{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:XS5F5J54IXQUL2QNDZLTGJZHOY","short_pith_number":"pith:XS5F5J54","canonical_record":{"source":{"id":"2502.09571","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-13T18:29:48Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"6dab0fcf7e098fa209849be9e2abe7abac062b5d326182c2278c662f206a97f6","abstract_canon_sha256":"664389ab5c7f6c6fed24213202a00df95ef9dcdb8edf024462b2668e0484b803"},"schema_version":"1.0"},"canonical_sha256":"bcba5ea7bc45e145ea0d1e5733272776251de62bde3d5aa2cb8c091634e47ac5","source":{"kind":"arxiv","id":"2502.09571","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.09571","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"arxiv_version","alias_value":"2502.09571v2","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.09571","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_12","alias_value":"XS5F5J54IXQU","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_16","alias_value":"XS5F5J54IXQUL2QN","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_8","alias_value":"XS5F5J54","created_at":"2026-07-05T11:10:52Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:XS5F5J54IXQUL2QNDZLTGJZHOY","target":"record","payload":{"canonical_record":{"source":{"id":"2502.09571","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-13T18:29:48Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"6dab0fcf7e098fa209849be9e2abe7abac062b5d326182c2278c662f206a97f6","abstract_canon_sha256":"664389ab5c7f6c6fed24213202a00df95ef9dcdb8edf024462b2668e0484b803"},"schema_version":"1.0"},"canonical_sha256":"bcba5ea7bc45e145ea0d1e5733272776251de62bde3d5aa2cb8c091634e47ac5","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:10:52.383027Z","signature_b64":"a4wyMh05opoOlj0BhSe/kVp8V8YVlwzsbahksWhmOKEeIJ4CtLXOpqN5y4iPytj01RWCbw0OoKGFvzfNvQOICQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"bcba5ea7bc45e145ea0d1e5733272776251de62bde3d5aa2cb8c091634e47ac5","last_reissued_at":"2026-07-05T11:10:52.382531Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:10:52.382531Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2502.09571","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T11:10:52Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"uGUCNywS19gf2E3pPoxM0DGJ2m0QKqzL0+MmhU9YNme5f2Sj1JmxBXhQXW0+O2CxPZy6Hwc9f9EXpPqQYQJ3AA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-07T03:46:34.702955Z"},"content_sha256":"471b38a6f59ee6c19d63245045673988dbc64bc17ac1e256a097fd3325cb5ef1","schema_version":"1.0","event_id":"sha256:471b38a6f59ee6c19d63245045673988dbc64bc17ac1e256a097fd3325cb5ef1"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:XS5F5J54IXQUL2QNDZLTGJZHOY","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"cs.LG","authors_text":"Connor W. Coley, Montgomery Bohde, Mrunali Manjrekar, Runzhong Wang, Shuiwang Ji","submitted_at":"2025-02-13T18:29:48Z","abstract_excerpt":"Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae an"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.09571","kind":"arxiv","version":2},"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/2502.09571/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":"2026-07-05T11:10:52Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"HkMC5ZDY/2shdTaqCdiw2M9IpDF0huUK4KL6MGktT1MhlhxBZX5m3h5pmRAJ2LuBIpMy2MkfD9KKeweQ/DzkAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-07T03:46:34.703509Z"},"content_sha256":"1df4076ff20a19c8fcd1c0d36d59c4a5ecf867f1ac187a89126dad2c895e426c","schema_version":"1.0","event_id":"sha256:1df4076ff20a19c8fcd1c0d36d59c4a5ecf867f1ac187a89126dad2c895e426c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/bundle.json","state_url":"https://pith.science/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/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":"2026-08-07T03:46:34Z","links":{"resolver":"https://pith.science/pith/XS5F5J54IXQUL2QNDZLTGJZHOY","bundle":"https://pith.science/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/bundle.json","state":"https://pith.science/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/state.json","well_known_bundle":"https://pith.science/.well-known/pith/XS5F5J54IXQUL2QNDZLTGJZHOY/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:XS5F5J54IXQUL2QNDZLTGJZHOY","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":"664389ab5c7f6c6fed24213202a00df95ef9dcdb8edf024462b2668e0484b803","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-13T18:29:48Z","title_canon_sha256":"6dab0fcf7e098fa209849be9e2abe7abac062b5d326182c2278c662f206a97f6"},"schema_version":"1.0","source":{"id":"2502.09571","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.09571","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"arxiv_version","alias_value":"2502.09571v2","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.09571","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_12","alias_value":"XS5F5J54IXQU","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_16","alias_value":"XS5F5J54IXQUL2QN","created_at":"2026-07-05T11:10:52Z"},{"alias_kind":"pith_short_8","alias_value":"XS5F5J54","created_at":"2026-07-05T11:10:52Z"}],"graph_snapshots":[{"event_id":"sha256:1df4076ff20a19c8fcd1c0d36d59c4a5ecf867f1ac187a89126dad2c895e426c","target":"graph","created_at":"2026-07-05T11:10:52Z","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/2502.09571/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae an","authors_text":"Connor W. Coley, Montgomery Bohde, Mrunali Manjrekar, Runzhong Wang, Shuiwang Ji","cross_cats":["q-bio.QM"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-13T18:29:48Z","title":"DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.09571","kind":"arxiv","version":2},"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":"sha256:471b38a6f59ee6c19d63245045673988dbc64bc17ac1e256a097fd3325cb5ef1","target":"record","created_at":"2026-07-05T11:10:52Z","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":"664389ab5c7f6c6fed24213202a00df95ef9dcdb8edf024462b2668e0484b803","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-13T18:29:48Z","title_canon_sha256":"6dab0fcf7e098fa209849be9e2abe7abac062b5d326182c2278c662f206a97f6"},"schema_version":"1.0","source":{"id":"2502.09571","kind":"arxiv","version":2}},"canonical_sha256":"bcba5ea7bc45e145ea0d1e5733272776251de62bde3d5aa2cb8c091634e47ac5","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"bcba5ea7bc45e145ea0d1e5733272776251de62bde3d5aa2cb8c091634e47ac5","first_computed_at":"2026-07-05T11:10:52.382531Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:10:52.382531Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"a4wyMh05opoOlj0BhSe/kVp8V8YVlwzsbahksWhmOKEeIJ4CtLXOpqN5y4iPytj01RWCbw0OoKGFvzfNvQOICQ==","signature_status":"signed_v1","signed_at":"2026-07-05T11:10:52.383027Z","signed_message":"canonical_sha256_bytes"},"source_id":"2502.09571","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:471b38a6f59ee6c19d63245045673988dbc64bc17ac1e256a097fd3325cb5ef1","sha256:1df4076ff20a19c8fcd1c0d36d59c4a5ecf867f1ac187a89126dad2c895e426c"],"state_sha256":"bed30608f1e574be84d21b82acd59e365c837c67aeda126a3edd16b8a4bedfc5"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"a2KiWmHBgYs0D0Dw/sUO0mqxsam14nKI8MGBWrf+G8Bgi7YveKu5BxO35xlieoIa9DEj46/RyYELSazyZk0QAQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-07T03:46:34.709930Z","bundle_sha256":"b357bafa529d5cee16160cd3414e4d5daac5a79c46d3ce7e88d45088a277bcca"}}