{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:AIEBGSVNIYUKBKDQWKPJI5VGOM","short_pith_number":"pith:AIEBGSVN","canonical_record":{"source":{"id":"2502.19397","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2025-02-11T10:10:33Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"5159e235b29280541ea8049e6edd3fc7190fed1ed9513a6e35b3d97a665154ab","abstract_canon_sha256":"2e41367c140f717ab8c6b4c0f9f051b5ab0b0cd572451f0dfc6c7f3cd5810808"},"schema_version":"1.0"},"canonical_sha256":"0208134aad4628a0a870b29e9476a6731573aa5523f0952f572dd8ecd18cffd0","source":{"kind":"arxiv","id":"2502.19397","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.19397","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"arxiv_version","alias_value":"2502.19397v1","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.19397","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_12","alias_value":"AIEBGSVNIYUK","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_16","alias_value":"AIEBGSVNIYUKBKDQ","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_8","alias_value":"AIEBGSVN","created_at":"2026-07-05T10:20:31Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:AIEBGSVNIYUKBKDQWKPJI5VGOM","target":"record","payload":{"canonical_record":{"source":{"id":"2502.19397","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2025-02-11T10:10:33Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"5159e235b29280541ea8049e6edd3fc7190fed1ed9513a6e35b3d97a665154ab","abstract_canon_sha256":"2e41367c140f717ab8c6b4c0f9f051b5ab0b0cd572451f0dfc6c7f3cd5810808"},"schema_version":"1.0"},"canonical_sha256":"0208134aad4628a0a870b29e9476a6731573aa5523f0952f572dd8ecd18cffd0","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:20:31.543110Z","signature_b64":"gRmxawL7CL8nm4/0koSz/AHmbGChl5tH6zDKCI6JJLi38ugL16iuiGCnM7m/Jx+r+gTh6Sbf76PLlc5wNRu9BQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"0208134aad4628a0a870b29e9476a6731573aa5523f0952f572dd8ecd18cffd0","last_reissued_at":"2026-07-05T10:20:31.542613Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:20:31.542613Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2502.19397","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":"2026-07-05T10:20:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"sHeB0K0KehgLiC2YjH/iFiSe7t/LLhB1kivKyAYvvXhx36WuuXV1j2kaMVXHMAYhZplCjyfX4prMM7iaDvEPCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-09T18:00:52.715989Z"},"content_sha256":"3a1e672435766e2fa616757807e82b9d10178239af79c42ab353f981d9e69bca","schema_version":"1.0","event_id":"sha256:3a1e672435766e2fa616757807e82b9d10178239af79c42ab353f981d9e69bca"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:AIEBGSVNIYUKBKDQWKPJI5VGOM","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Modelling Chemical Reaction Networks using Neural Ordinary Differential Equations","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.MN","authors_text":"Anna C. M. Th\\\"oni, Tal Kachman, Wilhelm T. S. Huck, William E. Robinson, Yoram Bachrach","submitted_at":"2025-02-11T10:10:33Z","abstract_excerpt":"In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an empirical model of the reaction network, it may be incomplete. Our approach aims to elucidate these hidden insights in the reaction network by combining dynamic modelling with deep learning in the form of neural ordinary differential equations. Our contributions not only help to identify the shortcomings of existing empirical models but also assist the design of fu"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.19397","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/2502.19397/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":"2026-07-05T10:20:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"F551QcI2/aahfBHoumo3T/z4wgGup8AXsuKlqwqDPsg/CljgyailOX4ghJWU9rOlc1/iXP8n5cxuQVOgsH7aCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-09T18:00:52.716555Z"},"content_sha256":"d5a7e97de988fcd3dfeeb0c3baada0a5d913abe6eba91293ca13a578ddb0a51f","schema_version":"1.0","event_id":"sha256:d5a7e97de988fcd3dfeeb0c3baada0a5d913abe6eba91293ca13a578ddb0a51f"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/bundle.json","state_url":"https://pith.science/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/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":"2026-08-09T18:00:52Z","links":{"resolver":"https://pith.science/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM","bundle":"https://pith.science/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/bundle.json","state":"https://pith.science/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/state.json","well_known_bundle":"https://pith.science/.well-known/pith/AIEBGSVNIYUKBKDQWKPJI5VGOM/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:AIEBGSVNIYUKBKDQWKPJI5VGOM","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":"2e41367c140f717ab8c6b4c0f9f051b5ab0b0cd572451f0dfc6c7f3cd5810808","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2025-02-11T10:10:33Z","title_canon_sha256":"5159e235b29280541ea8049e6edd3fc7190fed1ed9513a6e35b3d97a665154ab"},"schema_version":"1.0","source":{"id":"2502.19397","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.19397","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"arxiv_version","alias_value":"2502.19397v1","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.19397","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_12","alias_value":"AIEBGSVNIYUK","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_16","alias_value":"AIEBGSVNIYUKBKDQ","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_8","alias_value":"AIEBGSVN","created_at":"2026-07-05T10:20:31Z"}],"graph_snapshots":[{"event_id":"sha256:d5a7e97de988fcd3dfeeb0c3baada0a5d913abe6eba91293ca13a578ddb0a51f","target":"graph","created_at":"2026-07-05T10:20:31Z","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/2502.19397/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an empirical model of the reaction network, it may be incomplete. Our approach aims to elucidate these hidden insights in the reaction network by combining dynamic modelling with deep learning in the form of neural ordinary differential equations. Our contributions not only help to identify the shortcomings of existing empirical models but also assist the design of fu","authors_text":"Anna C. M. Th\\\"oni, Tal Kachman, Wilhelm T. S. Huck, William E. Robinson, Yoram Bachrach","cross_cats":["cs.LG"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2025-02-11T10:10:33Z","title":"Modelling Chemical Reaction Networks using Neural Ordinary Differential Equations"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.19397","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":"sha256:3a1e672435766e2fa616757807e82b9d10178239af79c42ab353f981d9e69bca","target":"record","created_at":"2026-07-05T10:20:31Z","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":"2e41367c140f717ab8c6b4c0f9f051b5ab0b0cd572451f0dfc6c7f3cd5810808","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2025-02-11T10:10:33Z","title_canon_sha256":"5159e235b29280541ea8049e6edd3fc7190fed1ed9513a6e35b3d97a665154ab"},"schema_version":"1.0","source":{"id":"2502.19397","kind":"arxiv","version":1}},"canonical_sha256":"0208134aad4628a0a870b29e9476a6731573aa5523f0952f572dd8ecd18cffd0","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"0208134aad4628a0a870b29e9476a6731573aa5523f0952f572dd8ecd18cffd0","first_computed_at":"2026-07-05T10:20:31.542613Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:20:31.542613Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"gRmxawL7CL8nm4/0koSz/AHmbGChl5tH6zDKCI6JJLi38ugL16iuiGCnM7m/Jx+r+gTh6Sbf76PLlc5wNRu9BQ==","signature_status":"signed_v1","signed_at":"2026-07-05T10:20:31.543110Z","signed_message":"canonical_sha256_bytes"},"source_id":"2502.19397","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3a1e672435766e2fa616757807e82b9d10178239af79c42ab353f981d9e69bca","sha256:d5a7e97de988fcd3dfeeb0c3baada0a5d913abe6eba91293ca13a578ddb0a51f"],"state_sha256":"d55f0add33d17bed2b3d54316f501131c6617315a0565e2f23e9904e764ccb40"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Obz9kC0cVp/qE9x5EhcRuTvyTWx3UCZSt/RvY8Yf05hWmujnZaPAOK0bTSA7QmZyk9U/iShcC3pueE9rdvaECg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-09T18:00:52.720100Z","bundle_sha256":"71ab645cd89372b1fa244381581848148b7532205c9ca418a34f2810b870150a"}}