{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2026:6TBFN5FVEAHKRQRQ6LQMB6CL6V","short_pith_number":"pith:6TBFN5FV","schema_version":"1.0","canonical_sha256":"f4c256f4b5200ea8c230f2e0c0f84bf57cd22de95f74d0fb051169a9b71860ef","source":{"kind":"arxiv","id":"2606.11868","version":1},"attestation_state":"computed","paper":{"title":"MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"cs.LG","authors_text":"Dongxin Lyu, Hongxin Xiang, Jingbo Zhou, Jun Xia, Yuqiang Li","submitted_at":"2026-06-10T09:43:30Z","abstract_excerpt":"De novo peptide sequencing from tandem mass spectrometry is pivotal in proteomics, enabling identification of novel peptides without reference databases. While recent Transformer-based encoder-decoder models have achieved remarkable performance, we uncover a critical pathology in their inference dynamics. Through comprehensive feature scaling experiments, we demonstrate that existing auto-regressive peptide decoders tend to over-rely on generated-sequence priors while progressively under-utilizing fine-grained physical evidence from the input mass spectrum. This phenomenon leads to suboptimal "},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"2606.11868","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-10T09:43:30Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"0d553086119b325f6ddbff45aaf0e6acf175e4ccae5277a2d0125538c546b0a4","abstract_canon_sha256":"962b7fbe3fd22151ad81dcfc0e642274d03d329376c06deed52ada91272af9fb"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-11T01:10:12.730070Z","signature_b64":"RreVdYkGUycHE3Y/CMGYLC44Jkw8NoxGoKAotgMWo7YCreDo+F1WS+93dQOOCSz8p3/sYDf+WUUDeH2PpMVbCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"f4c256f4b5200ea8c230f2e0c0f84bf57cd22de95f74d0fb051169a9b71860ef","last_reissued_at":"2026-06-11T01:10:12.729249Z","signature_status":"signed_v1","first_computed_at":"2026-06-11T01:10:12.729249Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"cs.LG","authors_text":"Dongxin Lyu, Hongxin Xiang, Jingbo Zhou, Jun Xia, Yuqiang Li","submitted_at":"2026-06-10T09:43:30Z","abstract_excerpt":"De novo peptide sequencing from tandem mass spectrometry is pivotal in proteomics, enabling identification of novel peptides without reference databases. While recent Transformer-based encoder-decoder models have achieved remarkable performance, we uncover a critical pathology in their inference dynamics. Through comprehensive feature scaling experiments, we demonstrate that existing auto-regressive peptide decoders tend to over-rely on generated-sequence priors while progressively under-utilizing fine-grained physical evidence from the input mass spectrum. This phenomenon leads to suboptimal "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.11868","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/2606.11868/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"},"aliases":[{"alias_kind":"arxiv","alias_value":"2606.11868","created_at":"2026-06-11T01:10:12.729377+00:00"},{"alias_kind":"arxiv_version","alias_value":"2606.11868v1","created_at":"2026-06-11T01:10:12.729377+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2606.11868","created_at":"2026-06-11T01:10:12.729377+00:00"},{"alias_kind":"pith_short_12","alias_value":"6TBFN5FVEAHK","created_at":"2026-06-11T01:10:12.729377+00:00"},{"alias_kind":"pith_short_16","alias_value":"6TBFN5FVEAHKRQRQ","created_at":"2026-06-11T01:10:12.729377+00:00"},{"alias_kind":"pith_short_8","alias_value":"6TBFN5FV","created_at":"2026-06-11T01:10:12.729377+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V","json":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V.json","graph_json":"https://pith.science/api/pith-number/6TBFN5FVEAHKRQRQ6LQMB6CL6V/graph.json","events_json":"https://pith.science/api/pith-number/6TBFN5FVEAHKRQRQ6LQMB6CL6V/events.json","paper":"https://pith.science/paper/6TBFN5FV"},"agent_actions":{"view_html":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V","download_json":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V.json","view_paper":"https://pith.science/paper/6TBFN5FV","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2606.11868&json=true","fetch_graph":"https://pith.science/api/pith-number/6TBFN5FVEAHKRQRQ6LQMB6CL6V/graph.json","fetch_events":"https://pith.science/api/pith-number/6TBFN5FVEAHKRQRQ6LQMB6CL6V/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V/action/timestamp_anchor","attest_storage":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V/action/storage_attestation","attest_author":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V/action/author_attestation","sign_citation":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V/action/citation_signature","submit_replication":"https://pith.science/pith/6TBFN5FVEAHKRQRQ6LQMB6CL6V/action/replication_record"}},"created_at":"2026-06-11T01:10:12.729377+00:00","updated_at":"2026-06-11T01:10:12.729377+00:00"}