{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:VXBRTODF5QACVHLQZ5ICLDIYIY","short_pith_number":"pith:VXBRTODF","canonical_record":{"source":{"id":"2604.02121","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2026-04-02T14:56:38Z","cross_cats_sorted":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"2febbe9c77849aabd6562d9456c395219b343f0205e651d658c0c282cbcdf2c1","abstract_canon_sha256":"5ed6c559a964112afd43b7dfd89c785c969d5c9ef07d3bf23339c757ea954ea3"},"schema_version":"1.0"},"canonical_sha256":"adc319b865ec002a9d70cf50258d18460311d5ef96221c838b7146a54986647c","source":{"kind":"arxiv","id":"2604.02121","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2604.02121","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"arxiv_version","alias_value":"2604.02121v2","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2604.02121","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_12","alias_value":"VXBRTODF5QAC","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_16","alias_value":"VXBRTODF5QACVHLQ","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_8","alias_value":"VXBRTODF","created_at":"2026-06-04T01:09:49Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:VXBRTODF5QACVHLQZ5ICLDIYIY","target":"record","payload":{"canonical_record":{"source":{"id":"2604.02121","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2026-04-02T14:56:38Z","cross_cats_sorted":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"2febbe9c77849aabd6562d9456c395219b343f0205e651d658c0c282cbcdf2c1","abstract_canon_sha256":"5ed6c559a964112afd43b7dfd89c785c969d5c9ef07d3bf23339c757ea954ea3"},"schema_version":"1.0"},"canonical_sha256":"adc319b865ec002a9d70cf50258d18460311d5ef96221c838b7146a54986647c","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-04T01:09:49.431099Z","signature_b64":"lcnt1eB+8vn5wNAL6Kf203Fb0D0gd0xqBCARrsubSoR/i3fL6Fan+TGZzRKp/E2pQTvAXEs+5qg/KC8LxNEjAA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"adc319b865ec002a9d70cf50258d18460311d5ef96221c838b7146a54986647c","last_reissued_at":"2026-06-04T01:09:49.430170Z","signature_status":"signed_v1","first_computed_at":"2026-06-04T01:09:49.430170Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2604.02121","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-06-04T01:09:49Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"iGfQf1Od594pEdGQE6td2DbwAS1kivJbuCFRIJEupXarJiygV4/vii3ggT6c+gYqQIIoGxrprS7Hhg6vYXC0Bw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-05T14:30:31.204953Z"},"content_sha256":"f3886234391f406dca99d45fbbcc0ff415c58fe0b43a3858f7e1fe3a8a822fe4","schema_version":"1.0","event_id":"sha256:f3886234391f406dca99d45fbbcc0ff415c58fe0b43a3858f7e1fe3a8a822fe4"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:VXBRTODF5QACVHLQZ5ICLDIYIY","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Gradient estimators for parameter inference in discrete stochastic kinetic models","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"primary_cat":"physics.comp-ph","authors_text":"Annalena Kofler, Ludwig Burger, Lukas Heinrich, Ulrich Gerland","submitted_at":"2026-04-02T14:56:38Z","abstract_excerpt":"Stochastic kinetic models are ubiquitous in physics, yet inferring their parameters from experimental data remains challenging. For deterministic models, parameter inference often relies on gradients, which can be obtained efficiently through automatic differentiation (AD). However, AD cannot be applied directly to the Gillespie stochastic simulation algorithm (SSA), since sampling from a discrete set of reactions introduces non-differentiable operations. In this work, we adopt three gradient estimators from machine learning for the Gillespie SSA: the Gumbel-Softmax Straight-Through (GS-ST) es"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2604.02121","kind":"arxiv","version":2},"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/2604.02121/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":"2026-06-04T01:09:49Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"bZ9g6TsLZkFceAqyJYUHQk6wBxbkrM3msN19OJ9RFTjUcLKqYNL2Ea/uK32qq75BBTD3lqIgsJOWypxYgT8gCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-05T14:30:31.205688Z"},"content_sha256":"ae29f945831f9697a90e5076f56960c42c973576e0f4db79ed2c384f5f319487","schema_version":"1.0","event_id":"sha256:ae29f945831f9697a90e5076f56960c42c973576e0f4db79ed2c384f5f319487"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/bundle.json","state_url":"https://pith.science/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/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":"2026-08-05T14:30:31Z","links":{"resolver":"https://pith.science/pith/VXBRTODF5QACVHLQZ5ICLDIYIY","bundle":"https://pith.science/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/bundle.json","state":"https://pith.science/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/state.json","well_known_bundle":"https://pith.science/.well-known/pith/VXBRTODF5QACVHLQZ5ICLDIYIY/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:VXBRTODF5QACVHLQZ5ICLDIYIY","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":"5ed6c559a964112afd43b7dfd89c785c969d5c9ef07d3bf23339c757ea954ea3","cross_cats_sorted":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2026-04-02T14:56:38Z","title_canon_sha256":"2febbe9c77849aabd6562d9456c395219b343f0205e651d658c0c282cbcdf2c1"},"schema_version":"1.0","source":{"id":"2604.02121","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2604.02121","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"arxiv_version","alias_value":"2604.02121v2","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2604.02121","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_12","alias_value":"VXBRTODF5QAC","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_16","alias_value":"VXBRTODF5QACVHLQ","created_at":"2026-06-04T01:09:49Z"},{"alias_kind":"pith_short_8","alias_value":"VXBRTODF","created_at":"2026-06-04T01:09:49Z"}],"graph_snapshots":[{"event_id":"sha256:ae29f945831f9697a90e5076f56960c42c973576e0f4db79ed2c384f5f319487","target":"graph","created_at":"2026-06-04T01:09:49Z","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/2604.02121/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Stochastic kinetic models are ubiquitous in physics, yet inferring their parameters from experimental data remains challenging. For deterministic models, parameter inference often relies on gradients, which can be obtained efficiently through automatic differentiation (AD). However, AD cannot be applied directly to the Gillespie stochastic simulation algorithm (SSA), since sampling from a discrete set of reactions introduces non-differentiable operations. In this work, we adopt three gradient estimators from machine learning for the Gillespie SSA: the Gumbel-Softmax Straight-Through (GS-ST) es","authors_text":"Annalena Kofler, Ludwig Burger, Lukas Heinrich, Ulrich Gerland","cross_cats":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2026-04-02T14:56:38Z","title":"Gradient estimators for parameter inference in discrete stochastic kinetic models"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2604.02121","kind":"arxiv","version":2},"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:f3886234391f406dca99d45fbbcc0ff415c58fe0b43a3858f7e1fe3a8a822fe4","target":"record","created_at":"2026-06-04T01:09:49Z","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":"5ed6c559a964112afd43b7dfd89c785c969d5c9ef07d3bf23339c757ea954ea3","cross_cats_sorted":["cond-mat.stat-mech","cs.LG","physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.comp-ph","submitted_at":"2026-04-02T14:56:38Z","title_canon_sha256":"2febbe9c77849aabd6562d9456c395219b343f0205e651d658c0c282cbcdf2c1"},"schema_version":"1.0","source":{"id":"2604.02121","kind":"arxiv","version":2}},"canonical_sha256":"adc319b865ec002a9d70cf50258d18460311d5ef96221c838b7146a54986647c","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"adc319b865ec002a9d70cf50258d18460311d5ef96221c838b7146a54986647c","first_computed_at":"2026-06-04T01:09:49.430170Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-06-04T01:09:49.430170Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"lcnt1eB+8vn5wNAL6Kf203Fb0D0gd0xqBCARrsubSoR/i3fL6Fan+TGZzRKp/E2pQTvAXEs+5qg/KC8LxNEjAA==","signature_status":"signed_v1","signed_at":"2026-06-04T01:09:49.431099Z","signed_message":"canonical_sha256_bytes"},"source_id":"2604.02121","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:f3886234391f406dca99d45fbbcc0ff415c58fe0b43a3858f7e1fe3a8a822fe4","sha256:ae29f945831f9697a90e5076f56960c42c973576e0f4db79ed2c384f5f319487"],"state_sha256":"d8d0598bfa3eba629d9f1a8947b5bc6f0a04ea0dc415c5a57fa268bff0c39b84"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"yKnUTDDPFgNd7FSj8+9pDAgzWScytxRSunptJcsfnZ0WEL+9533+mlyqm5D8wUqLPqwDf/q//WQpI7K6wh2dDg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-05T14:30:31.211825Z","bundle_sha256":"e61868776859458d5a27bb2a3dabb5280a48710079c3ba738977e1cdf679e339"}}