Archive MaleCNS research sources, provenance, bibliography and immutable data inventory
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Digital Drosophila Archive
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"""Isolated in-memory hypothesis overlays; all frozen model/data files read-only."""
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from pathlib import Path
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import argparse,json,time
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import numpy as np
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import pandas as pd
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import torch,yaml
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import phase4p,phase4p_finalize,phase4s,phase4v,phase4x
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from phase4p_revalidate import DeterministicAPLSim,door_inputs,make_drive
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from phase4r import save,digest,arrhash
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from phase4h_audit import verify_checksum
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from transmitter_roles_v1 import roles
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def checks(cfg):
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xc=yaml.safe_load((Path(cfg['prior_model'])/'phase4x.yaml').read_text());out=phase4x.checks(xc)
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for key in ('prior_root','prior_model'):
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root=Path(cfg[key]);out['X_'+key]=verify_checksum(root,root/'checksums.sha256')
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assert all(x['passed'] for x in out.values());return out
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class CountObserver:
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def __init__(self,rt,step):self.rt=rt;self.ext=rt.ext;self.step=step;self.before_late=None
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def __getattr__(self,name):return getattr(self.ext,name)
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def state_step(self,*args):
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if self.rt.step_index==self.step:self.before_late=self.rt.counts.cpu().numpy().copy()
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return self.ext.state_step(*args)
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def run(cfg,exp,model):
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for d in ('protocol','audit','events','states','observations','comparisons','regression','performance'):(exp/d).mkdir(parents=True,exist_ok=True)
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assert not (exp/'protocol/preregistered.json').exists(),'Refusing overwrite'
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save(exp/'audit/preflight.json',checks(cfg))
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vc=yaml.safe_load((Path(cfg['input_model'])/'phase4v.yaml').read_text())
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oc,panel,vectors,selection,mapping=door_inputs();panel=panel[panel.split=='calibration'].reset_index(drop=True);assert len(panel)==6
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save(exp/'protocol/preregistered.json',{'config':cfg,'input_config':vc,'panel':panel.to_dict('records'),
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'sources':{p.name:digest(p) for p in model.iterdir() if p.is_file()},'before_simulation':True,
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'no_candidate_selection':True,'new_seed_is_one_replication_not_generalization_gate':True})
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pcfg=yaml.safe_load((Path(cfg['runtime_root'])/'phase4p.yaml').read_text());rt=phase4p.CanonicalRuntime(pcfg,Path(cfg['runtime_root']),exp);sim=DeterministicAPLSim(rt)
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role=roles(sim.meta);dpm=np.flatnonzero(role.annotation_DPM).astype(np.int32)
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assert sorted(sim.meta.iloc[dpm].body_id.astype(int).tolist())==cfg['perturbation']['expected_bodies']
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ids=np.flatnonzero(np.isin(sim.sources,dpm)).astype(np.int64);eg=torch.as_tensor(ids,dtype=torch.int64,device=sim.device)
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assert not set(ids)&set(sim.apl_out_ids)
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sim.meta.iloc[dpm].to_parquet(exp/'audit/DPM-source-metadata.parquet',index=False)
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pd.DataFrame({'edge_id':ids,'source_neuron_idx':sim.sources[ids],'target_neuron_idx':rt.indices_np[ids],
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'raw_synapse_count':rt.raw_np[ids],'frozen_effective_weight':sim.base[eg].cpu().numpy()}).to_parquet(exp/'audit/perturbed-existing-edges.parquet',index=False)
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original_install=sim.install;original_base_hash=arrhash(sim.base.cpu().numpy());weightchecks=[]
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original_install(None);original_overlay=rt.weights.cpu().numpy().copy()
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factor=1.
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def install(E):
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assert E is None,'Learning forbidden in diagnostic branch'
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original_install(None)
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rt.weights[eg]=sim.base[eg]*float(factor)
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sim.install=install
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for spec in cfg['conditions']:
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factor=spec['factor'];sim.install(None);got=rt.weights.cpu().numpy()
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expected=original_overlay.copy();expected[ids]=original_overlay[ids]*np.float32(factor)
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assert np.array_equal(got,expected)
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changed=np.flatnonzero(got!=original_overlay)
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assert np.all(np.isin(changed,ids))
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weightchecks.append({'condition':spec['name'],'factor':factor,'changed_effective_edges':len(changed),
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'only_declared_DPM_edges':True,'edge_array_length':len(got),'raw_weight_changes':0})
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save(exp/'regression/overlay-scope.json',weightchecks)
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populations={'all':np.arange(sim.n),'KC':sim.kc,'PN_annotation':sim.pn,'MBON':sim.mbon,'DPM':dpm,
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'DAN_annotation':np.flatnonzero(role.annotation_DAN),'MBON_downstream':sim.downstream}
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for cls in ('descending','motor'):
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populations[cls]=np.flatnonzero(sim.meta.annotation_superclass.eq(cls).to_numpy())
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save(exp/'audit/populations.json',{k:{'count':len(v),'definition':('exact annotation_superclass' if k in ('descending','motor') else 'frozen IDs or exact annotation evidence')} for k,v in populations.items()})
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target=np.unique(sim.identity.loc[sim.identity.compartment.eq(vc['target_compartment']),'source_neuron_idx'].to_numpy(np.int32))
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reg=[];stats=[];watchrows=[];poprows=[];comparisons=[];inputs=[]
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start=time.perf_counter();torch.cuda.reset_peak_memory_stats()
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def trial(targets,forced,name):
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observer=CountObserver(rt,round(cfg['late_start_ms']/sim.dt));rt.ext=observer
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try:r=phase4v.observed(sim,targets,forced,target,vc)
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finally:rt.ext=observer.ext
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assert r['finite'],'Nonfinite state; stop branch analysis'
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r['late_counts']=r['counts']-observer.before_late
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assert np.all(r['late_counts']>=0)
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return r
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for oi in cfg['odor_indices']:
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odor=panel.iloc[oi];targets,rates=make_drive(oc,panel,vectors,selection,mapping,odor.odor_id,'physiological')
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for seed in cfg['seeds']:
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actual=vc['seed_namespace']+oi*vc['odor_seed_offset']+seed
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forced=phase4v.forcing(sim,targets,rates,actual,vc,'offset')
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inputs.append({'odor':oi,'seed':seed,'actual_seed':actual,'forcing_hash':arrhash(forced.cpu().numpy()),'targets_rates_hash':arrhash(targets,rates)})
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reference=None
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for spec in cfg['conditions']:
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factor=spec['factor'];condition=spec['name'];name=f'{oi}-{seed}-{condition}'
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r=trial(targets,forced,name)
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phase4s.persist_run(exp,name,r)
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np.savez_compressed(exp/'states'/f'{name}.npz',**{k:r[k] for k in ('counts','late_counts','final_v','final_g','trace')})
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pd.DataFrame(r['samples']).to_parquet(exp/'observations'/f'{name}.parquet',index=False)
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if condition=='frozen_reference':
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reference=r
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if seed==cfg['old_replay_seed']:
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oldname=f'{oi}-{seed}-offset';old=np.load(Path(cfg['input_experiment'])/'states'/f'{oldname}.npz')
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eq={k:bool(np.array_equal(old[k],r[k])) for k in ('counts','final_v','final_g','trace')}
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ev=pd.read_parquet(Path(cfg['input_experiment'])/'events'/f'{oldname}.parquet')
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eq['KC_events']=arrhash(ev.step.to_numpy(),ev.neuron_idx.to_numpy())==arrhash(r['kc_event_step'],r['kc_event_node'])
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assert all(eq.values());reg.append({'trial':name,'test':'frozen_V_reproduction',**eq})
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assert reference is not None
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if oi==cfg['odor_indices'][0]:
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rr=trial(targets,forced,name)
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keys=('counts','late_counts','final_v','final_g','kc_event_step','kc_event_node')
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eq={k:bool(np.array_equal(r[k],rr[k])) for k in keys};assert all(eq.values())
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reg.append({'trial':name,'test':'exact_repeat',**eq})
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es=r['kc_event_step'];en=r['kc_event_node'];late=es>=round(cfg['late_start_ms']/sim.dt)
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stats.append({'odor_index':oi,'odor_name':odor.odor_name,'seed':seed,'condition':condition,
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'whole_brain_spikes':int(r['counts'].astype(np.int64).sum()),'whole_brain_active':int(np.count_nonzero(r['counts'])),
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'late_whole_brain_spikes':int(r['late_counts'].astype(np.int64).sum()),'KC_spikes':len(es),'late_KC_spikes':int(late.sum()),
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'late_KC_active':int(np.unique(en[late]).size),'finite':r['finite'],'wall_seconds':r['wall_seconds']})
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for node in cfg['watch_neuron_idx']:
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t=es[en==node];watchrows.append({'odor_index':oi,'seed':seed,'condition':condition,'neuron_idx':node,
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'total_spikes':len(t),'late_spikes':int((t>=round(cfg['late_start_ms']/sim.dt)).sum()),
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'first_ms':float(t.min()*sim.dt) if len(t) else None,'last_ms':float(t.max()*sim.dt) if len(t) else None})
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for pop,idx in populations.items():
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poprows.append({'odor_index':oi,'seed':seed,'condition':condition,'population':pop,'neurons':len(idx),
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'total_spikes':int(r['counts'][idx].astype(np.int64).sum()),'active':int(np.count_nonzero(r['counts'][idx])),
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'late_spikes':int(r['late_counts'][idx].astype(np.int64).sum()),'late_active':int(np.count_nonzero(r['late_counts'][idx]))})
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comparisons.append({'odor_index':oi,'seed':seed,'condition':condition,
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'neurons_with_changed_counts':int(np.count_nonzero(r['counts']!=reference['counts'])),
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'max_abs_finalV_difference':float(np.abs(r['final_v'].astype(float)-reference['final_v']).max()),
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'KC_event_sequence_equal':arrhash(es,en)==arrhash(reference['kc_event_step'],reference['kc_event_node'])})
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save(exp/'regression/trials.json',reg)
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print(json.dumps({'odor_complete':oi,'seed':seed,'trials':len(stats)}),flush=True)
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sim.install=original_install;original_install(None)
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assert arrhash(sim.base.cpu().numpy())==original_base_hash
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assert np.array_equal(rt.weights.cpu().numpy(),original_overlay)
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save(exp/'regression/restore.json',{'immutable_memory_base_hash_exact':True,'frozen_APL_overlay_restored_exact':True})
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assert phase4s.evidence_regression(cfg,exp,rt,sim)
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for name,data in [('trials',stats),('watched-KC',watchrows),('populations',poprows),('paired-differences',comparisons)]:pd.DataFrame(data).to_parquet(exp/'comparisons'/f'{name}.parquet',index=False)
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save(exp/'protocol/input-hashes.json',inputs)
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save(exp/'audit/results.json',{'phase':'4Y','status':'COMPLETE-EXPERIMENTAL-HYPOTHESIS-AUDIT','trials':len(stats),'repeat_trials':6,
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'old_reference_reproductions':6,'frozen_reference_trials':5,'reference_pass':True,'all_finite':True,
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'DPM_neurons':len(dpm),'DPM_existing_edges':len(ids),'weight_training':False,'candidate_selected':False,
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'frozen_baseline_changed':False,'biological_sign_proven':False,'new_seed_count':1,'old_seed_count':1})
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save(exp/'performance/summary.json',{'wall_seconds_excluding_build':time.perf_counter()-start,'peak_VRAM_bytes':torch.cuda.max_memory_allocated(),
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'GPU':torch.cuda.get_device_name(0),'diagnostic_observation_overhead_included':True})
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def seal(cfg,exp,model):
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pre=json.loads((exp/'protocol/preregistered.json').read_text());now=checks(cfg);hist=phase4p_finalize.integrity()
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ok=hist['all_static_checks_passed'] and now==json.loads((exp/'audit/preflight.json').read_text()) and all(digest(model/n)==h for n,h in pre['sources'].items())
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save(exp/'audit/frozen-integrity.json',{'pass':ok,'history':hist,'current':now});assert ok
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result=json.loads((exp/'audit/results.json').read_text());result['integrity_pass']=True;save(exp/'audit/results.json',result)
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w=pd.read_parquet(exp/'comparisons/watched-KC.parquet');t=pd.read_parquet(exp/'comparisons/trials.parquet')
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lines=['# Phase 4Y — independent DPM fast-current hypotheses','',
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'Status: COMPLETE-EXPERIMENTAL-HYPOTHESIS-AUDIT. No candidate selection, training, game integration or frozen baseline changes.',
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'All conditions use identical PN forcing for 120ms, then off to 1000ms. Six old odors, one old seed and one new seed. Not a population-level independent generalization gate.',
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'Factors 0 and -1 are diagnostic model interventions, not corrections to raw labels or validated receptor-specific physiology. Only actual outgoing DPM effective currents change in RAM. Graph and raw counts stay intact.','',
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'| KC | condition | late spike range (12 trials) |','|---:|---|---:|']
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for (node,condition),g in w.groupby(['neuron_idx','condition']):lines.append(f'| {node} | {condition} | {g.late_spikes.min()}–{g.late_spikes.max()} |')
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lines+=['','| condition | mean whole-brain spikes | mean late KC spikes | mean late active KC |','|---|---:|---:|---:|']
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for condition,g in t.groupby('condition'):lines.append(f'| {condition} | {g.whole_brain_spikes.mean():.2f} | {g.late_KC_spikes.mean():.2f} | {g.late_KC_active.mean():.2f} |')
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lines+=['','Exact controls: six Phase4V original trials, six repeats, five frozen reference trials, unchanged in-memory base hash and restored frozen overlay.',
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'Finite states do not establish biological stability. No calibrated runaway threshold, biological sign conclusion, receptor kinetics or learning success is inferred.',
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'Whole-brain intervention outcomes may differ from prior isolated replay because all feedback responds. Report this difference, do not select a condition by favorable activity.']
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(exp/'REPORT.md').write_text('\n'.join(lines)+'\n',encoding='utf-8')
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for root in (model,exp):
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rows=[{'path':p.relative_to(root).as_posix(),'sha256':digest(p),'bytes':p.stat().st_size} for p in sorted(root.rglob('*')) if p.is_file() and p.name not in ('manifest.json','checksums.sha256')]
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save(root/'manifest.json',{'files':rows});rows.append({'path':'manifest.json','sha256':digest(root/'manifest.json')})
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(root/'checksums.sha256').write_text(''.join(x['sha256']+' '+x['path']+'\n' for x in rows));q=verify_checksum(root,root/'checksums.sha256');assert q['passed'];print(json.dumps(q),flush=True)
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if __name__=='__main__':
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p=argparse.ArgumentParser();p.add_argument('task',choices=['run','seal']);p.add_argument('--config',required=True);a=p.parse_args()
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cfg=yaml.safe_load(Path(a.config).read_text());(run if a.task=='run' else seal)(cfg,Path(cfg['experiment_root']),Path(cfg['model_root']))
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