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The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in which topology is implicit, forcing LLMs to reconstruct molecular structure before performing the requested chemical operation. Here we introduce MoleCode, an LLM-native, training-free, graph-explicit molecular language in which all molecular components are represented as typed entities with persistent identifiers and explicit relations. MoleCode makes molecular topology directly readable, editable and auditable within the language context, allowing an LLM to operate on structure rather than recover it from syntax. Across molecular reasoning, editing, generation and analysis tasks, this representational shift improves frontier LLMs most strongly when structural access is limiting: unfamiliar molecule","title":"MoleCode unlocks structural intelligence in large language models","url":"https://arxiv.org/abs/2605.16480","vendor":"arxiv_cs_ai"},"summary":"arXiv:2605.16480v1 Announce Type: cross \nAbstract: Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in which topology is implicit, forcing LLMs to reconstruct molecular structure before performing the requested chemical operation. Here we introduce MoleCode, an LLM-native, training-free, graph-explicit molecular language in which all molecular components are represented as typed entities with persistent identifiers and explicit relations. MoleCode makes molecular topology directly readable, editable and auditable within the language context, allowing an LLM to operate on structure rather than recover it from syntax. Across molecular reasoning, editing, generation and analysis tasks, this representational shift improves frontier LLMs most strongly when structural access is limiting: unfamiliar molecule","title":"MoleCode unlocks structural intelligence in large language models","vendor":"arxiv_cs_ai"},"confidence":{"method":"deterministic"},"decision":"POSITIVE","issued_at":"2026-05-19T04:43:36Z","notes":"Spider vendor_press (news) news.vendor_press.v1","object":{"captured_by":"crovia.spider.vendor_press","primary_source_url":"https://arxiv.org/abs/2605.16480"},"predecessors":[],"schema":"crovia.axiom.v1","signature":"ed25519:500ae35480118e566c05b2482a255bdbe2a3fcf50a2058aca46e6c960011d7b3f17effa44a662a8e5bdecf0616d70ddee298e7c7b893681ba11c1a020b3bd706","signer":"crovia.substrate","subject":{"observed_at":"2026-05-19T04:43:36Z","source_collector":"spider:vendor_press","target_id":"https://arxiv.org/abs/2605.16480"},"tsa":{"authority":"crovia.substrate.bootstrap","rfc3161_token":"{\"kind\":\"crovia.bootstrap.tsa\",\"source_jsonl\":\"/opt/crovia/spider/data/news/vendor_press_v1.jsonl\",\"source_seal_merkle_root\":\"spider_vendor_press_v1\",\"upgrade_path\":\"Sessione H \\u2014 OpenTimestamps weekly anchor\"}"},"zk_mode":"clear","zk_proof":null},"ledger":{"leaf_hash":"0a2b1eb209dbf2a8904b47d5a610c015ed4c0a5f8f053c7da3a01b169be6b5ba","leaf_index":142601,"ledger_path":"/opt/crovia/substrate/axiom_ledger.jsonl"},"merkle_proof":{"hash_alg":"sha256","leaf_prefix":"0x00","node_prefix":"0x01","odd_leaf_rule":"duplicate_last","path":[{"sibling":"fdced6e36f688e8d4057cccff7867a6f99bb309602682557e580535357c328b5","side":"left"},{"sibling":"dcd2ddc177aac5a38cdb4c433d6d1410d2af4b1516521805f32b31fef9239914","side":"right"},{"sibling":"6ba14ef83ab37ecdf17fb8c1e9203f427a719f8efc00f1c54caddbb573e69cbe","side":"right"},{"sibling":"87d2907e99da9e04dfa35e9a4df93ea2594159f674c4db4db75821b677c967fa","side":"left"},{"sibling":"e762f1bb67902431e69b3ac6fb4942b75f9cd4565ed2223e05c6dc22fa948fda","side":"right"},{"sibling":"036dbd29dff6b56d14c3fd8e8c155b6267e105ea923fb327307c91a3499e8016","side":"right"},{"sibling":"d1699c63b2a3c9d160a7dad72120a688f97fd9b9cc8ea79fe409f9e6aaaa5bbc","side":"right"},{"sibling":"0681a3895a908b2cd98c077a0abe5cdd8542f0ecb3a6294a35366c915b2e2e3e","side":"right"},{"sibling":"f1c796d3bd453570426dcee9ab20072f19762202f84b7993afba2c7c0ee9ec3b","side":"left"},{"sibling":"2e0ce989d789c88e796991ef014ce7e4e1f96c0d4ede9da8d31afcf5ba6a8f46","side":"right"},{"sibling":"202f1bead178ef3785968d50d3d188264a95192a077654c331612e04a34cbfbe","side":"left"},{"sibling":"72249c8c8b068386e35d16f4bd0bbeb9ba820ca217ef0f0d28396c9fe493f5f0","side":"left"},{"sibling":"ea64599340f7ffdf17ad0cbc1d9401ef8870a347e3847bdc106d06b1673df09c","side":"right"},{"sibling":"8f4c0fbe56b6c010fbb8c782ebcd478079bb3f991d8704e2534209a075d9163c","side":"left"},{"sibling":"4db1f363729507e27a60851cf6ed334d7b9acdef194ed7d419aba4d2bd367a4a","side":"right"},{"sibling":"a86ee18c45e7fcc408b6007eaece05aa75b2d9ae30252e9e878462b4dffbef7b","side":"right"},{"sibling":"1d18e7663d43ccff0122ecc7ee12645bb16afb607b218e81b1ea2408f863cb78","side":"right"},{"sibling":"d841ad93efda0869e5eb97678f348f03f5caab4353e05ff4bf18f47fb945b822","side":"left"}]},"schema":"crovia.axiom_proof.v1","seal":{"first_collector_run_id":"","first_receipt_hash":"","jsonl_path":"/opt/crovia/substrate/axiom_ledger.jsonl","key_id":"430895f101d38164","last_collector_run_id":"","last_receipt_hash":"","leaf_count":143302,"merkle_root":"999156d40a7c61d9ddd52b7338f3cbda3e68f53bace070c7b616ea194e23b123","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","run_id":"hourly_json_retrofit_20260519T053701Z","schema":"crovia.seal.v1","seal_family_version":"crovia-seal-family/1","seal_kind":"substrate_batch","sealed_at":"2026-05-19T05:37:30Z","sig_algorithm":"ed25519","signature":"b1a252cc66ff32bed1d10dd88a6b2a200e3856d3dbcfcc4ee55e02e00f3d548e854ed9c544704b222bd5d315492c4a935ba2d90d727c585a67899b0ad602fc05","signer_version":"1.1.0"},"trust_root":{"key_id":"430895f101d38164","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","signature_algorithm":"ed25519","url":"/registry/canon/TRUST_ROOT.md"},"verifier":{"spec":"/registry/canon/AXIOM_RECEIPT_v1.md","url":"/v/axm_c3bc49d94f9857cfbda8901ad50c242d5f8719db2a3de2341a4956b88e6f328e"}}