Human Model · HM(t) at day 160

State-timeSynthetic demo data⟨ I, S_t, H_0:t, E_t, Θ_t, T, U_t ⟩ — belief, not fact; uncertainty shown, not hiddenSteering view

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	59 ± 7.5	-0.01/d	0.36	15 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	53 ± 5.4	+0.25/d	0.54	4 d	Daily GI check-in · direct · today
Treatment toxicity	52 ± 11.6	-0.1/d	0.87	—	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	63 ± 11.4	+0.18/d	0.27	1 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	50 ± 10.7	-0.02/d	0.15	4 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	39 ± 8.5	-0.1/d	0.05	2 d	Weight, albumin, food log · proxy · days
Adherence	70 ± 6.8	-0.77/d	0.8	19 d	Dose + to-do completion · direct · today
Function / quality of life	46 ± 5.5	-0.19/d	0.59	1 d	PRO items · direct · today
Glycaemic control	129 ± 8	0/d	0	—	CGM daily mean · direct · today

High autocorrelation and slow recovery are early-warning signatures of a critical transition (Scheffer et al.), independent of the level.

Provenance — how did they arrive here?

The path H_0:t: baseline constraints, divergence, perturbations, actions and responses in order.

day 0baselineBaseline S11: LT phenotype; Rapid metabolizer; butyrate 41
day 22divergenceTrajectory diverged from the population model
day 22noteTrajectory diverged from prediction
day 26perturbationAntibiotic course (-4.7)
day 72perturbationPoor-sleep week (-3)
day 119perturbationDietary drift (-2.6)
day 122recommendedCR-01 recommended
day 123acceptedPatient accepted
day 128responseDeterioration detected before clinical escalation

Now: between basins, heading towards failing.

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.

T2 v2leading

confidence 49%

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 41/100
DeepGene: 4 keystone butyrate producers absent
Fat load → GI +5.1 next day
Diversity 2.7

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 5.1 over 39 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T1 v1competing

confidence 33%

Mucosal barrier loss: drug-induced epithelial injury amplified by a FUT2-dependent glycan deficit; histamine and inflammatory load add on top.

E+

DeepGene: host DNA fragmentation atypical
DeepGene: tissue recycling 46
Inflammatory load 63

E−

No FUT2 variant

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 0.05/day)

✓ holdsLow-residue meals should reduce GI within a week (not tested)

v1 baseline: genotype + phenotype

T4 v1competing

confidence 15%

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 6.9/10

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 3%

Drug-exposure toxicity: pharmacokinetic over-exposure drives GI and systemic toxicity together; dietary and microbial factors are secondary.

E+

Toxicity 52

E−

Rapid 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 (4 dietary detractors with ≥ 80% confidence)

v1 baseline: pharmacogenomics

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 53 → 57

Under GI-04

GI 53 → 43

Under ME-01

GI 53 → 55

Under NP-02

GI 53 → 44

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).

Action	pred ΔGI	obs ΔGI	ε	temporality	magnitude	dechallenge	rechallenge	cross-modal	confidence
CR-01 day 123	-7	2	+9	✗	✗	n/a	n/a	✗	0%

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
Treat	GI-04 GI Support Protocol 68% of 65 similar improved.	0.59	0.2	0.25	0.13	0.35	0.15	0.39
Maintain	Hold current regimen and content Protects a favourable trajectory.	0.35	0.05	0.05	0.05	0.05	0	0.31
Treat	NP-02 Dietary Support Protocol 62% of 37 similar improved.	0.45	0.2	0.25	0.13	0.25	0.15	0.3
Treat	DT-01 Dosing / Timing Recommendation 100% of 1 similar improved.	0.35	0.2	0.25	0.08	0.25	0.15	0.25
Treat	SC-12 Supportive Compound 83% of 24 similar improved.	0.38	0.2	0.25	0.08	0.25	0.4	0.23
Escalate	ME-01 Monitoring Escalation 100% of 44 similar improved.	0.22	0.2	0.25	0.08	0.1	0.15	0.2
Treat	BR-03 Behavioural Recommendation 100% of 2 similar improved.	0.28	0.2	0.25	0.08	0.25	0.15	0.18
Treat	HY-01 Hydration Protocol 0% of 1 similar improved.	0.15	0.2	0.25	0.08	0.25	0.15	0.05
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 bile acids Discriminates T2 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.2	0.01
Treat	AD-05 Adherence Support 0% of 0 similar improved.	0.1	0.2	0.25	0.08	0.25	0.15	0
Test	7α-hydroxy-4-cholesten-3-one (C4) Discriminates T2 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.5	-0.05

Excluded from the safe set

CR-01 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Rapid metabolizer; IL6, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 52, response 59
Labs / imaging, ≤ 14 d
0.77 (0.9·1·0.85)
Intervention response 1 within-patient responses recorded
ΔS after each action, accumulating
0.68 (0.75·1·0.9)
Deep biological state DeepGene retest day 90: damage 68/100, Shannon 2.38, butyrate 570 CPM, 2 opportunists above, 4 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 942603-R (compositional proxy)
0.39 (0.7·1·0.55)
Dynamic state GI 53, sleep 7.8 h, HRV 23, glucose 129
Companion + wearable, today
0.18 (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 70%
Food log + dose log, event-level
0.1 (0.55·0.9·0.2)

LLIFE OS insight · the five questions, in prose

grounded · add an LLM key for prose

P-02657 is on day 160 of META-24 (LT, baseline S11): response stable, tolerance improving, GI deteriorating. Over 14 days response moved +3 and GI +5; discontinuation risk is 59%. The state is between basins, heading towards failing, after diverging from the model on day 22.

Biology sets the gain: IL6 high-expression variant, Low microbial diversity; butyrate capacity 41/100, diversity 2.7. Pushing it down: Low butyrate capacity (-36.8), 4 keystone species absent (-27.5), Ultra-processed food (-25.7). Pulling it up: Protein (supports) (+27.7). From the daily log: ultra-processed +5.8 GI next day, protein -5.5 GI next day, fat +5.1 GI next day, simple carbs +5.1 GI next day.

Past actions: CR-01 on day 123 → improved (8%).

Next: GI-04 — 90% of 284 similar trajectories improved, 59% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.