Human Model · HM(t) at day 116
State-timeSynthetic demo data⟨ I, St, H0:t, Et, Θt, T, Ut ⟩ — belief, not fact; uncertainty shown, not hiddenSteering view
1
Localization — where is this individual biologically now?
Belief state b_t per dimension: value ± sd from within-person noise plus the observation model's semantic distance. Trajectory features (velocity, autocorrelation, recovery time) are state variables.
| Dimension | b_t | dS/dt | autocorr | recovery | observation model |
|---|---|---|---|---|---|
| Therapy response | 58 ± 9 | +0.62/d | 0.84 | 1 d | Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d |
| Gastrointestinal function | 54 ± 8.4 | -1.33/d | 0.82 | — | Daily GI check-in · direct · today |
| Treatment toxicity | 63 ± 12.3 | +1.69/d | 0.81 | — | Labs, interpolated between draws · proxy · last draw ≤ 7 d |
| Inflammatory activity | 62 ± 12.5 | +0.1/d | 0.19 | 2 d | CRP/ferritin + immune signature · inferred · weeks |
| Immune / metabolic | 56 ± 10.6 | +0.21/d | 0.03 | 7 d | Metabolic panel + wearable · inferred · weeks |
| Nutritional sufficiency | 39 ± 8.4 | +0.14/d | 0.4 | 2 d | Weight, albumin, food log · proxy · days |
| Adherence | 72 ± 6.4 | -0.22/d | 0.7 | 1 d | Dose + to-do completion · direct · today |
| Function / quality of life | 34 ± 5.7 | +0.27/d | 0.12 | 1 d | PRO items · direct · today |
High autocorrelation and slow recovery are early-warning signatures of a critical transition (Scheffer et al.), independent of the level.
2
Provenance — how did they arrive here?
The path H_0:t: baseline constraints, divergence, perturbations, actions and responses in order.
- day 0baselineBaseline S17: LT phenotype; Normal metabolizer; butyrate 28
- day 8perturbationDaily walks resumed (3.3)
- day 22perturbationPoor-sleep week (-3)
- day 34perturbationAntibiotic course (-4.7)
- day 41perturbationDietary drift (-2.6)
- day 82recommendedCR-01 recommended
- day 83divergenceTrajectory diverged from the population model
- day 83noteTrajectory diverged from prediction
Now: between basins, heading towards restoration.
3
Mechanism — which theories best explain the trajectory?
Versioned competing theories with supporting (E+), contradicting (E−) and missing-but-discriminative (E?) evidence. The contradiction engine lists what should NOT happen under each theory and whether it did.
T1 v2weakened
confidence 42%
Mucosal barrier loss: drug-induced epithelial injury amplified by a FUT2-dependent glycan deficit; histamine and inflammatory load add on top.
E+
- FUT2 non-secretor genotype (barrier glycan deficit)
- DeepGene: Escherichia coli above range (LPS / zonulin)
- DeepGene: host DNA fragmentation atypical
- DeepGene: tissue recycling 64
- Histamine load → GI +4.7 next day
- Inflammatory load 62
E−
- —
E? · would discriminate
- Faecal calprotectin (would separate barrier from motility)
- Serum DAO / histamine
- Zonulin
Forbidden under this theory
✗ violatedGI should not improve while histamine intake stays high (GI velocity -0.72/day)
✓ holdsLow-residue meals should reduce GI within a week (not tested)
v1 baseline: genotype + phenotype → v3 dietary attribution from 60-day log
T2 v2competing
confidence 39%
Bile-acid diarrhoea on a low-butyrate ecology: reduced SCFA production leaves bile acids unconjugated after fat-rich meals; GI burden tracks fat intake with a one-day lag.
E+
- Butyrate capacity 28/100
- DeepGene: 6 keystone butyrate producers absent
- DeepGene: H2S above band
- Fat load → GI +4.8 next day
- Diversity 1.8
E−
- —
E? · would discriminate
- Faecal bile acids
- 7α-hydroxy-4-cholesten-3-one (C4)
- Rechallenge: 3 high-fat days under observation
Forbidden under this theory
✓ holdsGI should not rise on low-fat days (fat effect 4.8 over 31 low-fat days)
v1 baseline: microbiome → v2 dietary attribution
T4 v1competing
confidence 10%
Behavioural spiral: symptomatic days cut adherence and sleep, which raise GI and stress, which cut adherence further; the biology is a follower, not the driver.
E+
- Stress 6.3/10
E−
- —
E? · would discriminate
- Dose-taking timestamps vs symptom timestamps
- Sleep-window rechallenge
Forbidden under this theory
✓ holdsGI should not worsen on days with full adherence and good sleep (insufficient paired days)
v1 from tracker trends
T3 v1falsified
confidence 9%
Drug-exposure toxicity: pharmacokinetic over-exposure drives GI and systemic toxicity together; dietary and microbial factors are secondary.
E+
- Toxicity 63
- GI autocorrelation 0.89 (slow recovery)
E−
- Normal metabolizer
E? · would discriminate
- Trough drug level
- Dose-timing rechallenge (evening vs morning)
Forbidden under this theory
✗ violatedGI should not move with diet if exposure is the driver (5 dietary detractors with ≥ 80% confidence)
v1 baseline: pharmacogenomics
4
Forecast — which futures are likely under alternative actions?
30-day rollout of GI burden under the baseline model T and under each safe candidate action (effect ramps over onset). Dashed = prediction, never fact.
No action
GI 54 → 61
Under GI-04
GI 54 → 46
Under ME-01
GI 54 → 59
Under NP-02
GI 54 → 47
8
Intervention as measurement
Each past action as a measurement of this patient's transition dynamics: predicted ΔGI vs observed, prediction error ε_t, and the within-patient evidence patterns → individualized response confidence (observational, kept separate from randomized evidence).
No action started yet.
5
Decision — the Restore controller
Safe set computed first, then A* = argmax E[HealthGain + λ₁·InformationGain + λ₂·ConfidenceGain − λ₃·Risk − λ₄·Burden − λ₅·Cost]. λ₁ = 0.6 (theories near-equiprobable), λ₃ = 1.4 (fragile state). Execution stays with the clinician or the informed patient (EU MDR Class I).
| Class | Action | Health | Info | Conf. | Risk | Burden | Cost | Utility |
|---|---|---|---|---|---|---|---|---|
| Treat | GI-04 GI Support Protocol 65% of 114 similar improved. | 0.58 | 0.2 | 0.25 | 0.13 | 0.35 | 0.15 | 0.39 |
| Escalate | CR-01 Clinician Review 100% of 8 similar improved. | 0.37 | 0.2 | 0.25 | 0.02 | 0.25 | 0.15 | 0.38 |
| Measure | Faecal calprotectin (would separate barrier from motility) Discriminates T1 from its competitors (E?). | 0 | 0.75 | 0.2 | 0.02 | 0.25 | 0.2 | 0.32 |
| Treat | NP-02 Dietary Support Protocol 64% of 61 similar improved. | 0.46 | 0.2 | 0.25 | 0.13 | 0.25 | 0.15 | 0.32 |
| Test | Serum DAO / histamine Discriminates T1 from its competitors (E?). | 0 | 0.75 | 0.2 | 0.02 | 0.25 | 0.5 | 0.26 |
| Treat | SC-12 Supportive Compound 67% of 43 similar improved. | 0.35 | 0.2 | 0.25 | 0.08 | 0.25 | 0.4 | 0.23 |
| Escalate | ME-01 Monitoring Escalation 100% of 63 similar improved. | 0.22 | 0.2 | 0.25 | 0.08 | 0.1 | 0.15 | 0.22 |
| Treat | DT-01 Dosing / Timing Recommendation 0% of 0 similar improved. | 0.18 | 0.2 | 0.25 | 0.08 | 0.25 | 0.15 | 0.11 |
| Observe | Continue passive collection, no perturbation A clean transition can be observed only without a new perturbation. | 0 | 0.15 | 0.05 | 0 | 0.05 | 0 | 0.08 |
| Treat | HY-01 Hydration Protocol 0% of 0 similar improved. | 0.15 | 0.2 | 0.25 | 0.08 | 0.25 | 0.15 | 0.08 |
| Maintain | Hold current regimen and content Protects nothing while the state deteriorates. | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0 | 0 |
Excluded from the safe set
- BR-03 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.
- AD-05 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.
Evidence weights · w = Authority × Relevance × Persistence
- Biological identity Normal metabolizer; FUT2, CYP2D6Germline panel, baseline0.86 (0.95·0.9·1)
- High-authority clinical Toxicity 63, response 58Labs / imaging, ≤ 14 d0.77 (0.9·1·0.85)
- Intervention response 0 within-patient responses recordedΔS after each action, accumulating0.68 (0.75·1·0.9)
- Deep biological state DeepGene retest day 90: damage 89/100, Shannon 1.92, butyrate 288 CPM, 5 opportunists above, 6 keystone absentSynthetic DeepGene metagenomics + host DNA, sample 913836-R (compositional proxy)0.54 (0.7·1·0.77)
- Dynamic state GI 54, sleep 6.5 h, HRV 37Companion + wearable, today0.18 (0.6·1·0.3)
- Exposure context Prepare a plain, low-fat pasta or rice meal and note how it feels afterwards; dosing per protocol; adherence 72%Food log + dose log, event-level0.1 (0.55·0.9·0.2)
LLIFE OS insight · the five questions, in prose
grounded · add an LLM key for proseP-01778 is on day 116 of NBL-101 (LT, baseline S17): response improving, tolerance unstable, GI improving. Over 14 days response moved +6 and GI -10; discontinuation risk is 55%. The state is between basins, heading towards restoration, after diverging from the model on day 83.
Biology sets the gain: FUT2 non-secretor, Low butyrate capacity, Low microbial diversity; butyrate capacity 28/100, diversity 1.8. Pushing it down: Escherichia coli 32.033% (LPS load) (-36), Low butyrate capacity (-28.3), 6 keystone species absent (-21.2). From the daily log: fat +4.8 GI next day, alcohol +4.8 GI next day, histamine +4.7 GI next day, spicy +3.7 GI next day.
Past actions: CR-01 on day 82 → declined.
Next: GI-04 — 81% of 284 similar trajectories improved, 56% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.