{"about":{"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.","site":"https://codewithpapers.app","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","syntology":{"site":"https://syntology.ai","developers":"https://syntology.ai/developers","mcp":{"server":"https://syntology.ai/mcp","transport":"streamable-http","server_card":"https://syntology.ai/.well-known/mcp/server-card.json","auth":{"type":"trial token, no account","trial_token":"https://syntology.ai/api/oauth/trial/token","method":"POST","docs":"https://syntology.ai/developers"}},"have":"https://syntology.ai/api/graph/have?x=<method, arXiv id or title> (free, answers coverage only)","paper_base":"https://syntology.ai/paper/","atlas_base":"https://app.syntology.ai/?focus="},"machine_readable":[{"url":"https://codewithpapers.app/llms.txt","what":"the machine catalog: every machine-readable file, counted"},{"url":"https://codewithpapers.app/index/manifest.json","what":"paper-to-code index by arXiv id, with Syntology's counts"},{"url":"https://codewithpapers.app/search/manifest.json","what":"site search index (titles, authors) and its files"},{"url":"https://codewithpapers.app/download","what":"bulk files: Syntology's layer, described there"},{"url":"https://codewithpapers.app/build_manifest.json","what":"the build record: inputs, counts, exclusions, probes"}]},"url":"/task/protein-design/papers/ran/1","list_of":"/task/protein-design","task":"Protein Design","archive":{"snapshot":"2025-07-28"},"key_notes":{"n_ran_checked":"legacy name, kept unchanged so existing readers do not break: it counts the samples that ran with no instrument failure (honoured, violated, and ran with no contract checked); it does not mean a contract was checked, and the pages print it as 'K with no instrument failure', not 'K checked'","n_constructed":"a sub-count of the samples that ran, never subtracted from them and never a failure: an executed sample whose run returned an instance of its own class (fixture_out_type equals the entry name): the run built an object and did not compute a result (Syntology's RAN record, counts.constructed)"},"syntology_read_at":"2026-09-28T10:30:06+00:00","order":"ran","order_definition":"only papers where Syntology ran at least one harvested sample; date (newest first), ties by arXiv id","caption":"We ran code from the paper's repository; we did not run it on this task or check it against the task's benchmarks.","absence":"A paper missing from this list is not a recorded non-run: it may have no arXiv id, no harvested code, or only samples that have not run yet.","page":1,"pages_in_order":1,"rows_per_page":100,"rows":[1,31],"of":31,"counts":{"archive_papers_tagged":175,"with_a_code_link":74,"where_syntology_ran_a_sample":31,"not_listed_spam_title":0,"listed":175,"listed_where_code_ran":31,"where_syntology_ran_a_sample_split":{"with_a_run_with_no_instrument_failure":24,"every_run_a_failure_of_syntologys_instrument":7,"listed_with_a_run_with_no_instrument_failure":24,"listed_every_run_a_failure_of_syntologys_instrument":7,"filter":{"states":["a run with no instrument failure","any run, instrument failures included"],"default":"a run with no instrument failure","note":"on the 'only where code ran' pages the default hides, in the browser, the rows where every run was a failure of Syntology's instrument; the second state shows them again. Rows are hidden, never re-ordered; these twins list every row"}},"definition":"distinct papers the archive tags; 'where Syntology ran a sample' counts papers with at least one harvested sample that ran, which is not a correctness claim"},"first_page":"/task/protein-design/papers/ran/1","prev":null,"next":null,"papers":[{"url":"/paper/scoring-assisted-generative-exploration-for","slug":"scoring-assisted-generative-exploration-for","title":"Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation","date":"2025-05-02","arxiv_id":"2505.01277","repositories_listed":1,"syntology":{"n":3,"n_ran":2,"n_constructed":0,"n_ran_checked":2,"n_instrument":0,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":2,"n_pointer_only":0,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 0 honoured, 0 violated, 2 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/scoring-assisted-generative-exploration-for#ran","syntology_url":"https://syntology.ai/paper/2505.01277","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2505.01277"}},"official":{"repos":["hclim0213/SAGE-Prot"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":2,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/proteina-scaling-flow-based-protein-structure","slug":"proteina-scaling-flow-based-protein-structure","title":"Proteina: Scaling Flow-based Protein Structure Generative Models","date":"2025-03-02","arxiv_id":"2503.00710","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":0,"n_instrument":1,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":1,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/proteina-scaling-flow-based-protein-structure#ran","syntology_url":"https://syntology.ai/paper/2503.00710","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2503.00710"}},"official":{"repos":["NVIDIA-Digital-Bio/proteina"],"state":"official: no sample here; runs from other or unrecorded repositories","n_ran":0,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["unlocated"]}}},{"url":"/paper/a-general-framework-for-inference-time","slug":"a-general-framework-for-inference-time","title":"A General Framework for Inference-time Scaling and Steering of Diffusion Models","date":"2025-01-12","arxiv_id":"2501.06848","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":0,"n_instrument":1,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":1,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/a-general-framework-for-inference-time#ran","syntology_url":"https://syntology.ai/paper/2501.06848","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2501.06848"}},"official":{"repos":["zacharyhorvitz/fk-diffusion-steering"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/concept-bottleneck-language-models-for","slug":"concept-bottleneck-language-models-for","title":"Concept Bottleneck Language Models For protein design","date":"2024-11-09","arxiv_id":"2411.06090","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":1,"n_instrument":0,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":1,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/concept-bottleneck-language-models-for#ran","syntology_url":"https://syntology.ai/paper/2411.06090","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2411.06090"}},"official":{"repos":["prescient-design/lobster"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":1,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/bridge-if-learning-inverse-protein-folding","slug":"bridge-if-learning-inverse-protein-folding","title":"Bridge-IF: Learning Inverse Protein Folding with Markov Bridges","date":"2024-11-04","arxiv_id":"2411.02120","repositories_listed":1,"syntology":{"n":3,"n_ran":1,"n_constructed":0,"n_ran_checked":1,"n_instrument":0,"n_unverified":2,"n_honours":0,"n_violates":0,"n_no_contract":1,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified","sample_list":"/paper/bridge-if-learning-inverse-protein-folding#ran","syntology_url":"https://syntology.ai/paper/2411.02120","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2411.02120"}},"official":{"repos":["violet-sto/bridge-if"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":1,"n_unverified":2,"ran_from_kinds":["official"]}}},{"url":"/paper/fine-tuning-discrete-diffusion-models-via","slug":"fine-tuning-discrete-diffusion-models-via","title":"Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design","date":"2024-10-17","arxiv_id":"2410.13643","repositories_listed":1,"syntology":{"n":8,"n_ran":7,"n_constructed":0,"n_ran_checked":7,"n_instrument":0,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":7,"n_pointer_only":8,"phrase":"7 ran (of which 0 constructed an object rather than computing a result; 7 with no instrument failure: 0 honoured, 0 violated, 7 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/fine-tuning-discrete-diffusion-models-via#ran","syntology_url":"https://syntology.ai/paper/2410.13643","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2410.13643"}},"official":{"repos":["chenyuwang-monica/drakes"],"state":"official (archive's flag): 7 ran","n_ran":7,"n_constructed":0,"n_ran_no_instrument_failure":7,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/geometric-trajectory-diffusion-models","slug":"geometric-trajectory-diffusion-models","title":"Geometric Trajectory Diffusion Models","date":"2024-10-16","arxiv_id":"2410.13027","repositories_listed":1,"syntology":{"n":10,"n_ran":10,"n_constructed":0,"n_ran_checked":8,"n_instrument":2,"n_unverified":0,"n_honours":3,"n_violates":0,"n_no_contract":5,"n_pointer_only":3,"phrase":"10 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 3 honoured, 0 violated, 5 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/geometric-trajectory-diffusion-models#ran","syntology_url":"https://syntology.ai/paper/2410.13027","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2410.13027"}},"official":{"repos":["hanjq17/geotdm"],"state":"official (archive's flag): 10 ran","n_ran":10,"n_constructed":0,"n_ran_no_instrument_failure":8,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/metalic-meta-learning-in-context-with-protein","slug":"metalic-meta-learning-in-context-with-protein","title":"Metalic: Meta-Learning In-Context with Protein Language Models","date":"2024-10-10","arxiv_id":"2410.08355","repositories_listed":1,"syntology":{"n":11,"n_ran":10,"n_constructed":0,"n_ran_checked":10,"n_instrument":0,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":10,"n_pointer_only":0,"phrase":"10 ran (of which 0 constructed an object rather than computing a result; 10 with no instrument failure: 0 honoured, 0 violated, 10 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/metalic-meta-learning-in-context-with-protein#ran","syntology_url":"https://syntology.ai/paper/2410.08355","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2410.08355"}},"official":{"repos":["instadeepai/metalic"],"state":"official (archive's flag): 10 ran","n_ran":10,"n_constructed":0,"n_ran_no_instrument_failure":10,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/context-guided-diffusion-for-out-of","slug":"context-guided-diffusion-for-out-of","title":"Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design","date":"2024-07-16","arxiv_id":"2407.11942","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":0,"n_instrument":1,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/context-guided-diffusion-for-out-of#ran","syntology_url":"https://syntology.ai/paper/2407.11942","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2407.11942"}},"official":{"repos":["leojklarner/context-guided-diffusion"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/rnaflow-rna-structure-sequence-design-via","slug":"rnaflow-rna-structure-sequence-design-via","title":"RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching","date":"2024-05-29","arxiv_id":"2405.18768","repositories_listed":1,"syntology":{"n":4,"n_ran":3,"n_constructed":0,"n_ran_checked":3,"n_instrument":0,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":3,"n_pointer_only":0,"phrase":"3 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/rnaflow-rna-structure-sequence-design-via#ran","syntology_url":"https://syntology.ai/paper/2405.18768","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2405.18768"}},"official":{"repos":["divnori/rnaflow"],"state":"official (archive's flag): 3 ran","n_ran":3,"n_constructed":0,"n_ran_no_instrument_failure":3,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/learning-the-language-of-protein-structure","slug":"learning-the-language-of-protein-structure","title":"Learning the Language of Protein Structure","date":"2024-05-24","arxiv_id":"2405.15840","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":0,"n_instrument":1,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/learning-the-language-of-protein-structure#ran","syntology_url":"https://syntology.ai/paper/2405.15840","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2405.15840"}},"official":{"repos":["instadeepai/protein-structure-tokenizer"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/improved-motif-scaffolding-with-se-3-flow","slug":"improved-motif-scaffolding-with-se-3-flow","title":"Improved motif-scaffolding with SE(3) flow matching","date":"2024-01-08","arxiv_id":"2401.04082","repositories_listed":2,"syntology":{"n":9,"n_ran":9,"n_constructed":0,"n_ran_checked":7,"n_instrument":2,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":7,"n_pointer_only":2,"phrase":"9 ran (of which 0 constructed an object rather than computing a result; 7 with no instrument failure: 0 honoured, 0 violated, 7 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/improved-motif-scaffolding-with-se-3-flow#ran","syntology_url":"https://syntology.ai/paper/2401.04082","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2401.04082"}},"official":{"repos":["microsoft/frame-flow","microsoft/protein-frame-flow"],"state":"official (archive's flag): 9 ran","n_ran":9,"n_constructed":0,"n_ran_no_instrument_failure":7,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/fast-non-autoregressive-inverse-folding-with","slug":"fast-non-autoregressive-inverse-folding-with","title":"Fast non-autoregressive inverse folding with discrete diffusion","date":"2023-12-05","arxiv_id":"2312.02447","repositories_listed":1,"syntology":{"n":2,"n_ran":2,"n_constructed":0,"n_ran_checked":0,"n_instrument":2,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/fast-non-autoregressive-inverse-folding-with#ran","syntology_url":"https://syntology.ai/paper/2312.02447","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2312.02447"}},"official":{"repos":["johnyang101/pmpnndiff"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/score-based-generative-models-for-designing","slug":"score-based-generative-models-for-designing","title":"Score-Based Generative Models for Designing Binding Peptide Backbones","date":"2023-10-10","arxiv_id":"2310.07051","repositories_listed":1,"syntology":{"n":5,"n_ran":4,"n_constructed":0,"n_ran_checked":4,"n_instrument":0,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":4,"n_pointer_only":5,"phrase":"4 ran (of which 0 constructed an object rather than computing a result; 4 with no instrument failure: 0 honoured, 0 violated, 4 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/score-based-generative-models-for-designing#ran","syntology_url":"https://syntology.ai/paper/2310.07051","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.07051"}},"official":{"repos":["mgreenig/loopgen"],"state":"official (archive's flag): 4 ran","n_ran":4,"n_constructed":0,"n_ran_no_instrument_failure":4,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/openproteinset-training-data-for-structural","slug":"openproteinset-training-data-for-structural","title":"OpenProteinSet: Training data for structural biology at scale","date":"2023-08-10","arxiv_id":"2308.05326","repositories_listed":1,"syntology":{"n":4,"n_ran":4,"n_constructed":0,"n_ran_checked":2,"n_instrument":2,"n_unverified":0,"n_honours":1,"n_violates":1,"n_no_contract":0,"n_pointer_only":0,"phrase":"4 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 1 honoured, 1 violated, 0 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/openproteinset-training-data-for-structural#ran","syntology_url":"https://syntology.ai/paper/2308.05326","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2308.05326"}},"official":{"repos":["aqlaboratory/openfold"],"state":"official (archive's flag): 4 ran","n_ran":4,"n_constructed":0,"n_ran_no_instrument_failure":2,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/metropolis-sampling-for-constrained-diffusion","slug":"metropolis-sampling-for-constrained-diffusion","title":"Metropolis Sampling for Constrained Diffusion Models","date":"2023-07-11","arxiv_id":"2307.05439","repositories_listed":0,"syntology":{"n":8,"n_ran":8,"n_constructed":0,"n_ran_checked":8,"n_instrument":0,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":8,"n_pointer_only":0,"phrase":"8 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 0 honoured, 0 violated, 8 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/metropolis-sampling-for-constrained-diffusion#ran","syntology_url":"https://syntology.ai/paper/2307.05439","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2307.05439"}},"official":null}},{"url":"/paper/practical-and-asymptotically-exact-1","slug":"practical-and-asymptotically-exact-1","title":"Practical and Asymptotically Exact Conditional Sampling in Diffusion Models","date":"2023-06-30","arxiv_id":"2306.17775","repositories_listed":2,"syntology":{"n":15,"n_ran":9,"n_constructed":1,"n_ran_checked":2,"n_instrument":7,"n_unverified":6,"n_honours":1,"n_violates":0,"n_no_contract":1,"n_pointer_only":15,"phrase":"9 ran (of which 1 constructed an object rather than computing a result; 2 with no instrument failure: 1 honoured, 0 violated, 1 with no contract checked; 7 where Syntology's instrument failed) · 6 unverified","sample_list":"/paper/practical-and-asymptotically-exact-1#ran","syntology_url":"https://syntology.ai/paper/2306.17775","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2306.17775"}},"official":{"repos":["blt2114/twisted_diffusion_sampler"],"state":"official (archive's flag): 9 ran","n_ran":9,"n_constructed":1,"n_ran_no_instrument_failure":2,"n_unverified":6,"ran_from_kinds":["official"]}}},{"url":"/paper/mol-instructions-a-large-scale-biomolecular","slug":"mol-instructions-a-large-scale-biomolecular","title":"Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models","date":"2023-06-13","arxiv_id":"2306.08018","repositories_listed":1,"syntology":{"n":2,"n_ran":2,"n_constructed":0,"n_ran_checked":2,"n_instrument":0,"n_unverified":0,"n_honours":2,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 2 with no instrument failure: 2 honoured, 0 violated, 0 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/mol-instructions-a-large-scale-biomolecular#ran","syntology_url":"https://syntology.ai/paper/2306.08018","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2306.08018"}},"official":{"repos":["zjunlp/mol-instructions"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":2,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/protein-design-with-guided-discrete-diffusion-1","slug":"protein-design-with-guided-discrete-diffusion-1","title":"Protein Design with Guided Discrete Diffusion","date":"2023-05-31","arxiv_id":"2305.20009","repositories_listed":1,"syntology":{"n":16,"n_ran":14,"n_constructed":0,"n_ran_checked":14,"n_instrument":0,"n_unverified":2,"n_honours":1,"n_violates":0,"n_no_contract":13,"n_pointer_only":1,"phrase":"14 ran (of which 0 constructed an object rather than computing a result; 14 with no instrument failure: 1 honoured, 0 violated, 13 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified","sample_list":"/paper/protein-design-with-guided-discrete-diffusion-1#ran","syntology_url":"https://syntology.ai/paper/2305.20009","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2305.20009"}},"official":{"repos":["ngruver/nos"],"state":"official (archive's flag): 14 ran","n_ran":14,"n_constructed":0,"n_ran_no_instrument_failure":14,"n_unverified":2,"ran_from_kinds":["official"]}}},{"url":"/paper/property-guided-generative-modelling-for","slug":"property-guided-generative-modelling-for","title":"Robust Model-Based Optimization for Challenging Fitness Landscapes","date":"2023-05-23","arxiv_id":"2305.13650","repositories_listed":1,"syntology":{"n":2,"n_ran":2,"n_constructed":0,"n_ran_checked":0,"n_instrument":2,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":2,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/property-guided-generative-modelling-for#ran","syntology_url":"https://syntology.ai/paper/2305.13650","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2305.13650"}},"official":{"repos":["sabagh1994/pgvae"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/a-text-guided-protein-design-framework","slug":"a-text-guided-protein-design-framework","title":"A Text-guided Protein Design Framework","date":"2023-02-09","arxiv_id":"2302.04611","repositories_listed":3,"syntology":{"n":3,"n_ran":2,"n_constructed":0,"n_ran_checked":1,"n_instrument":1,"n_unverified":1,"n_honours":1,"n_violates":0,"n_no_contract":0,"n_pointer_only":1,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/a-text-guided-protein-design-framework#ran","syntology_url":"https://syntology.ai/paper/2302.04611","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2302.04611"}},"official":{"repos":["QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling","chao1224/proteindt"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":1,"ran_from_kinds":["official","unlocated"]}}},{"url":"/paper/geometry-complete-diffusion-for-3d-molecule","slug":"geometry-complete-diffusion-for-3d-molecule","title":"Geometry-Complete Diffusion for 3D Molecule Generation and Optimization","date":"2023-02-08","arxiv_id":"2302.04313","repositories_listed":3,"syntology":{"n":10,"n_ran":7,"n_constructed":0,"n_ran_checked":7,"n_instrument":0,"n_unverified":3,"n_honours":0,"n_violates":0,"n_no_contract":7,"n_pointer_only":0,"phrase":"7 ran (of which 0 constructed an object rather than computing a result; 7 with no instrument failure: 0 honoured, 0 violated, 7 with no contract checked; 0 where Syntology's instrument failed) · 3 unverified","sample_list":"/paper/geometry-complete-diffusion-for-3d-molecule#ran","syntology_url":"https://syntology.ai/paper/2302.04313","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2302.04313"}},"official":{"repos":["bioinfomachinelearning/bio-diffusion","bioinfomachinelearning/gcdm-sbdd"],"state":"official (archive's flag): 7 ran","n_ran":7,"n_constructed":0,"n_ran_no_instrument_failure":7,"n_unverified":2,"ran_from_kinds":["official"]}}},{"url":"/paper/generating-novel-designable-and-diverse","slug":"generating-novel-designable-and-diverse","title":"Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds","date":"2023-01-29","arxiv_id":"2301.12485","repositories_listed":1,"syntology":{"n":5,"n_ran":5,"n_constructed":0,"n_ran_checked":5,"n_instrument":0,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":5,"n_pointer_only":0,"phrase":"5 ran (of which 0 constructed an object rather than computing a result; 5 with no instrument failure: 0 honoured, 0 violated, 5 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/generating-novel-designable-and-diverse#ran","syntology_url":"https://syntology.ai/paper/2301.12485","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2301.12485"}},"official":{"repos":["aqlaboratory/genie"],"state":"official (archive's flag): 5 ran","n_ran":5,"n_constructed":0,"n_ran_no_instrument_failure":5,"n_unverified":0,"ran_from_kinds":["official"]}}},{"url":"/paper/prodesign-toward-effective-and-efficient","slug":"prodesign-toward-effective-and-efficient","title":"PiFold: Toward effective and efficient protein inverse folding","date":"2022-09-22","arxiv_id":"2209.12643","repositories_listed":1,"syntology":{"n":2,"n_ran":1,"n_constructed":0,"n_ran_checked":1,"n_instrument":0,"n_unverified":1,"n_honours":1,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/prodesign-toward-effective-and-efficient#ran","syntology_url":"https://syntology.ai/paper/2209.12643","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2209.12643"}},"official":{"repos":["A4Bio/PiFold"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":1,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/few-shot-learning-of-accurate-folding","slug":"few-shot-learning-of-accurate-folding","title":"Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction","date":"2022-08-20","arxiv_id":"2208.09652","repositories_listed":2,"syntology":{"n":12,"n_ran":7,"n_constructed":0,"n_ran_checked":5,"n_instrument":2,"n_unverified":5,"n_honours":0,"n_violates":0,"n_no_contract":5,"n_pointer_only":2,"phrase":"7 ran (of which 0 constructed an object rather than computing a result; 5 with no instrument failure: 0 honoured, 0 violated, 5 with no contract checked; 2 where Syntology's instrument failed) · 5 unverified","sample_list":"/paper/few-shot-learning-of-accurate-folding#ran","syntology_url":"https://syntology.ai/paper/2208.09652","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2208.09652"}},"official":{"repos":["mindspore-ai/mindscience"],"state":"official (archive's flag): 5 ran","n_ran":5,"n_constructed":0,"n_ran_no_instrument_failure":5,"n_unverified":5,"ran_from_kinds":["listed","official"]}}},{"url":"/paper/progen2-exploring-the-boundaries-of-protein","slug":"progen2-exploring-the-boundaries-of-protein","title":"ProGen2: Exploring the Boundaries of Protein Language Models","date":"2022-06-27","arxiv_id":"2206.13517","repositories_listed":4,"syntology":{"n":18,"n_ran":13,"n_constructed":0,"n_ran_checked":8,"n_instrument":5,"n_unverified":5,"n_honours":0,"n_violates":0,"n_no_contract":8,"n_pointer_only":4,"phrase":"13 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 0 honoured, 0 violated, 8 with no contract checked; 5 where Syntology's instrument failed) · 5 unverified","sample_list":"/paper/progen2-exploring-the-boundaries-of-protein#ran","syntology_url":"https://syntology.ai/paper/2206.13517","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2206.13517"}},"official":{"repos":["salesforce/progen"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["listed","official","unlocated"]}}},{"url":"/paper/rita-a-study-on-scaling-up-generative-protein","slug":"rita-a-study-on-scaling-up-generative-protein","title":"RITA: a Study on Scaling Up Generative Protein Sequence Models","date":"2022-05-11","arxiv_id":"2205.05789","repositories_listed":4,"syntology":{"n":2,"n_ran":1,"n_constructed":0,"n_ran_checked":1,"n_instrument":0,"n_unverified":1,"n_honours":1,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/rita-a-study-on-scaling-up-generative-protein#ran","syntology_url":"https://syntology.ai/paper/2205.05789","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2205.05789"}},"official":{"repos":["lightonai/rita"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":1,"n_unverified":1,"ran_from_kinds":["official"]}}},{"url":"/paper/iterative-refinement-graph-neural-network-for-1","slug":"iterative-refinement-graph-neural-network-for-1","title":"Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design","date":"2021-10-09","arxiv_id":"2110.04624","repositories_listed":1,"syntology":{"n":11,"n_ran":8,"n_constructed":5,"n_ran_checked":6,"n_instrument":2,"n_unverified":3,"n_honours":0,"n_violates":0,"n_no_contract":6,"n_pointer_only":0,"phrase":"8 ran (of which 5 constructed an object rather than computing a result; 6 with no instrument failure: 0 honoured, 0 violated, 6 with no contract checked; 2 where Syntology's instrument failed) · 3 unverified","sample_list":"/paper/iterative-refinement-graph-neural-network-for-1#ran","syntology_url":"https://syntology.ai/paper/2110.04624","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2110.04624"}},"official":null}},{"url":"/paper/fold2seq-a-joint-sequence-1d-fold-3d-1","slug":"fold2seq-a-joint-sequence-1d-fold-3d-1","title":"Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design","date":"2021-06-24","arxiv_id":"2106.13058","repositories_listed":1,"syntology":{"n":4,"n_ran":2,"n_constructed":0,"n_ran_checked":1,"n_instrument":1,"n_unverified":2,"n_honours":0,"n_violates":0,"n_no_contract":1,"n_pointer_only":0,"phrase":"2 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 1 where Syntology's instrument failed) · 2 unverified","sample_list":"/paper/fold2seq-a-joint-sequence-1d-fold-3d-1#ran","syntology_url":"https://syntology.ai/paper/2106.13058","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2106.13058"}},"official":{"repos":["IBM/fold2seq"],"state":"official (archive's flag): 2 ran","n_ran":2,"n_constructed":0,"n_ran_no_instrument_failure":1,"n_unverified":2,"ran_from_kinds":["official"]}}},{"url":"/paper/learning-from-protein-structure-with","slug":"learning-from-protein-structure-with","title":"Learning from Protein Structure with Geometric Vector Perceptrons","date":"2020-09-03","arxiv_id":"2009.01411","repositories_listed":3,"syntology":{"n":6,"n_ran":5,"n_constructed":0,"n_ran_checked":1,"n_instrument":4,"n_unverified":1,"n_honours":0,"n_violates":0,"n_no_contract":1,"n_pointer_only":6,"phrase":"5 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 4 where Syntology's instrument failed) · 1 unverified","sample_list":"/paper/learning-from-protein-structure-with#ran","syntology_url":"https://syntology.ai/paper/2009.01411","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2009.01411"}},"official":{"repos":["drorlab/gvp-pytorch"],"state":"official: no sample here; runs from other or unrecorded repositories","n_ran":0,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["listed","named_in_paper"]}}},{"url":"/paper/energy-based-models-for-atomic-resolution-1","slug":"energy-based-models-for-atomic-resolution-1","title":"Energy-based models for atomic-resolution protein conformations","date":"2020-04-27","arxiv_id":"2004.13167","repositories_listed":1,"syntology":{"n":1,"n_ran":1,"n_constructed":0,"n_ran_checked":0,"n_instrument":1,"n_unverified":0,"n_honours":0,"n_violates":0,"n_no_contract":0,"n_pointer_only":0,"phrase":"1 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified","sample_list":"/paper/energy-based-models-for-atomic-resolution-1#ran","syntology_url":"https://syntology.ai/paper/2004.13167","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2004.13167"}},"official":{"repos":["facebookresearch/protein-ebm"],"state":"official (archive's flag): 1 ran","n_ran":1,"n_constructed":0,"n_ran_no_instrument_failure":0,"n_unverified":0,"ran_from_kinds":["official"]}}}],"record_sha256":"1de7712d5a174a7d08b420251411a5368238ecc73a6252a29a64290fa4b3a280","record_changed_at":"2026-09-28","record_changed_at_basis":"first_hashed"}