{"_canonicalization":{"envelope_id":"axm_ + sha256(envelope minus {signature, axiom_id, anchors})","envelope_signature":"ed25519(envelope minus {signature, axiom_id})","json":"sort_keys=True, separators=(',',':'), ensure_ascii=False, allow_nan=False, utf-8","leaf_hash":"sha256(0x00 || canonical_json(envelope_full))","seal_signature":"ed25519(seal minus {signature, sig_algorithm})"},"axiom_id":"axm_ff7269dfa81802789280ae7de341a480827f5f1793b7e53ccfabf0673273b504","bitcoin_anchor":{"bitcoin_attestations":[],"calendar_attestations":[],"ots_url":"","stamped_at":"","status":"pending_next_stamp"},"envelope":{"anchors":[{"chain":"crovia.axiom_graph","height":0,"merkle_proof":"spider_vendor_press_v1","root_at_anchor":"spider_vendor_press_v1"}],"axiom_id":"axm_ff7269dfa81802789280ae7de341a480827f5f1793b7e53ccfabf0673273b504","axiom_type":"AX.OBS","body":{"axiom_subtype":"news.vendor_press.v1","category":"news","fingerprint":"783d4cbf06041e39429c3498b0f9e2fd74f31a0b2f0fb999defc1ca5915e430d","published":"Wed, 03 Jun 2026 00:00:00 -0400","receipt_hash":"783d4cbf06041e39429c3498b0f9e2fd74f31a0b2f0fb999defc1ca5915e430d","schema":"spider.news.vendor_press.v1","spider":"vendor_press","spider_record":{"axiom_subtype":"news.vendor_press.v1","category":"news","decision_hint":"POSITIVE","envelope_target":"AX.OBS","fingerprint":"783d4cbf06041e39429c3498b0f9e2fd74f31a0b2f0fb999defc1ca5915e430d","observed_at":"2026-06-03T04:43:57.136784Z","parent_run_hash":"62ae9c8eda846b00bc49666345b338d00756c5203438666c4c1fc694cc364b84","published":"Wed, 03 Jun 2026 00:00:00 -0400","runtime_version":"0.1.0","schema":"spider.news.vendor_press.v1","source_status":200,"source_url":"https://export.arxiv.org/rss/cs.AI","spider":"vendor_press","summary_excerpt":"arXiv:2606.02629v1 Announce Type: cross \nAbstract: Protein-protein interactions (PPIs) are essential for many biological processes. However, existing PPI prediction approaches suffer from two major limitations: they overlook the hierarchical organization of proteins, particularly meso-scale motifs that critically regulate PPIs, and fail to effectively integrate sequence, structure, and function modalities. To address these limitations, we propose MMM-PPI, a Hierarchical Motif-based Multi-Modal protein Encoder for PPI Prediction that constructs PPI embeddings in a bottom-up multi-modal manner across three scales. At the micro-scale, we encode three modal residue features; at the meso-scale, a novel multimodal motif encoder aggregates residues into spatially-informed motif embeddings; at the macro-scale, a multimodal protein encoder integrates motifs into protein embeddings by jointly modeling motif importance and inter-modal correlations. The pre-trained encoder can be used off-the-shel","title":"Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding","url":"https://arxiv.org/abs/2606.02629","vendor":"arxiv_cs_ai"},"summary":"arXiv:2606.02629v1 Announce Type: cross \nAbstract: Protein-protein interactions (PPIs) are essential for many biological processes. However, existing PPI prediction approaches suffer from two major limitations: they overlook the hierarchical organization of proteins, particularly meso-scale motifs that critically regulate PPIs, and fail to effectively integrate sequence, structure, and function modalities. To address these limitations, we propose MMM-PPI, a Hierarchical Motif-based Multi-Modal protein Encoder for PPI Prediction that constructs PPI embeddings in a bottom-up multi-modal manner across three scales. At the micro-scale, we encode three modal residue features; at the meso-scale, a novel multimodal motif encoder aggregates residues into spatially-informed motif embeddings; at the macro-scale, a multimodal protein encoder integrates motifs into protein embeddings by jointly modeling motif importance and inter-modal correlations. The pre-trained encoder can be used off-the-shel","title":"Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding","vendor":"arxiv_cs_ai"},"confidence":{"method":"deterministic"},"decision":"POSITIVE","issued_at":"2026-06-03T04:43:57Z","notes":"Spider vendor_press (news) news.vendor_press.v1","object":{"captured_by":"crovia.spider.vendor_press","primary_source_url":"https://arxiv.org/abs/2606.02629"},"predecessors":[],"schema":"crovia.axiom.v1","signature":"ed25519:edc6f7071308bc7fea914ebc630f4f9edb8a1a0f39a51e6b4e448d77c20d79cc9cfd7b3050d54a227ed4916b5a952fe69d0c7c47eabfb3a4c445b7653e16e804","signer":"crovia.substrate","subject":{"observed_at":"2026-06-03T04:43:57Z","source_collector":"spider:vendor_press","target_id":"https://arxiv.org/abs/2606.02629"},"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":"2ed50254024b0084df2c8741f3402624dcb7aee0b1e5f2c212f7c286ed855005","leaf_index":209107,"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":"c7451e95702294434000bfd1f15e5fe41bf9b9021e4b6b33aac0863d4ee0fc10","side":"left"},{"sibling":"3070e81a604bb9e3653eef06df170c98f155d68f84004d4003fa3a70380f13ba","side":"left"},{"sibling":"d2247ada7d3a1dcc0609e67880d54d4464dbc9f2e9af767ec6962ef9b0807207","side":"right"},{"sibling":"78bcef28f1ce398da4c1cb64881c67378880e6a44fad052beb4cffdd810017fe","side":"right"},{"sibling":"1dd74fb8b94ab9a4206b688cb61f285835d411f1e06cc6d0ed9a06f6239ba364","side":"left"},{"sibling":"bbdc8533c8d8f5855c286968ddba9512cfc688ba8c32f801c9d86fbbeecf349b","side":"right"},{"sibling":"58746d6e8d96ba37e0b9e1ddb999eb39960ac9fbb6fc73c81cf5ab9ec0405d1e","side":"left"},{"sibling":"eae7f3d160253f87d5f2b594663f65cef3187784faa6d32d0ec2a662c29c4d98","side":"left"},{"sibling":"9924ce3405008f0c3a3b79e9066c574929b10c2965e0cc083262d3ac8aae2cb3","side":"right"},{"sibling":"2abcec6d14b256f82b270a3141886de6129141dec525543607b760f02588a877","side":"right"},{"sibling":"2b6b45743f97ac502854e489ac38a3366f8ae7ede58a2728b45daadbf29e9d03","side":"right"},{"sibling":"a81babbd79ea0da9e030dd7f43bffb6519d214317decd50727bea4e78189d970","side":"right"},{"sibling":"2dca509b3eb767a47cf215d4315f230ce9103a76264412008ae23a349b519ef1","side":"left"},{"sibling":"24d1bb4b13e0e46131b27b70a48e65fcf4e2e14b95e3bb83ade821e9df530f6b","side":"left"},{"sibling":"8d3baa674a45fd8bc6d3e8d25298f4bec86c72fa8259d576c330d12955c7b4f7","side":"right"},{"sibling":"e32819d1eff909db08066d1703f2db3f091cddac19378b2c0c625ab11e3fdbc0","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":209569,"merkle_root":"c852efc8ad7dfffc196c71380f79e6398bcaf566974cbae7c9950b0f600d5bc8","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","run_id":"hourly_json_retrofit_20260603T053701Z","schema":"crovia.seal.v1","seal_family_version":"crovia-seal-family/1","seal_kind":"substrate_batch","sealed_at":"2026-06-03T05:37:57Z","sig_algorithm":"ed25519","signature":"1ca417607effc813341721cfdade0a2d2d4ba96a90d361dbc3e864b6991b90abc326ec41d9ba3e7110cc04adb29d7b8d95abea7ff2ab8c591b2f864ed7270c03","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_ff7269dfa81802789280ae7de341a480827f5f1793b7e53ccfabf0673273b504"}}