{
  "note": "Every figure is a single run, measured values should be considered as follows: the BERTMap-family ranking runs were launched in pairs, one per GPU; a second matcher process was sharing the host's CPU and memory bandwidth throughout. The reasoner coherence checks reported above are separate steps that are not counted here.",
  "measured": "June 2026",
  "unit": "seconds",
  "pairs": ["NCIT-DOID", "SNOMED-FMA", "SNOMED-NCIT"],
  "hardware": {
    "host": "Every baseline runs locally on a machine with the following specifications.",
    "cpu": "AMD Ryzen Threadripper PRO 9965WX — 24 cores / 48 threads, boost to 5.49 GHz, 128 MB L3",
    "memory": "768 GB DDR5 ECC RDIMM",
    "gpu": "2 × NVIDIA RTX PRO 6000 Blackwell Max-Q Workstation Edition, 96 GB, 300 W",
    "storage": "PCIe Gen5 NVMe SSD 1 TB system volume, 4 TB working volume",
    "os": "Ubuntu 24.04 LTS"
  },
  "software": {
    "jvm": "OpenJDK 21 — heap 256 GB for AML / LogMap / LogMapLt, 48–128 GB for the BERTMap family",
    "python": "CPython 3.12",
    "bert": "DeepOnto 0.9.3, bert-base-uncased, max sequence length 256, 3 epochs, batch 32 (training) / 256 (prediction)",
    "reasoner": "ELK, for BERTMap's internal mapping repair"
  },
  "global": {
    "label": "Subtrack 1 — global equivalence alignment",
    "phase": "matching: producing each system's global alignment over the two full ontologies",
    "systems": {
      "LogMapLt": {
        "seconds": { "NCIT-DOID": 39.0, "SNOMED-FMA": 24.3, "SNOMED-NCIT": 59.3 },
        "total_seconds": 122.7,
        "resources": "CPU, 256 GB heap"
      },
      "AML": {
        "seconds": { "NCIT-DOID": 77.6, "SNOMED-FMA": 824.0, "SNOMED-NCIT": 767.4 },
        "total_seconds": 1669.1,
        "resources": "CPU, 256 GB heap"
      },
      "LogMap": {
        "seconds": { "NCIT-DOID": 429.2, "SNOMED-FMA": 86620.1, "SNOMED-NCIT": 9497.9 },
        "total_seconds": 96547.2,
        "resources": "CPU, 256 GB heap",
        "note": "The 24-hour SNOMED–FMA cell is the outlier; the other two pairs finish in minutes to hours."
      },
      "BERTMap": {
        "seconds": { "NCIT-DOID": 13812.0, "SNOMED-FMA": 65528.2, "SNOMED-NCIT": 89642.2 },
        "total_seconds": 168982.4,
        "resources": "1 GPU, 64 GB heap",
        "note": "Includes the in-run BERT fine-tune on each pair's own ontology synonyms."
      },
      "BERTMapLt": {
        "seconds": { "NCIT-DOID": 260.6, "SNOMED-FMA": 9840.7, "SNOMED-NCIT": 6183.5 },
        "total_seconds": 16284.8,
        "resources": "CPU, 128 GB heap"
      }
    },
    "source": "AML / LogMap / LogMapLt: per-cell wall-clock recorded, cells match, write and score. BERTMap / BERTMapLt: perform end-of-matching, excludes the ranking."
  },
  "local": {
    "label": "Subtrack 2 — local equivalence ranking",
    "phase": "ranking: scoring every candidate list in the test split",
    "systems": {
      "Lexical-Baseline": {
        "seconds": { "NCIT-DOID": 17.0, "SNOMED-FMA": 25.8, "SNOMED-NCIT": 80.1 },
        "total_seconds": 122.9,
        "resources": "CPU"
      },
      "SapBERT": {
        "seconds": { "NCIT-DOID": 207.9, "SNOMED-FMA": 408.7, "SNOMED-NCIT": 1477.9 },
        "total_seconds": 2094.5,
        "resources": "1 GPU"
      },
      "BERTMapLt": {
        "seconds": { "NCIT-DOID": 166.9, "SNOMED-FMA": 794.5, "SNOMED-NCIT": 1462.9 },
        "total_seconds": 2424.3,
        "resources": "CPU, 64 GB heap"
      },
      "BERTMap-ss": {
        "seconds": { "NCIT-DOID": 3852.4, "SNOMED-FMA": 28576.8, "SNOMED-NCIT": 31974.2 },
        "total_seconds": 64403.4,
        "resources": "1 GPU, 64 GB heap",
        "note": "Fine-tunes fresh on the public train+valid maps for every split — the fine-tune must not be shared across splits."
      },
      "BERTMap": {
        "seconds": { "NCIT-DOID": 285.1, "SNOMED-FMA": 652.0, "SNOMED-NCIT": 1443.7 },
        "total_seconds": 2380.8,
        "resources": "1 GPU, 48 GB heap",
        "note": "Reuses the fine-tuned checkpoint from its Subtrack-1 run, so the fine-tuning cost is counted in the matching table above and not here."
      }
    },
    "source": "Per-cell wall-clock recorded by the baseline runner for the ranking-only runs that produced the published MRR / Hits@k."
  }
}