O4-2

RetroSynthWAVE: An Open-Source Software Platform for
Efficient Chemical Synthesis Research12Haris Hasic 1, 2

Takashi Ishida 1

hasic@cb.cs.titech.ac.jp

ishida@c.titech.ac.jp

Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8 -85,
2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
Elix Inc., Daini Togo Park Building 3F, 8-34 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan

Keywords: Machine Learning – AI Method Development, Data Curation, Data Visualization
The RetroSynthWAVE project aims to establish a systematic, open -source software platform
focused on the field of chemical synthesis. It enables quick and efficient research for beginners aswell as advanced users by providing software packages that cover the foll owing synthesis-related
functionalities: Widgets and helpers, Aggregated chemical compound and chemical reaction data,
Variety of popular existing model implementations, and Evaluation metrics. Each of the software
packages can be used independently, as well as within the project software stack.
RetroSynthWAVE: HANA is the first and fundamental software package of the project. The nameis derived as an acronym for Helpers ANd Accessories, and it represents a utility wrapper modulethat encapsulates all of the essential libraries (e.g., RDKit [1], RDChiral [2]) and offers additional
fundamental functionalities while being easy to use.
RetroSynthWAVE: COCORO is the second software package of the project which is developed
using the functionalities from the previous one. The name is derived as an acronym for COllectionof Chemical COmpound and ReactiOn Data, and it represents an easy-to-use data platform thatautomates the retrieval, cleaning and featurization of available chemical information datasets. (e.g.,ChEMBL [3], USPTO [4])RetroSynthWAVE: CO-OP is the third software package of the project which is developed using
the functionalities from the previous two. The name is derived as an acronym for COllection Of
Popular Models, and it represents an easy-to-use model platform for the reimplementation of
popular existing (retro)synthesis models using the PyTorch library. It enables other users to submit
the implementation of new models in a standardized fashion.
RetroSynthWAVE: REFEREE is the final software package of the project. The name is derived as
an acronym for Retroactive EFficiency MEtRics Evaluation FramEwork, and it represents a utility
module that enables the definition of user-defined, pre-existing, and novel evaluation metrics for(retro)synthesis-focused models. Furthermore, by using the functionalities from all of the previous
software packages, it enables the retroactive application of new metrics on pre-existing models
thus enabling more advanced benchmarking of all relevant models.
[1] RDKit: Open-Source Cheminformatics Software. https://www.rdkit.org/. (2021.08.13)[2] Coley, C.W.; Green, W.H.; Jensen, K.F.; RDChiral: An RDKit Wrapper for HandlingStereochemistry in Retrosynthetic Template Extraction and Application, Journal of ChemicalInformation and Modeling, 2019, 59, 6, 2529-2537.
[3] ChEMBL Database - EMBL-EBI: https://www.ebi.ac.uk/chembl/. (2021.08.13)[4] Lowe, D. M. Extraction of Chemical Structures and Reactions from the Literature. Ph.D. Thesis,
University of Cambridge, Department of Chemistry, Pembroke College, 2012 .