{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:OPPEFI4GK2WRUICGVTDACZQGTC","short_pith_number":"pith:OPPEFI4G","canonical_record":{"source":{"id":"2410.08631","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-10-11T08:53:58Z","cross_cats_sorted":["cs.AI","cs.CE","cs.LG"],"title_canon_sha256":"1a315a8e2c8c6b73d58797468bee0e2875d3719b895713d7c19998935fc1b719","abstract_canon_sha256":"0355e4d75b3cb5c87df74dd1d4f2d8f932aa57980203daa51cd3648a8a181a15"},"schema_version":"1.0"},"canonical_sha256":"73de42a38656ad1a2046acc601660698908124e11c00445829805c56e68367b9","source":{"kind":"arxiv","id":"2410.08631","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2410.08631","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"arxiv_version","alias_value":"2410.08631v2","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2410.08631","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_12","alias_value":"OPPEFI4GK2WR","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_16","alias_value":"OPPEFI4GK2WRUICG","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_8","alias_value":"OPPEFI4G","created_at":"2026-07-05T09:44:15Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:OPPEFI4GK2WRUICGVTDACZQGTC","target":"record","payload":{"canonical_record":{"source":{"id":"2410.08631","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-10-11T08:53:58Z","cross_cats_sorted":["cs.AI","cs.CE","cs.LG"],"title_canon_sha256":"1a315a8e2c8c6b73d58797468bee0e2875d3719b895713d7c19998935fc1b719","abstract_canon_sha256":"0355e4d75b3cb5c87df74dd1d4f2d8f932aa57980203daa51cd3648a8a181a15"},"schema_version":"1.0"},"canonical_sha256":"73de42a38656ad1a2046acc601660698908124e11c00445829805c56e68367b9","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:44:15.416746Z","signature_b64":"kRvxC2zu0O85G7XlIp4DQl9yu0Bg6dxW3lyruhNuFXZJuxAngzV4uXvUNlXPXtwhkZQT5cEub+F4gjbBTANCDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"73de42a38656ad1a2046acc601660698908124e11c00445829805c56e68367b9","last_reissued_at":"2026-07-05T09:44:15.416246Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:44:15.416246Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2410.08631","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":"2026-07-05T09:44:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5T9jFYWN239/PGnxqCygnKdup+ccygf6logYT8du7vnRCd5dx2et8vtznWYQboCQR0sggQU68z4lwdK6JhAkBA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-06T07:50:50.129912Z"},"content_sha256":"ca5fd4c6f88436b6fe5d93dfc2fbc86be1cf119a0b070374b411439b8d9eeac9","schema_version":"1.0","event_id":"sha256:ca5fd4c6f88436b6fe5d93dfc2fbc86be1cf119a0b070374b411439b8d9eeac9"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:OPPEFI4GK2WRUICGVTDACZQGTC","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"CryoFM: A Flow-based Foundation Model for Cryo-EM Densities","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.AI","cs.CE","cs.LG"],"primary_cat":"q-bio.BM","authors_text":"Jing Yuan, Quanquan Gu, Yilai Li, Yi Zhou","submitted_at":"2024-10-11T08:53:58Z","abstract_excerpt":"Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2410.08631","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/2410.08631/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":"2026-07-05T09:44:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"iBcatygpMpckLBADjAl7HTzx92s040EfPvgVJBhDPlnSnc1Y5hJ+0WOGdE3x5e1/88d9XbKNZ27HrHSoav+5Cw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-06T07:50:50.130283Z"},"content_sha256":"8bb8a1cb49525d31efd174498f0d7e83280ad0adc3025ee40f15211c455d5f48","schema_version":"1.0","event_id":"sha256:8bb8a1cb49525d31efd174498f0d7e83280ad0adc3025ee40f15211c455d5f48"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/OPPEFI4GK2WRUICGVTDACZQGTC/bundle.json","state_url":"https://pith.science/pith/OPPEFI4GK2WRUICGVTDACZQGTC/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/OPPEFI4GK2WRUICGVTDACZQGTC/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":"2026-07-06T07:50:50Z","links":{"resolver":"https://pith.science/pith/OPPEFI4GK2WRUICGVTDACZQGTC","bundle":"https://pith.science/pith/OPPEFI4GK2WRUICGVTDACZQGTC/bundle.json","state":"https://pith.science/pith/OPPEFI4GK2WRUICGVTDACZQGTC/state.json","well_known_bundle":"https://pith.science/.well-known/pith/OPPEFI4GK2WRUICGVTDACZQGTC/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:OPPEFI4GK2WRUICGVTDACZQGTC","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":"0355e4d75b3cb5c87df74dd1d4f2d8f932aa57980203daa51cd3648a8a181a15","cross_cats_sorted":["cs.AI","cs.CE","cs.LG"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-10-11T08:53:58Z","title_canon_sha256":"1a315a8e2c8c6b73d58797468bee0e2875d3719b895713d7c19998935fc1b719"},"schema_version":"1.0","source":{"id":"2410.08631","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2410.08631","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"arxiv_version","alias_value":"2410.08631v2","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2410.08631","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_12","alias_value":"OPPEFI4GK2WR","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_16","alias_value":"OPPEFI4GK2WRUICG","created_at":"2026-07-05T09:44:15Z"},{"alias_kind":"pith_short_8","alias_value":"OPPEFI4G","created_at":"2026-07-05T09:44:15Z"}],"graph_snapshots":[{"event_id":"sha256:8bb8a1cb49525d31efd174498f0d7e83280ad0adc3025ee40f15211c455d5f48","target":"graph","created_at":"2026-07-05T09:44:15Z","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"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2410.08631/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning ","authors_text":"Jing Yuan, Quanquan Gu, Yilai Li, Yi Zhou","cross_cats":["cs.AI","cs.CE","cs.LG"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-10-11T08:53:58Z","title":"CryoFM: A Flow-based Foundation Model for Cryo-EM Densities"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2410.08631","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:ca5fd4c6f88436b6fe5d93dfc2fbc86be1cf119a0b070374b411439b8d9eeac9","target":"record","created_at":"2026-07-05T09:44:15Z","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":"0355e4d75b3cb5c87df74dd1d4f2d8f932aa57980203daa51cd3648a8a181a15","cross_cats_sorted":["cs.AI","cs.CE","cs.LG"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-10-11T08:53:58Z","title_canon_sha256":"1a315a8e2c8c6b73d58797468bee0e2875d3719b895713d7c19998935fc1b719"},"schema_version":"1.0","source":{"id":"2410.08631","kind":"arxiv","version":2}},"canonical_sha256":"73de42a38656ad1a2046acc601660698908124e11c00445829805c56e68367b9","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"73de42a38656ad1a2046acc601660698908124e11c00445829805c56e68367b9","first_computed_at":"2026-07-05T09:44:15.416246Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T09:44:15.416246Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"kRvxC2zu0O85G7XlIp4DQl9yu0Bg6dxW3lyruhNuFXZJuxAngzV4uXvUNlXPXtwhkZQT5cEub+F4gjbBTANCDQ==","signature_status":"signed_v1","signed_at":"2026-07-05T09:44:15.416746Z","signed_message":"canonical_sha256_bytes"},"source_id":"2410.08631","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:ca5fd4c6f88436b6fe5d93dfc2fbc86be1cf119a0b070374b411439b8d9eeac9","sha256:8bb8a1cb49525d31efd174498f0d7e83280ad0adc3025ee40f15211c455d5f48"],"state_sha256":"9c10d22c4f66c0471ba4220abeef604789465fdc3ba1399a0af6b2388001277f"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"SvjPvULLoH6KB3iwt40ydbAAigGdAzx5KG3ZnuOMFcXVgfVryK2dLujmdu+eCzxFdJdYXiCOQtECHLWsB1GCAA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-06T07:50:50.132370Z","bundle_sha256":"9faa06cd3c3d53fe187109fc4369ad25f7bb3b7bdbec754a07299abab614a934"}}