drive
Stanford
CA  US  94305-4401
Primary Place of Performance
Congressional District:
16
Unique Entity Identifier (UEI): HJD6G4D6TJY5
Parent UEI:
NSF Program(s): CMFP-Chem Mech Funct, and Prop
Primary Program Source: 01001718DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 7433, 7916, 8084
Program Element Code(s): 910200
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.049

ABSTRACT

With support from the Chemical Structure, Dynamics and Mechanisms - B Program in the Division of Chemistry and in response to the Data-Driven Discovery Science in Chemistry (D3SC) Dear Colleague Letter, Professor Richard N. Zare at Stanford University is working on optimizing chemical reactions in microdroplets with deep reinforcement learning. Unoptimized reactions are expensive because they waste time and reagents. A common way for chemists to explore reaction optimization is to change one variable at a time while all other variables remain fixed. This method, however, might not find the best conditions, that is the global optimum. Another way is to search across all combinations of reaction conditions by using batch chemistry. This approach gives a better chance to find the global optimal condition, but it is time-consuming and expensive. Deep reinforcement learning is believed to be a superior approach in which the computer analyzes a large data set and recognizes the pattern of features that lead to best reaction outcomes. It is like training a dog: suppose we want the dog to pick up a ball. If the dog does what we want, we say "Good dog!"; if it does not, we say "Bad dog!". Similarly, Professor Zare uses a machine learning method to give the system a positive reward if the reaction reaches a better result than previous ones, or a negative reward if it does not. A repeated process will eventually result in a set of best reaction conditions for certain reactions. Professor Zare and his group apply this approach to microdroplet chemistry, where many reactions can be carried out in small droplets and be accelerated by factors of one thousand to one million compared with the same reaction happening in bulk solution. Combining the efficient deep reinforcement learning method with accelerated microdroplet reactions, Professor Zare and his group are seeking to find optimal reaction conditions in a fast way. This combined approach can represent a significant step for enabling artificial intelligence to be used to optimize chemical reactions, which should have benefits in chemical production, drug screening, and materials discovery. The students in the Zare group enjoy the unique opportunity to experience micro-droplet chemical synthesis, fast chemical characterization, and deep learning-based complex data analysis.

A reaction can be thought of as a system having multiple inputs (parameters) and providing one or more outputs. Example inputs include: temperature; solvent composition; pH; catalyst; droplet size; and time. Example outputs include: product yield; selectivity; purity; and cost. The goal of reaction optimization described here is to select the best inputs to achieve a given output, which can be formulated as a reinforcement learning system. In order to find the optimal reaction conditions, Professor Zare is searching for critical reaction condition to try at the next step based on previous reaction conditions and product yields. A recurrent neural network is used to model the policy for reaction optimization. The reinforcement learning system is trained on mock reactions (random functions) and then real reactions for better performance. The approach, if successful, could help better understanding of fundamental features of reactivity and enable important industrial applications.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Zhou, Zhenpeng and Kearnes, Steven and Li, Li and Zare, Richard N. and Riley, Patrick "Optimization of Molecules via Deep Reinforcement Learning" Scientific Reports , v.9 , 2019 https://doi.org/10.1038/s41598-019-47148-x Citation Details
Zhou, Zhenpeng and Li, Xiaocheng and Zare, Richard N. "Optimizing Chemical Reactions with Deep Reinforcement Learning" ACS Central Science , v.3 , 2017 10.1021/acscentsci.7b00492 Citation Details
Zhou, Zhenpeng and Yan, Xin and Lai, Yin-Hung and Zare, Richard N. "Fluorescence Polarization Anisotropy in Microdroplets" The Journal of Physical Chemistry Letters , v.9 , 2018 10.1021/acs.jpclett.8b01129 Citation Details

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Various machine learning techniques were combined with the collection of large mass spectrometry data sets to predict whether tissue samples were benign or cancerous. Of particular importance was the application to oral squamous cell carcinoma (OSCC), a serious cancer of the mouth disease. This work used saliva (spit) for the purposes of making metabolic profiles using spray mass spectrometry from a conductive substrate. We also performed desorption electrospray ionization mass spectrometry imaging on tissue samples. Saliva samples from 373 volunteers, 124 who are healthy, 124 who have premalignant lesions, and 125 who are OSCC patients, were collected for discovering and validating dysregulated metabolites and determining altered metabolic pathways. With the aid of machine learning (ML), OSCC and premalignant lesions can be distinguished from the normal physical condition in real time with an accuracy of 86.7%, on a person-by-person basis. These results suggest that the combination of CPSI-MS and ML is a feasible tool for accurate, automated diagnosis of OSCC in clinical practice. This study is being continued elsewhere in a hospital setting, which is a most encouraging outcome. Transcending the application to this particular disease is the demonstration that machine learning combined with reliable mass spectrometric data can be applied in a much shorter time than traditional approaches to make medical diagnoses of high statistical significance. As mass spectrometers become portable and compact, it is anticipated that this type of analysis will become an important new tool for the treatment of many different medical conditions.


Last Modified: 01/04/2021
Modified by: Richard N Zare

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