{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2022:ROCKDM4D4MVPPUKIGG7Z4KHPDE","short_pith_number":"pith:ROCKDM4D","canonical_record":{"source":{"id":"2211.04020","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.QM","submitted_at":"2022-11-08T05:46:02Z","cross_cats_sorted":["cs.LG","q-bio.GN","q-bio.TO"],"title_canon_sha256":"d3879b14deeac7c4b30ac0b224248058c798e5c83fd8b0720b12e8be89f3cd01","abstract_canon_sha256":"359cca0d553902089f98c11bb327619208722f60798c1ae05ebabb021179bfd6"},"schema_version":"1.0"},"canonical_sha256":"8b84a1b383e32af7d14831bf9e28ef1933a4ffb2a01e3ccbb9202c2f6ac97dd3","source":{"kind":"arxiv","id":"2211.04020","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2211.04020","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"arxiv_version","alias_value":"2211.04020v2","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2211.04020","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_12","alias_value":"ROCKDM4D4MVP","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_16","alias_value":"ROCKDM4D4MVPPUKI","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_8","alias_value":"ROCKDM4D","created_at":"2026-07-05T07:00:43Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2022:ROCKDM4D4MVPPUKIGG7Z4KHPDE","target":"record","payload":{"canonical_record":{"source":{"id":"2211.04020","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.QM","submitted_at":"2022-11-08T05:46:02Z","cross_cats_sorted":["cs.LG","q-bio.GN","q-bio.TO"],"title_canon_sha256":"d3879b14deeac7c4b30ac0b224248058c798e5c83fd8b0720b12e8be89f3cd01","abstract_canon_sha256":"359cca0d553902089f98c11bb327619208722f60798c1ae05ebabb021179bfd6"},"schema_version":"1.0"},"canonical_sha256":"8b84a1b383e32af7d14831bf9e28ef1933a4ffb2a01e3ccbb9202c2f6ac97dd3","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T07:00:43.491995Z","signature_b64":"4gTM5/R4OJR5LodxdJhits9d1sGqJ7Y9cTBSoSstPhAT2IqyGc0joJ42ti6P/STKdCDaKO2hrzeasDFk/oPHDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"8b84a1b383e32af7d14831bf9e28ef1933a4ffb2a01e3ccbb9202c2f6ac97dd3","last_reissued_at":"2026-07-05T07:00:43.491430Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T07:00:43.491430Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2211.04020","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":"2026-07-05T07:00:43Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"nRNeEhELidjblNkZdffrH/LwWJiYeDFVYP86d44XdGAVmjFHsPgBjOXA2peGDAiKPiokkUiIl6J6hDDqt5o1AA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-06T22:45:05.895995Z"},"content_sha256":"3dc981c9141ba22806461fe69a58faafc3c2b56c092416395dd327c19f8436d9","schema_version":"1.0","event_id":"sha256:3dc981c9141ba22806461fe69a58faafc3c2b56c092416395dd327c19f8436d9"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2022:ROCKDM4D4MVPPUKIGG7Z4KHPDE","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Generating counterfactual explanations of tumor spatial proteomes to discover effective strategies for enhancing immune infiltration","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["cs.LG","q-bio.GN","q-bio.TO"],"primary_cat":"q-bio.QM","authors_text":"Alexander M. Xu, Aman Bhargava, Matt W. Thomson, Zitong Jerry Wang","submitted_at":"2022-11-08T05:46:02Z","abstract_excerpt":"The tumor microenvironment (TME) significantly impacts cancer prognosis due to its immune composition. While therapies for altering the immune composition, including immunotherapies, have shown exciting results for treating hematological cancers, they are less effective for immunologically-cold, solid tumors. Spatial omics technologies capture the spatial organization of the TME with unprecedented molecular detail, revealing the relationship between immune cell localization and molecular signals. Here, we formulate T-cell infiltration prediction as a self-supervised machine learning problem an"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2211.04020","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/2211.04020/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":"2026-07-05T07:00:43Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5BAUQLWZH5GUIRsN2G1nR5eDMxlZ+lLRBotJAOZ7o4PI7Li4jsdxiDWmhVtwtr5NKEtBZ0Tsu4KUiP2BkZOuDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-06T22:45:05.896485Z"},"content_sha256":"7e6308d52fa81438101d91c2a75044b9e7d5143cadb8dd8d6d3bcac829c515f5","schema_version":"1.0","event_id":"sha256:7e6308d52fa81438101d91c2a75044b9e7d5143cadb8dd8d6d3bcac829c515f5"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/bundle.json","state_url":"https://pith.science/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/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":"2026-08-06T22:45:05Z","links":{"resolver":"https://pith.science/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE","bundle":"https://pith.science/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/bundle.json","state":"https://pith.science/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/state.json","well_known_bundle":"https://pith.science/.well-known/pith/ROCKDM4D4MVPPUKIGG7Z4KHPDE/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2022:ROCKDM4D4MVPPUKIGG7Z4KHPDE","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":"359cca0d553902089f98c11bb327619208722f60798c1ae05ebabb021179bfd6","cross_cats_sorted":["cs.LG","q-bio.GN","q-bio.TO"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.QM","submitted_at":"2022-11-08T05:46:02Z","title_canon_sha256":"d3879b14deeac7c4b30ac0b224248058c798e5c83fd8b0720b12e8be89f3cd01"},"schema_version":"1.0","source":{"id":"2211.04020","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2211.04020","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"arxiv_version","alias_value":"2211.04020v2","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2211.04020","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_12","alias_value":"ROCKDM4D4MVP","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_16","alias_value":"ROCKDM4D4MVPPUKI","created_at":"2026-07-05T07:00:43Z"},{"alias_kind":"pith_short_8","alias_value":"ROCKDM4D","created_at":"2026-07-05T07:00:43Z"}],"graph_snapshots":[{"event_id":"sha256:7e6308d52fa81438101d91c2a75044b9e7d5143cadb8dd8d6d3bcac829c515f5","target":"graph","created_at":"2026-07-05T07:00:43Z","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/2211.04020/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The tumor microenvironment (TME) significantly impacts cancer prognosis due to its immune composition. While therapies for altering the immune composition, including immunotherapies, have shown exciting results for treating hematological cancers, they are less effective for immunologically-cold, solid tumors. Spatial omics technologies capture the spatial organization of the TME with unprecedented molecular detail, revealing the relationship between immune cell localization and molecular signals. Here, we formulate T-cell infiltration prediction as a self-supervised machine learning problem an","authors_text":"Alexander M. Xu, Aman Bhargava, Matt W. Thomson, Zitong Jerry Wang","cross_cats":["cs.LG","q-bio.GN","q-bio.TO"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.QM","submitted_at":"2022-11-08T05:46:02Z","title":"Generating counterfactual explanations of tumor spatial proteomes to discover effective strategies for enhancing immune infiltration"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2211.04020","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":"sha256:3dc981c9141ba22806461fe69a58faafc3c2b56c092416395dd327c19f8436d9","target":"record","created_at":"2026-07-05T07:00:43Z","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":"359cca0d553902089f98c11bb327619208722f60798c1ae05ebabb021179bfd6","cross_cats_sorted":["cs.LG","q-bio.GN","q-bio.TO"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.QM","submitted_at":"2022-11-08T05:46:02Z","title_canon_sha256":"d3879b14deeac7c4b30ac0b224248058c798e5c83fd8b0720b12e8be89f3cd01"},"schema_version":"1.0","source":{"id":"2211.04020","kind":"arxiv","version":2}},"canonical_sha256":"8b84a1b383e32af7d14831bf9e28ef1933a4ffb2a01e3ccbb9202c2f6ac97dd3","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"8b84a1b383e32af7d14831bf9e28ef1933a4ffb2a01e3ccbb9202c2f6ac97dd3","first_computed_at":"2026-07-05T07:00:43.491430Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T07:00:43.491430Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"4gTM5/R4OJR5LodxdJhits9d1sGqJ7Y9cTBSoSstPhAT2IqyGc0joJ42ti6P/STKdCDaKO2hrzeasDFk/oPHDw==","signature_status":"signed_v1","signed_at":"2026-07-05T07:00:43.491995Z","signed_message":"canonical_sha256_bytes"},"source_id":"2211.04020","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3dc981c9141ba22806461fe69a58faafc3c2b56c092416395dd327c19f8436d9","sha256:7e6308d52fa81438101d91c2a75044b9e7d5143cadb8dd8d6d3bcac829c515f5"],"state_sha256":"779b6cb89dd746602356fe1dd689ac7257c62b5ae72d81660e3bf14bb794a593"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"XvKzUbpHEXkBqRBJf8K+77B5gPV+0FGpzqHY1FwxYPuusbPQ9UQQBV8B12C6NlCJSwNRXsftUpg2k1BVkLhkDg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-06T22:45:05.900049Z","bundle_sha256":"70f59ff01ace61d5bcff429be8bee84caec70cdc1b4118d53bc7388db43a02e3"}}