{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/123133"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/123133","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Message passing neural networks for molecular property prediction","abstract":"Developing new drugs relies heavily on understanding the various molecular properties of potential drug candidates. While experimental assays performed in the lab are the best source of information about molecular properties, these assays are slow and expensive. For this reason, there has been great interest in the potential of machine learning models to predict molecular properties without the need for experimental assays. However, recent literature has not yet clearly determined which machine learning models are optimal for molecular property prediction. In this thesis, I apply the Direct Message Passing Neural Network (D-MPNN) from [47, 48] to 19 publicly available property prediction datasets, and I demonstrate that it consistently outperforms prior machine learning models. Additionally, I introduce several optimizations to the D-MPNN which further enhance its performance and lead to new state-of-the-art results.","abstract_html":"Developing new drugs relies heavily on understanding the various molecular properties of potential drug candidates. While experimental assays performed in the lab are the best source of information about molecular properties, these assays are slow and expensive. For this reason, there has been great interest in the potential of machine learning models to predict molecular properties without the need for experimental assays. However, recent literature has not yet clearly determined which machine learning models are optimal for molecular property prediction. In this thesis, I apply the Direct Message Passing Neural Network (D-MPNN) from [47, 48] to 19 publicly available property prediction datasets, and I demonstrate that it consistently outperforms prior machine learning models. Additionally, I introduce several optimizations to the D-MPNN which further enhance its performance and lead to new state-of-the-art results.","abstract_has_math":false,"creators":["Swanson, Kyle(Kyle W.)"],"institution":"Massachusetts Institute of Technology","degree_name":"Master","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","school":null,"contributors":[],"advisors":["Regina Barzilay."],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019","date_published":"2019","updated_at":"2026-07-22T22:20:44Z","subjects":["Electrical Engineering and Computer Science."],"languages":["eng"],"rights":["MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/1721.1/123133","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Regina Barzilay."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","EECS"]},{"key":"dc:contributor.other","label":"Dc Contributor Other","values":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science."]},{"key":"dc:creator","label":"Author","values":["Swanson, Kyle(Kyle W.)"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2019-12-05T18:05:17Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2019-12-05T18:05:17Z"]},{"key":"dc:date.issued","label":"Date","values":["2019"]},{"key":"dc:publisher","label":"Institution","values":["Massachusetts Institute of Technology"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Electrical Engineering and Computer Science."]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1721.1/123133"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.","Thesis: M. Eng. in Computer Science and Engineering, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2019","Cataloged from student-submitted PDF version of thesis.","Includes bibliographical references (pages 81-84)."]},{"key":"dc:description.abstract","label":"Abstract","values":["Developing new drugs relies heavily on understanding the various molecular properties of potential drug candidates. While experimental assays performed in the lab are the best source of information about molecular properties, these assays are slow and expensive. For this reason, there has been great interest in the potential of machine learning models to predict molecular properties without the need for experimental assays. However, recent literature has not yet clearly determined which machine learning models are optimal for molecular property prediction. In this thesis, I apply the Direct Message Passing Neural Network (D-MPNN) from [47, 48] to 19 publicly available property prediction datasets, and I demonstrate that it consistently outperforms prior machine learning models. Additionally, I introduce several optimizations to the D-MPNN which further enhance its performance and lead to new state-of-the-art results."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["M. Eng. in Computer Science and Engineering"]},{"key":"dc:title","label":"Title","values":["Message passing neural networks for molecular property prediction"]}]}],"canonical_facts":{"dc:contributor.advisor":["Regina Barzilay."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","EECS"],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science."],"dc:creator":["Swanson, Kyle(Kyle W.)"],"dc:date.accessioned":["2019-12-05T18:05:17Z"],"dc:date.available":["2019-12-05T18:05:17Z"],"dc:date.issued":["2019"],"dc:description":["This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.","Thesis: M. Eng. in Computer Science and Engineering, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2019","Cataloged from student-submitted PDF version of thesis.","Includes bibliographical references (pages 81-84)."],"dc:description.abstract":["Developing new drugs relies heavily on understanding the various molecular properties of potential drug candidates. While experimental assays performed in the lab are the best source of information about molecular properties, these assays are slow and expensive. For this reason, there has been great interest in the potential of machine learning models to predict molecular properties without the need for experimental assays. However, recent literature has not yet clearly determined which machine learning models are optimal for molecular property prediction. In this thesis, I apply the Direct Message Passing Neural Network (D-MPNN) from [47, 48] to 19 publicly available property prediction datasets, and I demonstrate that it consistently outperforms prior machine learning models. Additionally, I introduce several optimizations to the D-MPNN which further enhance its performance and lead to new state-of-the-art results."],"dc:description.degree":["M. Eng. in Computer Science and Engineering"],"dc:identifier.uri":["https://hdl.handle.net/1721.1/123133"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Electrical Engineering and Computer Science."],"dc:title":["Message passing neural networks for molecular property prediction"],"dc:type":["Thesis"],"thesis:degree_name":["Master"]},"updated_at":"2026-07-22T22:20:44Z"}