{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:EAGIQR5D62TNHBG7VL7EGNT65U","short_pith_number":"pith:EAGIQR5D","canonical_record":{"source":{"id":"2505.04300","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-07T10:14:31Z","cross_cats_sorted":["cs.AI","cs.LG"],"title_canon_sha256":"a82aed8613915db0c43dba48a03ef35dbf8497881c93234c78e6f881451a3533","abstract_canon_sha256":"e93cb425deff143ee77c5b41723e2bc1a7e71365d048b1862d4b3af14d628366"},"schema_version":"1.0"},"canonical_sha256":"200c8847a3f6a6d384dfaafe43367eed196e8e9fc23d8897b3426d8aa7d9b594","source":{"kind":"arxiv","id":"2505.04300","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2505.04300","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"arxiv_version","alias_value":"2505.04300v1","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2505.04300","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_12","alias_value":"EAGIQR5D62TN","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_16","alias_value":"EAGIQR5D62TNHBG7","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_8","alias_value":"EAGIQR5D","created_at":"2026-07-05T10:59:39Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:EAGIQR5D62TNHBG7VL7EGNT65U","target":"record","payload":{"canonical_record":{"source":{"id":"2505.04300","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-07T10:14:31Z","cross_cats_sorted":["cs.AI","cs.LG"],"title_canon_sha256":"a82aed8613915db0c43dba48a03ef35dbf8497881c93234c78e6f881451a3533","abstract_canon_sha256":"e93cb425deff143ee77c5b41723e2bc1a7e71365d048b1862d4b3af14d628366"},"schema_version":"1.0"},"canonical_sha256":"200c8847a3f6a6d384dfaafe43367eed196e8e9fc23d8897b3426d8aa7d9b594","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:59:39.652904Z","signature_b64":"QDS+WdQcUPrIdZmewiEWrLR5Fb3MPNnfnrxvNoLoCle/IHG+KsgKppF2T8V8k43F4RIear35507zPJdILngqBg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"200c8847a3f6a6d384dfaafe43367eed196e8e9fc23d8897b3426d8aa7d9b594","last_reissued_at":"2026-07-05T10:59:39.652312Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:59:39.652312Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2505.04300","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":"2026-07-05T10:59:39Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"okDOUy4dS4MzQKmSxmdWH9Y7QP/yED+hNms/e9mhApM9O/Zrfk+yLMpicBfjQ/LEE77qf2ASh4entyDVbY40Bg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-19T22:46:22.991042Z"},"content_sha256":"91c68af084abf002fc002ec155aa91dbfd77a64b726e288379cfa224dcd077e1","schema_version":"1.0","event_id":"sha256:91c68af084abf002fc002ec155aa91dbfd77a64b726e288379cfa224dcd077e1"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:EAGIQR5D62TNHBG7VL7EGNT65U","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI","cs.LG"],"primary_cat":"q-bio.QM","authors_text":"Cesare Rollo, Corrado Pancotti, Flavio Sartori, Isabella Caranzano, Piero Fariselli, Pietro Li\\`o, Tiziana Sanavia","submitted_at":"2025-05-07T10:14:31Z","abstract_excerpt":"Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art dee"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2505.04300","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/2505.04300/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":"2026-07-05T10:59:39Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ZZzWcq6EEEcbagUXd1BM4h2FrDdu5kdox1iB+VAON1MDarTU7UWSi9eZgJE3MgskurH2aD8tR3R0DD2qR2dZDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-19T22:46:22.991710Z"},"content_sha256":"82b49a564dc23e6f63623f675a2d8a538a8c012b56c77b319136696ba8f8f183","schema_version":"1.0","event_id":"sha256:82b49a564dc23e6f63623f675a2d8a538a8c012b56c77b319136696ba8f8f183"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/EAGIQR5D62TNHBG7VL7EGNT65U/bundle.json","state_url":"https://pith.science/pith/EAGIQR5D62TNHBG7VL7EGNT65U/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/EAGIQR5D62TNHBG7VL7EGNT65U/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":"2026-08-19T22:46:22Z","links":{"resolver":"https://pith.science/pith/EAGIQR5D62TNHBG7VL7EGNT65U","bundle":"https://pith.science/pith/EAGIQR5D62TNHBG7VL7EGNT65U/bundle.json","state":"https://pith.science/pith/EAGIQR5D62TNHBG7VL7EGNT65U/state.json","well_known_bundle":"https://pith.science/.well-known/pith/EAGIQR5D62TNHBG7VL7EGNT65U/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:EAGIQR5D62TNHBG7VL7EGNT65U","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":"e93cb425deff143ee77c5b41723e2bc1a7e71365d048b1862d4b3af14d628366","cross_cats_sorted":["cs.AI","cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-07T10:14:31Z","title_canon_sha256":"a82aed8613915db0c43dba48a03ef35dbf8497881c93234c78e6f881451a3533"},"schema_version":"1.0","source":{"id":"2505.04300","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2505.04300","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"arxiv_version","alias_value":"2505.04300v1","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2505.04300","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_12","alias_value":"EAGIQR5D62TN","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_16","alias_value":"EAGIQR5D62TNHBG7","created_at":"2026-07-05T10:59:39Z"},{"alias_kind":"pith_short_8","alias_value":"EAGIQR5D","created_at":"2026-07-05T10:59:39Z"}],"graph_snapshots":[{"event_id":"sha256:82b49a564dc23e6f63623f675a2d8a538a8c012b56c77b319136696ba8f8f183","target":"graph","created_at":"2026-07-05T10:59:39Z","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/2505.04300/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art dee","authors_text":"Cesare Rollo, Corrado Pancotti, Flavio Sartori, Isabella Caranzano, Piero Fariselli, Pietro Li\\`o, Tiziana Sanavia","cross_cats":["cs.AI","cs.LG"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-07T10:14:31Z","title":"Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2505.04300","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":"sha256:91c68af084abf002fc002ec155aa91dbfd77a64b726e288379cfa224dcd077e1","target":"record","created_at":"2026-07-05T10:59:39Z","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":"e93cb425deff143ee77c5b41723e2bc1a7e71365d048b1862d4b3af14d628366","cross_cats_sorted":["cs.AI","cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-07T10:14:31Z","title_canon_sha256":"a82aed8613915db0c43dba48a03ef35dbf8497881c93234c78e6f881451a3533"},"schema_version":"1.0","source":{"id":"2505.04300","kind":"arxiv","version":1}},"canonical_sha256":"200c8847a3f6a6d384dfaafe43367eed196e8e9fc23d8897b3426d8aa7d9b594","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"200c8847a3f6a6d384dfaafe43367eed196e8e9fc23d8897b3426d8aa7d9b594","first_computed_at":"2026-07-05T10:59:39.652312Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:59:39.652312Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"QDS+WdQcUPrIdZmewiEWrLR5Fb3MPNnfnrxvNoLoCle/IHG+KsgKppF2T8V8k43F4RIear35507zPJdILngqBg==","signature_status":"signed_v1","signed_at":"2026-07-05T10:59:39.652904Z","signed_message":"canonical_sha256_bytes"},"source_id":"2505.04300","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:91c68af084abf002fc002ec155aa91dbfd77a64b726e288379cfa224dcd077e1","sha256:82b49a564dc23e6f63623f675a2d8a538a8c012b56c77b319136696ba8f8f183"],"state_sha256":"ca020e2d2f2f70bed6c3769cdd754c56bafb52dd94d57e94d9520b0f6b0124ea"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"OKvzTeBikfDIhaoLF/r04EUGKcxuUuS+51MZpkphq2H70vt3+QtTznWMIQSC5NhlsZ9DgX0LCbPSHEGphmTUCg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-19T22:46:22.995749Z","bundle_sha256":"ece47855fc235b4946a616693a1c67b6416c6756909acee301e68f9c60242ddd"}}