Human Model · HM(t) at day 117
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 | 94 ± 10.4 | +1.13/d | 0.77 | — | Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d |
| Gastrointestinal function | 16 ± 5.1 | +0.13/d | 0.16 | 7 d | Daily GI check-in · direct · today |
| Treatment toxicity | 14 ± 8.5 | -0.36/d | 0.63 | 3 d | Labs, interpolated between draws · proxy · last draw ≤ 7 d |
| Inflammatory activity | 18 ± 11.4 | -0.03/d | -0.18 | 3 d | CRP/ferritin + immune signature · inferred · weeks |
| Immune / metabolic | 76 ± 11.1 | +0.32/d | 0.25 | 3 d | Metabolic panel + wearable · inferred · weeks |
| Nutritional sufficiency | 68 ± 7.5 | -0.11/d | 0.28 | 6 d | Weight, albumin, food log · proxy · days |
| Adherence | 93 ± 4 | +0.07/d | 0.31 | 11 d | Dose + to-do completion · direct · today |
| Function / quality of life | 84 ± 5.3 | +0.38/d | 0.29 | 2 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: SR phenotype; Rapid metabolizer; butyrate 70
- day 11perturbationDaily walks resumed (3.3)
- day 25perturbationAlcohol on dosing days (-1.8)
- day 53perturbationAntibiotic course (-4.7)
- day 73perturbationDietary drift (-2.6)
Now: in the restoration basin, 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 v2leading
confidence 47%
Mucosal barrier loss: drug-induced epithelial injury amplified by a FUT2-dependent glycan deficit; histamine and inflammatory load add on top.
E+
- DeepGene: Klebsiella pneumoniae above range (LPS / zonulin)
E−
- No FUT2 variant
- No histamine signal in the log
E? · would discriminate
- Faecal calprotectin (would separate barrier from motility)
- Serum DAO / histamine
- Zonulin
Forbidden under this theory
✓ holdsGI should not improve while histamine intake stays high (GI velocity -0.39/day)
✓ holdsLow-residue meals should reduce GI within a week (not tested)
v1 baseline: genotype + phenotype → v3 dietary attribution from 60-day log
T2 v2weakened
confidence 18%
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+
- —
E−
- Butyrate producers intact
- No fat-load signal in the log
E? · would discriminate
- Faecal bile acids
- 7α-hydroxy-4-cholesten-3-one (C4)
- Rechallenge: 3 high-fat days under observation
Forbidden under this theory
✗ violatedGI should not rise on low-fat days (fat effect 0.5 over 45 low-fat days)
v1 baseline: microbiome → v2 dietary attribution
T3 v1weakened
confidence 18%
Drug-exposure toxicity: pharmacokinetic over-exposure drives GI and systemic toxicity together; dietary and microbial factors are secondary.
E+
- DPYD variant
E−
- Rapid metabolizer
- Toxicity within range
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 (1 dietary detractors with ≥ 80% confidence)
v1 baseline: pharmacogenomics
T4 v1competing
confidence 18%
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+
- —
E−
- Adherence intact
- Sleep and stress stable
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
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 16 → 16
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 = 0.3 (a theory leads), λ₃ = 1 (stable enough). Execution stays with the clinician or the informed patient (EU MDR Class I).
| Class | Action | Health | Info | Conf. | Risk | Burden | Cost | Utility |
|---|---|---|---|---|---|---|---|---|
| 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 | 0.03 |
| Measure | Faecal calprotectin (would separate barrier from motility) Discriminates T1 from its competitors (E?). | 0 | 0.45 | 0.2 | 0.02 | 0.25 | 0.2 | 0.01 |
| Maintain | Hold current regimen and content Protects nothing while the state deteriorates. | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0 | 0 |
| Test | Serum DAO / histamine Discriminates T1 from its competitors (E?). | 0 | 0.45 | 0.2 | 0.02 | 0.25 | 0.5 | -0.05 |
Excluded from the safe set
- GI-04 Not indicated for the current state.
- DT-01 Not indicated for the current state.
- HY-01 Not indicated for the current state.
- CR-01 Not indicated for the current state.
- BR-03 Not indicated for the current state.
- ME-01 Not indicated for the current state.
- AD-05 Not indicated for the current state.
- NP-02 Not indicated for the current state.
- SC-12 Not indicated for the current state.
Evidence weights · w = Authority × Relevance × Persistence
- Biological identity Rapid metabolizer; DPYD, CYP2D6, MTHFRGermline panel, baseline0.86 (0.95·0.9·1)
- High-authority clinical Toxicity 14, response 94Labs / 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 30/100, Shannon 3.08, butyrate 707 CPM, 2 opportunists above, 2 keystone absentSynthetic DeepGene metagenomics + host DNA, sample 910860-R (compositional proxy)0.54 (0.7·1·0.765)
- Dynamic state GI 16, sleep 7.2 h, HRV 43Companion + wearable, today0.18 (0.6·1·0.3)
- Exposure context Keep meals regular; three to four moderate portions spaced through the day; dosing per protocol; adherence 93%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-01448 is on day 117 of NBL-101 (SR, baseline S17): response improving, tolerance favorable, GI deteriorating. Over 14 days response moved +14 and GI +6; discontinuation risk is 18%. The state is in the restoration basin, heading towards restoration.
Butyrate capacity 70/100, diversity 3.7, rapid metabolizer. Pushing it down: Klebsiella pneumoniae 3.956% (LPS load) (-19.3), Alcohol (-17.1), Rapid metabolizer (-13). Pulling it up: Butyrate producers intact (+12.1), Daily walks resumed (+3.3). From the daily log: alcohol +5.1 GI next day.
No action has been tried yet.
No action is indicated now; the trajectory is stable relative to similar patients.