{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2020:FGDDE46DG5HIQXS5IP5ONOI4VO","short_pith_number":"pith:FGDDE46D","canonical_record":{"source":{"id":"2010.03068","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2020-10-06T22:45:19Z","cross_cats_sorted":["math.CO"],"title_canon_sha256":"bb690235d306ed3a5674754bc67af5a883bd04e64fd59b42857cc31bd1faf643","abstract_canon_sha256":"5f529d19579a4afda4078420a0cd9dcdfb320ed34d49dab7d28fc9792027c560"},"schema_version":"1.0"},"canonical_sha256":"29863273c3374e885e5d43fae6b91cab8e3fc9de67eaffbcbca0a8f51a5510df","source":{"kind":"arxiv","id":"2010.03068","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2010.03068","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"arxiv_version","alias_value":"2010.03068v1","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2010.03068","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_12","alias_value":"FGDDE46DG5HI","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_16","alias_value":"FGDDE46DG5HIQXS5","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_8","alias_value":"FGDDE46D","created_at":"2026-07-05T01:40:59Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2020:FGDDE46DG5HIQXS5IP5ONOI4VO","target":"record","payload":{"canonical_record":{"source":{"id":"2010.03068","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2020-10-06T22:45:19Z","cross_cats_sorted":["math.CO"],"title_canon_sha256":"bb690235d306ed3a5674754bc67af5a883bd04e64fd59b42857cc31bd1faf643","abstract_canon_sha256":"5f529d19579a4afda4078420a0cd9dcdfb320ed34d49dab7d28fc9792027c560"},"schema_version":"1.0"},"canonical_sha256":"29863273c3374e885e5d43fae6b91cab8e3fc9de67eaffbcbca0a8f51a5510df","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T01:40:59.239332Z","signature_b64":"AAdfkiwfJ5mwy6TCxuDmrfU8Yj3VUt9G83GaQKSaDspbDUV41x1emyPSwlHJ2YEYDXGOQpPzTWSR6K8Rekq2Dg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"29863273c3374e885e5d43fae6b91cab8e3fc9de67eaffbcbca0a8f51a5510df","last_reissued_at":"2026-07-05T01:40:59.238837Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T01:40:59.238837Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2010.03068","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":"2026-07-05T01:40:59Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"mtuIBbo5X6lcqj7tKJWY0+p1p9Z+zx9+A6zJ1L3+UHkZklsMXVvI3lprjDNkcr3WOlmlvAIa0Sth2blUbOvIBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T16:13:39.793144Z"},"content_sha256":"436739e38584bd76d714e30b5037dff724df0808b69190566c68874bf76c530d","schema_version":"1.0","event_id":"sha256:436739e38584bd76d714e30b5037dff724df0808b69190566c68874bf76c530d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2020:FGDDE46DG5HIQXS5IP5ONOI4VO","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["math.CO"],"primary_cat":"q-bio.QM","authors_text":"Adam S. Cockrell, Amie J. Eisfeld, Amy C. Sims, Brenda Praggastis, Brett Jefferson, Cliff Joslyn, Danielle Westhoff-Smith, Emilie Purvine, Emily Heath, Henry Kvinge, Hugh D. Mitchell, Jacob F. Kocher, Jason E. McDermott, Katrina M. Waters, Kelly G. Stratton, Kevin B. Walters, Larissa B. Thackray, Lisa M. Bramer, Michael S. Diamond, Natalie C. Heller, Peter J. Halfmann, Qing Tan, Ralph S. Baric, Shufang Fan, Song Feng, Timothy P. Sheahan, Vineet D. Menachery, Yoshihiro Kawaoka","submitted_at":"2020-10-06T22:45:19Z","abstract_excerpt":"Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, imp"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2010.03068","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/2010.03068/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":"2026-07-05T01:40:59Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"rNi2InLnCrmO+QycnV94hgGxhI698w1Tf47lK5z4bDxFtJlLTArb7PdHyQMuNU2kYdNO02Jjpm0E5Cs5J5kkAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T16:13:39.794103Z"},"content_sha256":"d6f6a7f868748b157810eb42dfcb4db7274141164cac802dcf54e4f085b5fa28","schema_version":"1.0","event_id":"sha256:d6f6a7f868748b157810eb42dfcb4db7274141164cac802dcf54e4f085b5fa28"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/bundle.json","state_url":"https://pith.science/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/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":"2026-08-13T16:13:39Z","links":{"resolver":"https://pith.science/pith/FGDDE46DG5HIQXS5IP5ONOI4VO","bundle":"https://pith.science/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/bundle.json","state":"https://pith.science/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/state.json","well_known_bundle":"https://pith.science/.well-known/pith/FGDDE46DG5HIQXS5IP5ONOI4VO/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2020:FGDDE46DG5HIQXS5IP5ONOI4VO","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":"5f529d19579a4afda4078420a0cd9dcdfb320ed34d49dab7d28fc9792027c560","cross_cats_sorted":["math.CO"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2020-10-06T22:45:19Z","title_canon_sha256":"bb690235d306ed3a5674754bc67af5a883bd04e64fd59b42857cc31bd1faf643"},"schema_version":"1.0","source":{"id":"2010.03068","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2010.03068","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"arxiv_version","alias_value":"2010.03068v1","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2010.03068","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_12","alias_value":"FGDDE46DG5HI","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_16","alias_value":"FGDDE46DG5HIQXS5","created_at":"2026-07-05T01:40:59Z"},{"alias_kind":"pith_short_8","alias_value":"FGDDE46D","created_at":"2026-07-05T01:40:59Z"}],"graph_snapshots":[{"event_id":"sha256:d6f6a7f868748b157810eb42dfcb4db7274141164cac802dcf54e4f085b5fa28","target":"graph","created_at":"2026-07-05T01:40:59Z","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/2010.03068/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, imp","authors_text":"Adam S. Cockrell, Amie J. Eisfeld, Amy C. Sims, Brenda Praggastis, Brett Jefferson, Cliff Joslyn, Danielle Westhoff-Smith, Emilie Purvine, Emily Heath, Henry Kvinge, Hugh D. Mitchell, Jacob F. Kocher, Jason E. McDermott, Katrina M. Waters, Kelly G. Stratton, Kevin B. Walters, Larissa B. Thackray, Lisa M. Bramer, Michael S. Diamond, Natalie C. Heller, Peter J. Halfmann, Qing Tan, Ralph S. Baric, Shufang Fan, Song Feng, Timothy P. Sheahan, Vineet D. Menachery, Yoshihiro Kawaoka","cross_cats":["math.CO"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2020-10-06T22:45:19Z","title":"Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2010.03068","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":"sha256:436739e38584bd76d714e30b5037dff724df0808b69190566c68874bf76c530d","target":"record","created_at":"2026-07-05T01:40:59Z","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":"5f529d19579a4afda4078420a0cd9dcdfb320ed34d49dab7d28fc9792027c560","cross_cats_sorted":["math.CO"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2020-10-06T22:45:19Z","title_canon_sha256":"bb690235d306ed3a5674754bc67af5a883bd04e64fd59b42857cc31bd1faf643"},"schema_version":"1.0","source":{"id":"2010.03068","kind":"arxiv","version":1}},"canonical_sha256":"29863273c3374e885e5d43fae6b91cab8e3fc9de67eaffbcbca0a8f51a5510df","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"29863273c3374e885e5d43fae6b91cab8e3fc9de67eaffbcbca0a8f51a5510df","first_computed_at":"2026-07-05T01:40:59.238837Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T01:40:59.238837Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"AAdfkiwfJ5mwy6TCxuDmrfU8Yj3VUt9G83GaQKSaDspbDUV41x1emyPSwlHJ2YEYDXGOQpPzTWSR6K8Rekq2Dg==","signature_status":"signed_v1","signed_at":"2026-07-05T01:40:59.239332Z","signed_message":"canonical_sha256_bytes"},"source_id":"2010.03068","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:436739e38584bd76d714e30b5037dff724df0808b69190566c68874bf76c530d","sha256:d6f6a7f868748b157810eb42dfcb4db7274141164cac802dcf54e4f085b5fa28"],"state_sha256":"561aca0de43f51166ce8dad059af00078124492d6ebea8df066e23e2abb19f03"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"v0zmecetDLSqwOHMcvoOZhcwvCoadjbD8aDCCT1fMaVw2oUVSeCIqX8Kr/2g86n7z5Vjs0QzXzxnSQhLZrNUBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-13T16:13:39.821551Z","bundle_sha256":"f8a154e8a70d7d4b1a949a5d0e769431a1d050f4f5d3aa18c2bf0c66ac169acb"}}