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Inspired by classical enhanced sampling, we introduce an implicit, history-dependent bias in the generative space of a pretrained emulator. Specifically, a history-aware score estimator augments the frozen emulator with a distance-weighted bias that steers reverse-time sampling away from previously generated structures, regularized by an environment-support term. To preserve structural validity at long horizons, a score-based refinement step re-projects drifted samples onto the data manifold using the frozen emulator. Our experiments demonstrate that the method (i) raises diversity by $35\\%$ on DynamicPDB-80; (ii) on $12$ zero-shot Fast-Folding proteins, the learned bias alone re","title":"Learning Implicit Bias in Generative Spaces for Accelerating Protein Dynamics Emulation","url":"https://arxiv.org/abs/2606.01833","vendor":"arxiv_cs_ai"},"summary":"arXiv:2606.01833v1 Announce Type: cross \nAbstract: Generative emulators of protein dynamics produce plausible trajectories at a fraction of the cost of molecular dynamics, but they inherit their training distribution and tend to revisit known states rather than reach rare ones under long-horizon extrapolation. Inspired by classical enhanced sampling, we introduce an implicit, history-dependent bias in the generative space of a pretrained emulator. 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Our experiments demonstrate that the method (i) raises diversity by $35\\%$ on DynamicPDB-80; (ii) on $12$ zero-shot Fast-Folding proteins, the learned bias alone re","title":"Learning Implicit Bias in Generative Spaces for Accelerating Protein Dynamics Emulation","vendor":"arxiv_cs_ai"},"confidence":{"method":"deterministic"},"decision":"POSITIVE","issued_at":"2026-06-02T04:43:38Z","notes":"Spider vendor_press (news) news.vendor_press.v1","object":{"captured_by":"crovia.spider.vendor_press","primary_source_url":"https://arxiv.org/abs/2606.01833"},"predecessors":[],"schema":"crovia.axiom.v1","signature":"ed25519:90576efe41f573b5caf09f973f8a50dd13b3f459c2521764e6b2b087c0fcd853dd914fb79c4d9e4ec9c703b01b957302d85ed3c8679b4b0dbedc20ac6c79770c","signer":"crovia.substrate","subject":{"observed_at":"2026-06-02T04:43:38Z","source_collector":"spider:vendor_press","target_id":"https://arxiv.org/abs/2606.01833"},"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":"0228a1244e2b0d9abe1f36b3a50af4c66c75f9a133c6b4906c31e30cf1da0730","leaf_index":205663,"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":"39edd9c5687a19fb3efca6e0329417d7a2ccac0d4b6bf64f3a45e704230cf7bf","side":"left"},{"sibling":"c20a13ea70151a9ee7f1ae20f19608853ca49eea8cdb7a327d40d8eaa65451bf","side":"left"},{"sibling":"d8c8ed53ac27ff29a432e4c42cde13e9dbde82da88943764aa4501be6c188a2a","side":"left"},{"sibling":"95fa0bb97fa80837431335c9b5d6c2fe9d74dd3f727bb42f9310cbc50cb6b033","side":"left"},{"sibling":"d233ba86d24caac142980431a76ee06f0f96b536f4b2a94025c47656581fed6a","side":"left"},{"sibling":"2e054db6710d2da07a243b6c7bf8c0c4b9a0c1bbf0d38bd040eb7e66f2336296","side":"right"},{"sibling":"ed8954602c8dc2208f9836b8ffc4c53db7b272b0fd703c7c7d1edc5f7b9ace8c","side":"left"},{"sibling":"41924649fb2045a8eb1c76bcccd1d2cd8c7e0ab0bba7b07a79bf25a0c1677263","side":"right"},{"sibling":"21332ee1c3955bf1803955bf945ab0966ce5e0aa48d8642320cdbc044a72b935","side":"left"},{"sibling":"6620a5008acf732cd3e57b0f2d1437293e88366c2e5b175ebeb7d796fc1e0c62","side":"left"},{"sibling":"a82575bfb494af7afcc13aaae718afa6f74030f09d71b02819ea25efd4186fc4","side":"right"},{"sibling":"e6adead8216db4cae92f0a036d53baebf30eed95a99c0d10758aa75bb7780f2f","side":"right"},{"sibling":"1acc2b7ff453ffd8c97b80ae4db5358780f0c6796874fd75403791dbe99f8cd7","side":"right"},{"sibling":"24d1bb4b13e0e46131b27b70a48e65fcf4e2e14b95e3bb83ade821e9df530f6b","side":"left"},{"sibling":"5f86f58c28b1a86ae06dfff4666bb9fba8866021a81fd4f1d200aa9af4722dfb","side":"right"},{"sibling":"f6cc6f94f6944ae21390afc65ac9e91dc31f84ee6e060681bba5ae08058294bd","side":"right"},{"sibling":"c300cf0154c136afc09b1702a0be98f4ba5b6dc5cf57e8cc714ec1eaf4196eff","side":"left"},{"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":206226,"merkle_root":"d2a6d32b13cbf343fb143b21a756d0533864ae6577a376ee84ba867b949207ec","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","run_id":"hourly_json_retrofit_20260602T053701Z","schema":"crovia.seal.v1","seal_family_version":"crovia-seal-family/1","seal_kind":"substrate_batch","sealed_at":"2026-06-02T05:37:46Z","sig_algorithm":"ed25519","signature":"abd9956cfb19dd1fb8142c46a220bac2514848c6abb0e79b8b0940206cc3ebb00894d4daaf9f786427f82a7cc12482e7fda79054ebb06bceaa9b4b97e23fb30e","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_fa333ae406b96035681a65f8593c9c0a85bd8b083f6313a82a2e92be104886a2"}}