Human Model · HM(t) at day 117

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	48 ± 8.1	+0.33/d	0.6	3 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	72 ± 8.9	+1.51/d	0.8	1 d	Daily GI check-in · direct · today
Treatment toxicity	45 ± 8.9	-0.52/d	0.65	2 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	57 ± 12.4	+0.45/d	0.32	1 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	51 ± 11	0/d	0.13	1 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	34 ± 8.2	-0.45/d	0.56	14 d	Weight, albumin, food log · proxy · days
Adherence	51 ± 5.1	+0.22/d	0.67	2 d	Dose + to-do completion · direct · today
Function / quality of life	30 ± 5.3	-0.2/d	0.12	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 S14: EC-03 phenotype; Normal metabolizer; butyrate 27
day 22perturbationLow-HRV stretch (-2.7)
day 46divergenceTrajectory diverged from the population model
day 46noteTrajectory diverged from prediction
day 59recommendedGI-04 recommended
day 60acceptedPatient accepted
day 64perturbationDaily walks resumed (3.3)
day 68responseGI symptom burden −19% vs expected
day 74state 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.

T1 v3leading

confidence 46%

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

E+

FUT2 non-secretor genotype (barrier glycan deficit)
DeepGene: Escherichia coli above range (LPS / zonulin)
DeepGene: tissue recycling 55
Histamine load → GI +6.2 next day
Inflammatory load 57
GI-04 (barrier-support protocol) improved GI

E−

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 1.13/day)

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

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

T2 v2competing

confidence 31%

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 27/100
DeepGene: 6 keystone butyrate producers absent
Fat load → GI +6 next day
Diversity 2.0

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 6 over 38 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T4 v1competing

confidence 22%

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 51%
Sleep quality worsening
Stress 7.9/10

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 1%

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

E+

GI autocorrelation 0.83 (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 (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 72 → 63

Under ME-01

GI 72 → 60

Under NP-02

GI 72 → 49

Under SC-12

GI 72 → 54

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
GI-04 day 60	-24	-30	-6	✓	✓	n/a	n/a	✓	53%

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 = 1.4 (fragile state). 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	0.32
Treat	NP-02 Dietary Support Protocol 63% of 63 similar improved.	0.45	0.2	0.25	0.13	0.25	0.15	0.25
Treat	SC-12 Supportive Compound 67% of 43 similar improved.	0.35	0.2	0.25	0.08	0.25	0.4	0.17
Escalate	ME-01 Monitoring Escalation 100% of 66 similar improved.	0.22	0.2	0.25	0.08	0.1	0.15	0.16
Treat	DT-01 Dosing / Timing Recommendation 0% of 0 similar improved.	0.18	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
Treat	HY-01 Hydration Protocol 0% of 0 similar improved.	0.15	0.2	0.25	0.08	0.25	0.15	0.02
Measure	Faecal calprotectin (would separate barrier from motility) Discriminates T1 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.2	0
Test	Serum DAO / histamine Discriminates T1 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.5	-0.06
Maintain	Hold current regimen and content Protects a favourable trajectory.	0.35	0.05	0.05	0.4	0.05	0	-0.2

Excluded from the safe set

GI-04 Not indicated for the current state.
BR-03 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.
AD-05 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; FUT2, IL6, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 45, response 48
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 78/100, Shannon 2.05, butyrate 312 CPM, 5 opportunists above, 6 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 909869-R (compositional proxy)
0.54 (0.7·1·0.765)
Dynamic state GI 72, sleep 5.8 h, HRV 31
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 51%
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-01339 is on day 117 of NBL-101 (EC-03, baseline S14): response improving, tolerance improving, GI unstable. Over 14 days response moved +11 and GI +20; discontinuation risk is 96%. The state is between basins, heading towards failing, after diverging from the model on day 46.

Biology sets the gain: FUT2 non-secretor, IL6 high-expression variant, Low butyrate capacity, Low microbial diversity, Baseline state S14, Cluster EC-03 (high response / high intolerance), Adherence < 60%; butyrate capacity 27/100, diversity 2.0. Pushing it down: Escherichia coli 31.089% (LPS load) (-36.3), Low butyrate capacity (-28.5), Histamine load (-22.5). Pulling it up: GI Support Protocol GI-04 (+31.2). From the daily log: histamine +6.2 GI next day, fat +6 GI next day, simple carbs +5.8 GI next day, spicy +5.6 GI next day.

Past actions: GI-04 on day 60 → improved (19%).

Next: NP-02 — 77% of 284 similar trajectories improved, 67% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.