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LAnA-v3

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Upload MIMIC test evaluation results

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Files changed (6) hide show
  1. README.md +22 -22
  2. evaluations/mimic_test_findings_only_metrics.json +20 -20
  3. evaluations/mimic_test_findings_only_predictions.csv +0 -0
  4. evaluations/mimic_test_metrics.json +60 -60
  5. evaluations/mimic_test_predictions.csv +0 -0
  6. run_summary.json +60 -60
README.md CHANGED
@@ -105,34 +105,34 @@ These comparison tables are refreshed across the full LAnA collection whenever a
105
  | Metric | LAnA | LAnA-MIMIC | LAnA-MIMIC-CHEXPERT | LAnA-v2 | LAnA-v3 |
106
  | --- | --- | --- | --- | --- | --- |
107
  | Number of studies | `3041` | `3041` | `3041` | `3041` | `3041` |
108
- | ROUGE-L | `0.1686` | `0.1653` | `0.1513` | `0.1670` | `0.1526` |
109
- | BLEU-1 | `0.2091` | `0.1916` | `0.1707` | `0.2174` | `0.1650` |
110
- | BLEU-4 | `0.0417` | `0.0386` | `0.0357` | `0.0417` | `0.0334` |
111
- | METEOR | `0.2298` | `0.2202` | `0.2079` | `0.2063` | `0.2057` |
112
- | RadGraph F1 | `0.1024` | `0.0921` | `0.0918` | `0.1057` | `0.0941` |
113
- | RadGraph entity F1 | `0.1587` | `0.1459` | `0.1399` | `0.1569` | `0.1454` |
114
- | RadGraph relation F1 | `0.1443` | `0.1322` | `0.1246` | `0.1474` | `0.1296` |
115
- | CheXpert F1 14-micro | `0.2116` | `0.1565` | `0.1829` | `0.1401` | `0.2607` |
116
- | CheXpert F1 5-micro | `0.2512` | `0.1530` | `0.2183` | `0.2506` | `0.2470` |
117
- | CheXpert F1 14-macro | `0.1095` | `0.0713` | `0.1095` | `0.0401` | `0.1240` |
118
- | CheXpert F1 5-macro | `0.1644` | `0.1007` | `0.1634` | `0.1004` | `0.1682` |
119
 
120
  ### Cross-Model Comparison: Findings-Only Frontal Test Studies
121
 
122
  | Metric | LAnA | LAnA-MIMIC | LAnA-MIMIC-CHEXPERT | LAnA-v2 | LAnA-v3 |
123
  | --- | --- | --- | --- | --- | --- |
124
  | Number of studies | `2210` | `2210` | `2210` | `2210` | `2210` |
125
- | ROUGE-L | `0.1771` | `0.1720` | `0.1576` | `0.1771` | `0.1613` |
126
- | BLEU-1 | `0.2177` | `0.2003` | `0.1754` | `0.2263` | `0.1749` |
127
- | BLEU-4 | `0.0484` | `0.0449` | `0.0405` | `0.0487` | `0.0397` |
128
- | METEOR | `0.2466` | `0.2347` | `0.2207` | `0.2240` | `0.2231` |
129
- | RadGraph F1 | `0.1119` | `0.1000` | `0.1010` | `0.1181` | `0.1047` |
130
- | RadGraph entity F1 | `0.1713` | `0.1577` | `0.1517` | `0.1739` | `0.1595` |
131
- | RadGraph relation F1 | `0.1549` | `0.1413` | `0.1347` | `0.1628` | `0.1419` |
132
- | CheXpert F1 14-micro | `0.1907` | `0.1442` | `0.1651` | `0.1365` | `0.2501` |
133
- | CheXpert F1 5-micro | `0.2415` | `0.1716` | `0.2152` | `0.2455` | `0.2375` |
134
- | CheXpert F1 14-macro | `0.1039` | `0.0700` | `0.1047` | `0.0381` | `0.1203` |
135
- | CheXpert F1 5-macro | `0.1578` | `0.1112` | `0.1611` | `0.0952` | `0.1627` |
136
 
137
  ## Data
138
 
 
105
  | Metric | LAnA | LAnA-MIMIC | LAnA-MIMIC-CHEXPERT | LAnA-v2 | LAnA-v3 |
106
  | --- | --- | --- | --- | --- | --- |
107
  | Number of studies | `3041` | `3041` | `3041` | `3041` | `3041` |
108
+ | ROUGE-L | `0.1686` | `0.1653` | `0.1513` | `0.1670` | `0.1745` |
109
+ | BLEU-1 | `0.2091` | `0.1916` | `0.1707` | `0.2174` | `0.2346` |
110
+ | BLEU-4 | `0.0417` | `0.0386` | `0.0357` | `0.0417` | `0.0484` |
111
+ | METEOR | `0.2298` | `0.2202` | `0.2079` | `0.2063` | `0.2129` |
112
+ | RadGraph F1 | `0.1024` | `0.0921` | `0.0918` | `0.1057` | `0.0939` |
113
+ | RadGraph entity F1 | `0.1587` | `0.1459` | `0.1399` | `0.1569` | `0.1441` |
114
+ | RadGraph relation F1 | `0.1443` | `0.1322` | `0.1246` | `0.1474` | `0.1280` |
115
+ | CheXpert F1 14-micro | `0.2116` | `0.1565` | `0.1829` | `0.1401` | `0.3116` |
116
+ | CheXpert F1 5-micro | `0.2512` | `0.1530` | `0.2183` | `0.2506` | `0.2486` |
117
+ | CheXpert F1 14-macro | `0.1095` | `0.0713` | `0.1095` | `0.0401` | `0.1363` |
118
+ | CheXpert F1 5-macro | `0.1644` | `0.1007` | `0.1634` | `0.1004` | `0.1686` |
119
 
120
  ### Cross-Model Comparison: Findings-Only Frontal Test Studies
121
 
122
  | Metric | LAnA | LAnA-MIMIC | LAnA-MIMIC-CHEXPERT | LAnA-v2 | LAnA-v3 |
123
  | --- | --- | --- | --- | --- | --- |
124
  | Number of studies | `2210` | `2210` | `2210` | `2210` | `2210` |
125
+ | ROUGE-L | `0.1771` | `0.1720` | `0.1576` | `0.1771` | `0.1848` |
126
+ | BLEU-1 | `0.2177` | `0.2003` | `0.1754` | `0.2263` | `0.2480` |
127
+ | BLEU-4 | `0.0484` | `0.0449` | `0.0405` | `0.0487` | `0.0573` |
128
+ | METEOR | `0.2466` | `0.2347` | `0.2207` | `0.2240` | `0.2310` |
129
+ | RadGraph F1 | `0.1119` | `0.1000` | `0.1010` | `0.1181` | `0.1046` |
130
+ | RadGraph entity F1 | `0.1713` | `0.1577` | `0.1517` | `0.1739` | `0.1584` |
131
+ | RadGraph relation F1 | `0.1549` | `0.1413` | `0.1347` | `0.1628` | `0.1405` |
132
+ | CheXpert F1 14-micro | `0.1907` | `0.1442` | `0.1651` | `0.1365` | `0.2921` |
133
+ | CheXpert F1 5-micro | `0.2415` | `0.1716` | `0.2152` | `0.2455` | `0.2394` |
134
+ | CheXpert F1 14-macro | `0.1039` | `0.0700` | `0.1047` | `0.0381` | `0.1326` |
135
+ | CheXpert F1 5-macro | `0.1578` | `0.1112` | `0.1611` | `0.0952` | `0.1636` |
136
 
137
  ## Data
138
 
evaluations/mimic_test_findings_only_metrics.json CHANGED
@@ -4,35 +4,35 @@
4
  "dataset": "mimic-cxr",
5
  "view_filter": "frontal-only (PA/AP), structured Findings section only",
6
  "num_examples": 2210,
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- "bleu_1": 0.17491187190057955,
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- "meteor": 0.22311507091428398,
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- "rouge_l": 0.1612770175038926,
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- "chexpert_f1_14_micro": 0.2501020547013199,
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- "chexpert_f1_5_micro": 0.23749208359721344,
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- "chexpert_f1_14_macro": 0.12030236160434729,
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- "chexpert_f1_5_macro": 0.16269249240448827,
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- "chexpert_f1_micro": 0.2501020547013199,
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- "chexpert_f1_macro": 0.12030236160434729,
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  "chexpert_per_label_f1": {
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- "Enlarged Cardiomediastinum": 0.0625,
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- "Cardiomegaly": 0.3613109512390088,
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  "Lung Opacity": 0.005772005772005772,
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  "Lung Lesion": 0.0,
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- "Edema": 0.26058631921824105,
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  "Consolidation": 0.0,
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  "Pneumonia": 0.0,
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  "Atelectasis": 0.013186813186813187,
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  "Pneumothorax": 0.0,
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- "Pleural Effusion": 0.1783783783783784,
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  "Pleural Other": 0.0,
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- "Fracture": 0.022988505747126436,
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- "Support Devices": 0.415625,
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- "No Finding": 0.36388508891928867
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  },
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- "radgraph_f1": 0.10468134329680011,
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- "radgraph_f1_entity": 0.1595464585348944,
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- "radgraph_f1_relation": 0.14191739966668873,
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  "radgraph_available": true,
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  "radgraph_error": null
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  }
 
4
  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP), structured Findings section only",
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  "num_examples": 2210,
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+ "bleu_1": 0.24804371044734913,
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+ "meteor": 0.2309676565725014,
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+ "chexpert_f1_14_micro": 0.2921437031188314,
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+ "chexpert_f1_5_micro": 0.23939202026599113,
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+ "chexpert_f1_5_macro": 0.1635857001735776,
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+ "chexpert_f1_micro": 0.2921437031188314,
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+ "chexpert_f1_macro": 0.13259269532627468,
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  "chexpert_per_label_f1": {
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+ "Enlarged Cardiomediastinum": 0.06293706293706294,
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+ "Cardiomegaly": 0.3652312599681021,
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  "Lung Opacity": 0.005772005772005772,
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  "Lung Lesion": 0.0,
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+ "Edema": 0.2601626016260163,
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  "Consolidation": 0.0,
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  "Pneumonia": 0.0,
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  "Atelectasis": 0.013186813186813187,
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  "Pneumothorax": 0.0,
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+ "Pleural Effusion": 0.1793478260869565,
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  "Pleural Other": 0.0,
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+ "Fracture": 0.023255813953488372,
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+ "Support Devices": 0.5962264150943396,
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+ "No Finding": 0.3501779359430605
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  },
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+ "radgraph_f1": 0.10463721960424775,
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+ "radgraph_f1_entity": 0.15836826410474694,
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+ "radgraph_f1_relation": 0.1404934373559056,
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  "radgraph_available": true,
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  "radgraph_error": null
38
  }
evaluations/mimic_test_findings_only_predictions.csv CHANGED
The diff for this file is too large to render. See raw diff
 
evaluations/mimic_test_metrics.json CHANGED
@@ -4,35 +4,35 @@
4
  "dataset": "mimic-cxr",
5
  "view_filter": "frontal-only (PA/AP)",
6
  "num_examples": 3041,
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- "bleu_1": 0.16499879686902857,
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- "rouge_l": 0.15262886260140987,
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- "chexpert_f1_14_micro": 0.26065662978414655,
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- "chexpert_f1_5_micro": 0.246974358974359,
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- "chexpert_f1_14_macro": 0.1239880617810402,
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- "chexpert_f1_5_macro": 0.16818421256006927,
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- "chexpert_f1_micro": 0.26065662978414655,
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- "chexpert_f1_macro": 0.1239880617810402,
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  "chexpert_per_label_f1": {
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- "Enlarged Cardiomediastinum": 0.0776255707762557,
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  "Lung Opacity": 0.004073319755600814,
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  "Lung Lesion": 0.0,
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- "Edema": 0.24839400428265523,
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- "Pleural Effusion": 0.192274678111588,
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- "Fracture": 0.017391304347826087,
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  },
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- "radgraph_f1": 0.09410311365933419,
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- "radgraph_f1_entity": 0.14542321670985509,
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- "radgraph_f1_relation": 0.12964295145994836,
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  "radgraph_available": true,
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  "radgraph_error": null,
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  "evaluation_suite": "mimic_test_dual",
@@ -42,35 +42,35 @@
42
  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP)",
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  "num_examples": 3041,
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- "bleu_1": 0.16499879686902857,
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- "chexpert_f1_micro": 0.26065662978414655,
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- "chexpert_f1_macro": 0.1239880617810402,
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  "chexpert_per_label_f1": {
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- "Enlarged Cardiomediastinum": 0.0776255707762557,
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- "Cardiomegaly": 0.39155672823218995,
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  "Lung Opacity": 0.004073319755600814,
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- "Edema": 0.24839400428265523,
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  "Atelectasis": 0.008695652173913044,
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  },
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  "radgraph_available": true,
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  "radgraph_error": null
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  },
@@ -80,35 +80,35 @@
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  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP), structured Findings section only",
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  "num_examples": 2210,
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- "bleu_1": 0.17491187190057955,
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  "chexpert_per_label_f1": {
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- "Enlarged Cardiomediastinum": 0.0625,
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- "Cardiomegaly": 0.3613109512390088,
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  "Lung Opacity": 0.005772005772005772,
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  "Lung Lesion": 0.0,
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- "Edema": 0.26058631921824105,
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  "Consolidation": 0.0,
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  "radgraph_available": true,
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  "radgraph_error": null
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  }
 
4
  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP)",
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  "num_examples": 3041,
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  "evaluation_suite": "mimic_test_dual",
 
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  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP)",
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  "num_examples": 3041,
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  "Pneumonia": 0.0,
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  "Atelectasis": 0.008695652173913044,
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  "Pneumothorax": 0.0,
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  "Pleural Other": 0.0,
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  },
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  },
 
80
  "dataset": "mimic-cxr",
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  "view_filter": "frontal-only (PA/AP), structured Findings section only",
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  "num_examples": 2210,
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evaluations/mimic_test_predictions.csv CHANGED
The diff for this file is too large to render. See raw diff
 
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