{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/supervised-learning-and-the-finite","title":"Supervised Learning and the Finite-Temperature String Method for Computing Committor Functions and Reaction Rates","arxiv_id":"2107.13522","date":"2021-07-28","proceeding":null,"authors":["Muhammad R. Hasyim","Clay H. Batton","Kranthi K. Mandadapu"],"abstract":"A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction rates and transition-state ensembles. Under the framework of transition path theory (TPT), recent work [1] proposes an algorithm where a feedback loop couples a neural network that models the committor function with importance sampling, mainly umbrella sampling, which collects data needed for adaptive training. In this work, we show additional modifications are needed to improve the accuracy of the algorithm. The first modification adds elements of supervised learning, which allows the neural network to improve its prediction by fitting to sample-mean estimates of committor values obtained from short molecular dynamics trajectories. The second modification replaces the committor-based umbrella sampling with the finite-temperature string (FTS) method, which enables homogeneous sampling in regions where transition pathways are located. We test our modifications on low-dimensional systems with non-convex potential energy where reference solutions can be found via analytical or the finite element methods, and show how combining supervised learning and the FTS method yields accurate computation of committor functions and reaction rates. We also provide an error analysis for algorithms that use the FTS method, using which reaction rates can be accurately estimated during training with a small number of samples. The methods are then applied to a molecular system in which no reference solution is known, where accurate computations of committor functions and reaction rates can still be obtained.","url_abs":"https://arxiv.org/abs/2107.13522v2","url_pdf":"https://arxiv.org/pdf/2107.13522v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"supervised-learning-and-the-finite","repo_url":"https://github.com/muhammadhasyim/tps-torch","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2107.13522","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2107.13522"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/muhammadhasyim/tps-torch","reach":null}],"summary":{"ran_fixture":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"5a2dcb6f4de562b9","entry":"nullspace","repo":"muhammadhasyim/tps-torch","repo_kind":"official","path":"tpstorch/ml/nn.py","file_url":"https://github.com/muhammadhasyim/tps-torch/blob/HEAD/tpstorch/ml/nn.py","link_basis":"first_harvest_node","language":"python","status":"ran_fixture","verification_level":1,"contract_check":"RAISES","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":"BSD-3-Clause","inline_ok":true,"mcp_get_code":{"code_sha256":"5a2dcb6f4de562b9"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}