{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:DLVEO3OKKAL3WDMZZO6KQE6AO4","short_pith_number":"pith:DLVEO3OK","canonical_record":{"source":{"id":"2506.08954","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-06-10T16:24:09Z","cross_cats_sorted":["cs.LG","q-bio.BM"],"title_canon_sha256":"902c9dd69b12a1396a296d14d558126dc287a8786de7050ddcd58aefc88ed95b","abstract_canon_sha256":"8a6169692917d7a2062b040c4dac0296157e48879fee8e465b45612068795015"},"schema_version":"1.0"},"canonical_sha256":"1aea476dca5017bb0d99cbbca813c0770174d8eebb8af76c2589b18ba9fef9eb","source":{"kind":"arxiv","id":"2506.08954","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2506.08954","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"arxiv_version","alias_value":"2506.08954v1","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2506.08954","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_12","alias_value":"DLVEO3OKKAL3","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_16","alias_value":"DLVEO3OKKAL3WDMZ","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_8","alias_value":"DLVEO3OK","created_at":"2026-07-05T11:19:15Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:DLVEO3OKKAL3WDMZZO6KQE6AO4","target":"record","payload":{"canonical_record":{"source":{"id":"2506.08954","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-06-10T16:24:09Z","cross_cats_sorted":["cs.LG","q-bio.BM"],"title_canon_sha256":"902c9dd69b12a1396a296d14d558126dc287a8786de7050ddcd58aefc88ed95b","abstract_canon_sha256":"8a6169692917d7a2062b040c4dac0296157e48879fee8e465b45612068795015"},"schema_version":"1.0"},"canonical_sha256":"1aea476dca5017bb0d99cbbca813c0770174d8eebb8af76c2589b18ba9fef9eb","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:19:15.816430Z","signature_b64":"mQmmX5OBhWGlXXRx+b12khX6BiZO5VSBiISY/tcL3pyUGsDx0saDIHZN+NihCeNEhox++QjWKi6VSEWRuu+7Aw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"1aea476dca5017bb0d99cbbca813c0770174d8eebb8af76c2589b18ba9fef9eb","last_reissued_at":"2026-07-05T11:19:15.815905Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:19:15.815905Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2506.08954","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":"2026-07-05T11:19:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"kmlq9Ui7zwMmer0hEka4u0pYR3hGnh2oFTmNRfMkJBlDUBOvhAGsfWIftq1aD+VLBpvjoIjmUelCn3e8YIQrDw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T20:03:16.264805Z"},"content_sha256":"f5cd25ee3f8ec192a41f45d458d958843824a3805126bb17ac80fcc893bb3a5a","schema_version":"1.0","event_id":"sha256:f5cd25ee3f8ec192a41f45d458d958843824a3805126bb17ac80fcc893bb3a5a"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:DLVEO3OKKAL3WDMZZO6KQE6AO4","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG","q-bio.BM"],"primary_cat":"q-bio.QM","authors_text":"Aoi Otani, Debora Marks, Lood Van Niekerk, Pascal Notin, Peter M{\\o}rch Groth, Ruben Weitzman, Yarin Gal","submitted_at":"2025-06-10T16:24:09Z","abstract_excerpt":"Retrieving homologous protein sequences is essential for a broad range of protein modeling tasks such as fitness prediction, protein design, structure modeling, and protein-protein interactions. Traditional workflows have relied on a two-step process: first retrieving homologs via Multiple Sequence Alignments (MSA), then training models on one or more of these alignments. However, MSA-based retrieval is computationally expensive, struggles with highly divergent sequences or complex insertions & deletions patterns, and operates independently of the downstream modeling objective. We introduce Pr"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2506.08954","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/2506.08954/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":"2026-07-05T11:19:15Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"MHtEsbJz85l04WmV1Rci90qs5RTSlIccuZJoR9snIE1zdVs998Cq2IF6G1qBMUm73ZdjXHLPntRYep65evgvAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T20:03:16.265327Z"},"content_sha256":"b6a3cdc3f172814fb1b3b7a038b2e15334760a7b6f98dbf3a1df9bd14c5c5833","schema_version":"1.0","event_id":"sha256:b6a3cdc3f172814fb1b3b7a038b2e15334760a7b6f98dbf3a1df9bd14c5c5833"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/bundle.json","state_url":"https://pith.science/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/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":"2026-08-04T20:03:16Z","links":{"resolver":"https://pith.science/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4","bundle":"https://pith.science/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/bundle.json","state":"https://pith.science/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/state.json","well_known_bundle":"https://pith.science/.well-known/pith/DLVEO3OKKAL3WDMZZO6KQE6AO4/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:DLVEO3OKKAL3WDMZZO6KQE6AO4","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":"8a6169692917d7a2062b040c4dac0296157e48879fee8e465b45612068795015","cross_cats_sorted":["cs.LG","q-bio.BM"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-06-10T16:24:09Z","title_canon_sha256":"902c9dd69b12a1396a296d14d558126dc287a8786de7050ddcd58aefc88ed95b"},"schema_version":"1.0","source":{"id":"2506.08954","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2506.08954","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"arxiv_version","alias_value":"2506.08954v1","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2506.08954","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_12","alias_value":"DLVEO3OKKAL3","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_16","alias_value":"DLVEO3OKKAL3WDMZ","created_at":"2026-07-05T11:19:15Z"},{"alias_kind":"pith_short_8","alias_value":"DLVEO3OK","created_at":"2026-07-05T11:19:15Z"}],"graph_snapshots":[{"event_id":"sha256:b6a3cdc3f172814fb1b3b7a038b2e15334760a7b6f98dbf3a1df9bd14c5c5833","target":"graph","created_at":"2026-07-05T11:19:15Z","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/2506.08954/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Retrieving homologous protein sequences is essential for a broad range of protein modeling tasks such as fitness prediction, protein design, structure modeling, and protein-protein interactions. Traditional workflows have relied on a two-step process: first retrieving homologs via Multiple Sequence Alignments (MSA), then training models on one or more of these alignments. However, MSA-based retrieval is computationally expensive, struggles with highly divergent sequences or complex insertions & deletions patterns, and operates independently of the downstream modeling objective. We introduce Pr","authors_text":"Aoi Otani, Debora Marks, Lood Van Niekerk, Pascal Notin, Peter M{\\o}rch Groth, Ruben Weitzman, Yarin Gal","cross_cats":["cs.LG","q-bio.BM"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-06-10T16:24:09Z","title":"Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2506.08954","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:f5cd25ee3f8ec192a41f45d458d958843824a3805126bb17ac80fcc893bb3a5a","target":"record","created_at":"2026-07-05T11:19:15Z","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":"8a6169692917d7a2062b040c4dac0296157e48879fee8e465b45612068795015","cross_cats_sorted":["cs.LG","q-bio.BM"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-06-10T16:24:09Z","title_canon_sha256":"902c9dd69b12a1396a296d14d558126dc287a8786de7050ddcd58aefc88ed95b"},"schema_version":"1.0","source":{"id":"2506.08954","kind":"arxiv","version":1}},"canonical_sha256":"1aea476dca5017bb0d99cbbca813c0770174d8eebb8af76c2589b18ba9fef9eb","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"1aea476dca5017bb0d99cbbca813c0770174d8eebb8af76c2589b18ba9fef9eb","first_computed_at":"2026-07-05T11:19:15.815905Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:19:15.815905Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"mQmmX5OBhWGlXXRx+b12khX6BiZO5VSBiISY/tcL3pyUGsDx0saDIHZN+NihCeNEhox++QjWKi6VSEWRuu+7Aw==","signature_status":"signed_v1","signed_at":"2026-07-05T11:19:15.816430Z","signed_message":"canonical_sha256_bytes"},"source_id":"2506.08954","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:f5cd25ee3f8ec192a41f45d458d958843824a3805126bb17ac80fcc893bb3a5a","sha256:b6a3cdc3f172814fb1b3b7a038b2e15334760a7b6f98dbf3a1df9bd14c5c5833"],"state_sha256":"3bdd899b578758b4ae004915ad18b2c582062cb9720ea8b3149d621b8309fdd1"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"tnSoSOC5hRmF819SZy3Grz1x8JHFBEwuTNbtzHdeT7QFO3HKyOfCC1zD/zfPR8xlyUPGLYFskZ3hpuWk8aUKCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T20:03:16.271366Z","bundle_sha256":"530a49bda1760d28877ce3cd1ac6ea94ff52b3954d98d12b550c754bc26871f6"}}