Human Model · HM(t) at day 109

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	49 ± 7.2	+0.05/d	0.38	1 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	42 ± 6.1	+0.34/d	0.57	12 d	Daily GI check-in · direct · today
Treatment toxicity	48 ± 7.5	+0.19/d	0.59	1 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	52 ± 11.4	+0.34/d	0.61	2 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	46 ± 11.2	-0.16/d	-0.2	1 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	49 ± 8.2	-0.27/d	0.25	1 d	Weight, albumin, food log · proxy · days
Adherence	49 ± 4.3	-0.17/d	0.71	—	Dose + to-do completion · direct · today
Function / quality of life	39 ± 4.9	-0.14/d	0.51	2 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 23
day 11perturbationAntibiotic course (-4.7)
day 46divergenceTrajectory diverged from the population model
day 46noteTrajectory diverged from prediction
day 52perturbationDaily walks resumed (3.3)
day 58perturbationLow-HRV stretch (-2.7)
day 60recommendedGI-04 recommended
day 61acceptedPatient accepted
day 69responseGI symptom burden −31% vs expected
day 71perturbationDietary drift (-2.6)
day 75state 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 48%

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: Klebsiella pneumoniae above range (LPS / zonulin)
DeepGene: host DNA fragmentation atypical
DeepGene: tissue recycling 65
Histamine load → GI +5.1 next day
Inflammatory load 52
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 -0.37/day)

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

v1 baseline: genotype + phenotype → v2 day 61: GI-04 response added to E+ → v3 dietary attribution from 60-day log

T2 v2competing

confidence 29%

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 23/100
DeepGene: 6 keystone butyrate producers absent
Fat load → GI +6 next day
Diversity 1.9

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 40 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T4 v1competing

confidence 15%

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 49%
Stress 6.6/10

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 8%

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

E+

Toxicity 48
GI autocorrelation 0.66 (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 (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 42 → 52

Under ME-01

GI 42 → 50

Under NP-02

GI 42 → 41

Under SC-12

GI 42 → 45

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 61	-21	-14	+7	✓	✓	n/a	n/a	✓	43%

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
Escalate	CR-01 Clinician Review 100% of 5 similar improved.	0.37	0.2	0.25	0.02	0.25	0.15	0.33
Treat	NP-02 Dietary Support Protocol 63% of 63 similar improved.	0.45	0.2	0.25	0.13	0.25	0.15	0.3
Escalate	ME-01 Monitoring Escalation 100% of 67 similar improved.	0.22	0.2	0.25	0.08	0.1	0.15	0.2
Treat	SC-12 Supportive Compound 67% of 45 similar improved.	0.35	0.2	0.25	0.08	0.25	0.4	0.2
Treat	DT-01 Dosing / Timing Recommendation 0% of 0 similar improved.	0.18	0.2	0.25	0.08	0.25	0.15	0.08
Treat	HY-01 Hydration Protocol 0% of 0 similar improved.	0.15	0.2	0.25	0.08	0.25	0.15	0.05
Treat	BR-03 Behavioural Recommendation 0% of 0 similar improved.	0.14	0.2	0.25	0.08	0.25	0.15	0.04
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 calprotectin (would separate barrier from motility) Discriminates T1 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.2	0.01
Treat	AD-05 Adherence Support 0% of 0 similar improved.	0.1	0.2	0.25	0.08	0.25	0.15	0
Test	Serum DAO / histamine Discriminates T1 from its competitors (E?).	0	0.45	0.2	0.02	0.25	0.5	-0.05
Maintain	Hold current regimen and content Protects nothing while the state deteriorates.	0.05	0.05	0.05	0.4	0.05	0	-0.34

Excluded from the safe set

GI-04 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; FUT2, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 48, response 49
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 75/100, Shannon 1.84, butyrate 293 CPM, 1 opportunists above, 6 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 910728-R (compositional proxy)
0.56 (0.7·1·0.805)
Dynamic state GI 42, sleep 7.0 h, HRV 37
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 49%
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-01400 is on day 109 of NBL-101 (EC-03, baseline S14): response stable, tolerance deteriorating, GI stable. Over 14 days response moved -2 and GI +4; discontinuation risk is 66%. The state is between basins, heading towards failing, after diverging from the model on day 46.

Biology sets the gain: FUT2 non-secretor, Low butyrate capacity, Low microbial diversity, Baseline state S14, Cluster EC-03 (high response / high intolerance), Adherence < 60%; butyrate capacity 23/100, diversity 1.9. Pushing it down: Low butyrate capacity (-27), Klebsiella pneumoniae 10.192% (LPS load) (-25.4), Alcohol (-22.2). Pulling it up: GI Support Protocol GI-04 (+46.6). From the daily log: alcohol +7 GI next day, fat +6 GI next day, histamine +5.1 GI next day, fibre +3.4 GI next day.

Past actions: GI-04 on day 61 → improved (31%).

Next: AD-05 — 50% of 284 similar trajectories improved, 45% probability here. Adherence is 49% and stable; nothing else works if the dose is missed → adherence support first. This would be contradicted by a further GI rise within the onset window or falling adherence.