Human Model · HM(t) at day 129

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	82 ± 7.8	-0.07/d	0.34	5 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	19 ± 6.6	+0.47/d	0.65	5 d	Daily GI check-in · direct · today
Treatment toxicity	0 ± 7.3	-0.14/d	0.13	2 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	14 ± 11.7	+0.11/d	0.41	2 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	76 ± 10.8	+0.07/d	-0.15	2 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	72 ± 8.5	-0.08/d	0.42	1 d	Weight, albumin, food log · proxy · days
Adherence	96 ± 5.2	-0.5/d	0.86	10 d	Dose + to-do completion · direct · today
Function / quality of life	80 ± 5.4	-0.17/d	0.11	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.

Provenance — how did they arrive here?

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

day 0baselineBaseline S08: SR phenotype; Normal metabolizer; butyrate 72
day 17perturbationLow-HRV stretch (-2.7)
day 19perturbationAntibiotic course (-4.7)
day 59perturbationDietary drift (-2.6)
day 99perturbationAlcohol on dosing days (-1.8)

Now: in the restoration basin, heading towards restoration.

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.

T4 v1leading

confidence 38%

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+

Sleep quality worsening

E−

Adherence intact

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 v1weakened

confidence 33%

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

E+

DPYD variant
GI autocorrelation 0.75 (slow recovery)

E−

Normal 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

T1 v2competing

confidence 21%

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

E+

DeepGene: Escherichia coli 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 0.59/day)

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

v1 baseline: genotype + phenotype → v3 dietary attribution from 60-day log

T2 v2falsified

confidence 8%

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 45 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

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 19 → 16

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
Maintain	Hold current regimen and content Protects a favourable trajectory.	0.35	0.05	0.05	0.05	0.05	0	0.32
Measure	Dose-taking timestamps vs symptom timestamps Discriminates T4 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.2	0.32
Test	Sleep-window rechallenge Discriminates T4 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.5	0.27
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

Excluded from the safe set

ME-01 Not indicated for the current state.
BR-03 Not indicated for the current state.
NP-02 Not indicated for the current state.
CR-01 Not indicated for the current state.
SC-12 Not indicated for the current state.
AD-05 Not indicated for the current state.
DT-01 Not indicated for the current state.
HY-01 Not indicated for the current state.
GI-04 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; DPYD, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 0, response 82
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 23/100, Shannon 3.5, butyrate 858 CPM, 3 opportunists above, 1 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 966657-R (compositional proxy)
0.49 (0.7·1·0.7050000000000001)
Dynamic state GI 19, sleep 6.9 h, HRV 35
Companion + wearable, today
0.18 (0.6·1·0.3)
Exposure context Keep meals regular; three to four moderate portions spaced through the day; dosing per protocol; adherence 96%
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-03065 is on day 129 of ONX-7 (SR, baseline S08): response favorable, tolerance improving, GI deteriorating. Over 14 days response moved +3 and GI +6; discontinuation risk is 14%. The state is in the restoration basin, heading towards restoration.

Butyrate capacity 72/100, diversity 4.4, normal metabolizer. Pushing it down: Escherichia coli 6.179% (LPS load) (-23.8), Alcohol (-14.3), Bacteroides fragilis elevated (-13). Pulling it up: Protein (supports) (+13.3), Butyrate producers intact (+13.1). From the daily log: alcohol +4.3 GI next day, protein -3.5 GI next day.

No action has been tried yet.

No action is indicated now; the trajectory is stable relative to similar patients.