Human Model · HM(t) at day 178

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	61 ± 9.4	-0.39/d	0.86	—	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	44 ± 6.4	+0.67/d	0.51	16 d	Daily GI check-in · direct · today
Treatment toxicity	21 ± 8.4	+0.23/d	0.44	3 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	44 ± 11.9	+0.49/d	0.29	16 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	57 ± 11.4	-0.34/d	0.46	1 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	49 ± 9	-0.45/d	0.18	16 d	Weight, albumin, food log · proxy · days
Adherence	99 ± 4.9	+0.17/d	0.73	—	Dose + to-do completion · direct · today
Function / quality of life	54 ± 6	-0.46/d	0.52	9 d	PRO items · direct · today
Glycaemic control	138 ± 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 S05: MR phenotype; Intermediate metabolizer; butyrate 66
day 41perturbationPoor-sleep week (-3)
day 101perturbationLow-HRV stretch (-2.7)
day 171divergenceTrajectory diverged from the population model
day 171noteTrajectory diverged from prediction

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.

T1 v1leading

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

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 0.48/day)

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

v1 baseline: genotype + phenotype

T3 v1competing

confidence 41%

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

E+

GI autocorrelation 0.62 (slow recovery)

E−

Toxicity within range

E? · would discriminate

Trough drug level
Dose-timing rechallenge (evening vs morning)

Forbidden under this theory

✓ holdsGI should not move with diet if exposure is the driver (0 dietary detractors with ≥ 80% confidence)

v1 baseline: pharmacogenomics

T2 v2falsified

confidence 6%

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+

DeepGene: H2S above band

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 0.1 over 40 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T4 v1competing

confidence 6%

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

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 44 → 26

Under HY-01

GI 44 → 23

Under DT-01

GI 44 → 23

Under NP-02

GI 44 → 20

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.

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 (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	NP-02 Dietary Support Protocol 50% of 4 similar improved.	0.42	0.2	0.25	0.13	0.25	0.15	0.33
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	DT-01 Dosing / Timing Recommendation 83% of 6 similar improved.	0.32	0.2	0.25	0.08	0.25	0.15	0.28
Test	Serum DAO / histamine Discriminates T1 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.5	0.27
Treat	HY-01 Hydration Protocol 57% of 7 similar improved.	0.23	0.2	0.25	0.08	0.25	0.15	0.19
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
Maintain	Hold current regimen and content Protects nothing while the state deteriorates.	0.05	0.05	0.05	0.05	0.05	0	0.02

Excluded from the safe set

GI-04 Not indicated for the current state.
ME-01 Not indicated for the current state.
BR-03 Not indicated for the current state.
SC-12 Not indicated for the current state.
AD-05 Not indicated for the current state.
CR-01 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Intermediate metabolizer; CYP2D6, GLP1R
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 21, response 61
Labs / imaging, ≤ 14 d
0.77 (0.9·1·0.85)
Intervention response 0 within-patient responses recorded
ΔS after each action, accumulating
0.68 (0.75·1·0.9)
Deep biological state DeepGene retest day 90: damage 36/100, Shannon 3.2, butyrate 768 CPM, 3 opportunists above, 2 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 936680-R (compositional proxy)
0.32 (0.7·1·0.46)
Dynamic state GI 44, sleep 6.8 h, HRV 61, glucose 138
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 99%
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-02005 is on day 178 of META-24 (MR, baseline S05): response declining, tolerance favorable, GI deteriorating. Over 14 days response moved -6 and GI +8; discontinuation risk is 35%. The state is between basins, heading towards failing, after diverging from the model on day 171.

Butyrate capacity 66/100, diversity 3.6, intermediate metabolizer. Pushing it down: Enterococcus faecium 5.484% (LPS load) (-29.8), Enterobacteriaceae elevated (-16.9), H2S production above band (-15.2). Pulling it up: Protein (supports) (+29.5), Butyrate producers intact (+17.1). From the daily log: protein -5.6 GI next day.

No action has been tried yet.

Next: DT-01 — 91% of 284 similar trajectories improved, 61% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.