{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:MVZ6R5XIW5LH2R3WWPAZEO7TIU","short_pith_number":"pith:MVZ6R5XI","canonical_record":{"source":{"id":"2412.02882","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"cs.MS","submitted_at":"2024-12-03T22:34:38Z","cross_cats_sorted":["cs.GR","q-bio.GN"],"title_canon_sha256":"270330820250d7ed559de40852bd3ce93685f66fdfd19aea8892775610ba7937","abstract_canon_sha256":"faec1bb52afdaa30998239146c4da8a36e639a7382b743d0ec2dbee4849e28f5"},"schema_version":"1.0"},"canonical_sha256":"6573e8f6e8b7567d4776b3c1923bf345381b105242747d3fa4faa9c6fb5ec2b8","source":{"kind":"arxiv","id":"2412.02882","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.02882","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"arxiv_version","alias_value":"2412.02882v2","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.02882","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_12","alias_value":"MVZ6R5XIW5LH","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_16","alias_value":"MVZ6R5XIW5LH2R3W","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_8","alias_value":"MVZ6R5XI","created_at":"2026-07-05T09:44:55Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:MVZ6R5XIW5LH2R3WWPAZEO7TIU","target":"record","payload":{"canonical_record":{"source":{"id":"2412.02882","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"cs.MS","submitted_at":"2024-12-03T22:34:38Z","cross_cats_sorted":["cs.GR","q-bio.GN"],"title_canon_sha256":"270330820250d7ed559de40852bd3ce93685f66fdfd19aea8892775610ba7937","abstract_canon_sha256":"faec1bb52afdaa30998239146c4da8a36e639a7382b743d0ec2dbee4849e28f5"},"schema_version":"1.0"},"canonical_sha256":"6573e8f6e8b7567d4776b3c1923bf345381b105242747d3fa4faa9c6fb5ec2b8","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:44:55.506447Z","signature_b64":"2UCvDyxaL4Tz9RAhOfFAnG7skm8TxYsky8vRA02qIO/wHpF53Fd+tE7YjBnQZDx6zDWR0fY/78k238j/cOCFBw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"6573e8f6e8b7567d4776b3c1923bf345381b105242747d3fa4faa9c6fb5ec2b8","last_reissued_at":"2026-07-05T09:44:55.505886Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:44:55.505886Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2412.02882","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":"2026-07-05T09:44:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"vFyL/qEmHmtbfi5OEsMwE5R7gkLenTs5YGm50fxfS6xf5aofcqzhks8vspEaD7NeCU2R0L/iEjz2bo20cPOqCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-20T10:22:31.753936Z"},"content_sha256":"80b083d9d604be1ea39fbacb3ff063d4536b3993e6e85cde468e7bb412924d6c","schema_version":"1.0","event_id":"sha256:80b083d9d604be1ea39fbacb3ff063d4536b3993e6e85cde468e7bb412924d6c"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:MVZ6R5XIW5LH2R3WWPAZEO7TIU","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"iSEEtree: interactive explorer for hierarchical data","license":"http://creativecommons.org/licenses/by-sa/4.0/","headline":"","cross_cats":["cs.GR","q-bio.GN"],"primary_cat":"cs.MS","authors_text":"Akewak Jeba, Ely Seraidarian, Giulio Benedetti, Leo Lahti, Theotime Pralas, Tuomas Borman","submitted_at":"2024-12-03T22:34:38Z","abstract_excerpt":"$\\textbf{Motivation:}$ Hierarchical data structures are prevalent across several fields of research, as they represent an organised and efficient approach to study complex interconnected systems. Their significance is particularly evident in microbiome analysis, where microbial communities are classified at various taxonomic levels along the phylogenetic tree. In light of this trend, the R/Bioconductor community has established a reproducible analytical framework for hierarchical data, which relies on the highly generic and optimised TreeSummarizedExperiment data container. However, using this"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.02882","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/2412.02882/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":"2026-07-05T09:44:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"BW2HEBVrvm7LpmkIdotL3dcwcxjjTc3fKOE4kcM1TK/5FoqVAZRX2RBuGOeM9lKKjdjO446Hzg2HTkGj8riqBQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-20T10:22:31.754543Z"},"content_sha256":"09ae2ed33bc098fdaaae7d8926921ec9978a9b60f3ad942e8914530e01ffe6d5","schema_version":"1.0","event_id":"sha256:09ae2ed33bc098fdaaae7d8926921ec9978a9b60f3ad942e8914530e01ffe6d5"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/bundle.json","state_url":"https://pith.science/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/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":"2026-08-20T10:22:31Z","links":{"resolver":"https://pith.science/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU","bundle":"https://pith.science/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/bundle.json","state":"https://pith.science/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/state.json","well_known_bundle":"https://pith.science/.well-known/pith/MVZ6R5XIW5LH2R3WWPAZEO7TIU/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:MVZ6R5XIW5LH2R3WWPAZEO7TIU","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":"faec1bb52afdaa30998239146c4da8a36e639a7382b743d0ec2dbee4849e28f5","cross_cats_sorted":["cs.GR","q-bio.GN"],"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"cs.MS","submitted_at":"2024-12-03T22:34:38Z","title_canon_sha256":"270330820250d7ed559de40852bd3ce93685f66fdfd19aea8892775610ba7937"},"schema_version":"1.0","source":{"id":"2412.02882","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.02882","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"arxiv_version","alias_value":"2412.02882v2","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.02882","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_12","alias_value":"MVZ6R5XIW5LH","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_16","alias_value":"MVZ6R5XIW5LH2R3W","created_at":"2026-07-05T09:44:55Z"},{"alias_kind":"pith_short_8","alias_value":"MVZ6R5XI","created_at":"2026-07-05T09:44:55Z"}],"graph_snapshots":[{"event_id":"sha256:09ae2ed33bc098fdaaae7d8926921ec9978a9b60f3ad942e8914530e01ffe6d5","target":"graph","created_at":"2026-07-05T09:44:55Z","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/2412.02882/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"$\\textbf{Motivation:}$ Hierarchical data structures are prevalent across several fields of research, as they represent an organised and efficient approach to study complex interconnected systems. Their significance is particularly evident in microbiome analysis, where microbial communities are classified at various taxonomic levels along the phylogenetic tree. In light of this trend, the R/Bioconductor community has established a reproducible analytical framework for hierarchical data, which relies on the highly generic and optimised TreeSummarizedExperiment data container. However, using this","authors_text":"Akewak Jeba, Ely Seraidarian, Giulio Benedetti, Leo Lahti, Theotime Pralas, Tuomas Borman","cross_cats":["cs.GR","q-bio.GN"],"headline":"","license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"cs.MS","submitted_at":"2024-12-03T22:34:38Z","title":"iSEEtree: interactive explorer for hierarchical data"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.02882","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":"sha256:80b083d9d604be1ea39fbacb3ff063d4536b3993e6e85cde468e7bb412924d6c","target":"record","created_at":"2026-07-05T09:44:55Z","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":"faec1bb52afdaa30998239146c4da8a36e639a7382b743d0ec2dbee4849e28f5","cross_cats_sorted":["cs.GR","q-bio.GN"],"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"cs.MS","submitted_at":"2024-12-03T22:34:38Z","title_canon_sha256":"270330820250d7ed559de40852bd3ce93685f66fdfd19aea8892775610ba7937"},"schema_version":"1.0","source":{"id":"2412.02882","kind":"arxiv","version":2}},"canonical_sha256":"6573e8f6e8b7567d4776b3c1923bf345381b105242747d3fa4faa9c6fb5ec2b8","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"6573e8f6e8b7567d4776b3c1923bf345381b105242747d3fa4faa9c6fb5ec2b8","first_computed_at":"2026-07-05T09:44:55.505886Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T09:44:55.505886Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"2UCvDyxaL4Tz9RAhOfFAnG7skm8TxYsky8vRA02qIO/wHpF53Fd+tE7YjBnQZDx6zDWR0fY/78k238j/cOCFBw==","signature_status":"signed_v1","signed_at":"2026-07-05T09:44:55.506447Z","signed_message":"canonical_sha256_bytes"},"source_id":"2412.02882","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:80b083d9d604be1ea39fbacb3ff063d4536b3993e6e85cde468e7bb412924d6c","sha256:09ae2ed33bc098fdaaae7d8926921ec9978a9b60f3ad942e8914530e01ffe6d5"],"state_sha256":"8c28488a6a127be53d7d2b5f35579a50e1a25065e2618ba8c37d0400aa455fe2"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"tP0WasaNSgG84vqcY7T04GBsbViYl3qNpNwKiZlfgyRCrjD/NMNyt8oJXErQHZuMF6ONfR/KfuqMtQmRjJ9zCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-20T10:22:31.758197Z","bundle_sha256":"5045b1475c2fceeaedd19b6e91ee646086a3631dcde40fb11fa2d4d0962c2ef6"}}