{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T13:15:40Z","timestamp":1775913340513,"version":"3.50.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T00:00:00Z","timestamp":1631059200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100002923","name":"National Scientific and Technical Research Council","doi-asserted-by":"publisher","award":["PIP 112-2017-0100829"],"award-info":[{"award-number":["PIP 112-2017-0100829"]}],"id":[{"id":"10.13039\/501100002923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"National Agency for Science and Technology, Argentina","doi-asserted-by":"publisher","award":["PICT-2019-03350"],"award-info":[{"award-number":["PICT-2019-03350"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>With the consolidation of deep learning in drug discovery, several novel algorithms for learning molecular representations have been proposed. Despite the interest of the community in developing new methods for learning molecular embeddings and their theoretical benefits, comparing molecular embeddings with each other and with traditional representations is not straightforward, which in turn hinders the process of choosing a suitable representation for Quantitative Structure\u2013Activity Relationship (QSAR) modeling. A reason behind this issue is the difficulty of conducting a fair and thorough comparison of the different existing embedding approaches, which requires numerous experiments on various datasets and training scenarios. To close this gap, we reviewed the literature on methods for molecular embeddings and reproduced three unsupervised and two supervised molecular embedding techniques recently proposed in the literature. We compared these five methods concerning their performance in QSAR scenarios using different classification and regression datasets. We also compared these representations to traditional molecular representations, namely molecular descriptors and fingerprints. As opposed to the expected outcome, our experimental setup consisting of over $25 000$ trained models and statistical tests revealed that the predictive performance using molecular embeddings did not significantly surpass that of traditional representations. Although supervised embeddings yielded competitive results compared with those using traditional molecular representations, unsupervised embeddings tended to perform worse than traditional representations. Our results highlight the need for conducting a careful comparison and analysis of the different embedding techniques prior to using them in drug design tasks and motivate a discussion about the potential of molecular embeddings in computer-aided drug design.<\/jats:p>","DOI":"10.1093\/bib\/bbab365","type":"journal-article","created":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T19:11:27Z","timestamp":1629313887000},"source":"Crossref","is-referenced-by-count":37,"title":["Using molecular embeddings in QSAR modeling: does it make a difference?"],"prefix":"10.1093","volume":"23","author":[{"given":"Mar\u00eda Virginia","family":"Sabando","sequence":"first","affiliation":[{"name":"Institute for Computer Science and Engineering, UNS-CONICET, Bah\u00eda Blanca, Argentina"}]},{"given":"Ignacio","family":"Ponzoni","sequence":"additional","affiliation":[{"name":"Institute for Computer Science and Engineering, UNS-CONICET, Bah\u00eda Blanca, Argentina"},{"name":"Department of Computer Science and Engineering, Universidad Nacional del Sur, Bah\u00eda Blanca, Argentina"}]},{"given":"Evangelos E","family":"Milios","sequence":"additional","affiliation":[{"name":"Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada"}]},{"given":"Axel J","family":"Soto","sequence":"additional","affiliation":[{"name":"Institute for Computer Science and Engineering, UNS-CONICET, Bah\u00eda Blanca, Argentina"},{"name":"Department of Computer Science and Engineering, Universidad Nacional del Sur, Bah\u00eda Blanca, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2021,9,8]]},"reference":[{"issue":"4","key":"2022011921021386600_ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa321","article-title":"Do we need different machine learning algorithms for QSAR modeling? 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