Human Model · HM(t) at day 125

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	40 ± 8.9	-0.14/d	0.49	3 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	19 ± 4.7	-0.28/d	0.23	1 d	Daily GI check-in · direct · today
Treatment toxicity	2 ± 8.1	-0.19/d	0.58	3 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	19 ± 11	-0.17/d	0.36	1 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	57 ± 10.9	-0.03/d	-0.11	1 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	66 ± 8	+0.18/d	0.39	6 d	Weight, albumin, food log · proxy · days
Adherence	84 ± 5.2	-0.51/d	0.8	1 d	Dose + to-do completion · direct · today
Function / quality of life	54 ± 5.5	-0.05/d	-0.24	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 S18: EC-01 phenotype; Normal metabolizer; butyrate 37
day 17perturbationPoor-sleep week (-3)
day 26perturbationAntibiotic course (-4.7)
day 63perturbationDaily walks resumed (3.3)
day 64perturbationAlcohol on dosing days (-1.8)
day 77perturbationLow-HRV stretch (-2.7)
day 90perturbationDietary drift (-2.6)
day 90recommendedBR-03 recommended
day 91acceptedPatient accepted
day 98responseGI symptom burden −12% vs expected
day 104state changeTolerance state changed
day 105divergenceTrajectory diverged from the population model
day 105noteTrajectory diverged from prediction

Now: between basins, 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.

T2 v2leading

confidence 88%

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 37/100
DeepGene: 4 keystone butyrate producers absent
DeepGene: H2S above band
Fat load → GI +3.7 next day
Diversity 2.2

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 3.7 over 42 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T1 v2competing

confidence 7%

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

E+

DeepGene: tissue recycling 46

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 -0.13/day)

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

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

T3 v1falsified

confidence 3%

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

E+

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 (2 dietary detractors with ≥ 80% confidence)

v1 baseline: pharmacogenomics

T4 v1competing

confidence 3%

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+

Behavioural protocol improved state

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 19 → 17

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
BR-03 day 91	-2	12	+14	✗	✓	n/a	n/a	✗	18%

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 bile acids Discriminates T2 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	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

DT-01 Not indicated for the current state.
GI-04 Not indicated for the current state.
BR-03 Not indicated for the current state.
HY-01 Not indicated for the current state.
AD-05 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.
ME-01 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 2, response 40
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 63/100, Shannon 2.63, butyrate 578 CPM, 2 opportunists above, 4 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 970349-R (compositional proxy)
0.51 (0.7·1·0.7250000000000001)
Dynamic state GI 19, sleep 6.0 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 84%
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-03418 is on day 125 of ONX-7 (EC-01, baseline S18): response unstable, tolerance favorable, GI improving. Over 14 days response moved +3 and GI -8; discontinuation risk is 11%. The state is between basins, heading towards restoration, after diverging from the model on day 105.

Biology sets the gain: Low butyrate capacity, Low microbial diversity; butyrate capacity 37/100, diversity 2.2. Pushing it down: Low butyrate capacity (-30), Enterococcus faecium 9.962% (LPS load) (-28), 4 keystone species absent (-22.5). Pulling it up: Behavioural Recommendation BR-03 (+15.1), Protein (supports) (+14.2). From the daily log: fat +3.7 GI next day, lactose +3.6 GI next day, protein -3.6 GI next day.

Past actions: BR-03 on day 91 → improved (12%).

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