{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:J7CFJCDT63FZNXOAYXHWSFQHXQ","short_pith_number":"pith:J7CFJCDT","canonical_record":{"source":{"id":"2404.07194","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2024-04-10T17:50:29Z","cross_cats_sorted":["cs.AI","q-bio.BM"],"title_canon_sha256":"6527f63a7f656154a896ae8f06d986ed3fe32349ca1bb3e4e14fbdbfb83bcd19","abstract_canon_sha256":"4161b646bf33db8dc6aa24d8ed59e16525fbbcb995a8a2cf52b5f4eb35fb9f72"},"schema_version":"1.0"},"canonical_sha256":"4fc4548873f6cb96ddc0c5cf691607bc1af0cc5abbfcea75c142fe00ecfce10c","source":{"kind":"arxiv","id":"2404.07194","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2404.07194","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"arxiv_version","alias_value":"2404.07194v1","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2404.07194","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_12","alias_value":"J7CFJCDT63FZ","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_16","alias_value":"J7CFJCDT63FZNXOA","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_8","alias_value":"J7CFJCDT","created_at":"2026-07-05T08:06:36Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:J7CFJCDT63FZNXOAYXHWSFQHXQ","target":"record","payload":{"canonical_record":{"source":{"id":"2404.07194","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2024-04-10T17:50:29Z","cross_cats_sorted":["cs.AI","q-bio.BM"],"title_canon_sha256":"6527f63a7f656154a896ae8f06d986ed3fe32349ca1bb3e4e14fbdbfb83bcd19","abstract_canon_sha256":"4161b646bf33db8dc6aa24d8ed59e16525fbbcb995a8a2cf52b5f4eb35fb9f72"},"schema_version":"1.0"},"canonical_sha256":"4fc4548873f6cb96ddc0c5cf691607bc1af0cc5abbfcea75c142fe00ecfce10c","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T08:06:36.718780Z","signature_b64":"w39jj8vEL2aTtSR9kPuAeNbFdOrCDwN32/Y20/SOmg7w1Tn+9Cm1JOiUbLun5aBIlxUZi0aTwG1qWY2u16XcBw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"4fc4548873f6cb96ddc0c5cf691607bc1af0cc5abbfcea75c142fe00ecfce10c","last_reissued_at":"2026-07-05T08:06:36.718196Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T08:06:36.718196Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2404.07194","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":"2026-07-05T08:06:36Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"esOohjekNGAn0wJyX3cxBlGcLc/Up4QjmtKn+SEk2vOJeR4CU8QlUHaIFTuS2vwIfxSxsIaBzJwpuKJwRdLSCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-17T20:17:22.618662Z"},"content_sha256":"b7bce82fcda9cf62cdc9fc6f2e18ec199a7b203c74ec8ccdc9f3c7991b47f59d","schema_version":"1.0","event_id":"sha256:b7bce82fcda9cf62cdc9fc6f2e18ec199a7b203c74ec8ccdc9f3c7991b47f59d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:J7CFJCDT63FZNXOAYXHWSFQHXQ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI","q-bio.BM"],"primary_cat":"cs.LG","authors_text":"Andreas Mayr, Florian Sestak, G\\\"unter Klambauer, Johannes Brandstetter, Lisa Schneckenreiter, Sepp Hochreiter","submitted_at":"2024-04-10T17:50:29Z","abstract_excerpt":"Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D structures in protein structure databases or from AlphaFold predictions. Current binding site identification methods heavily rely on graph neural networks (GNNs), usually designed to output E(3)-equivariant predictions. Such methods turned out to be very beneficial for physics-related tasks like binding energy or motion trajectory prediction. However, the perfor"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2404.07194","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/2404.07194/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":"2026-07-05T08:06:36Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"2JmT7eLBgovn8ctviTrKwQ2BdP73WdjlhthGJcBplDeleaf4c8oDaANpSXzAWB0psRuobOGqVReaHN0tZ+t/Dg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-17T20:17:22.619052Z"},"content_sha256":"26746032d1a8800998622c92bf5cfde1cd902c9885bd19034508307583b3eaf9","schema_version":"1.0","event_id":"sha256:26746032d1a8800998622c92bf5cfde1cd902c9885bd19034508307583b3eaf9"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/bundle.json","state_url":"https://pith.science/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/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":"2026-08-17T20:17:22Z","links":{"resolver":"https://pith.science/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ","bundle":"https://pith.science/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/bundle.json","state":"https://pith.science/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/J7CFJCDT63FZNXOAYXHWSFQHXQ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:J7CFJCDT63FZNXOAYXHWSFQHXQ","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":"4161b646bf33db8dc6aa24d8ed59e16525fbbcb995a8a2cf52b5f4eb35fb9f72","cross_cats_sorted":["cs.AI","q-bio.BM"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2024-04-10T17:50:29Z","title_canon_sha256":"6527f63a7f656154a896ae8f06d986ed3fe32349ca1bb3e4e14fbdbfb83bcd19"},"schema_version":"1.0","source":{"id":"2404.07194","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2404.07194","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"arxiv_version","alias_value":"2404.07194v1","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2404.07194","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_12","alias_value":"J7CFJCDT63FZ","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_16","alias_value":"J7CFJCDT63FZNXOA","created_at":"2026-07-05T08:06:36Z"},{"alias_kind":"pith_short_8","alias_value":"J7CFJCDT","created_at":"2026-07-05T08:06:36Z"}],"graph_snapshots":[{"event_id":"sha256:26746032d1a8800998622c92bf5cfde1cd902c9885bd19034508307583b3eaf9","target":"graph","created_at":"2026-07-05T08:06:36Z","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/2404.07194/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D structures in protein structure databases or from AlphaFold predictions. Current binding site identification methods heavily rely on graph neural networks (GNNs), usually designed to output E(3)-equivariant predictions. Such methods turned out to be very beneficial for physics-related tasks like binding energy or motion trajectory prediction. However, the perfor","authors_text":"Andreas Mayr, Florian Sestak, G\\\"unter Klambauer, Johannes Brandstetter, Lisa Schneckenreiter, Sepp Hochreiter","cross_cats":["cs.AI","q-bio.BM"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2024-04-10T17:50:29Z","title":"VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2404.07194","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:b7bce82fcda9cf62cdc9fc6f2e18ec199a7b203c74ec8ccdc9f3c7991b47f59d","target":"record","created_at":"2026-07-05T08:06:36Z","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":"4161b646bf33db8dc6aa24d8ed59e16525fbbcb995a8a2cf52b5f4eb35fb9f72","cross_cats_sorted":["cs.AI","q-bio.BM"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2024-04-10T17:50:29Z","title_canon_sha256":"6527f63a7f656154a896ae8f06d986ed3fe32349ca1bb3e4e14fbdbfb83bcd19"},"schema_version":"1.0","source":{"id":"2404.07194","kind":"arxiv","version":1}},"canonical_sha256":"4fc4548873f6cb96ddc0c5cf691607bc1af0cc5abbfcea75c142fe00ecfce10c","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"4fc4548873f6cb96ddc0c5cf691607bc1af0cc5abbfcea75c142fe00ecfce10c","first_computed_at":"2026-07-05T08:06:36.718196Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T08:06:36.718196Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"w39jj8vEL2aTtSR9kPuAeNbFdOrCDwN32/Y20/SOmg7w1Tn+9Cm1JOiUbLun5aBIlxUZi0aTwG1qWY2u16XcBw==","signature_status":"signed_v1","signed_at":"2026-07-05T08:06:36.718780Z","signed_message":"canonical_sha256_bytes"},"source_id":"2404.07194","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:b7bce82fcda9cf62cdc9fc6f2e18ec199a7b203c74ec8ccdc9f3c7991b47f59d","sha256:26746032d1a8800998622c92bf5cfde1cd902c9885bd19034508307583b3eaf9"],"state_sha256":"564bbb4cb1dde594de2062bccc65b56b4755c758d747816983b419444a6b003c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"2b06t/NxDPfkvUXGoP5TIjCeIoT2wCV8I2hZ4yQUbl39ubc9XvhzFigDDuxR3Hy9X7H1rF3GdHcha0PRMj2PCA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-17T20:17:22.622305Z","bundle_sha256":"026e40de31c1b5f473e26958150ba7517b61a1a9e2fc1bd044f0baf985eb3d1b"}}