{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:UTF6PVSQPEFZGPQ7ELLB3KMDFY","short_pith_number":"pith:UTF6PVSQ","canonical_record":{"source":{"id":"2412.17780","kind":"arxiv","version":4},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-23T18:38:49Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"0ef2f1b7c7527c71bbb8fbf874524dff0c5cf92ea32f25b3bd1108edca27aecf","abstract_canon_sha256":"731f62fa06307de4aea819969c0d220a99d014bbc66cf140f493e0b550dff798"},"schema_version":"1.0"},"canonical_sha256":"a4cbe7d650790b933e1f22d61da9832e16383016902200d926b38518fbf47d12","source":{"kind":"arxiv","id":"2412.17780","version":4},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.17780","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"arxiv_version","alias_value":"2412.17780v4","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.17780","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_12","alias_value":"UTF6PVSQPEFZ","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_16","alias_value":"UTF6PVSQPEFZGPQ7","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_8","alias_value":"UTF6PVSQ","created_at":"2026-07-05T11:14:01Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:UTF6PVSQPEFZGPQ7ELLB3KMDFY","target":"record","payload":{"canonical_record":{"source":{"id":"2412.17780","kind":"arxiv","version":4},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-23T18:38:49Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"0ef2f1b7c7527c71bbb8fbf874524dff0c5cf92ea32f25b3bd1108edca27aecf","abstract_canon_sha256":"731f62fa06307de4aea819969c0d220a99d014bbc66cf140f493e0b550dff798"},"schema_version":"1.0"},"canonical_sha256":"a4cbe7d650790b933e1f22d61da9832e16383016902200d926b38518fbf47d12","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:14:01.181876Z","signature_b64":"M0tPMi94oTQ7gtdeqiwRlPB5gRAIJDR3x4IAbsuFnCAr11NDPBXUix4hgHwh53dHatGtMtdXym43DUQZJcXEAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"a4cbe7d650790b933e1f22d61da9832e16383016902200d926b38518fbf47d12","last_reissued_at":"2026-07-05T11:14:01.181278Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:14:01.181278Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2412.17780","source_version":4,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T11:14:01Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Nb0+emTTIC87WmEdLUWkLRe/kmAAplWXNO3a7k71JiIRhZnwAuJTTtfHtgRR23PVyOj1p867DOGS0vYmFWNBDw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-06T06:07:58.806317Z"},"content_sha256":"c8450ca3c5005b5230f3aa9b48985d4d8c9a0b1938145f76bdbba33b9e72c970","schema_version":"1.0","event_id":"sha256:c8450ca3c5005b5230f3aa9b48985d4d8c9a0b1938145f76bdbba33b9e72c970"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:UTF6PVSQPEFZGPQ7ELLB3KMDFY","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Pranam Chatterjee, Sophia Tang, Yinuo Zhang","submitted_at":"2024-12-23T18:38:49Z","abstract_excerpt":"We present PepTune, a multi-objective discrete diffusion model for simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with a novel bond-dependent masking schedule and invalid loss function. To guide the diffusion process, we introduce Monte Carlo Tree Guidance (MCTG), an inference-time multi-objective guidance algorithm that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTG integrates classifier-based rewards with search-tree expan"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.17780","kind":"arxiv","version":4},"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/2412.17780/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":"2026-07-05T11:14:01Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"TugfnJxN2RmtPL1SJVzZWk3ypfDr3PpVS6uDzrl81bnL5Kn9LWGsLK3hLPEf5v0D14jojZTqO8jXoKhGPIPzDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-06T06:07:58.806700Z"},"content_sha256":"e4b48771c0c24152f68a73919dbe62a830d6e5fa4faf91185d285fee17f6e488","schema_version":"1.0","event_id":"sha256:e4b48771c0c24152f68a73919dbe62a830d6e5fa4faf91185d285fee17f6e488"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/bundle.json","state_url":"https://pith.science/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/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":"2026-08-06T06:07:58Z","links":{"resolver":"https://pith.science/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY","bundle":"https://pith.science/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/bundle.json","state":"https://pith.science/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/state.json","well_known_bundle":"https://pith.science/.well-known/pith/UTF6PVSQPEFZGPQ7ELLB3KMDFY/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:UTF6PVSQPEFZGPQ7ELLB3KMDFY","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":"731f62fa06307de4aea819969c0d220a99d014bbc66cf140f493e0b550dff798","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-23T18:38:49Z","title_canon_sha256":"0ef2f1b7c7527c71bbb8fbf874524dff0c5cf92ea32f25b3bd1108edca27aecf"},"schema_version":"1.0","source":{"id":"2412.17780","kind":"arxiv","version":4}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.17780","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"arxiv_version","alias_value":"2412.17780v4","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.17780","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_12","alias_value":"UTF6PVSQPEFZ","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_16","alias_value":"UTF6PVSQPEFZGPQ7","created_at":"2026-07-05T11:14:01Z"},{"alias_kind":"pith_short_8","alias_value":"UTF6PVSQ","created_at":"2026-07-05T11:14:01Z"}],"graph_snapshots":[{"event_id":"sha256:e4b48771c0c24152f68a73919dbe62a830d6e5fa4faf91185d285fee17f6e488","target":"graph","created_at":"2026-07-05T11:14:01Z","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/2412.17780/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"We present PepTune, a multi-objective discrete diffusion model for simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with a novel bond-dependent masking schedule and invalid loss function. To guide the diffusion process, we introduce Monte Carlo Tree Guidance (MCTG), an inference-time multi-objective guidance algorithm that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTG integrates classifier-based rewards with search-tree expan","authors_text":"Pranam Chatterjee, Sophia Tang, Yinuo Zhang","cross_cats":["cs.AI"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-23T18:38:49Z","title":"PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.17780","kind":"arxiv","version":4},"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:c8450ca3c5005b5230f3aa9b48985d4d8c9a0b1938145f76bdbba33b9e72c970","target":"record","created_at":"2026-07-05T11:14:01Z","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":"731f62fa06307de4aea819969c0d220a99d014bbc66cf140f493e0b550dff798","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-23T18:38:49Z","title_canon_sha256":"0ef2f1b7c7527c71bbb8fbf874524dff0c5cf92ea32f25b3bd1108edca27aecf"},"schema_version":"1.0","source":{"id":"2412.17780","kind":"arxiv","version":4}},"canonical_sha256":"a4cbe7d650790b933e1f22d61da9832e16383016902200d926b38518fbf47d12","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"a4cbe7d650790b933e1f22d61da9832e16383016902200d926b38518fbf47d12","first_computed_at":"2026-07-05T11:14:01.181278Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:14:01.181278Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"M0tPMi94oTQ7gtdeqiwRlPB5gRAIJDR3x4IAbsuFnCAr11NDPBXUix4hgHwh53dHatGtMtdXym43DUQZJcXEAQ==","signature_status":"signed_v1","signed_at":"2026-07-05T11:14:01.181876Z","signed_message":"canonical_sha256_bytes"},"source_id":"2412.17780","source_kind":"arxiv","source_version":4}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:c8450ca3c5005b5230f3aa9b48985d4d8c9a0b1938145f76bdbba33b9e72c970","sha256:e4b48771c0c24152f68a73919dbe62a830d6e5fa4faf91185d285fee17f6e488"],"state_sha256":"fc999f02a5b6beaddd002c42387e767e84c349dc93f7fe6f2dc1a3045c9f8fee"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"LJPVYMNQznYPbG8K9OyB/bFONu0fSBV/Wbx1VJexMafmmQH7sy1KxrO4WU1yWA9VLxrYXVH0kLoziWsRrKbzDw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-06T06:07:58.810586Z","bundle_sha256":"21422f748e0f800d1b4789b945e8710fb72fb0be2ec0c0e1d1a1e31afaf5716e"}}