Human Model · HM(t) at day 112

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	44 ± 8	-0.27/d	0.69	11 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	54 ± 7.5	+0.53/d	0.77	—	Daily GI check-in · direct · today
Treatment toxicity	46 ± 9.6	+0.21/d	0.79	1 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	51 ± 11.6	+0.39/d	0.6	3 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	50 ± 10.5	-0.14/d	0.04	1 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	42 ± 8.8	-0.38/d	0.44	1 d	Weight, albumin, food log · proxy · days
Adherence	43 ± 5	-0.19/d	0.7	—	Dose + to-do completion · direct · today
Function / quality of life	31 ± 5.1	-0.24/d	0.3	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 S06: EC-03 phenotype; Normal metabolizer; butyrate 28
day 0perturbationAlcohol on dosing days (-1.8)
day 2perturbationDietary drift (-2.6)
day 31recommendedNP-02 recommended
day 32acceptedPatient accepted
day 42responseGI symptom burden −17% vs expected
day 48state changeTolerance state changed
day 50recommendedGI-04 recommended
day 51acceptedPatient accepted
day 53divergenceTrajectory diverged from the population model
day 53noteTrajectory diverged from prediction
day 59responseGI symptom burden −18% vs expected
day 60perturbationDaily walks resumed (3.3)
day 65state changeTolerance state changed

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 37%

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 28/100
DeepGene: 6 keystone butyrate producers absent
Fat load → GI +4.4 next day
Diversity 2.1

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 4.4 over 39 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T1 v3competing

confidence 34%

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)
DeepGene: host DNA fragmentation atypical
DeepGene: tissue recycling 64
Inflammatory load 51
GI-04 (barrier-support protocol) improved GI

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 0.19/day)

✓ holdsLow-residue meals should reduce GI within a week (NP-02 → improved)

v1 baseline: genotype + phenotype → v2 day 51: GI-04 response added to E+ → v3 dietary attribution from 60-day log

T4 v1competing

confidence 19%

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+

Adherence 43%
Sleep quality worsening

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 11%

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

E+

Toxicity 46
GI autocorrelation 0.83 (slow recovery)

E−

Normal 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 (3 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 54 → 58

Under ME-01

GI 54 → 56

Under SC-12

GI 54 → 50

Under DT-01

GI 54 → 51

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
NP-02 day 32	-2	22	+24	✗	✓	no	n/a	✗	18%
GI-04 day 51	-10	28	+38	✗	✓	no	n/a	✗	18%

Learning curve · |ε| per cycle:NP-02 24 (prior 24)GI-04 30 (prior 38)not yet improving

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
Escalate	CR-01 Clinician Review 100% of 4 similar improved.	0.37	0.2	0.25	0.02	0.25	0.15	0.39
Measure	Faecal bile acids Discriminates T2 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.2	0.32
Test	7α-hydroxy-4-cholesten-3-one (C4) Discriminates T2 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.5	0.27
Escalate	ME-01 Monitoring Escalation 100% of 67 similar improved.	0.22	0.2	0.25	0.08	0.1	0.15	0.26
Treat	SC-12 Supportive Compound 67% of 45 similar improved.	0.35	0.2	0.25	0.08	0.25	0.4	0.26
Treat	DT-01 Dosing / Timing Recommendation 0% of 0 similar improved.	0.18	0.2	0.25	0.08	0.25	0.15	0.14
Treat	HY-01 Hydration Protocol 0% of 0 similar improved.	0.15	0.2	0.25	0.08	0.25	0.15	0.11
Treat	BR-03 Behavioural Recommendation 0% of 0 similar improved.	0.14	0.2	0.25	0.08	0.25	0.15	0.1
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
Treat	AD-05 Adherence Support 0% of 0 similar improved.	0.1	0.2	0.25	0.08	0.25	0.15	0.06
Maintain	Hold current regimen and content Protects nothing while the state deteriorates.	0.05	0.05	0.05	0.4	0.05	0	-0.33

Excluded from the safe set

GI-04 Not indicated for the current state.
NP-02 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; IL6, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 46, response 44
Labs / imaging, ≤ 14 d
0.77 (0.9·1·0.85)
Intervention response 2 within-patient responses recorded
ΔS after each action, accumulating
0.68 (0.75·1·0.9)
Deep biological state DeepGene retest day 90: damage 85/100, Shannon 1.63, butyrate 323 CPM, 4 opportunists above, 6 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 910829-R (compositional proxy)
0.55 (0.7·1·0.79)
Dynamic state GI 54, sleep 5.6 h, HRV 30
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 43%
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-01438 is on day 112 of NBL-101 (EC-03, baseline S06): response declining, tolerance deteriorating, GI stable. Over 14 days response moved -8 and GI -2; discontinuation risk is 60%. The state is between basins, heading towards failing, after diverging from the model on day 53.

Biology sets the gain: IL6 high-expression variant, Low butyrate capacity, Low microbial diversity, Cluster EC-03 (high response / high intolerance), Adherence < 60%; butyrate capacity 28/100, diversity 2.1. Pushing it down: Enterococcus faecium 15.941% (LPS load) (-32.6), Low butyrate capacity (-27.5), 6 keystone species absent (-20.6). Pulling it up: Dietary Support Protocol NP-02 (+32.1), GI Support Protocol GI-04 (+30.5). From the daily log: fat +4.4 GI next day, simple carbs +3.4 GI next day, spicy +3.4 GI next day.

Past actions: NP-02 on day 32 → improved (17%); GI-04 on day 51 → improved (18%).

Next: ME-01 — 100% of 284 similar trajectories improved, 71% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.