{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2018:7FGJ275HRSE23IRXQWI7GO7RG6","short_pith_number":"pith:7FGJ275H","canonical_record":{"source":{"id":"1804.10647","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2018-04-27T18:54:15Z","cross_cats_sorted":[],"title_canon_sha256":"a40083171d57501a27b922640de94a5ee07dd363a8b2c5974496516bc96a2711","abstract_canon_sha256":"ec39f0ddf647f547cf64fac070d29b8897307b2151a8b880886021f41b40e8fb"},"schema_version":"1.0"},"canonical_sha256":"f94c9d7fa78c89ada2378591f33bf137ba0b6aa42d5fe6774a311371b75c4e29","source":{"kind":"arxiv","id":"1804.10647","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1804.10647","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"arxiv_version","alias_value":"1804.10647v1","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1804.10647","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"pith_short_12","alias_value":"7FGJ275HRSE2","created_at":"2026-05-18T12:32:11Z"},{"alias_kind":"pith_short_16","alias_value":"7FGJ275HRSE23IRX","created_at":"2026-05-18T12:32:11Z"},{"alias_kind":"pith_short_8","alias_value":"7FGJ275H","created_at":"2026-05-18T12:32:11Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2018:7FGJ275HRSE23IRXQWI7GO7RG6","target":"record","payload":{"canonical_record":{"source":{"id":"1804.10647","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2018-04-27T18:54:15Z","cross_cats_sorted":[],"title_canon_sha256":"a40083171d57501a27b922640de94a5ee07dd363a8b2c5974496516bc96a2711","abstract_canon_sha256":"ec39f0ddf647f547cf64fac070d29b8897307b2151a8b880886021f41b40e8fb"},"schema_version":"1.0"},"canonical_sha256":"f94c9d7fa78c89ada2378591f33bf137ba0b6aa42d5fe6774a311371b75c4e29","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:17:15.981065Z","signature_b64":"no0E6k0ceth3t31RhadHaD0YLr7++qh6S+izu/O0SZjgGnpwxQdxoWlCR33KFzNqYYAdyJrMkZdy+DtC7JvBDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"f94c9d7fa78c89ada2378591f33bf137ba0b6aa42d5fe6774a311371b75c4e29","last_reissued_at":"2026-05-18T00:17:15.980565Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:17:15.980565Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1804.10647","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":"2026-05-18T00:17:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"8NFXgVKis8wj1MoDihQHUMeLEW3Xqxs10KArujdlKQUY2enqEr4WhFqaoUo93MHAUbbNy8PyEPl6wHTj/u5hDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T15:01:54.085565Z"},"content_sha256":"d53bc1804383d7b6bf313aac098f29129d23fdb83b71b77c3ccd6fccc714ed8f","schema_version":"1.0","event_id":"sha256:d53bc1804383d7b6bf313aac098f29129d23fdb83b71b77c3ccd6fccc714ed8f"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2018:7FGJ275HRSE23IRXQWI7GO7RG6","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.BM","authors_text":"Duc Duy Nguyen, Guo-Wei Wei, Kedi Wu, Menglun Wang, Yin Cao, Zixuan Cang","submitted_at":"2018-04-27T18:54:15Z","abstract_excerpt":"Advanced mathematics, such as multiscale weighted colored graph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affinity prediction and ranking in the last two D3R grand challenges in computer-aided drug design and discovery. D3R Grand Challenge 2 (GC2) focused on the pose prediction and binding affinity ranking and free energy prediction for Farnesoid X receptor ligands. Our models obtained the top place in absolute free energy prediction for free energy Set 1 in S"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1804.10647","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":""},"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":"2026-05-18T00:17:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"SkFSJdp2/6AUu09UsM7crLFh6wtbgdfq/yNikXZyAQpqP6G0296F/n6JyP2PwS1ueokfEl+NoFcgfTbRe4Y7BA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T15:01:54.085935Z"},"content_sha256":"b41ac0257334ad907e32d50a9c9d9a93181f3ae383c7bc11ff8c6a32e5f4662d","schema_version":"1.0","event_id":"sha256:b41ac0257334ad907e32d50a9c9d9a93181f3ae383c7bc11ff8c6a32e5f4662d"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/7FGJ275HRSE23IRXQWI7GO7RG6/bundle.json","state_url":"https://pith.science/pith/7FGJ275HRSE23IRXQWI7GO7RG6/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/7FGJ275HRSE23IRXQWI7GO7RG6/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":"2026-05-26T15:01:54Z","links":{"resolver":"https://pith.science/pith/7FGJ275HRSE23IRXQWI7GO7RG6","bundle":"https://pith.science/pith/7FGJ275HRSE23IRXQWI7GO7RG6/bundle.json","state":"https://pith.science/pith/7FGJ275HRSE23IRXQWI7GO7RG6/state.json","well_known_bundle":"https://pith.science/.well-known/pith/7FGJ275HRSE23IRXQWI7GO7RG6/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2018:7FGJ275HRSE23IRXQWI7GO7RG6","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":"ec39f0ddf647f547cf64fac070d29b8897307b2151a8b880886021f41b40e8fb","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2018-04-27T18:54:15Z","title_canon_sha256":"a40083171d57501a27b922640de94a5ee07dd363a8b2c5974496516bc96a2711"},"schema_version":"1.0","source":{"id":"1804.10647","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1804.10647","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"arxiv_version","alias_value":"1804.10647v1","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1804.10647","created_at":"2026-05-18T00:17:15Z"},{"alias_kind":"pith_short_12","alias_value":"7FGJ275HRSE2","created_at":"2026-05-18T12:32:11Z"},{"alias_kind":"pith_short_16","alias_value":"7FGJ275HRSE23IRX","created_at":"2026-05-18T12:32:11Z"},{"alias_kind":"pith_short_8","alias_value":"7FGJ275H","created_at":"2026-05-18T12:32:11Z"}],"graph_snapshots":[{"event_id":"sha256:b41ac0257334ad907e32d50a9c9d9a93181f3ae383c7bc11ff8c6a32e5f4662d","target":"graph","created_at":"2026-05-18T00:17:15Z","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"},"paper":{"abstract_excerpt":"Advanced mathematics, such as multiscale weighted colored graph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affinity prediction and ranking in the last two D3R grand challenges in computer-aided drug design and discovery. D3R Grand Challenge 2 (GC2) focused on the pose prediction and binding affinity ranking and free energy prediction for Farnesoid X receptor ligands. Our models obtained the top place in absolute free energy prediction for free energy Set 1 in S","authors_text":"Duc Duy Nguyen, Guo-Wei Wei, Kedi Wu, Menglun Wang, Yin Cao, Zixuan Cang","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2018-04-27T18:54:15Z","title":"Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1804.10647","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:d53bc1804383d7b6bf313aac098f29129d23fdb83b71b77c3ccd6fccc714ed8f","target":"record","created_at":"2026-05-18T00:17:15Z","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":"ec39f0ddf647f547cf64fac070d29b8897307b2151a8b880886021f41b40e8fb","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2018-04-27T18:54:15Z","title_canon_sha256":"a40083171d57501a27b922640de94a5ee07dd363a8b2c5974496516bc96a2711"},"schema_version":"1.0","source":{"id":"1804.10647","kind":"arxiv","version":1}},"canonical_sha256":"f94c9d7fa78c89ada2378591f33bf137ba0b6aa42d5fe6774a311371b75c4e29","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"f94c9d7fa78c89ada2378591f33bf137ba0b6aa42d5fe6774a311371b75c4e29","first_computed_at":"2026-05-18T00:17:15.980565Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:17:15.980565Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"no0E6k0ceth3t31RhadHaD0YLr7++qh6S+izu/O0SZjgGnpwxQdxoWlCR33KFzNqYYAdyJrMkZdy+DtC7JvBDQ==","signature_status":"signed_v1","signed_at":"2026-05-18T00:17:15.981065Z","signed_message":"canonical_sha256_bytes"},"source_id":"1804.10647","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:d53bc1804383d7b6bf313aac098f29129d23fdb83b71b77c3ccd6fccc714ed8f","sha256:b41ac0257334ad907e32d50a9c9d9a93181f3ae383c7bc11ff8c6a32e5f4662d"],"state_sha256":"85b2d2b80f5a322f92d4a78c6b9a7585fb576edfa6f77db59640d2aee8cc7334"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ueKJotLZFw0MSIexlszYhw+SFEpomkCflO1C2LPM7k2K/Y5RGG/bsrK8aKl+5krLxc014QlQodEDS9xSExZoAg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-26T15:01:54.088443Z","bundle_sha256":"257864c4476301142624ee0f68c162288e4be617011395b619389154de2c5786"}}