{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:6FT5RJHD4CNQXOOWAAH425XTLL","short_pith_number":"pith:6FT5RJHD","canonical_record":{"source":{"id":"2607.18144","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-20T16:43:54Z","cross_cats_sorted":["cs.AI","cs.CL"],"title_canon_sha256":"f456b31164bc20eab091ebae67b14b65b8a560ae270dd6a1630d7e633c003f79","abstract_canon_sha256":"4eb30ee71d9d3da7a96105721a5790e55b293fa5010ad22a1e52cb38457ae59d"},"schema_version":"1.0"},"canonical_sha256":"f167d8a4e3e09b0bb9d6000fcd76f35ad4423588195de266d5b0eb793baee3d6","source":{"kind":"arxiv","id":"2607.18144","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.18144","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"arxiv_version","alias_value":"2607.18144v1","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.18144","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_12","alias_value":"6FT5RJHD4CNQ","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_16","alias_value":"6FT5RJHD4CNQXOOW","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_8","alias_value":"6FT5RJHD","created_at":"2026-07-21T02:22:18Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:6FT5RJHD4CNQXOOWAAH425XTLL","target":"record","payload":{"canonical_record":{"source":{"id":"2607.18144","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-20T16:43:54Z","cross_cats_sorted":["cs.AI","cs.CL"],"title_canon_sha256":"f456b31164bc20eab091ebae67b14b65b8a560ae270dd6a1630d7e633c003f79","abstract_canon_sha256":"4eb30ee71d9d3da7a96105721a5790e55b293fa5010ad22a1e52cb38457ae59d"},"schema_version":"1.0"},"canonical_sha256":"f167d8a4e3e09b0bb9d6000fcd76f35ad4423588195de266d5b0eb793baee3d6","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-21T02:22:18.946430Z","signature_b64":"C9s9yrqgCS6t9IJPFTrNHVhdvLtTXBNfueFRELld3niDcR9o18R0kyhOLVxvNTwYGdCETzh1DIUNhNF+22vBCQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"f167d8a4e3e09b0bb9d6000fcd76f35ad4423588195de266d5b0eb793baee3d6","last_reissued_at":"2026-07-21T02:22:18.945577Z","signature_status":"signed_v1","first_computed_at":"2026-07-21T02:22:18.945577Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2607.18144","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":"2026-07-21T02:22:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"3cjTtZxpvroZdQoGGXrTDhdnpwKkzwV4/N65HmMM8VoMbtJIqAEh2o/6cuZhQFumd1+lHAMa/lQUi0SUqX2WBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T16:03:13.165492Z"},"content_sha256":"09fa8e7955c0695b1f2a230391108d918d66f5e6e55accf01660bf7f95cbd062","schema_version":"1.0","event_id":"sha256:09fa8e7955c0695b1f2a230391108d918d66f5e6e55accf01660bf7f95cbd062"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:6FT5RJHD4CNQXOOWAAH425XTLL","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["cs.AI","cs.CL"],"primary_cat":"cs.LG","authors_text":"Alex Aliper, Alex Zhavoronkov, Maksim Kuznetsov, Maxim Malkov, Rim Shayakhmetov, Roman Schutski, Thomas MacDougall, Vladimir Aladinskiy","submitted_at":"2026-07-20T16:43:54Z","abstract_excerpt":"Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While diffusion models have dominated as a leading paradigm for high-quality 3D molecule generation, LLM-based methods are rapidly emerging in molecular design and have shown competitive performance in pocket-conditioned molecular generation. However, their ability to reason about physics and 3D spatial environments is largely underexplored. In this work, we systematically analyze whether current general-purpose LLMs are cap"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.18144","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/2607.18144/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":"2026-07-21T02:22:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"sJD1mP9Kh7KBEA9NaD8JUIJS/HW1B0m1Ia/EgEBfXiOccTXx+hpqnkLDa8lioO0HjNoW6VzuTuVBnokGOtRABw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T16:03:13.166554Z"},"content_sha256":"08d7c66d6c3af250810aa65854965087baef1fcd83776f2235a5dfd360352745","schema_version":"1.0","event_id":"sha256:08d7c66d6c3af250810aa65854965087baef1fcd83776f2235a5dfd360352745"},{"event_type":"integrity_finding","subject_pith_number":"pith:2026:6FT5RJHD4CNQXOOWAAH425XTLL","target":"integrity","payload":{"note":"DOI is split by whitespace or line breaks in the printed bibliography. Reconstructed DOI 10.1016/j.cell.2026.01.003 resolves to 'Unified modeling of 3D molecular generation via atomic interactions with PocketXMol'. A reader following the printed text alone cannot reach it.","snippet":"Xingang Peng, Ruihan Guo, Fenglin Guo, Ziyi Wang, Jiayu Sun, Jiaqi Guan, Yinjun Jia, Yan Xu, Yanwen Huang, Muhan Zhang, Jian Peng, Xinquan Wang, Chuanhui Han, Zihua Wang, and Jianzhu Ma. Unified modeling of 3d molecular generation via atomi","arxiv_id":"2607.18144","detector":"doi_compliance","evidence":{"ref_index":48,"verdict_class":"incontrovertible","resolved_title":"Unified modeling of 3D molecular generation via atomic interactions with PocketXMol","printed_excerpt":"10.1016/j.cell","reconstructed_doi":"10.1016/j.cell.2026.01.003"},"severity":"advisory","ref_index":48,"audited_at":"2026-08-01T15:59:47.073721Z","event_type":"pith.integrity.v1","detected_doi":"10.1016/j.cell.2026.01.003","detector_url":"https://pith.science/pith-integrity-protocol#doi_compliance","external_url":null,"finding_type":"recoverable_identifier","evidence_hash":"5337dbd668edf17a619b27dc116174b103447cfeb3d959969f2e5ea62ed17bbf","paper_version":1,"verdict_class":"incontrovertible","resolved_title":"Unified modeling of 3D molecular generation via atomic interactions with PocketXMol","detector_version":"1.1.0","detected_arxiv_id":null,"integrity_event_id":16157,"payload_sha256":"6234c7d2c8c28b7909467d88f7ad9797fc48a8ffe862a89923a0560bc9bc71f6","signature_b64":"oJFFXhmJnQfDUPJVuoCUcUbzIZH1ABQfYL/TvSLWe+2sddvYQ1x78N73/6nYFo6yPMDE5roxhJUcIU+YwLxsDA==","signing_key_id":"pith-v1-2026-05"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-08-01T16:03:29Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"UlA5fO7sRWWrfzXnRGovXoKy4ec13HRO1heWWUcCEEcoDEVTFSlSKK+MeLcefb2pNKXQGDuMjHmwPzUGmC4lCA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T16:03:13.172034Z"},"content_sha256":"e99e070433864a9ab3c4f7f0e0e6061e4ad101285c2e80f17f0229098e2f652c","schema_version":"1.0","event_id":"sha256:e99e070433864a9ab3c4f7f0e0e6061e4ad101285c2e80f17f0229098e2f652c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/6FT5RJHD4CNQXOOWAAH425XTLL/bundle.json","state_url":"https://pith.science/pith/6FT5RJHD4CNQXOOWAAH425XTLL/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/6FT5RJHD4CNQXOOWAAH425XTLL/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":"2026-08-03T16:03:13Z","links":{"resolver":"https://pith.science/pith/6FT5RJHD4CNQXOOWAAH425XTLL","bundle":"https://pith.science/pith/6FT5RJHD4CNQXOOWAAH425XTLL/bundle.json","state":"https://pith.science/pith/6FT5RJHD4CNQXOOWAAH425XTLL/state.json","well_known_bundle":"https://pith.science/.well-known/pith/6FT5RJHD4CNQXOOWAAH425XTLL/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:6FT5RJHD4CNQXOOWAAH425XTLL","merge_version":"pith-open-graph-merge-v1","event_count":3,"valid_event_count":3,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"4eb30ee71d9d3da7a96105721a5790e55b293fa5010ad22a1e52cb38457ae59d","cross_cats_sorted":["cs.AI","cs.CL"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-20T16:43:54Z","title_canon_sha256":"f456b31164bc20eab091ebae67b14b65b8a560ae270dd6a1630d7e633c003f79"},"schema_version":"1.0","source":{"id":"2607.18144","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.18144","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"arxiv_version","alias_value":"2607.18144v1","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.18144","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_12","alias_value":"6FT5RJHD4CNQ","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_16","alias_value":"6FT5RJHD4CNQXOOW","created_at":"2026-07-21T02:22:18Z"},{"alias_kind":"pith_short_8","alias_value":"6FT5RJHD","created_at":"2026-07-21T02:22:18Z"}],"graph_snapshots":[{"event_id":"sha256:08d7c66d6c3af250810aa65854965087baef1fcd83776f2235a5dfd360352745","target":"graph","created_at":"2026-07-21T02:22:18Z","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/2607.18144/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While diffusion models have dominated as a leading paradigm for high-quality 3D molecule generation, LLM-based methods are rapidly emerging in molecular design and have shown competitive performance in pocket-conditioned molecular generation. However, their ability to reason about physics and 3D spatial environments is largely underexplored. In this work, we systematically analyze whether current general-purpose LLMs are cap","authors_text":"Alex Aliper, Alex Zhavoronkov, Maksim Kuznetsov, Maxim Malkov, Rim Shayakhmetov, Roman Schutski, Thomas MacDougall, Vladimir Aladinskiy","cross_cats":["cs.AI","cs.CL"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-20T16:43:54Z","title":"Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.18144","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":"sha256:09fa8e7955c0695b1f2a230391108d918d66f5e6e55accf01660bf7f95cbd062","target":"record","created_at":"2026-07-21T02:22:18Z","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":"4eb30ee71d9d3da7a96105721a5790e55b293fa5010ad22a1e52cb38457ae59d","cross_cats_sorted":["cs.AI","cs.CL"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-20T16:43:54Z","title_canon_sha256":"f456b31164bc20eab091ebae67b14b65b8a560ae270dd6a1630d7e633c003f79"},"schema_version":"1.0","source":{"id":"2607.18144","kind":"arxiv","version":1}},"canonical_sha256":"f167d8a4e3e09b0bb9d6000fcd76f35ad4423588195de266d5b0eb793baee3d6","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"f167d8a4e3e09b0bb9d6000fcd76f35ad4423588195de266d5b0eb793baee3d6","first_computed_at":"2026-07-21T02:22:18.945577Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-21T02:22:18.945577Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"C9s9yrqgCS6t9IJPFTrNHVhdvLtTXBNfueFRELld3niDcR9o18R0kyhOLVxvNTwYGdCETzh1DIUNhNF+22vBCQ==","signature_status":"signed_v1","signed_at":"2026-07-21T02:22:18.946430Z","signed_message":"canonical_sha256_bytes"},"source_id":"2607.18144","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:09fa8e7955c0695b1f2a230391108d918d66f5e6e55accf01660bf7f95cbd062","sha256:08d7c66d6c3af250810aa65854965087baef1fcd83776f2235a5dfd360352745","sha256:e99e070433864a9ab3c4f7f0e0e6061e4ad101285c2e80f17f0229098e2f652c"],"state_sha256":"bc0f5439fd50739a00aaacba822d81aec059f2589fe74d588c3bddd46c26a965"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"kiVw1ZThfcWn9IcUz1n2k8hMcepl8mazmypPZM1KhN4lyNfENq44h96eq4qBpAF4Cq1JRLbm19II9JTbqE5EBw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-03T16:03:13.176188Z","bundle_sha256":"ad9fab750daac5faaba8392324b4393f43c0594bd8cec06440f93c70d9d681c9"}}