{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2021:KRPYBUBRM7UBZHAGX4X5C3K5OZ","short_pith_number":"pith:KRPYBUBR","canonical_record":{"source":{"id":"2106.04464","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.chem-ph","submitted_at":"2021-06-08T15:49:21Z","cross_cats_sorted":["cs.LG","math.AT"],"title_canon_sha256":"f5b3ef9446a4468cc2bfd87bd4a366730b7352aa1a53f46194b9ea1c7fce8334","abstract_canon_sha256":"3f69959fe41ccf833c8cc0ead8985bcb322e45aff0f53447bed218f9e4a077ad"},"schema_version":"1.0"},"canonical_sha256":"545f80d03167e81c9c06bf2fd16d5d767dd8686cc6ea473bf7843e3f9becf495","source":{"kind":"arxiv","id":"2106.04464","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2106.04464","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"arxiv_version","alias_value":"2106.04464v2","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2106.04464","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_12","alias_value":"KRPYBUBRM7UB","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_16","alias_value":"KRPYBUBRM7UBZHAG","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_8","alias_value":"KRPYBUBR","created_at":"2026-07-05T03:57:26Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2021:KRPYBUBRM7UBZHAGX4X5C3K5OZ","target":"record","payload":{"canonical_record":{"source":{"id":"2106.04464","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.chem-ph","submitted_at":"2021-06-08T15:49:21Z","cross_cats_sorted":["cs.LG","math.AT"],"title_canon_sha256":"f5b3ef9446a4468cc2bfd87bd4a366730b7352aa1a53f46194b9ea1c7fce8334","abstract_canon_sha256":"3f69959fe41ccf833c8cc0ead8985bcb322e45aff0f53447bed218f9e4a077ad"},"schema_version":"1.0"},"canonical_sha256":"545f80d03167e81c9c06bf2fd16d5d767dd8686cc6ea473bf7843e3f9becf495","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T03:57:26.896751Z","signature_b64":"+dgOVo8RMxEFujPeauLiGVBkcaxcqYQVXoldQP3zhgKnmr0doLj92HFzMHJwXURv1D7kdqHamTfPW1TQZKj0Bg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"545f80d03167e81c9c06bf2fd16d5d767dd8686cc6ea473bf7843e3f9becf495","last_reissued_at":"2026-07-05T03:57:26.896401Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T03:57:26.896401Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2106.04464","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":"2026-07-05T03:57:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"/kg0LvrmbKZWDg1izL2yMLjbxPWFAHz7UNN6wa/cv/6pF5ffGZlsp30XCh5fRrYO8oCfdQp03nOyZL7lMje6Aw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T06:52:26.034734Z"},"content_sha256":"f83a2a6d186b0a610822ad0e796c4665b57d8fc0212ab3f8b11317f21936f171","schema_version":"1.0","event_id":"sha256:f83a2a6d186b0a610822ad0e796c4665b57d8fc0212ab3f8b11317f21936f171"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2021:KRPYBUBRM7UBZHAGX4X5C3K5OZ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.LG","math.AT"],"primary_cat":"physics.chem-ph","authors_text":"Karthikeyan Natesan Ramamurthy, Payel Das, Samuel Hoffman, Vijil Chenthamarakshan, Yair Schiff","submitted_at":"2021-06-08T15:49:21Z","abstract_excerpt":"Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep generative models are restricted due to lack of spatial information. Here we propose augmentation of deep generative models with topological data analysis (TDA) representations, known as persistence images, for robust encoding of 3D molecular geometry. We show that the TDA augmentation of a character-based Variational Auto-Encoder (VAE) outperforms state-of"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2106.04464","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/2106.04464/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":"2026-07-05T03:57:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"K665DehKy9LCqwo+jJi43iz895OKmADIa8jT7VZzo905fr8coyFdEfw0Mf4v9QfDI/eRFBs8+4Xq+wA3KN4cDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T06:52:26.035642Z"},"content_sha256":"39e98a277297f29e6bda999f8b090714a6c857774a1e77a7b5bfdf63b50b17b1","schema_version":"1.0","event_id":"sha256:39e98a277297f29e6bda999f8b090714a6c857774a1e77a7b5bfdf63b50b17b1"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/bundle.json","state_url":"https://pith.science/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/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":"2026-08-04T06:52:26Z","links":{"resolver":"https://pith.science/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ","bundle":"https://pith.science/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/bundle.json","state":"https://pith.science/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/KRPYBUBRM7UBZHAGX4X5C3K5OZ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2021:KRPYBUBRM7UBZHAGX4X5C3K5OZ","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":"3f69959fe41ccf833c8cc0ead8985bcb322e45aff0f53447bed218f9e4a077ad","cross_cats_sorted":["cs.LG","math.AT"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.chem-ph","submitted_at":"2021-06-08T15:49:21Z","title_canon_sha256":"f5b3ef9446a4468cc2bfd87bd4a366730b7352aa1a53f46194b9ea1c7fce8334"},"schema_version":"1.0","source":{"id":"2106.04464","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2106.04464","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"arxiv_version","alias_value":"2106.04464v2","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2106.04464","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_12","alias_value":"KRPYBUBRM7UB","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_16","alias_value":"KRPYBUBRM7UBZHAG","created_at":"2026-07-05T03:57:26Z"},{"alias_kind":"pith_short_8","alias_value":"KRPYBUBR","created_at":"2026-07-05T03:57:26Z"}],"graph_snapshots":[{"event_id":"sha256:39e98a277297f29e6bda999f8b090714a6c857774a1e77a7b5bfdf63b50b17b1","target":"graph","created_at":"2026-07-05T03:57:26Z","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/2106.04464/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep generative models are restricted due to lack of spatial information. Here we propose augmentation of deep generative models with topological data analysis (TDA) representations, known as persistence images, for robust encoding of 3D molecular geometry. We show that the TDA augmentation of a character-based Variational Auto-Encoder (VAE) outperforms state-of","authors_text":"Karthikeyan Natesan Ramamurthy, Payel Das, Samuel Hoffman, Vijil Chenthamarakshan, Yair Schiff","cross_cats":["cs.LG","math.AT"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.chem-ph","submitted_at":"2021-06-08T15:49:21Z","title":"Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2106.04464","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:f83a2a6d186b0a610822ad0e796c4665b57d8fc0212ab3f8b11317f21936f171","target":"record","created_at":"2026-07-05T03:57:26Z","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":"3f69959fe41ccf833c8cc0ead8985bcb322e45aff0f53447bed218f9e4a077ad","cross_cats_sorted":["cs.LG","math.AT"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.chem-ph","submitted_at":"2021-06-08T15:49:21Z","title_canon_sha256":"f5b3ef9446a4468cc2bfd87bd4a366730b7352aa1a53f46194b9ea1c7fce8334"},"schema_version":"1.0","source":{"id":"2106.04464","kind":"arxiv","version":2}},"canonical_sha256":"545f80d03167e81c9c06bf2fd16d5d767dd8686cc6ea473bf7843e3f9becf495","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"545f80d03167e81c9c06bf2fd16d5d767dd8686cc6ea473bf7843e3f9becf495","first_computed_at":"2026-07-05T03:57:26.896401Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T03:57:26.896401Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"+dgOVo8RMxEFujPeauLiGVBkcaxcqYQVXoldQP3zhgKnmr0doLj92HFzMHJwXURv1D7kdqHamTfPW1TQZKj0Bg==","signature_status":"signed_v1","signed_at":"2026-07-05T03:57:26.896751Z","signed_message":"canonical_sha256_bytes"},"source_id":"2106.04464","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:f83a2a6d186b0a610822ad0e796c4665b57d8fc0212ab3f8b11317f21936f171","sha256:39e98a277297f29e6bda999f8b090714a6c857774a1e77a7b5bfdf63b50b17b1"],"state_sha256":"03bffc868aa8455de2c51dd1b7bb0ddd44c955e8babe719823a4996462b67cc5"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"BZ9OKHxGYH6CxMcMll3O4sfQsH23UMDcHFSjTYR7h2iyVsOr0DsSGpyyRFSJMhN23rojJiACo3RE1R3eKfUFDw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T06:52:26.041545Z","bundle_sha256":"9faf7c6981edcefd4fead4495bf89155296ba822cc7daa569bf8beb61d86a20d"}}