Human Model · HM(t) at day 105

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	62 ± 8.8	-0.51/d	0.69	5 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	52 ± 5.6	+0.5/d	0.57	2 d	Daily GI check-in · direct · today
Treatment toxicity	54 ± 10.1	+0.91/d	0.81	—	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	55 ± 12	+0.4/d	0.45	2 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	53 ± 11.2	-0.14/d	-0.07	2 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	42 ± 8.8	-0.44/d	0.28	6 d	Weight, albumin, food log · proxy · days
Adherence	69 ± 6.7	-0.91/d	0.79	—	Dose + to-do completion · direct · today
Function / quality of life	41 ± 6.5	-0.79/d	0.61	1 d	PRO items · direct · today
Glycaemic control	156 ± 8	0/d	0	—	CGM daily mean · 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 45
day 42perturbationDaily walks resumed (3.3)
day 47recommendedNP-02 recommended
day 48acceptedPatient accepted
day 55perturbationPoor-sleep week (-3)
day 58responseGI symptom burden −19% vs expected
day 59perturbationLow-HRV stretch (-2.7)
day 64state changeTolerance state changed
day 71divergenceTrajectory diverged from the population model
day 71noteTrajectory diverged from prediction
day 92recommendedME-01 recommended
day 93acceptedPatient accepted
day 96responseDeterioration detected before clinical escalation

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.

T1 v1leading

confidence 54%

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: host DNA fragmentation atypical
DeepGene: tissue recycling 61
Inflammatory load 55

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 0.57/day)

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

v1 baseline: genotype + phenotype

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+

Sleep quality worsening
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

T2 v2falsified

confidence 12%

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: 6 keystone butyrate producers absent
DeepGene: H2S above band
Diversity 2.4

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 41 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T3 v1falsified

confidence 12%

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

E+

Toxicity 54
GI autocorrelation 0.78 (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 (2 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 52 → 59

Under GI-04

GI 52 → 44

Under SC-12

GI 52 → 50

Under CR-01

GI 52 → 53

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 48	-5	19	+24	✗	✓	n/a	n/a	✗	18%
ME-01 day 93	-2	5	+7	✗	✗	n/a	n/a	✗	0%

Learning curve · |ε| per cycle:NP-02 24 (prior 24)ME-01 5 (prior 7)improving over cycles

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
Treat	GI-04 GI Support Protocol 77% of 56 similar improved.	0.62	0.2	0.25	0.13	0.35	0.15	0.37
Escalate	CR-01 Clinician Review 100% of 12 similar improved.	0.37	0.2	0.25	0.02	0.25	0.15	0.32
Treat	SC-12 Supportive Compound 80% of 25 similar improved.	0.38	0.2	0.25	0.08	0.25	0.4	0.2
Treat	DT-01 Dosing / Timing Recommendation 50% of 2 similar improved.	0.26	0.2	0.25	0.08	0.25	0.15	0.13
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 1 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 nothing while the state deteriorates.	0.05	0.05	0.05	0.4	0.05	0	-0.5

Excluded from the safe set

ME-01 Not indicated for the current state.
NP-02 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, GLP1R
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 54, response 62
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 88/100, Shannon 1.58, butyrate 304 CPM, 5 opportunists above, 6 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 942538-R (compositional proxy)
0.58 (0.7·1·0.8250000000000001)
Dynamic state GI 52, sleep 5.1 h, HRV 36, glucose 156
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 69%
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-02634 is on day 105 of META-24 (EC-03, baseline S14): response favorable, tolerance deteriorating, GI stable. Over 14 days response moved -1 and GI -3; discontinuation risk is 80%. The state is between basins, heading towards restoration, after diverging from the model on day 71.

Biology sets the gain: FUT2 non-secretor, IL6 high-expression variant, Low microbial diversity, Baseline state S14, Cluster EC-03 (high response / high intolerance); butyrate capacity 45/100, diversity 2.4. Pushing it down: Escherichia coli 33.687% (LPS load) (-33.3), 6 keystone species absent (-19.6), FUT2 non-secretor (-15.9). Pulling it up: Dietary Support Protocol NP-02 (+30.8), Butyrate producers intact (+11.2). From the daily log: simple carbs +3.5 GI next day, ultra-processed +3.1 GI next day, protein -2.8 GI next day.

Past actions: NP-02 on day 48 → improved (19%); ME-01 on day 93 → improved (3%).

Next: GI-04 — 91% of 284 similar trajectories improved, 92% probability here. This would be contradicted by a further GI rise within the onset window or falling adherence.