Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/palette/secS_scratch_rare_states.palette.json

@@ -0,0 +1,88 @@
+{
+  "schema": "pbisc.vector-method-palette.v1",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_scratch_rare_states.pdf",
+  "source_sha256": "69c1c1c9783bc1b1e7f3b874a2832e5a77ac67168bb8bc623271b305bd50bb4d",
+  "destination": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/palette/secS_scratch_rare_states.pdf",
+  "destination_sha256": "34f15bd49fac9d65fdda1454c5ffc6f5defb4d8e46918697358254b90cdcb9fc",
+  "mapping": {
+    "#D55E00": "#C5AA4B",
+    "#882255": "#806A25",
+    "#0072B2": "#B59A50",
+    "#44AA99": "#D4BE75",
+    "#332288": "#665522"
+  },
+  "rgb_absolute_tolerance": 1e-08,
+  "streams_inspected": 1,
+  "modified_streams": 1,
+  "stream_checks": [
+    {
+      "stream": "page0/Contents0",
+      "noncolor_operator_sha256_before": "ee9ed80e548368d0f09ec0046c3a352f337ee49c6b59ffaa33586bb0a6fd2f37",
+      "noncolor_operator_sha256_after": "ee9ed80e548368d0f09ec0046c3a352f337ee49c6b59ffaa33586bb0a6fd2f37",
+      "colour_operators_changed": 158
+    }
+  ],
+  "colour_counts": [
+    {
+      "old": "#0072B2",
+      "new": "#B59A50",
+      "operator": "rg",
+      "count": 18
+    },
+    {
+      "old": "#332288",
+      "new": "#665522",
+      "operator": "rg",
+      "count": 18
+    },
+    {
+      "old": "#44AA99",
+      "new": "#D4BE75",
+      "operator": "rg",
+      "count": 18
+    },
+    {
+      "old": "#882255",
+      "new": "#806A25",
+      "operator": "rg",
+      "count": 52
+    },
+    {
+      "old": "#D55E00",
+      "new": "#C5AA4B",
+      "operator": "rg",
+      "count": 52
+    }
+  ],
+  "image_payload_count": 0,
+  "image_payloads": [],
+  "rectangle_rules_matched": 0,
+  "rectangle_checks": [],
+  "scope_insertions": "Only balanced q/RGB/RGB/paint/Q wrappers; original non-colour operators preserved",
+  "preservation": {
+    "noncolor_operators": true,
+    "text_geometry": true,
+    "page_rectangles": true,
+    "image_payloads": true,
+    "source_unchanged": true
+  },
+  "preservation_pass": true,
+  "render": {
+    "pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/palette/secS_scratch_rare_states.pdf",
+    "png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/palette/secS_scratch_rare_states.png",
+    "dpi": 200,
+    "page_rect": [
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+      0.0,
+      801.5868530273438,
+      364.0645751953125
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+    "width": 2227,
+    "height": 1012,
+    "png_sha256": "221eefd848c035982a9786596818086cc69ece55dd2cd8e54ac9a1f869d77904",
+    "rendering": "native PDF rendering; no raster recolouring"
+  },
+  "semantic_reason": "PBISC pretrained/scratch and cross-cohort adaptations use distinct gold shades; markers and acceptable-error grey band retained.",
+  "original_png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_scratch_rare_states.png",
+  "original_png_sha256": "af53b558820bb87fe64d7a5ebc96d7477479370efce817c08908cbb278bd5ad2"
+}

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/tools/build_expanded_master_20261013.py

@@ -0,0 +1,270 @@
+"""Expand all 76 original PBISC slides with existing, source-bound evidence.
+
+No experiment launches. Saved-table plotting runs on CPU. Original deck files
+and original source figures are preserved; additions and colour variants have
+separate destinations and a complete coverage map.
+"""
+from pathlib import Path
+from datetime import datetime, timezone, timedelta
+import copy,csv,hashlib,json,os,sys,tempfile
+if os.environ.get('CUDA_VISIBLE_DEVICES')!='':
+    raise SystemExit('Set CUDA_VISIBLE_DEVICES empty for CPU-only deck production')
+D=Path(__file__).resolve().parents[1];A=D/'data/expanded_master_20261013'
+sys.path.insert(0,str(D))
+import generate_deck as G
+from pptx import Presentation
+from pptx.util import Inches
+from review_palette_pdf import recolor_pdf,render_pdf_to_png
+from expanded_legacy_rare import build as build_legacy_rare
+
+OUT='PBISC-Diffusion_expanded_master_20261013'
+SOURCES={};PALETTE_RECORDS=[];CACHE={}
+
+def sha(path):
+    with Path(path).open('rb') as stream:return hashlib.file_digest(stream,'sha256').hexdigest()
+
+def source(path,role):
+    p=Path(path).resolve()
+    if not p.is_file():raise FileNotFoundError(p)
+    SOURCES[str(p)]={'sha256':sha(p),'role':role}
+    return p
+
+def rel(path):
+    p=Path(path).resolve()
+    try:return str(p.relative_to(D))
+    except ValueError:return str(p)
+
+def reuse_or_build(name,builder):
+    """Avoid replotting unchanged saved evidence during slide-layout fixes."""
+    cache=A/'build_cache';cache.mkdir(exist_ok=True)
+    file=cache/(name+'.json');module=Path(builder.__code__.co_filename).resolve()
+    if file.is_file():
+        saved=json.loads(file.read_text())
+        if saved.get('module_sha256')==sha(module) and all(Path(p).is_file() and sha(p)==h for p,h in saved.get('bindings',{}).items()):
+            print('reuse verified saved plots:',name)
+            return saved['result']
+    result=builder();bindings={}
+    for row in result.get('sources',[]):
+        p=Path(row['path'] if isinstance(row,dict) else row).resolve();h=sha(p)
+        if isinstance(row,dict) and row.get('sha256'):assert h==row['sha256'],p
+        bindings[str(p)]=h
+    for p in result.get('assets',[]):bindings[str(Path(p).resolve())]=sha(p)
+    file.write_text(json.dumps({'module_sha256':sha(module),'bindings':bindings,'result':result},indent=2)+'\n')
+    return result
+
+def ledger(slide):
+    if 'original_slide' in slide:return 'original:'+str(slide['original_slide'])
+    return slide['addition_key']
+
+def note(title,section,rows,after,key,foot):
+    return {'kind':'evidence_note','title':title,'section_label':section,'rows':rows,
+        'after_original':after,'addition_key':key,'footnote':foot,'footnote_full':foot}
+
+def normalize_footnote(s):
+    # Retain complete sources/citations in speaker notes while keeping the slide readable.
+    if 'footnote' not in s:s['footnote']=s.get('footnote_short','')
+    if s.get('refs') and len(G.wrap(s['footnote'],G.FOOT_PT,G.FOOT_W))>1:s.pop('refs')
+    if len(G.wrap(s.get('footnote',''),G.FOOT_PT,G.FOOT_W))>2:
+        raise ValueError('Shorten slide footnote: '+s['title'])
+
+def original_slide(number,item,review_by_old):
+    s=copy.deepcopy(item);s['original_slide']=number
+    s['original_title']=item['title'];s['original_footnote']=item.get('footnote','')
+    if s['kind']=='title':
+        s['title']='PBISC-Diffusion: expanded evidence deck'
+        s['subtitle']='Original 76-slide coverage + existing analyses · 13 October 2026'
+    elif s['kind']=='agenda':
+        s['title']='Full evidence map'
+    elif s['kind']=='content':
+        s['footnote_full']='Original slide '+str(number)+': '+item.get('footnote_full',item.get('footnote',''))
+        if number in review_by_old:
+            update=review_by_old[number]
+            s['footnote']=update.get('footnote',s.get('footnote',''))
+            s['footnote_full']='Current scope: '+s['footnote']+'\n\n'+s['footnote_full']
+        if number in [3,5,16,29,36,48,54,57]:
+            s['section_label']='Original roadmap'
+            s['footnote']='Original 8 October planning snapshot, retained for context. Current evidence and incomplete work are distinguished in this expanded deck.'
+            s['footnote_full']=s['footnote']+'\n\n'+s['footnote_full']
+        if number==31:
+            s['title']='Healthy paired-data learning curves'
+            s['footnote']='LoRA: n training + 7 validation. scSemi: n + 7 representatives, with CV-HVG reuse. Not the strict total-n protocol.'
+        if number==37:
+            s['keywords']=['403 paired samples, 275 donors','Identity screening where available; donor-level splits','Ji bulk: whole blood, not PBMC']
+        if number in (32,63):
+            s['title']='Representative-dependent composition' if number==32 else 'scSemiProfiler and the representative-copy baseline'
+        if number==46:
+            s['keywords']=['PBISC closer than BayesPrism in 22/25 draws, than CIBERSORTx in 24/25',
+                           'Composition compared with held-out observed cells',
+                           'Five-fold: PBISC lowest error in 4 of 5 cohorts']
+        if number==38:
+            s['title']='Disease signals with five training donors'
+        if number in [49,50,51]:
+            s['title']={49:'Rare-state fractions: original analysis',50:'Rare-state ranking: original analysis',51:'Rare states: original five-fold analysis'}[number]
+            s['section_label']='Historical scorer'
+            s['footnote']='Historical scoring: zero-draw and sample-unit limitations apply. Corrected five-donor analyses follow; five-fold correction is separate.'
+            s['keywords']=['Original output retained for traceability','Use the corrected donor-level analysis for updated conclusions']
+            s['footnote_full']=s['footnote']+'\n\n'+s['footnote_full']
+        if number==52:
+            s['footnote']='Historical Behcet diagnostic; reference is unmatched and includes training donors. This is not independent patient-level subtype validation.'
+        if number==55:
+            s['title']='Bulk-only cohort plan: original snapshot'
+            s['section_label']='Historical plan'
+            s['keywords']=['Original cohort/sample inventory','Later exploratory outputs follow','New-data reproduction is a separate step']
+            s['footnote']='Historical cohort counts. Existing exploratory outputs are reviewed separately; reproduction with the user-prepared new dataset remains pending.'
+            s['say']='Historical planned cohort map. Later exploratory outputs exist; this slide does not claim new-data reproduction is complete.'
+        normalize_footnote(s)
+    return s
+
+def method_palette(s,policy):
+    old=list(s.get('figures',[]))
+    if not old:return
+    s['figures_before_palette']=old
+    out=[]
+    for item in old:
+        p=source(D/item,'original or added figure image')
+        stem=p.stem
+        if stem not in policy['rules']:
+            mode=s.get('palette','')
+            if isinstance(mode,dict):mode=mode.get('mode','')
+            mode={'native-gold-blue':'native','biological/preserved':'biological'}.get(mode,mode)
+            if mode not in ('native','preserved','biological'):
+                raise ValueError('Missing semantic palette for '+str(p)+' in '+s['title'])
+            out.append(rel(p));PALETTE_RECORDS.append({'slide_key':ledger(s),'asset':str(p),'action':mode,'reason':s.get('palette_reason','New native plot or non-method colour encoding.')})
+            continue
+        rule=policy['rules'][stem]
+        original_p=p
+        if rule.get('precolored_source_png'):
+            p=source(rule['precolored_source_png'],'mixed-cohort/method figure rendered from unchanged saved values')
+            if rule.get('precolored_proof'):source(rule['precolored_proof'],'legacy rare-state numerical identity proof')
+        mapping=rule.get('mapping',{})
+        if not mapping and not rule.get('rectangle_rules'):
+            out.append(rel(p));PALETTE_RECORDS.append({'slide_key':ledger(s),'asset':str(original_p),'output':str(p),'action':'preserved' if p==original_p else 'precolored','reason':rule['reason']})
+            continue
+        cachekey=(str(p),stem)
+        if cachekey not in CACHE:
+            inp=source(rule.get('source_pdf',p.with_suffix('.pdf')),'vector source for method palette')
+            target=D/'figures/expanded_master_20261013/palette';target.mkdir(parents=True,exist_ok=True)
+            final_pdf=target/(stem+'.pdf');final_png=target/(stem+'.png')
+            with tempfile.TemporaryDirectory(prefix='.build-',dir=target) as temp:
+                pdf=Path(temp)/(stem+'.pdf');png=Path(temp)/(stem+'.png')
+                proof=recolor_pdf(inp,pdf,mapping,rectangle_rules=rule.get('rectangle_rules'),rgb_tolerance=rule.get('rgb_tolerance',5.1e-7 if stem=='fig1b_overview_nature' else 1e-8))
+                render=render_pdf_to_png(pdf,png,dpi=300 if stem=='fig1b_overview_nature' else 200)
+                pdf.replace(final_pdf);png.replace(final_png)
+            proof['destination']=str(final_pdf);render['pdf']=str(final_pdf);render['png']=str(final_png)
+            proof.update({'render':render,'semantic_reason':rule['reason'],'original_png':str(original_p),'original_png_sha256':sha(original_p)})
+            receipt=target/(stem+'.palette.json');receipt.write_text(json.dumps(proof,indent=2)+'\n')
+            for f in (final_pdf,final_png,receipt):source(f,'expanded-master colour variant or preservation proof')
+            CACHE[cachekey]=(final_png,receipt)
+        png,receipt=CACHE[cachekey]
+        out.append(rel(png));PALETTE_RECORDS.append({'slide_key':ledger(s),'asset':str(original_p),'output':str(png),'proof':str(receipt),'action':'recolored','preservation_pass':True})
+    s['figures']=out
+
+def draw_note(prs,s,number):
+    slide=prs.slides.add_slide(prs.slide_layouts[6]);G.white_bg(slide);G.add_title(slide,s['title'],s.get('section_label'))
+    rows=s['rows'];step=4.95/max(len(rows),1)
+    for i,(head,body) in enumerate(rows):
+        y=1.2+i*step
+        G.add_text(slide,G.X0,y,11.8,.38,[head],18,bold=True)
+        lines=G.wrap(body,15,11.8)
+        assert len(lines)<=3,(s['title'],head)
+        G.add_text(slide,G.X0,y+.43,11.8,min(step-.48,.9),[body],15,color=G.GREY)
+    G.add_footer(slide,s.get('footnote'),number);G.add_notes(slide,s)
+
+def main():
+    from expanded_healthy_materials import build as build_healthy
+    from expanded_disease_materials import build as build_disease
+    A.mkdir(exist_ok=True)
+    master_path=source(D/'data/slides_spec.json','original 76-slide structure and provenance')
+    original=json.loads(master_path.read_text())['slides'];assert len(original)==76
+    review=json.loads(source(D/'data/results_review_20261013_spec.json','audited subset for six additional views and protocol corrections').read_text())['slides']
+    review_by_old={x['original_slide']:x for x in review if x.get('original_slide')}
+    policy=json.loads(source(A/'palette.json','semantic gold/blue policy for complete original deck').read_text())
+    legacy=build_legacy_rare()
+    for row in legacy.get('inputs',[]):
+        if isinstance(row,dict):source(row['path'],row.get('role','legacy rare source'))
+        else:source(row,'legacy rare source')
+    if legacy.get('proof'):source(legacy['proof'],'legacy rare numeric preservation proof')
+    additions=[];modules=[]
+    for name,builder in [('healthy',build_healthy),('disease',build_disease)]:
+        result=reuse_or_build(name,builder);modules.append({'name':name,'result':result})
+        for row in result.get('sources',[]):
+            p=row['path'] if isinstance(row,dict) else row
+            source(p,row.get('role','additional evidence source') if isinstance(row,dict) else 'additional evidence source')
+            if isinstance(row,dict) and row.get('sha256'):assert SOURCES[str(Path(p).resolve())]['sha256']==row['sha256'],p
+        for p in result.get('assets',[]):source(p,'new source-bound analysis figure or table')
+        for j,item in enumerate(result['slides']):
+            s=copy.deepcopy(item);s['addition_key']=s.get('addition_key',s.get('key',name+':'+str(j+1)))
+            s.setdefault('kind','content');s.setdefault('keywords',[])
+            s.setdefault('section_label','Additional evidence');s.setdefault('after_original',76)
+            s.setdefault('footnote_full',s.get('footnote',''))
+            s['footnote_full']+='\nEvidence source: '+str(s.get('sources',''))
+            normalize_footnote(s);additions.append(s)
+    for i,after in [(6,12),(8,27),(13,30),(22,49),(23,50),(24,52)]:
+        s=copy.deepcopy(review[i-1]);s.pop('original_slide',None)
+        s['figures']=s.get('figures_before_palette',s.get('figures',[]))
+        s.pop('figures_before_palette',None)
+        s['addition_key']='review:'+str(i);s['after_original']=after
+        s['footnote_full']='Additional view from the audited results review. '+s.get('footnote_full',s.get('footnote',''))
+        normalize_footnote(s);additions.append(s)
+    additions += [
+        note('How to read this expanded evidence deck','Evidence scope',[
+            ('Complete original coverage','All 76 original slides are retained in order, with protocol labels corrected where needed.'),
+            ('Additional existing evidence','New views use completed figures, stored coordinates or saved score tables; no new training or cell generation.'),
+            ('Scope stays visible','Historical diagnostics, completed strict subsets, exploratory bulk-only analyses and pending reproduction are labelled separately.')],2,'guide:scope','Original figures retain their data and evidence lineage; sources and limitations are in the speaker notes.'),
+        note('Availability is not the same as a new experiment','Evidence map',[
+            ('Available now','Pretraining/architecture, LoRA and rank controls, paired benchmarks, external diagnostics and rare-state analyses.'),
+            ('Protocol update','Only receipt-verified scored strict units enter the added result panels; generated-only outputs are not scored evidence.'),
+            ('Figure 6 boundary','Historical bulk-only explorations are included as exploratory evidence. The user-prepared independent reproduction dataset is still pending.')],3,'guide:availability','Planning cards from the original deck are retained as dated snapshots, not a fresh list of experiments to rerun.'),
+        note('Why the historical and strict protocols differ','Protocol boundary',[
+            ('Historical healthy learning curves','LoRA used n training plus 7 validation pairs. Historical scSemi budget curves also reused CV-derived highly variable genes.'),
+            ('Five donors versus five samples','Sepsis support is five samples; multi-visit Imperial, Giroux and Ji support can include more than five samples.'),
+            ('New strict evaluation','Fixed-step, exact-sample support is a distinct protocol. Its partial results are labelled by completed cohort and draw.')],21,'guide:protocol','Support draws overlap in donors. Displayed draw variation is not independent population replication.'),
+        note('What remains to establish Figure 6','Figure 6',[
+            ('Existing exploratory outputs','Historical bulk-only generation and candidate audits are available and shown with their validation outcomes.'),
+            ('Independent reproduction','The new user-prepared cohort is a separate evaluation; no completed finding is claimed here.'),
+            ('Evidence required','Prespecified endpoint, exact sample/visit linkage, population definition and confirmation beyond the input-bulk signal.')],55,'guide:figure6','Historical candidate analyses do not substitute for independent reproduction in the new cohort.')
+    ]
+    keys=[x['addition_key'] for x in additions];assert len(keys)==len(set(keys)),keys
+    by_after={n:[] for n in range(77)}
+    for item in additions:
+        assert 0<=int(item['after_original'])<=76
+        by_after[int(item['after_original'])].append(item)
+    slides=list(by_after[0])
+    for number,item in enumerate(original,1):
+        slides.append(original_slide(number,item,review_by_old));slides.extend(by_after[number])
+    for s in slides:method_palette(s,policy)
+    prs=Presentation();prs.slide_width=Inches(G.SLIDE_W);prs.slide_height=Inches(G.SLIDE_H)
+    for i,s in enumerate(slides,1):
+        kind=s['kind']
+        if kind=='title':G.build_title(prs,s)
+        elif kind=='agenda':G.build_agenda(prs,s,i)
+        elif kind=='divider':G.build_divider(prs,s,i)
+        elif kind=='content':G.build_content(prs,s,i)
+        elif kind=='evidence_note':draw_note(prs,s,i)
+        else:raise ValueError(kind)
+        for f in s.get('figures',[]):
+            source(D/f,'embedded figure')
+            vector=(D/f).with_suffix('.pdf')
+            if vector.is_file():source(vector,'figure vector companion')
+    prs.save(D/(OUT+'.pptx'))
+    for p in [Path(__file__),D/'generate_deck.py',D/'tools/style.py',D/'tools/review_palette_pdf.py',D/'tools/expanded_legacy_rare.py',D/'tools/expanded_healthy_materials.py',D/'tools/expanded_disease_materials.py']:
+        source(p,'expanded deck builder or plotting source')
+    coverage=[{'original_slide':s['original_slide'],'expanded_slide':i,'original_title':s['original_title'],'current_title':s['title']} for i,s in enumerate(slides,1) if 'original_slide' in s]
+    assert [r['original_slide'] for r in coverage]==list(range(1,77))
+    spec={'deck':{'output_pptx':OUT+'.pptx','output_pdf':OUT+'.pdf'},'slides':slides}
+    (A/'spec.json').write_text(json.dumps(spec,indent=2)+'\n')
+    with (A/'original_76_coverage.csv').open('w') as f:
+        w=csv.DictWriter(f,fieldnames=list(coverage[0]));w.writeheader();w.writerows(coverage)
+    with (A/'slide_map.csv').open('w') as f:
+        w=csv.DictWriter(f,fieldnames=['slide','original_slide','addition_key','title','section','footnote']);w.writeheader()
+        for i,s in enumerate(slides,1):w.writerow({'slide':i,'original_slide':s.get('original_slide',''),'addition_key':s.get('addition_key',''),'title':s['title'],'section':s.get('section_label',''),'footnote':s.get('footnote','')})
+    manifest={'schema':'pbisc.expanded-master.v1','as_of_kst':datetime.now(timezone(timedelta(hours=9))).isoformat(),
+        'slides':slides,'sources':SOURCES,'original_slides':76,'added_slides':len(additions),'total_slides':len(slides),
+        'coverage':coverage,'palette_records':PALETTE_RECORDS,'modules':modules,
+        'output':{'pptx':{'path':str(D/(OUT+'.pptx')),'sha256':sha(D/(OUT+'.pptx'))},'pdf':'pending export'},
+        'new_training':False,'new_generation':False,'new_scoring':False,
+        'cpu_work':'existing figure reuse; saved-table and stored-coordinate plotting only'}
+    (A/'manifest.json').write_text(json.dumps(manifest,indent=2)+'\n')
+    print(json.dumps({'original':76,'added':len(additions),'total':len(slides),'sources':len(SOURCES),'pptx':str(D/(OUT+'.pptx'))}))
+
+if __name__=='__main__':main()