Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues

2019/08/21 ISMB/ECCB 2019読み会にて "Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues"という論文を紹介する際に使用したスライド

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1. Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues Dan Guo, Kylie Bemis, Catherine Rawlins, Jeffrey Agar and Olga Vitek., Bioinformatics, 35, 2019, i208–i217 ඌ࡚ྒྷʢஜ೾େʣ
   !ZVJGV 2019/08/21 ISMB/ECCB 2019ಡΈձ
2. ཁ໿ ໰୊: Mass spectrometry imaging (MSI) ͷσʔλ͔ΒۭؒతύλʔϯΛࣔ͢ ΠΦϯΛڭࢣͳ͠Ͱݟ͚͍ͭͨ ҙٛ: ૊৫ͷܗଶߏ଄Λ൓өۭͨؒ͠෼෍Λࣔ͢ΠΦϯ͸ྟচతʹ΋ੜ෺ֶత ʹ΋ॏཁɻݱঢ়Ͱ͸ਓखͰ୳ͯ͠ΔʢΒ͍͠ʣ ͕ը૾਺͕ଟ͗͢Δɻ ํࡦ: σΟϦΫϨ-Ψ΢εࠞ߹Ϟσϧʹۭؒతͳ੍໿ΛՃ͑ͨ spatial-DGMM͓ ΑͼσʔλॲཧϫʔΫϑϩʔΛఏҊɻ ධՁ: ਓ޻σʔλɾ࣮σʔλʹͯΠΦϯը૾ͷηάϝϯςʔγϣϯ͕Ͱ͖͍ͯ Δ͜ͱΛࣔ͠ɺ࣮σʔλͷܭࢉ݁Ռ͕Լྲྀͷղੳʹ༗༻Ͱ͋Δ͜ͱΛࣔͨ͠
   
3. എܠ̍ Mass spectrometry imaging (MSI) ۭؒ࠲ඪଆɿ͋Δ࠲ඪʹ͓͚Δ਺ඦʙ਺ສछྨͷ෺࣭ͷྔ ΠΦϯଆɿ͋ΔΠΦϯͷۭؒ෼෍ʢΠΦϯϚοϓʣ͕Θ͔Δ
    Li+ Trends in Food Science & Technology (2019) DOI: 10.1016/j.tifs.2015.10.018 ૊৫੾ย্Ͱͻͨ͢ΒϚεεϖΫτϩϝτϦʔܭଌΛ͢Δ ˒ΠΦϯϚοϓ ˒ ˒ ˒ ˒ ˒ ˒
4. എܠ̎ܗଶ ΠΦϯϚοϓͷΠΦϯͷہࡏΛௐ΂Δ͜ͱ͸ҩֶɾੜ෺ֶ తʹॏཁ ࣬ױ΍࣏ྍͷػংͷݚڀɿλϯύΫ࣭ɾ୅ँ෺ͷྔ͕૊৫ܗଶಛҟతʹมԽ͍ͯ͠ Δ͜ͱ͕͋Δ ࣏ྍޮ཰ͷݚڀɿ౤༩ͨ͠ༀࡎͷ෼෍ → ૊৫தͰͷྖҬಛҟੑ ϘτϧωοΫɿΠΦϯϚοϓ͕ଟ͗͢Δ ਺ඦ͔Β਺ສछྨͷ෺࣭ʹରԠ͢ΔΠΦϯϚοϓ x ܁Γฦ࣮͠ݧʢϨϓϦέΠτʣ ਺ x ࣮ݧ৚݅਺ ਓखͩͱେม
   
5. ໰୊ઃఆɿΠΦϯϚοϓͷΫϥελϦϯά σʔλ఺ͷ཭ࢄજࡏม਺Λ
    ೖྗɿҰͭͷ෺࣭ͷ ΠΦϯϚοϓ ʢεΧϥʔʣ ग़ྗɿ֤ଌఆ఺ͷ જࡏม਺ ʢ཭ࢄͳΫϥελʣ ҰछྨͷΠΦϯʹ͍ͭͯ Ґஔ i ʹ͓͚ΔΠΦϯڧ౓ Ґஔ i ͷજࡏม਺
6. ઌߦݚڀͱͷҧ͍ vs. PCA, Spatial K-means, Spatial centroid segmentation ͜ΕΒͷख๏͸ʢ୯छྨΠΦϯͷΠΦϯϚοϓͰ͸ͳ͘ʣଟछྨͷΠΦϯͷΠΦϯ ڧ౓ϕΫτϧΛσʔλ఺ͱͯ͠ద༻͞ΕΔ ը૾ͷηάϝϯςʔγϣϯ͸Ͱ͖Δ͕ɺΠΦϯ͝ͱͷҧ͍͸Θ͔Βͳ͍ ΠΦϯಛҟతͳۭؒ෼෍͕Θ͔Βͳ͍ vs. DGMM σʔλ఺ಉ࢜ͷۭؒ෼෍Λߟྀ͍ͯ͠ͳ͍
   
7. ఏҊख๏: Spatial-DGMM
    Dirichlet GMM (DGMM): GMMͷΫϥελׂΓ౰ͯͷࣄલ෼෍ͷ ௒ࣄલ෼෍ͱͯ͠σΟϦΫϨ෼෍Λઃఆ GMM Ґஔ i ͷΫϥελॴଐͷࣄલ෼෍ Ґஔ i ͷΫϥελॴଐͷࣄޙ෼෍ Spatial DGMM: DGMMʹۭؒґଘੑΛಋೖ Linear filter: EMͷiteration͝ͱʹ ࣄޙ֬཰Λ i पลͷҐஔʹ͓͚Δࣄޙ෼෍Ͱฏۉ ۭ͕͍ؒۙ΄Ͳେ͖͍ શ෺࣭ͷεϖΫτϧڧ౓͕ ࣅ͍ͯΔ΄Ͳେ͖͍ ɹɹͰΫϥελʔॴଐͷࣄલ෼෍͕ॏΈ෇͚͞ΕΔ
8. ఏҊख๏: ίϯϙʔωϯτ਺ͷܾఆ 1. GMMͱBICͰKͷ਺Λܾఆ 2. spatial-DGMMΛKͰԿ౓΋ॳظԽͱneighborhoodͷൣ ғΛม࣮͑ͯߦ ʢ(BIC͸K͕େ͖͘ͳΓ͕ͪͳͷͰ) ద੾ͳίϯϙʔωϯτ਺Λબͼ͍ͨʣ 3. σʔλ఺ׂ͕Γ౰ͯΒΕ͍ͯΔίϯϙʔωϯτͷ਺ɺ K' ͷ࠷ස஋Λબ୒ 4. Spatial-DGMMΛK'Λίϯϙʔωϯτ਺ͱͯ͠࠶౓࣮ߦ
    K' ΛܾΊΔ 1 2 3 3
9. ධՁ̍: ਓ޻σʔλʹΑΔධՁ
    ྖҬʢ˓ɺ˚ɺഎܠʣ͝ͱʹ ΠΦϯڧ౓͕ҟͳΔ ϊΠζͷڧ͞Λม͍͑ͯ͘ GMMͱSpatial DGMMΛൺֱͨ͠ → Spatial DGMMͷํ͕ϊΠζʹڧ͔ͬͨ ※Ͳͷ͘Β͍ͷϊΠζ͕࣮σʔλͰ૝ఆ͞ΕΔͷ͔ʹ͍ͭͯهࡌͳ͠ ίϯϙʔωϯτฏۉͷਪఆޡࠩ ίϯϙʔωϯτޡ෼ྨ
10. ධՁ̎: ࣮σʔλͰͪΌΜͱࡱΕΔ (Fig. 5͔Fig. 6) ΠΦϯಛҟతͳۭؒύλʔϯ͕औΕΔ
     શ෺࣭ͷΠΦϯڧ౓Λ ࢖ͬͨΫϥελϦϯά ͋ΔΠΦϯʹ͍ͭͯͷ ΫϥελϦϯά ALSϞσϧϚ΢εͷ೴ Ϛ΢ε೴ͷαϒߏ଄͕ औΕ͍ͯΔ ̍ͭͷίϯϙʔωϯτ͸ ࢄࡏ͍ͯ͠Δ ʢϊΠζͷ͍ͤͩͱओுʣ փന࣭ɺന࣭ͱରԠ͢Δ͜ͱ͕஌ΒΕ͍ͯΔ ࢷ࣭ (phosphatidylcholines)ͷ෼෍͕૊৫ߏ଄ͱ੔߹
11. ධՁ̏: ԼྲྀղੳͰͷ༗༻ੑ
     ROIͱۭؒ෼෍͕ྨࣅͨ͠ ίϯϙʔωϯτ͕୳ͤΔ ࣅ͍ͯΔΠΦϯͷ ΫϥελϦϯά͕Ͱ͖Δ ίϯϙʔωϯτ͝ͱʹ ৚݅ؒͰࠩ෼ΛͱΔ ఏҊ๏ ROIͱ֤ίϯϙʔω ϯτͷJaccard܎਺ →είΞ͕ߴ͍ طଘ๏ ROIΛόΠφϦͷϚο ϓͱͯ͠ϐΞιϯ૬ؔ → ஋͕௿͍ spatial shrunken centroid segmentation Ͱग़͖ͯͨROI (೴ྊ) طଘ๏ɿϢʔΫϦουڑ཭ ఏҊ๏ɿಉ͡ίϯϙʔωϯτʹؚ·ΕΔ ఺ͷׂ߹Λڑ཭ ίϯϙʔωϯτؒͷൺΛ৚݅ؒ Ͱൺֱ͢Δ ʢ۩ମతʹ࢖͑ͦ͏ͳղੳʣ ※ࠩͷ౷ܭݕఆ͸͍ͯ͠ͳ͍
12. ٞ࿦ αϒߏ଄಺ͷΠΦϯڧ౓ʹ͍ͭͯΨ΢ε෼෍ΛԾఆ͍ͯ͠ Δ → σʔλ͕ΑΓෳࡶͳ෼෍ʢܗଶߏ଄ɺμΠφϛοΫϨϯ δɺϊΠζͳͲʣ΍ੑ࣭ʢίϯϙʔωϯτؒͰͷฏۉͷࠩ ͕Ͳͷఔ౓͔ʣΛ͍࣋ͬͯͨ৔߹ʹ͸ద੾Ͱͳ͍͔΋͠Ε ͳ͍
    
13. ײ૝ ී௨ͷηάϝϯςʔγϣϯٕज़ʢڭࢣ͋Γʣ νϟωϧͷ਺͕ଟ ਺͔ͩΒ߹Θͳ͍ʢͱॻ͍ͯ͋Δ͕ɺ࣮ࡍʹ͸ΠΦϯ͝ͱʹ΍ͬ ͍ͯΔʣ scRNA-seqͱͷؔ࿈ (SLIDE-seqσʔλΛ࢖ͬͨ΍ͭʣ ୯ʹεϜʔδϯά͢Ε͹͍͍ͷͰ͸ʁ BIC͸ద੾Ͱ͸ͳ͍ʁ ͏·͍͍ͬͯ͘ΔͷΛݟͤΒΕ͍ͯΔײ͡ʁ
    
14. ͳͥISMB/ECCBʹ࠾୒͞Εͨͷ͔ʁ 1. ϒϧʔΦʔγϟϯ͔ͩΒઆɿ MS͕গͳ͍ɺMSI͕গͳ͍ʁ "GENERAL COMPUTATIONAL BIOLOGY" 2. ࣮ݧ΋͍ͯ͠Δ͔Βઆɿ ౷ܭ: Olga Vitek ࣮ݧ: Jeffrey Agar 3. ܭଌٕज़ʹ߹Θٕͤͨज़తߩݙʢपล఺ͷॏΈʣ