Skip to content

Commit 8015c6e

Browse files
aivukaivuk
committed
paper: add Levine_13dim results, real stability figure, 11 pages
1 parent 46e80f1 commit 8015c6e

6 files changed

Lines changed: 93 additions & 60 deletions

File tree

‎paper/densitree.aux‎

Lines changed: 21 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
\@writefile{toc}{\contentsline {paragraph}{Hungarian-aligned majority vote.}{3}{section*.5}\protected@file@percent }
2525
\@writefile{toc}{\contentsline {subsection}{\numberline {2.4}Decoupled downsampling and tree construction}{3}{subsection.2.4}\protected@file@percent }
2626
\citation{levine2015phenograph}
27+
\citation{levine2015phenograph}
2728
\@writefile{loa}{\contentsline {algorithm}{\numberline {1}{\ignorespaces Mixed-linkage consensus metaclustering}}{4}{algorithm.1}\protected@file@percent }
2829
\newlabel{alg:consensus}{{1}{4}{Mixed-linkage consensus metaclustering}{algorithm.1}{}}
2930
\@writefile{toc}{\contentsline {subsection}{\numberline {2.5}Rationale for decoupling}{4}{subsection.2.5}\protected@file@percent }
@@ -34,40 +35,43 @@
3435
\newlabel{tab:levine}{{1}{5}{Benchmark results on Levine\_32dim (104{,}184 cells, 32 markers, 14 populations). Bold indicates best. Mean $\pm $ std over 3 runs}{table.caption.6}{}}
3536
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Compared methods}{5}{subsection.3.2}\protected@file@percent }
3637
\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Evaluation metrics}{5}{subsection.3.3}\protected@file@percent }
37-
\@writefile{toc}{\contentsline {subsection}{\numberline {3.4}Results on Levine\_32dim}{5}{subsection.3.4}\protected@file@percent }
3838
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces ARI comparison on Levine\_32dim. Error bars show standard deviation over 3 runs. \texttt {densitree}{} achieves the highest ARI with the lowest variance.}}{6}{figure.caption.7}\protected@file@percent }
3939
\newlabel{fig:benchmark}{{2}{6}{ARI comparison on Levine\_32dim. Error bars show standard deviation over 3 runs. \densitree {} achieves the highest ARI with the lowest variance}{figure.caption.7}{}}
40+
\@writefile{toc}{\contentsline {subsection}{\numberline {3.4}Results on Levine\_32dim}{6}{subsection.3.4}\protected@file@percent }
4041
\@writefile{toc}{\contentsline {subsection}{\numberline {3.5}Results on synthetic data}{6}{subsection.3.5}\protected@file@percent }
41-
\@writefile{toc}{\contentsline {subsection}{\numberline {3.6}Ablation: contribution of each component}{6}{subsection.3.6}\protected@file@percent }
42+
\@writefile{toc}{\contentsline {subsection}{\numberline {3.6}Results on Levine\_13dim}{6}{subsection.3.6}\protected@file@percent }
4243
\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Benchmark results on synthetic data (50{,}000 cells, 15 features, 12 populations). Bold indicates best.}}{7}{table.caption.8}\protected@file@percent }
4344
\newlabel{tab:synthetic}{{2}{7}{Benchmark results on synthetic data (50{,}000 cells, 15 features, 12 populations). Bold indicates best}{table.caption.8}{}}
44-
\@writefile{lot}{\contentsline {table}{\numberline {3}{\ignorespaces Ablation study on Levine\_32dim. Each row adds one component cumulatively. MBK = MiniBatchKMeans.}}{7}{table.caption.9}\protected@file@percent }
45-
\newlabel{tab:ablation}{{3}{7}{Ablation study on Levine\_32dim. Each row adds one component cumulatively. MBK = MiniBatchKMeans}{table.caption.9}{}}
46-
\@writefile{toc}{\contentsline {subsection}{\numberline {3.7}Stability analysis}{7}{subsection.3.7}\protected@file@percent }
45+
\@writefile{lot}{\contentsline {table}{\numberline {3}{\ignorespaces Benchmark results on Levine\_13dim (13 markers, 24 populations). Bold indicates best.}}{7}{table.caption.9}\protected@file@percent }
46+
\newlabel{tab:levine13}{{3}{7}{Benchmark results on Levine\_13dim (13 markers, 24 populations). Bold indicates best}{table.caption.9}{}}
47+
\@writefile{toc}{\contentsline {subsection}{\numberline {3.7}Ablation: contribution of each component}{7}{subsection.3.7}\protected@file@percent }
48+
\@writefile{toc}{\contentsline {subsection}{\numberline {3.8}Stability analysis}{7}{subsection.3.8}\protected@file@percent }
4749
\@writefile{toc}{\contentsline {section}{\numberline {4}Discussion}{7}{section.4}\protected@file@percent }
4850
\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Mixed-linkage diversity}{7}{subsection.4.1}\protected@file@percent }
49-
\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Decoupling as a general principle}{7}{subsection.4.2}\protected@file@percent }
50-
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Ablation study on Levine\_32dim. Each bar adds one component cumulatively. Error bars show ARI standard deviation. The mixed-linkage consensus eliminates the high variance introduced by decoupled clustering while further improving accuracy.}}{8}{figure.caption.10}\protected@file@percent }
51-
\newlabel{fig:ablation}{{3}{8}{Ablation study on Levine\_32dim. Each bar adds one component cumulatively. Error bars show ARI standard deviation. The mixed-linkage consensus eliminates the high variance introduced by decoupled clustering while further improving accuracy}{figure.caption.10}{}}
51+
\@writefile{lot}{\contentsline {table}{\numberline {4}{\ignorespaces Ablation study on Levine\_32dim. Each row adds one component cumulatively. MBK = MiniBatchKMeans.}}{8}{table.caption.10}\protected@file@percent }
52+
\newlabel{tab:ablation}{{4}{8}{Ablation study on Levine\_32dim. Each row adds one component cumulatively. MBK = MiniBatchKMeans}{table.caption.10}{}}
53+
\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Decoupling as a general principle}{8}{subsection.4.2}\protected@file@percent }
5254
\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Limitations}{8}{subsection.4.3}\protected@file@percent }
53-
\@writefile{toc}{\contentsline {paragraph}{Runtime.}{8}{section*.12}\protected@file@percent }
54-
\@writefile{toc}{\contentsline {paragraph}{Rare population F1.}{8}{section*.13}\protected@file@percent }
55-
\@writefile{toc}{\contentsline {paragraph}{Synthetic data.}{8}{section*.14}\protected@file@percent }
55+
\@writefile{toc}{\contentsline {paragraph}{Runtime.}{8}{section*.13}\protected@file@percent }
56+
\@writefile{toc}{\contentsline {paragraph}{Rare population F1.}{8}{section*.14}\protected@file@percent }
57+
\@writefile{toc}{\contentsline {paragraph}{Synthetic data.}{8}{section*.15}\protected@file@percent }
5658
\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}Applicability beyond cytometry}{8}{subsection.4.4}\protected@file@percent }
5759
\bibcite{fred2005evidence}{Fred and Jain(2005)}
60+
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Ablation study on Levine\_32dim. Each bar adds one component cumulatively. Error bars show ARI standard deviation. The mixed-linkage consensus eliminates the high variance introduced by decoupled clustering while further improving accuracy.}}{9}{figure.caption.11}\protected@file@percent }
61+
\newlabel{fig:ablation}{{3}{9}{Ablation study on Levine\_32dim. Each bar adds one component cumulatively. Error bars show ARI standard deviation. The mixed-linkage consensus eliminates the high variance introduced by decoupled clustering while further improving accuracy}{figure.caption.11}{}}
62+
\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusion}{9}{section.5}\protected@file@percent }
5863
\bibcite{kuhn1955hungarian}{Kuhn(1955)}
5964
\bibcite{levine2015phenograph}{Levine et~al.(2015)}
6065
\bibcite{monti2003consensus}{Monti et~al.(2003)}
61-
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Distribution of ARI over 20 independent runs on Levine\_32dim. \texttt {densitree}{} (left) achieves consistently high ARI with minimal variance, while FlowSOM-style (right) exhibits a bimodal distribution with frequent low-quality runs. Dashed lines indicate mean ARI.}}{9}{figure.caption.11}\protected@file@percent }
62-
\newlabel{fig:stability}{{4}{9}{Distribution of ARI over 20 independent runs on Levine\_32dim. \densitree {} (left) achieves consistently high ARI with minimal variance, while FlowSOM-style (right) exhibits a bimodal distribution with frequent low-quality runs. Dashed lines indicate mean ARI}{figure.caption.11}{}}
63-
\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusion}{9}{section.5}\protected@file@percent }
6466
\bibcite{qiu2011spade}{Qiu et~al.(2011)}
6567
\bibcite{qiu2017deterministic}{Qiu(2017)}
6668
\bibcite{sculley2010web}{Sculley(2010)}
6769
\bibcite{strehl2002cluster}{Strehl and Ghosh(2002)}
6870
\bibcite{vangassen2015flowsom}{Van~Gassen et~al.(2015)}
6971
\bibcite{weber2016comparison}{Weber and Robinson(2016)}
7072
\bibcite{wilkerson2010consensus}{Wilkerson and Hayes(2010)}
71-
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Example \texttt {densitree}{} tree output on Levine\_32dim with 20 clusters. Left: nodes colored by median CD45 expression (viridis colormap). Right: nodes sized proportionally to cell count. The tree captures the phenotypic hierarchy of the bone marrow compartment.}}{10}{figure.caption.15}\protected@file@percent }
72-
\newlabel{fig:tree}{{5}{10}{Example \densitree {} tree output on Levine\_32dim with 20 clusters. Left: nodes colored by median CD45 expression (viridis colormap). Right: nodes sized proportionally to cell count. The tree captures the phenotypic hierarchy of the bone marrow compartment}{figure.caption.15}{}}
73-
\gdef \@abspage@last{10}
73+
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Distribution of ARI over 20 independent runs on Levine\_32dim. \texttt {densitree}{} (left) achieves consistently high ARI with minimal variance, while FlowSOM-style (right) exhibits a bimodal distribution with frequent low-quality runs. Dashed lines indicate mean ARI.}}{10}{figure.caption.12}\protected@file@percent }
74+
\newlabel{fig:stability}{{4}{10}{Distribution of ARI over 20 independent runs on Levine\_32dim. \densitree {} (left) achieves consistently high ARI with minimal variance, while FlowSOM-style (right) exhibits a bimodal distribution with frequent low-quality runs. Dashed lines indicate mean ARI}{figure.caption.12}{}}
75+
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Example \texttt {densitree}{} tree output on Levine\_32dim with 20 clusters. Left: nodes colored by median CD45 expression (viridis colormap). Right: nodes sized proportionally to cell count. The tree captures the phenotypic hierarchy of the bone marrow compartment.}}{11}{figure.caption.16}\protected@file@percent }
76+
\newlabel{fig:tree}{{5}{11}{Example \densitree {} tree output on Levine\_32dim with 20 clusters. Left: nodes colored by median CD45 expression (viridis colormap). Right: nodes sized proportionally to cell count. The tree captures the phenotypic hierarchy of the bone marrow compartment}{figure.caption.16}{}}
77+
\gdef \@abspage@last{11}

‎paper/densitree.log‎

Lines changed: 35 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex 2026.3.30) 10 APR 2026 17:10
1+
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex 2026.3.30) 10 APR 2026 17:12
22
entering extended mode
33
restricted \write18 enabled.
44
%&-line parsing enabled.
@@ -658,7 +658,7 @@ LaTeX Font Info: External font `lmex10' loaded for size
658658
dvips/lm/lm-ec.enc}{/usr/share/texmf/fonts/enc/dvips/lm/lm-rm.enc}{/usr/share/t
659659
exmf/fonts/enc/dvips/lm/lm-mathit.enc}{/usr/share/texmf/fonts/enc/dvips/lm/lm-m
660660
athsy.enc}]
661-
<figures/fig1_algorithm_overview.pdf, id=119, 500.83109pt x 321.47893pt>
661+
<figures/fig1_algorithm_overview.pdf, id=123, 500.83109pt x 321.47893pt>
662662
File: figures/fig1_algorithm_overview.pdf Graphic file (type pdf)
663663
<use figures/fig1_algorithm_overview.pdf>
664664
Package pdftex.def Info: figures/fig1_algorithm_overview.pdf used on input lin
@@ -676,82 +676,83 @@ _overview.pdf>]
676676

677677
[4]
678678
LaTeX Font Info: Trying to load font information for TS1+lmr on input line 2
679-
11.
679+
14.
680680
(/usr/share/texmf/tex/latex/lm/ts1lmr.fd
681681
File: ts1lmr.fd 2015/05/01 v1.6.1 Font defs for Latin Modern
682682
)
683683
LaTeX Font Info: Font shape `T1/lmtt/bx/n' in size <10.95> not available
684-
(Font) Font shape `T1/lmtt/b/n' tried instead on input line 211.
684+
(Font) Font shape `T1/lmtt/b/n' tried instead on input line 214.
685685
LaTeX Font Info: Font shape `T1/lmtt/bx/n' in size <10> not available
686-
(Font) Font shape `T1/lmtt/b/n' tried instead on input line 242.
687-
<figures/fig2_benchmark_comparison.pdf, id=283, 251.88165pt x 198.1075pt>
686+
(Font) Font shape `T1/lmtt/b/n' tried instead on input line 245.
687+
<figures/fig2_benchmark_comparison.pdf, id=288, 251.88165pt x 198.1075pt>
688688
File: figures/fig2_benchmark_comparison.pdf Graphic file (type pdf)
689689
<use figures/fig2_benchmark_comparison.pdf>
690690
Package pdftex.def Info: figures/fig2_benchmark_comparison.pdf used on input l
691-
ine 254.
691+
ine 257.
692692
(pdftex.def) Requested size: 452.9679pt x 356.26974pt.
693693

694694

695695
[5{/usr/share/texmf/fonts/enc/dvips/lm/lm-ts1.enc}]
696-
<figures/fig3_ablation_study.pdf, id=297, 247.33435pt x 195.97768pt>
696+
697+
[6 <./figures/fig2_benchmark_comparison.pdf>]
698+
<figures/fig3_ablation_study.pdf, id=383, 247.33435pt x 195.97768pt>
697699
File: figures/fig3_ablation_study.pdf Graphic file (type pdf)
698700
<use figures/fig3_ablation_study.pdf>
699-
Package pdftex.def Info: figures/fig3_ablation_study.pdf used on input line 31
700-
1.
701+
Package pdftex.def Info: figures/fig3_ablation_study.pdf used on input line 33
702+
8.
701703
(pdftex.def) Requested size: 452.9679pt x 358.94362pt.
702704

703-
Overfull \hbox (3.86278pt too wide) in paragraph at lines 322--325
705+
Overfull \hbox (3.86278pt too wide) in paragraph at lines 349--352
704706
\T1/lmr/m/n/10.95 (-20) We as-sessed \T1/lmtt/m/n/10.95 densitree\T1/lmr/m/n/10
705707
.95 (-20) 's sta-bil-ity by run-ning it 20 times with dif-fer-ent base seeds on
706708
Levine_32dim
707709
[]
708710

709-
710-
711-
[6 <./figures/fig2_benchmark_comparison.pdf>]
712-
<figures/fig4_stability_comparison.pdf, id=379, 508.86143pt x 187.69875pt>
711+
<figures/fig4_stability_comparison.pdf, id=385, 500.23546pt x 201.71912pt>
713712
File: figures/fig4_stability_comparison.pdf Graphic file (type pdf)
714713
<use figures/fig4_stability_comparison.pdf>
715714
Package pdftex.def Info: figures/fig4_stability_comparison.pdf used on input l
716-
ine 328.
717-
(pdftex.def) Requested size: 452.9679pt x 167.08571pt.
715+
ine 355.
716+
(pdftex.def) Requested size: 452.9679pt x 182.66283pt.
718717

719718

720719
[7]
721-
<figures/fig5_spade_tree.pdf, id=386, 500.83109pt x 257.64255pt>
720+
<figures/fig5_spade_tree.pdf, id=393, 500.83109pt x 257.64255pt>
722721
File: figures/fig5_spade_tree.pdf Graphic file (type pdf)
723722
<use figures/fig5_spade_tree.pdf>
724-
Package pdftex.def Info: figures/fig5_spade_tree.pdf used on input line 369.
723+
Package pdftex.def Info: figures/fig5_spade_tree.pdf used on input line 396.
725724
(pdftex.def) Requested size: 452.9679pt x 233.02802pt.
726725

727726

728-
[8 <./figures/fig3_ablation_study.pdf>]
729-
Overfull \hbox (5.97566pt too wide) in paragraph at lines 391--395
727+
[8]
728+
Overfull \hbox (5.97566pt too wide) in paragraph at lines 418--422
730729
\T1/lmr/m/n/10.95 (-20) mark dataset is avail-able from [][]$\T1/lmtt/m/n/10.95
731730
https : / / github . com / lmweber / benchmark-[]data-[]Levine-[]32-[]dim$[][]
732731
\T1/lmr/m/n/10.95 (-20) .
733732
[]
734733

735734

736735

737-
[9 <./figures/fig4_stability_comparison.pdf>]
736+
[9 <./figures/fig3_ablation_study.pdf>]
737+
738+
[10 <./figures/fig4_stability_comparison.pdf>]
738739

739-
[10 <./figures/fig5_spade_tree.pdf>] (./densitree.aux)
740+
[11 <./figures/fig5_spade_tree.pdf>] (./densitree.aux)
740741
***********
741742
LaTeX2e <2024-11-01> patch level 2
742743
L3 programming layer <2025-01-18>
743744
***********
744745
Package rerunfilecheck Info: File `densitree.out' has not changed.
745-
(rerunfilecheck) Checksum: 09BB963463BA1FBB894893396951E065;3575.
746+
(rerunfilecheck) Checksum: F91397A2CE3086E40F1BC79E15C4BDA9;3757.
746747
)
747748
Here is how much of TeX's memory you used:
748-
15673 strings out of 475102
749-
249416 string characters out of 5764877
750-
679894 words of memory out of 5000000
751-
38148 multiletter control sequences out of 15000+600000
749+
15678 strings out of 475102
750+
249483 string characters out of 5764877
751+
681008 words of memory out of 5000000
752+
38150 multiletter control sequences out of 15000+600000
752753
661007 words of font info for 214 fonts, out of 8000000 for 9000
753754
59 hyphenation exceptions out of 8191
754-
75i,11n,79p,1006b,570s stack positions out of 10000i,1000n,20000p,200000b,200000s
755+
75i,11n,79p,1006b,574s stack positions out of 10000i,1000n,20000p,200000b,200000s
755756
</usr/share/texmf/fonts/type1/public/lm/lmbx10.pfb></usr/share/texmf/fonts/ty
756757
pe1/public/lm/lmbx12.pfb></usr/share/texmf/fonts/type1/public/lm/lmex10.pfb></u
757758
sr/share/texmf/fonts/type1/public/lm/lmmi10.pfb></usr/share/texmf/fonts/type1/p
@@ -766,10 +767,10 @@ c/lm/lmsy8.pfb></usr/share/texmf/fonts/type1/public/lm/lmtk10.pfb></usr/share/t
766767
exmf/fonts/type1/public/lm/lmtt10.pfb></usr/share/texmf/fonts/type1/public/lm/l
767768
mtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/ms
768769
bm10.pfb>
769-
Output written on densitree.pdf (10 pages, 500001 bytes).
770+
Output written on densitree.pdf (11 pages, 504252 bytes).
770771
PDF statistics:
771-
746 PDF objects out of 1000 (max. 8388607)
772-
324 compressed objects within 4 object streams
773-
68 named destinations out of 1000 (max. 500000)
774-
60106 words of extra memory for PDF output out of 61914 (max. 10000000)
772+
764 PDF objects out of 1000 (max. 8388607)
773+
334 compressed objects within 4 object streams
774+
71 named destinations out of 1000 (max. 500000)
775+
60114 words of extra memory for PDF output out of 61914 (max. 10000000)
775776

0 commit comments

Comments
 (0)