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"""Phase 4S: independently calibrated timing, fixed-event credit, isolated transfer."""
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from pathlib import Path
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import argparse
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import hashlib
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import json
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import resource
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import time
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import numpy as np
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import pandas as pd
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import torch
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import yaml
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import phase4p
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import phase4p_finalize
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from phase4p_revalidate import DeterministicAPLSim, IsolatedReplay, door_inputs, make_drive
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from phase4h_audit import verify_checksum
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from phase4q import last_spike_trace, edge_elig, update_E, group_metrics, v2_trace, replay_metrics
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from phase4r import save, digest, arrhash, curves, quick_integrity
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def checks(cfg):
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out=quick_integrity(cfg)
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for name,key in [('R','phase4r_root'),('R_model','phase4r_model')]:
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root=Path(cfg[key]);out[name]=verify_checksum(root,root/'checksums.sha256')
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return out
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def timing_test(rows,cfg,w,u):
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x=pd.DataFrame(rows);x=x[(x.window_ms==w)&(x.US_ms==u)];details=[]
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gate=cfg['timing_gate']
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for label,g in x.groupby('label'):
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m=float(g.matched.mean());r=float(g.random_expectation.mean())
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ratio=m/r if r else None
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n=int((g.ratio>=gate['per_seed_ratio_at_least']).sum())
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details.append({'label':label,'mean_matched':m,'mean_random':r,'ratio':ratio,'qualifying_seeds':n,
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'pass':bool(ratio is not None and ratio>=gate['mean_matched_random_ratio_each_odor'] and n>=gate['qualifying_seeds_each_odor'])})
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return {'window_ms':w,'US_ms':u,'tau_ms':w/3,'odors':details,'pass':len(details)==2 and all(g['pass'] for g in details)}
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def persist_run(exp,name,run):
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frame=pd.DataFrame({'step':run['kc_event_step'],'neuron_idx':run['kc_event_node']})
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frame.to_parquet(exp/'events'/f'{name}.parquet',index=False)
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return arrhash(run['kc_event_step'],run['kc_event_node'])
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def evidence_regression(cfg,exp,rt,sim):
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rt.weights.copy_(sim.base);rows=[]
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for spec in rt.cfg['reference_trials']:
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ref=Path(cfg['phase4p_root'])/'phase4c-v2/reference'/spec['name'];ev=pd.read_parquet(ref/'spike-events.parquet')
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expect={'step':ev.step.to_numpy(),'neuron_idx':ev.neuron_idx.to_numpy(),'counts':np.load(ref/'per-neuron-spike-counts.int32.npy'),
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'v':np.load(ref/'final-voltage.float32.npy'),'g':np.load(ref/'final-g.float32.npy')}
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run=rt.run(np.flatnonzero(rt.pops[spec['population']]),spec['rate_hz'],spec['seed'],spec['duration_ms'])
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exact={k:arrhash(run[k])==arrhash(expect[k].astype(run[k].dtype)) for k in expect}
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rows.append({'trial':spec['name'],'exact':exact,'pass':all(exact.values())})
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save(exp/'regression/frozen-trials.json',{'rows':rows,'pass':all(x['pass'] for x in rows)})
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return all(x['pass'] for x in rows)
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def run(cfg,exp,model):
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for d in ('protocol','calibration','heldout','formal','isolated','whole-brain','events','audit','regression','performance'):(exp/d).mkdir(parents=True,exist_ok=True)
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if (exp/'protocol/preregistered.json').exists():raise RuntimeError('Run already exists: refusing overwrite')
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pre=checks(cfg);save(exp/'audit/preflight.json',pre)
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assert all(v['passed'] for v in pre.values())
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ocfg,panel,vectors,selection,mapping=door_inputs();cal=panel[panel.split=='calibration'].iloc[:2]
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assert set(cal.odor_id).isdisjoint({selection['ODOR_A']['odor_id'],selection['ODOR_B']['odor_id']})
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prereg={'config':cfg,'calibration_odors':cal[['odor_id','odor_name']].to_dict('records'),
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'created_before_simulation':True,'source_hashes':{p.name:digest(p) for p in model.glob('phase4s.*')},
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'protocol_basis':'Phase4R onset response identified at 15-25ms; this informs predeclared finite grid, not formal A/B outcomes'}
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save(exp/'protocol/preregistered.json',prereg)
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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)
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sim=DeterministicAPLSim(rt);identity=sim.identity;assert identity.identity_group.value_counts().to_dict()==cfg['formal']['fixed_groups']
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assert len(identity)==14232
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lookup=np.full(sim.n,-1,np.int32);lookup[sim.kc]=np.arange(len(sim.kc),dtype=np.int32)
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loc=lookup[identity.source_neuron_idx.to_numpy(np.int32)];assert np.all(loc>=0)
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comp=identity.compartment.astype(str).to_numpy()==cfg['target_compartment'];multi=np.bincount(loc[comp],minlength=len(sim.kc)).astype(np.float32)
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dan=sim.dan_targets(cfg['matched_DAN'],cfg['target_compartment']);duration=cfg['duration_ms'];nsteps=round(duration/sim.dt)
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identity.to_parquet(exp/'protocol/frozen-edge-identity.parquet',index=False)
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calrows=[];cached={};wall0=time.perf_counter();cpu0=resource.getrusage(resource.RUSAGE_SELF);torch.cuda.reset_peak_memory_stats()
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for oi,(_,odor) in enumerate(cal.iterrows()):
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label='CAL_'+chr(65+oi);targets,rates=make_drive(ocfg,panel,vectors,selection,mapping,odor.odor_id,'physiological')
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pd.DataFrame({'neuron_idx':targets,'rate_hz':rates}).to_parquet(exp/'protocol'/f'{label}-drive.parquet',index=False)
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for seed in cfg['calibration_seeds']:
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actual=seed+oi*cfg['odor_seed_offset'];r=sim.run(targets,rates,actual,duration,collect_events=True);assert r['finite']
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cached[(label,seed)]=(targets,rates,actual,r);persist_run(exp,f'cal-{label}-{seed}',r)
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cs=curves(r,lookup,multi,cfg['windows_ms'],sim.dt,nsteps)
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for i,w in enumerate(cfg['windows_ms']):
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den=float(cs[i].mean())
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for u in cfg['candidate_US_ms']:
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m=float(cs[i][round(u/sim.dt)])
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calrows.append({'label':label,'seed':seed,'window_ms':w,'US_ms':u,'matched':m,'random_expectation':den,'ratio':m/den if den else None})
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pd.DataFrame(calrows).to_parquet(exp/'calibration/grid.parquet',index=False)
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grid=[timing_test(calrows,cfg,w,u) for w in cfg['windows_ms'] for u in cfg['candidate_US_ms']]
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good=[x for x in grid if x['pass']];chosen=min(good,key=lambda x:(x['window_ms'],x['US_ms'])) if good else None
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# Persist the selection BEFORE accessing heldout data or formal odor responses.
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save(exp/'calibration/selection.json',{'grid':grid,'chosen':chosen,'pass':chosen is not None,'formal_AB_used':False})
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summary={'phase':'4S','calibration':chosen,'heldout':None,'formal':None,'isolated':None,'whole':None,
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'timing_candidate':False,'credit_candidate':False,'associative_memory_claim':False}
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if chosen:
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w=chosen['window_ms'];u=chosen['US_ms'];us=round(u/sim.dt);tau=w/3
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held=[];gate_exact=[]
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for oi,(_,odor) in enumerate(cal.iterrows()):
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label='CAL_'+chr(65+oi);targets,rates=make_drive(ocfg,panel,vectors,selection,mapping,odor.odor_id,'physiological')
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for seed in cfg['heldout_seeds']:
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actual=seed+oi*cfg['odor_seed_offset'];r=sim.run(targets,rates,actual,duration,collect_events=True);assert r['finite']
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cs=curves(r,lookup,multi,[w],sim.dt,nsteps)[0];den=float(cs.mean());m=float(cs[us])
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held.append({'label':label,'seed':seed,'window_ms':w,'US_ms':u,'matched':m,'random_expectation':den,'ratio':m/den if den else None})
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persist_run(exp,f'held-{label}-{seed}',r)
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for pulse in (us,int(np.random.default_rng(actual+975000).integers(nsteps))):
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forced=sim.run(targets,rates,actual,duration,dan_targets=dan,dan_pulses=[pulse*sim.dt],collect_events=True)
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t,_=last_spike_trace(r['kc_event_step'],r['kc_event_node'],lookup,pulse,w,tau,sim.dt)
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tt,_=last_spike_trace(forced['kc_event_step'],forced['kc_event_node'],lookup,pulse,w,tau,sim.dt)
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v2check=v2_trace(forced['kc_event_step'],forced['kc_event_node'],lookup,pulse,sim.dt)
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gate_exact.append({'label':label,'seed':seed,'US_step':pulse,'credit_exact':bool(np.array_equal(t,tt)),
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'v2_CPU_trace_exact_to_runtime':bool(np.array_equal(v2check,forced['trace']))})
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pd.DataFrame(held).to_parquet(exp/'heldout/results.parquet',index=False)
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h=timing_test(held,cfg,w,u);h['same_event_vs_live_US_credit_exact']=all(x['credit_exact'] and x['v2_CPU_trace_exact_to_runtime'] for x in gate_exact)
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h['pass']=h['pass'] and h['same_event_vs_live_US_credit_exact'];save(exp/'heldout/gate.json',h);save(exp/'regression/live-US-gates.json',gate_exact)
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summary['heldout']=h;print(json.dumps({'selection':chosen,'heldout':h}),flush=True)
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if h['pass']:
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summary['timing_candidate']=True
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formal(cfg,exp,sim,identity,lookup,loc,comp,w,u,ocfg,panel,vectors,selection,mapping,summary)
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summary['regression_pass']=evidence_regression(cfg,exp,rt,sim)
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summary['status']='TIMING-PASS-CREDIT-PASS' if summary['credit_candidate'] else ('TIMING-PASS-CREDIT-NOT-ESTABLISHED' if summary['timing_candidate'] else 'FAIL-TIMING-VALIDATION')
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summary['timing_candidate'] &= summary['regression_pass'];summary['credit_candidate'] &= summary['regression_pass']
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save(exp/'audit/results.json',summary)
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cpu1=resource.getrusage(resource.RUSAGE_SELF);wall=time.perf_counter()-wall0
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save(exp/'performance/summary.json',{'wall_seconds':wall,'peak_VRAM_bytes':int(torch.cuda.max_memory_allocated()),
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'peak_RAM_bytes':int(cpu1.ru_maxrss*1024),'CPU_percent_one_core':100*(cpu1.ru_utime+cpu1.ru_stime-cpu0.ru_utime-cpu0.ru_stime)/wall,
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'GPU':'RTX 4090','GPU_utilization':'not sampled','runtime':'deterministic-runtime-v2'})
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print(json.dumps(summary),flush=True)
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def formal(cfg,exp,sim,identity,lookup,loc,comp,w,u,ocfg,panel,vectors,selection,mapping,summary):
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spec=cfg['formal'];us=round(u/sim.dt);nsteps=round(cfg['duration_ms']/sim.dt);names=spec['arms'];points=spec['checkpoints']
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targets,rates=make_drive(ocfg,panel,vectors,selection,mapping,selection['ODOR_A']['odor_id'],'physiological')
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states={};rows=[];audit=[];contam=[];repeat=[];groups=identity.identity_group.astype(str).to_numpy()
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for seed in spec['train_seed_bases']:
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E={name:np.ones(len(identity),np.float32) for name in names}
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for name in names:
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states[f'{seed}_{name}_0']=E[name].copy()
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for x in group_metrics(E[name],sim.base_candidate,identity):rows.append({'seed':seed,'pairing':0,'arm':name,**x})
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for pairing in range(1,max(points)+1):
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actual=seed+pairing;r=sim.run(targets,rates,actual,cfg['duration_ms'],collect_events=True);assert r['finite']
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s=r['kc_event_step'];n=r['kc_event_node'];rand=int(np.random.default_rng(actual+spec['random_seed_offset']).integers(nsteps))
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e3,last=last_spike_trace(s,n,lookup,us,w,w/3,sim.dt);er,lastr=last_spike_trace(s,n,lookup,rand,w,w/3,sim.dt)
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v2=v2_trace(s,n,lookup,us,sim.dt);v90=v2_trace(s,n,lookup,900,sim.dt)
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elig={'v2_same_US':edge_elig(v2,loc,comp),'v2_90ms':edge_elig(v90,loc,comp),
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'v3_matched':edge_elig(e3,loc,comp),'v3_random':edge_elig(er,loc,comp),'D0':np.zeros(len(identity),np.float32)}
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event_hash=persist_run(exp,f'formal-{seed}-{pairing}',r)
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audit.append({'seed':seed,'pairing':pairing,'actual_seed':actual,'random_US_step':rand,'matched_US_step':us,'KC_hash_all_arms':event_hash,
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'no_weight_overlay_during_event_collection':True,'same_KC_events_all_arms':True})
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for name in names:
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E[name],delta=update_E(E[name],elig[name])
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for j in np.flatnonzero((groups=='B-specific')&(delta!=0)):
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gate=rand if name=='v3_random' else (900 if name=='v2_90ms' else us)
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ts=s[n==int(identity.source_neuron_idx.iloc[j])];ts=ts[ts<=gate];ls=int(ts[-1]) if len(ts) else None
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contam.append({'seed':seed,'pairing':pairing,'arm':name,'edge_id':int(identity.edge_id.iloc[j]),
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'KC_body_id':int(identity.source_body_id.iloc[j]),'last_KC_step':ls,'US_step':gate,'eligibility':float(elig[name][j]),'delta_E':float(delta[j])})
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if pairing in points:
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for name in names:
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states[f'{seed}_{name}_{pairing}']=E[name].copy()
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for x in group_metrics(E[name],sim.base_candidate,identity):rows.append({'seed':seed,'pairing':pairing,'arm':name,**x})
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# Checkpoint each independent trajectory for recoverability.
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np.savez_compressed(exp/'formal'/f'states-{seed}.npz',**{k:v for k,v in states.items() if k.startswith(str(seed)+'_')})
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if pairing%20==0:print(json.dumps({'formal_seed':seed,'pairings':pairing}),flush=True)
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if seed==spec['train_seed_bases'][0]:
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rr=sim.run(targets,rates,seed+100,cfg['duration_ms'],collect_events=True)
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repeat.append({'seed':seed+100,'events_exact':arrhash(rr['kc_event_step'],rr['kc_event_node'])==event_hash,
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'states_exact':arrhash(rr['final_v'],rr['final_g'])==arrhash(r['final_v'],r['final_g'])})
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f=pd.DataFrame(rows);f.to_parquet(exp/'formal/group-trajectory.parquet',index=False)
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pd.DataFrame(audit).to_parquet(exp/'formal/event-audit.parquet',index=False);pd.DataFrame(contam).to_parquet(exp/'formal/B-contamination.parquet',index=False)
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save(exp/'regression/formal-repeat.json',repeat)
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endpoints=f[f.pairing==spec['primary_endpoint']];gates=[]
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for seed in spec['train_seed_bases']:
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z=endpoints[endpoints.seed==seed]
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def val(arm,group):return float(z[(z.arm==arm)&(z.group==group)].total_abs_delta_E.iloc[0])
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ma=val('v3_matched','A-specific');ra=val('v3_random','A-specific');b2=val('v2_same_US','B-specific');b3=val('v3_matched','B-specific')
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ratio=ma/ra if ra else None;red=(1-b3/b2) if b2 else None
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ag=ma>0 and (ra==0 or ma>=spec['minimum_A_credit_matched_random_ratio']*ra)
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bg=(red is not None and red>=spec['minimum_B_reduction_vs_v2_same_US']) or (b2==0 and b3==0)
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gates.append({'seed':seed,'A_credit':ma,'random_A_credit':ra,'A_ratio':ratio,'B_v2':b2,'B_v3':b3,'B_reduction':red,'pass':ag and bg})
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fp=sum(x['pass'] for x in gates)>=spec['minimum_seed_majority']
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summary['formal']={'gate_pass':fp,'primary_endpoint':spec['primary_endpoint'],'seeds':gates,'open_loop_shadow_only':True}
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save(exp/'formal/gate.json',summary['formal'])
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# Always measure isolated transfer after independently validated timing; its own gate controls whole-brain overlays.
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replay=IsolatedReplay(sim,cfg['target_compartment']);evals={};results=[]
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for odor in ('ODOR_A','ODOR_B'):
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t,rates=make_drive(ocfg,panel,vectors,selection,mapping,selection[odor]['odor_id'],'physiological')
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for es in spec['evaluation_seeds']:
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er=sim.run(t,rates,es,cfg['duration_ms'],collect_events=True);evals[(odor,es)]=er;persist_run(exp,f'eval-{odor}-{es}',er)
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for pairing in spec['isolated_checkpoints']:
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for odor in ('ODOR_A','ODOR_B'):
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for seed,es in zip(spec['train_seed_bases'],spec['evaluation_seeds']):
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er=evals[(odor,es)];base=replay.run(er['kc_event_step'],er['kc_event_node'],None,cfg['duration_ms'])
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for name in names:
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post=replay.run(er['kc_event_step'],er['kc_event_node'],states[f'{seed}_{name}_{pairing}'],cfg['duration_ms'])
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results.append({'pairing':pairing,'odor':odor,'seed':seed,'evaluation_seed':es,'arm':name,**replay_metrics(base,post,sim.dt)})
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z=pd.DataFrame(results);z.to_parquet(exp/'isolated/results.parquet',index=False);ig=[];trajectory=[]
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for pairing in spec['isolated_checkpoints']:
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for seed in spec['train_seed_bases']:
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def L(arm,odor):return int(z[(z.pairing==pairing)&(z.seed==seed)&(z.arm==arm)&(z.odor==odor)].spike_L1.iloc[0])
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a,b,ra,rb=L('v3_matched','ODOR_A'),L('v3_matched','ODOR_B'),L('v3_random','ODOR_A'),L('v3_random','ODOR_B')
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trajectory.append({'pairing':pairing,'seed':seed,'A':a,'B':b,'random_A':ra,'random_B':rb,'A_specific':a>0 and a>b,'random_specific':ra>0 and ra>rb,'matched_beats_random':a>ra})
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endpoint=[x for x in trajectory if x['pairing']==spec['primary_endpoint']];major=spec['minimum_seed_majority']
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ip=sum(x['A_specific'] for x in endpoint)>=major and sum(x['random_specific'] for x in endpoint)<major and sum(x['matched_beats_random'] for x in endpoint)>=major and bool((z[z.arm=='D0'].spike_L1==0).all())
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summary['isolated']={'gate_pass':ip,'endpoint':endpoint,'trajectory':trajectory,'D0_zero':bool((z[z.arm=='D0'].spike_L1==0).all()),'no_checkpoint_selected_posthoc':True}
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save(exp/'isolated/gate.json',summary['isolated'])
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if fp and ip:
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whole=[]
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for odor in ('ODOR_A','ODOR_B'):
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t,rates=make_drive(ocfg,panel,vectors,selection,mapping,selection[odor]['odor_id'],'physiological')
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for seed,es in zip(spec['train_seed_bases'],spec['evaluation_seeds']):
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base=evals[(odor,es)]
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for name in ('v3_matched','v3_random','v2_same_US','D0'):
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post=sim.run(t,rates,es,cfg['duration_ms'],E=states[f'{seed}_{name}_100'])
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whole.append({'seed':seed,'odor':odor,'arm':name,'MBON_L1':int(np.abs(post['mbon_counts']-base['mbon_counts']).sum()),
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'downstream_L1':int(np.abs(post['downstream_counts']-base['downstream_counts']).sum()),'finite':post['finite']})
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wf=pd.DataFrame(whole);wf.to_parquet(exp/'whole-brain/results.parquet',index=False);wg=[]
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for seed in spec['train_seed_bases']:
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def v(arm,odor):return int(wf[(wf.seed==seed)&(wf.arm==arm)&(wf.odor==odor)].MBON_L1.iloc[0])
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a,b,ra,rb=v('v3_matched','ODOR_A'),v('v3_matched','ODOR_B'),v('v3_random','ODOR_A'),v('v3_random','ODOR_B')
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wg.append({'seed':seed,'A':a,'B':b,'random_A':ra,'random_B':rb,'specific':a>b and a>ra,'random_specific':ra>rb})
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wp=sum(x['specific'] for x in wg)>=major and sum(x['random_specific'] for x in wg)<major and bool(wf.finite.all()) and bool((wf[wf.arm=='D0'].MBON_L1==0).all())
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summary['whole']={'run':True,'pass':wp,'seeds':wg};summary['credit_candidate']=bool(wp)
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else:summary['whole']={'run':False,'reason':'formal credit or isolated specificity gate failed'}
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save(exp/'whole-brain/gate.json',summary['whole'])
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def finalize(cfg,exp,model):
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old=phase4p_finalize.integrity();now=checks(cfg);before=json.loads((exp/'audit/preflight.json').read_text())
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pre=json.loads((exp/'protocol/preregistered.json').read_text());same=all(digest(model/n)==h for n,h in pre['source_hashes'].items())
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integrity={'Phase1_4O':old,'Phase4P_4R':now,'before_after_equal':now==before,'preregistered_source_hashes_unchanged':same,
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'pass':old['all_static_checks_passed'] and all(x['passed'] for x in now.values()) and now==before and same}
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save(exp/'audit/frozen-integrity.json',integrity);summary=json.loads((exp/'audit/results.json').read_text())
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summary['integrity_pass']=integrity['pass'];summary['timing_candidate'] &= integrity['pass'];summary['credit_candidate'] &= integrity['pass']
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if summary['timing_candidate']:
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save(model/'MaleCNS-CSUS-Timing-v1-candidate.json',{'scope':'independent calibration and seed-heldout matched/random credit timing only; no memory claim',
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'selection':summary['calibration'],'heldout':summary['heldout'],'brain_unchanged':True})
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if summary['credit_candidate']:
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save(model/'MaleCNS-CreditAssignment-v1-candidate.json',{'scope':'open-loop shadow credit and replay; no online learning claim','source':str(exp/'audit/results.json')})
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save(exp/'audit/results.json',summary)
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for root in (model,exp):
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ps=[p for p in sorted(root.rglob('*')) if p.is_file() and p.name not in ('checksums.sha256','manifest.json')]
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rows=[{'path':p.relative_to(root).as_posix(),'sha256':digest(p),'bytes':p.stat().st_size} for p in ps]
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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))
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test=verify_checksum(root,root/'checksums.sha256');assert test['passed'];print(json.dumps(test),flush=True)
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print(json.dumps({'status':summary['status'],'timing_candidate':summary['timing_candidate'],'credit_candidate':summary['credit_candidate'],'integrity_pass':integrity['pass']}),flush=True)
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if __name__=='__main__':
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p=argparse.ArgumentParser();p.add_argument('task',choices=['run','finalize']);p.add_argument('--config',required=True);a=p.parse_args()
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cfg=yaml.safe_load(Path(a.config).read_text());exp=Path(cfg['experiment_root']);model=Path(cfg['model_root'])
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(run if a.task=='run' else finalize)(cfg,exp,model)
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Digital Drosophila Archive