{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:ZWFK34MJCHYP4IUKB45UMD3Z2M","short_pith_number":"pith:ZWFK34MJ","canonical_record":{"source":{"id":"2402.13297","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2024-02-20T05:41:46Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"e4cb8c5b3d2b784da467bf4d75875071a2888393595e10c60c711acedb62d78a","abstract_canon_sha256":"6ca2f21e44341a35823f04235808da4998f69d6ef0de225fa91705e4b0610c60"},"schema_version":"1.0"},"canonical_sha256":"cd8aadf18911f0fe228a0f3b460f79d3198097ae17f88d255823c7ba1499a26e","source":{"kind":"arxiv","id":"2402.13297","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2402.13297","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"arxiv_version","alias_value":"2402.13297v1","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2402.13297","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_12","alias_value":"ZWFK34MJCHYP","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_16","alias_value":"ZWFK34MJCHYP4IUK","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_8","alias_value":"ZWFK34MJ","created_at":"2026-07-05T07:47:30Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:ZWFK34MJCHYP4IUKB45UMD3Z2M","target":"record","payload":{"canonical_record":{"source":{"id":"2402.13297","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2024-02-20T05:41:46Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"e4cb8c5b3d2b784da467bf4d75875071a2888393595e10c60c711acedb62d78a","abstract_canon_sha256":"6ca2f21e44341a35823f04235808da4998f69d6ef0de225fa91705e4b0610c60"},"schema_version":"1.0"},"canonical_sha256":"cd8aadf18911f0fe228a0f3b460f79d3198097ae17f88d255823c7ba1499a26e","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T07:47:30.175466Z","signature_b64":"JcHbmdyB8x+4qtUUeYqZQoK/aO585gk/uHV5ZLqxmkqtTgFoZLqcGUCCjOKhkOBLY6mWuJ0qDqAGtR8kOqFvBQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"cd8aadf18911f0fe228a0f3b460f79d3198097ae17f88d255823c7ba1499a26e","last_reissued_at":"2026-07-05T07:47:30.175043Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T07:47:30.175043Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2402.13297","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T07:47:30Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5/xc7FXbWU4/kmLvowkkPYQFswF1Q+eSxULN4OwNrmzJFvDXzTLUXt0QPXhsls7E1ftu65l3iuf7M9SmL5QkDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-19T07:40:48.932853Z"},"content_sha256":"fa96b018de4eb2328837e72273b7efd5be7440275431490d5da7a8d0ab057917","schema_version":"1.0","event_id":"sha256:fa96b018de4eb2328837e72273b7efd5be7440275431490d5da7a8d0ab057917"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:ZWFK34MJCHYP4IUKB45UMD3Z2M","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-terminal Coding Sequences","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.QM","authors_text":"Kaiwen Tang, Shida Wang, Weiran Chu, Weng-Fai Wong, Yanfeng Liu, Yuhua Sheng, Zhanglu Yan","submitted_at":"2024-02-20T05:41:46Z","abstract_excerpt":"N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology co-designed few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2402.13297","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2402.13297/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T07:47:30Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"j+QvFoRMgnxpmOovsYuVfFGb+DSMDdEY5CEa0ebT+hAmoGCp86avUYqfF7IRAcK0c3UJZaGHK+avcxTVyXkwCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-19T07:40:48.933235Z"},"content_sha256":"4802e3afd092d8813355994dbe677009744d3323853ffd30e52a4dea5f231817","schema_version":"1.0","event_id":"sha256:4802e3afd092d8813355994dbe677009744d3323853ffd30e52a4dea5f231817"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/bundle.json","state_url":"https://pith.science/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-07-19T07:40:48Z","links":{"resolver":"https://pith.science/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M","bundle":"https://pith.science/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/bundle.json","state":"https://pith.science/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/state.json","well_known_bundle":"https://pith.science/.well-known/pith/ZWFK34MJCHYP4IUKB45UMD3Z2M/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:ZWFK34MJCHYP4IUKB45UMD3Z2M","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"6ca2f21e44341a35823f04235808da4998f69d6ef0de225fa91705e4b0610c60","cross_cats_sorted":["cs.AI"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2024-02-20T05:41:46Z","title_canon_sha256":"e4cb8c5b3d2b784da467bf4d75875071a2888393595e10c60c711acedb62d78a"},"schema_version":"1.0","source":{"id":"2402.13297","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2402.13297","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"arxiv_version","alias_value":"2402.13297v1","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2402.13297","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_12","alias_value":"ZWFK34MJCHYP","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_16","alias_value":"ZWFK34MJCHYP4IUK","created_at":"2026-07-05T07:47:30Z"},{"alias_kind":"pith_short_8","alias_value":"ZWFK34MJ","created_at":"2026-07-05T07:47:30Z"}],"graph_snapshots":[{"event_id":"sha256:4802e3afd092d8813355994dbe677009744d3323853ffd30e52a4dea5f231817","target":"graph","created_at":"2026-07-05T07:47:30Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2402.13297/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology co-designed few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then ","authors_text":"Kaiwen Tang, Shida Wang, Weiran Chu, Weng-Fai Wong, Yanfeng Liu, Yuhua Sheng, Zhanglu Yan","cross_cats":["cs.AI"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2024-02-20T05:41:46Z","title":"Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-terminal Coding Sequences"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2402.13297","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:fa96b018de4eb2328837e72273b7efd5be7440275431490d5da7a8d0ab057917","target":"record","created_at":"2026-07-05T07:47:30Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"6ca2f21e44341a35823f04235808da4998f69d6ef0de225fa91705e4b0610c60","cross_cats_sorted":["cs.AI"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2024-02-20T05:41:46Z","title_canon_sha256":"e4cb8c5b3d2b784da467bf4d75875071a2888393595e10c60c711acedb62d78a"},"schema_version":"1.0","source":{"id":"2402.13297","kind":"arxiv","version":1}},"canonical_sha256":"cd8aadf18911f0fe228a0f3b460f79d3198097ae17f88d255823c7ba1499a26e","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"cd8aadf18911f0fe228a0f3b460f79d3198097ae17f88d255823c7ba1499a26e","first_computed_at":"2026-07-05T07:47:30.175043Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T07:47:30.175043Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"JcHbmdyB8x+4qtUUeYqZQoK/aO585gk/uHV5ZLqxmkqtTgFoZLqcGUCCjOKhkOBLY6mWuJ0qDqAGtR8kOqFvBQ==","signature_status":"signed_v1","signed_at":"2026-07-05T07:47:30.175466Z","signed_message":"canonical_sha256_bytes"},"source_id":"2402.13297","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:fa96b018de4eb2328837e72273b7efd5be7440275431490d5da7a8d0ab057917","sha256:4802e3afd092d8813355994dbe677009744d3323853ffd30e52a4dea5f231817"],"state_sha256":"e83690f65f46dbb836ad885bfda67c467fbb1744f15513dbec80038866a7a15c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ty+hy+Fp9N8mCUCesgB0c40FrwthUvgL7vpoW8qiPZfbLanWMcraalYF3FPoEbVqOy7bwcqD+bYqtc0w7/CUBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-19T07:40:48.935529Z","bundle_sha256":"66a450ab506790288b1b68a17dc00b8323a6861892f140ad2abbdd6ef92ebe45"}}