{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/162989"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/162989","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Inference Time Search for Protein Structure Prediction","abstract":"Scaling inference-time compute for deep learning models has led to superhuman performance in games and enhanced reasoning capabilities for language models. However, similar gains have not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement algorithms for searching and sampling in this discrete latent space and conduct experiments on a small model, demonstrating an increase in oracle and top-1-selected accuracy for predicted protein-protein complex structures.","abstract_html":"Scaling inference-time compute for deep learning models has led to superhuman performance in games and enhanced reasoning capabilities for language models. However, similar gains have not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement algorithms for searching and sampling in this discrete latent space and conduct experiments on a small model, demonstrating an increase in oracle and top-1-selected accuracy for predicted protein-protein complex structures.","abstract_has_math":false,"creators":["Qi, Richard"],"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":["Barzilay, Regina"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-05","date_published":"2025-05","updated_at":"2026-07-22T22:21:30Z","subjects":[],"languages":[],"rights":["In Copyright - Educational Use Permitted","Copyright retained by author(s)"],"rights_urls":["https://rightsstatements.org/page/InC-EDU/1.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/1721.1/162989","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Barzilay, Regina"]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science"]},{"key":"dc:creator","label":"Author","values":["Qi, Richard"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-10-06T17:38:25Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-10-06T17:38:25Z"]},{"key":"dc:date.issued","label":"Date","values":["2025-05"]},{"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","Master of Engineering in Electrical Engineering and Computer Science"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["In Copyright - Educational Use Permitted","Copyright retained by author(s)"]},{"key":"dc:rights.uri","label":"Rights URI","values":["https://rightsstatements.org/page/InC-EDU/1.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1721.1/162989"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Scaling inference-time compute for deep learning models has led to superhuman performance in games and enhanced reasoning capabilities for language models. However, similar gains have not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement algorithms for searching and sampling in this discrete latent space and conduct experiments on a small model, demonstrating an increase in oracle and top-1-selected accuracy for predicted protein-protein complex structures."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["M.Eng."]},{"key":"dc:title","label":"Title","values":["Inference Time Search for Protein Structure Prediction"]}]}],"canonical_facts":{"dc:contributor.advisor":["Barzilay, Regina"],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science"],"dc:creator":["Qi, Richard"],"dc:date.accessioned":["2025-10-06T17:38:25Z"],"dc:date.available":["2025-10-06T17:38:25Z"],"dc:date.issued":["2025-05"],"dc:description.abstract":["Scaling inference-time compute for deep learning models has led to superhuman performance in games and enhanced reasoning capabilities for language models. However, similar gains have not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement algorithms for searching and sampling in this discrete latent space and conduct experiments on a small model, demonstrating an increase in oracle and top-1-selected accuracy for predicted protein-protein complex structures."],"dc:description.degree":["M.Eng."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/162989"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["In Copyright - Educational Use Permitted","Copyright retained by author(s)"],"dc:rights.uri":["https://rightsstatements.org/page/InC-EDU/1.0/"],"dc:title":["Inference Time Search for Protein Structure Prediction"],"dc:type":["Thesis"],"thesis:degree_name":["Master","Master of Engineering in Electrical Engineering and Computer Science"]},"updated_at":"2026-07-22T22:21:30Z"}