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Existing unbalanced Optimal Transport (OT) methods treat mass as a continuous fluid, performing inference at the population level. However, this macroscopic view often fails to capture the discrete, jump-like nature of birth-death events at single-cell resolution, which is essential for understanding lineage branching and fate decisions. We present Unbalanced Schr\\\"odinger Bridge (USB), a simulation-free framework for learning underlying dynamics that effectively integrates both stochastic and unbalanced effects which also models the discrete, jump-like birth-death dynamics at single-cell resolution. Theoretically, USB provides a tractable solution to the Branching Schr\\\"odinger Bridge (BSB) problem, offering a rigorous microscopic interpretatio","title":"Beyond Continuity: Simulation-free Reconstruction of Discrete Branching Dynamics from Single-cell Snapshots","url":"https://arxiv.org/abs/2605.00545","vendor":"arxiv_cs_ai"},"summary":"arXiv:2605.00545v2 Announce Type: replace-cross \nAbstract: Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis. Existing unbalanced Optimal Transport (OT) methods treat mass as a continuous fluid, performing inference at the population level. However, this macroscopic view often fails to capture the discrete, jump-like nature of birth-death events at single-cell resolution, which is essential for understanding lineage branching and fate decisions. We present Unbalanced Schr\\\"odinger Bridge (USB), a simulation-free framework for learning underlying dynamics that effectively integrates both stochastic and unbalanced effects which also models the discrete, jump-like birth-death dynamics at single-cell resolution. Theoretically, USB provides a tractable solution to the Branching Schr\\\"odinger Bridge (BSB) problem, offering a rigorous microscopic interpretatio","title":"Beyond Continuity: Simulation-free Reconstruction of Discrete Branching Dynamics from Single-cell Snapshots","vendor":"arxiv_cs_ai"},"confidence":{"method":"deterministic"},"decision":"POSITIVE","issued_at":"2026-06-11T04:43:37Z","notes":"Spider vendor_press (news) news.vendor_press.v1","object":{"captured_by":"crovia.spider.vendor_press","primary_source_url":"https://arxiv.org/abs/2605.00545"},"predecessors":[],"schema":"crovia.axiom.v1","signature":"ed25519:e1cb9ba37a9d3f9f1b2bd5f5119288e95a152a427cb015fe4997b8a396ca4ee89da5ae376d9560b744ec1eaef2c27b8a0c3be94653aaaa211043b111cedaf606","signer":"crovia.substrate","subject":{"observed_at":"2026-06-11T04:43:37Z","source_collector":"spider:vendor_press","target_id":"https://arxiv.org/abs/2605.00545"},"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":"4dc579c9eede3a74767a17c6685d55564052ed8b77caa7e3505568dae6711dfb","leaf_index":227617,"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":"9469e7c70c9d732853a3588e0eef27cd8da5776f24fa1f390f09b7b788c8843c","side":"left"},{"sibling":"bec074b75e9acbf176a4e0889f3da62660cbc8f5cd02fbe8c1b01ce8c23a6706","side":"right"},{"sibling":"a26f7544145b9f59703130efb147f1cdcf5f1e30c4d60a548ba98a37d3943620","side":"right"},{"sibling":"ad6db35f0660e336e7231f347bee77ed974d8753f1cab78e04555fe93d4bdc2f","side":"right"},{"sibling":"696baab52c8dd7da00eec185cbbf6d57c893178092dfa3f22b70aabd97d81169","side":"right"},{"sibling":"bf0a852b6519918429c7e01817ee3e63de5ebb9c3bf1960b2f07a5135d3a4194","side":"left"},{"sibling":"b3e44c169468247ff310527cf2f90f2c6c7fb8fa20f54d288a0ad8da5e1aeaae","side":"right"},{"sibling":"8a3e5c7ea49dd66cd71ed0760cc762c1e6d233215488abe34cb40cd8d01bc326","side":"right"},{"sibling":"f76de2250b6d1132375cb2a9c157faf5c22b74a7ca5c8df342d778d0e08e1216","side":"left"},{"sibling":"04e399458c5b36988cae0bf1c6dbe1b01349003b15cb5aa43f95c55acffe4ec3","side":"right"},{"sibling":"1383228337d54218bd8e5563aebb0b0dfe15c5269e3d5138e64c261d6130a88b","side":"right"},{"sibling":"57cb49c192550231071a0bf53a0821da2f79c585ec6c8d0fc76cebd62ccd78b2","side":"left"},{"sibling":"cdb58f86163046d3b15f857b03372ec75e1ad9ea4548e086793d528b9eed364d","side":"left"},{"sibling":"533d82482604463aa4a281b9d8b85917b383b7c5f924b2b494039524c55e8797","side":"left"},{"sibling":"b2590791b920ca2a4ed39de126d2c0b1a10d9e7e62f572f12425f214e767b6e1","side":"left"},{"sibling":"6cea4964f32722eb370847c2f7c9d6a9f0622c239538b07e6815a59d6fd8d49c","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":228173,"merkle_root":"7e416202c0bfd759bd2eea4236713b403993d99793fe8badb5065040080bece3","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","run_id":"hourly_json_retrofit_20260611T143708Z","schema":"crovia.seal.v1","seal_family_version":"crovia-seal-family/1","seal_kind":"substrate_batch","sealed_at":"2026-06-11T21:59:35Z","sig_algorithm":"ed25519","signature":"231c80024bc3982dd493c45b31af95097e97aabc6d712a4e5bad7d0cbdd3c08e01ff395b0f8e72754bac97016e0cd0eed88b8a13cb71edbbcb9b6d72c10a7b03","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_189dd765c38c1751ef93736c53f4b72066b3bc5a6e18613f2bdf3f33e9131026"}}