Human Phenotype Project · predictive benchmark
What can each measurement predict?
PhenoBench maps predictive information across 90 clinically grounded tasks, from blood markers and body composition to sleep, glucose dynamics, and longitudinal physiology.
measurement>representation>task>matched evaluation
160 matched cells · 52 tasks
Matched model-family leaderboard
Mean rank compares methods only where task, cohort, feature set, split, and metric are fixed. Lower is better. The 10-method comparison includes tuned XGBoost and CatBoost. Averaged within each cell, the six pretrained models improved over ridge by a median of 0.004 R² (95% task-cluster bootstrap CI, 0.003–0.007).
| # | Method | Mean rank | Matched cells |
|---|---|---|---|
| 1 | TabPFN 3.5 | 3.52 | 160 |
| 2 | TabDPT | 3.87 | 160 |
| 3 | TabFM | 4.14 | 160 |
| 4 | TabICL | 4.77 | 160 |
| 5 | TabPFN v2 | 5.03 | 160 |
| 6 | TabSwift | 5.28 | 160 |
| 7 | RealMLP | 6.01 | 160 |
| 8 | Ridge | 6.77 | 160 |
| 9 | CatBoost | 7.16 | 160 |
| 10 | XGBoost | 8.46 | 160 |
Machine-readable evidence: model_family_summary.csv · model_family_contrast.json · model_family_cells.csv
Benchmark atlas
90 clinical tasks across 15 domains
3 framework diagnostics test benchmark mechanics alongside the clinical task set.
Each card links a clinical question to its valid comparison routes. Aggregate result rows contain no participant-level records or private execution identifiers.
- 1-minute orthostatic SBP dropcardiovascular_lipid · vascular_measurement4 tracks · 36 result rows · r2
- Absolute Basophil Countimmune · blood_test7 tracks · 39 result rows · r2
- Absolute Eosinophil Countimmune · blood_test7 tracks · 39 result rows · r2
- Absolute Lymphocyte Countimmune · blood_test7 tracks · 39 result rows · r2
- Absolute Monocyte Countimmune · blood_test7 tracks · 39 result rows · r2
- Absolute Neutrophil Countimmune · blood_test7 tracks · 39 result rows · r2
- Alanine aminotransferase (ALT)hepatobiliary · blood_test5 tracks · 21 result rows · r2
- Albuminhepatobiliary · blood_test5 tracks · 21 result rows · r2
- Apnea–hypopnea index (AHI)respiratory_hypoxaemia · sleep_wearable3 tracks · 6 result rows · r2
- ApoBcardiovascular_lipid · blood_test3 tracks · 18 result rows · r2
- Asthma Statusrespiratory_hypoxaemia · condition_status3 tracks · 6 result rows · roc_auc
- Basophil Percentageimmune · blood_test0 tracks · 0 result rows · r2
- Body Weightanthropometric_body_composition · anthropometry0 tracks · 0 result rows · r2
- Carotid intima-media thicknesscardiovascular_lipid · ultrasound3 tracks · 18 result rows · r2
- CGM coefficient of variationmetabolic_metabolomics · cgm2 tracks · 18 result rows · r2
- CGM mean glucosemetabolic_metabolomics · cgm2 tracks · 18 result rows · r2
- CGM time in range (70–180 mg/dL)metabolic_metabolomics · cgm2 tracks · 18 result rows · r2
- Chronological Ageaging · demographic7 tracks · 9 result rows · r2
- Diastolic blood pressurecardiovascular_lipid · vascular_measurement4 tracks · 36 result rows · r2
- Diet Sleep Causal Effectsleep_physiology · event_level0 tracks · 0 result rows · ate_bpm
- Eosinophil Percentageimmune · blood_test0 tracks · 0 result rows · r2
- Estimated glomerular filtration rate (eGFR)renal_metabolic · derived_clinical_score2 tracks · 0 result rows · r2
- Fasting plasma glucose (FPG)metabolic_metabolomics · blood_test5 tracks · 21 result rows · r2
- Fatty Liver Disease Statushepatobiliary · condition_status3 tracks · 18 result rows · roc_auc
- Fatty liver index (FLI)hepatobiliary · derived_clinical_score6 tracks · 18 result rows · r2
- Femoral neck bone mineral density (BMD)musculoskeletal · dxa_body_composition0 tracks · 0 result rows · r2
- Ferritinhematologic · blood_test5 tracks · 21 result rows · r2
- Fibrosis-3 index (FIB-3)hepatobiliary · derived_clinical_score6 tracks · 21 result rows · r2
- Fibrosis-4 index (FIB-4)hepatobiliary · derived_clinical_score6 tracks · 18 result rows · r2
- Fundus Artery Average Widthophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- Fundus Artery Fractal Dimensionophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- Fundus Artery Tortuosity Densityophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- Fundus Artery Vessel Densityophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- Fundus Vein Average Widthophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- Fundus Vein Tortuosity Densityophthalmic_retinal · fundus_imaging8 tracks · 57 result rows · r2
- GlycAmetabolic_metabolomics · nmr_metabolomics5 tracks · 21 result rows · r2
- Glycine (NMR)metabolic_metabolomics · nmr_metabolomics4 tracks · 21 result rows · r2
- Gut Microbiome Identity Retrievalgut_microbiome · microbiome0 tracks · 0 result rows · recall_at_1
- Gut Shannon Diversitygut_microbiome · microbiome2 tracks · 4 result rows · r2
- Gut Species Richnessgut_microbiome · microbiome2 tracks · 4 result rows · r2
- HbA1cmetabolic_metabolomics · blood_test14 tracks · 25 result rows · r2
- HDL cholesterol (NMR)cardiovascular_lipid · nmr_metabolomics4 tracks · 36 result rows · r2
- Hemoglobinhematologic · blood_test5 tracks · 21 result rows · r2
- Hyperlipidemia statuscardiovascular_lipid · condition_status3 tracks · 18 result rows · roc_auc
- Hypertension statuscardiovascular_lipid · condition_status3 tracks · 18 result rows · roc_auc
- Hypothyroidism Statusendocrine · condition_status3 tracks · 18 result rows · roc_auc
- Intrinsic Geometryframework · framework_diagnostic0 tracks · 0 result rows · rankme_normalized
- Irritable Bowel Syndrome Statusgut_microbiome · condition_status3 tracks · 4 result rows · roc_auc
- LDL cholesterolcardiovascular_lipid · blood_test3 tracks · 18 result rows · r2
- LDL cholesterol (NMR)cardiovascular_lipid · nmr_metabolomics3 tracks · 18 result rows · r2
- Lean Body Massanthropometric_body_composition · dxa_body_composition7 tracks · 21 result rows · r2
- Liver Attenuationhepatobiliary · ultrasound5 tracks · 21 result rows · r2
- Liver Stiffnesshepatobiliary · ultrasound5 tracks · 21 result rows · r2
- Loneliness Statusneurologic_psychosocial · questionnaire2 tracks · 3 result rows · balanced_accuracy
- Lumbar spine bone mineral density (BMD)musculoskeletal · dxa_body_composition0 tracks · 0 result rows · r2
- Lymphocyte Percentageimmune · blood_test0 tracks · 0 result rows · r2
- Maximum Bilateral Grip Strengthmusculoskeletal · functional_test5 tracks · 21 result rows · r2
- Meal-conditioned CGM trajectorymetabolic_metabolomics · event_level2 tracks · 4 result rows · rmse
- Mean ankle pressurecardiovascular_lipid · vascular_measurement4 tracks · 36 result rows · r2
- Migraine Statusneurologic_psychosocial · condition_status3 tracks · 6 result rows · roc_auc
- Minimum bilateral ABIcardiovascular_lipid · vascular_measurement4 tracks · 36 result rows · r2
- Minimum nocturnal oxygen saturation (SpO₂)respiratory_hypoxaemia · sleep_wearable2 tracks · 6 result rows · r2
- Monocyte Percentageimmune · blood_test0 tracks · 0 result rows · r2
- Neutrophil Percentageimmune · blood_test0 tracks · 0 result rows · r2
- Next Night Sleepsleep_physiology · event_level3 tracks · 6 result rows · r2
- Non-HDL cholesterolcardiovascular_lipid · blood_test4 tracks · 36 result rows · r2
- Obesity Statusanthropometric_body_composition · condition_status0 tracks · 0 result rows · roc_auc
- Oxygen desaturation index (ODI)respiratory_hypoxaemia · sleep_wearable2 tracks · 6 result rows · r2
- Participant Synthetic Regressionframework · framework_diagnostic0 tracks · 0 result rows · r2
- Postprandial glucose response (PPGR)metabolic_metabolomics · event_level2 tracks · 4 result rows · r2
- PR intervalcardiovascular_lipid · ecg4 tracks · 36 result rows · r2
- Prediabetes Statusmetabolic_metabolomics · condition_status3 tracks · 18 result rows · roc_auc
- QRS durationcardiovascular_lipid · ecg4 tracks · 36 result rows · r2
- QT intervalcardiovascular_lipid · ecg4 tracks · 36 result rows · r2
- QTccardiovascular_lipid · ecg4 tracks · 36 result rows · r2
- Resting heart ratecardiovascular_lipid · ecg2 tracks · 18 result rows · r2
- Sleep Efficiencysleep_physiology · sleep_wearable2 tracks · 4 result rows · r2
- Synthetic Regressionframework · framework_diagnostic0 tracks · 0 result rows · r2
- Systolic blood pressurecardiovascular_lipid · vascular_measurement3 tracks · 18 result rows · r2
- T2D Statusmetabolic_metabolomics · condition_status2 tracks · 9 result rows · roc_auc
- Thigh-ankle pulse-wave velocitycardiovascular_lipid · vascular_measurement2 tracks · 18 result rows · r2
- Thyroid-stimulating hormone (TSH)endocrine · blood_test5 tracks · 21 result rows · r2
- Total branched-chain amino acids (NMR)metabolic_metabolomics · nmr_metabolomics4 tracks · 21 result rows · r2
- Total Sleep Timesleep_physiology · sleep_wearable2 tracks · 4 result rows · r2
- Triglyceridescardiovascular_lipid · blood_test3 tracks · 18 result rows · r2
- Triglycerides (NMR)cardiovascular_lipid · nmr_metabolomics3 tracks · 18 result rows · r2
- Triglyceride–glucose index (TyG)metabolic_metabolomics · derived_clinical_score6 tracks · 21 result rows · r2
- Uraterenal_metabolic · blood_test2 tracks · 6 result rows · r2
- Visceral adipose tissue (VAT)anthropometric_body_composition · dxa_body_composition0 tracks · 0 result rows · r2
- Vitamin Dendocrine · blood_test5 tracks · 21 result rows · r2
- Waistanthropometric_body_composition · anthropometry0 tracks · 0 result rows · r2
- Waist Hip Ratioanthropometric_body_composition · anthropometry0 tracks · 0 result rows · r2
- White blood cell count (WBC)immune · blood_test7 tracks · 39 result rows · r2
Machine-readable catalog: catalog.json
Proof of concept
PhenoBench-LLM
Descriptive validation results on 11 shared tasks. Win rate is the fraction of same-task model comparisons won. It does not measure participant-level prediction accuracy. Models fitted on the same fields generally performed better. The all-available analysis remains downloadable with task coverage.
82.5%Gemini 3.7 Flash
73.4%Claude Opus 4.8
72.7%Claude Sonnet 5
63.3%Gemini 3.1 Pro
62.2%GPT 5.6 Luna
56.6%Gemini 3.1 Flash Lite
47.2%Claude Haiku 4.5
46.9%Nova Pro
46.2%Grok 4.3
39.5%Llama 4 Maverick
32.9%Llama 3.3 70B
30.1%DeepSeek V4 Pro
25.9%Pixtral Large
20.6%GPT 5.4 Nano
Machine-readable results: common-task win rates · all-available win rates · task rows
Reproducibility package: Prompts, schemas, synthetic example, and evaluation code.
Maintainer-run evaluation
Submit a container
Develop against fabricated, schema-faithful examples. Then send an OCI image pinned by digest. Maintainers run accepted images on private evaluation data when capacity allows.
- Choose a synthetic task bundle
- Package the prediction contract
- Open a submission issue with the immutable image digest
Source, Task Cards, and contribution guide on GitHub.
Manual intake. No automated queue, turnaround guarantee, or guarantee of publication.