Multiple kernel learning applied to the integration of Tara oceans datasets
1. Multiple kernel learning applied to the integration of
Tara oceans datasets
Nathalie Villa-Vialaneix
Joint work with Jérôme Mariette
http://www.nathalievilla.org
7 Février 2017
Institut Élie Cartan, Université de Lorraine
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 1/41
2. Sommaire
1 Metagenomic datasets and associated questions
2 A typical (and rich) case study: TARA Oceans datasets
3 A UMKL framework for integrating multiple metagenomic data
4 Application to TARA Oceans datasets
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 2/41
3. Sommaire
1 Metagenomic datasets and associated questions
2 A typical (and rich) case study: TARA Oceans datasets
3 A UMKL framework for integrating multiple metagenomic data
4 Application to TARA Oceans datasets
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 3/41
4. What are metagenomic data?
Source: [Sommer et al., 2010]
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 4/41
5. What are metagenomic data?
Source: [Sommer et al., 2010]
abundance data sparse
n × p-matrices with count data
of samples in rows and
descriptors (species, OTUs,
KEGG groups, k-mer, ...) in
columns. Generally p n.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 4/41
6. What are metagenomic data?
Source: [Sommer et al., 2010]
abundance data sparse
n × p-matrices with count data
of samples in rows and
descriptors (species, OTUs,
KEGG groups, k-mer, ...) in
columns. Generally p n.
philogenetic tree (evolution
history between species,
OTUs...). One tree with p leaves
built from the sequences
collected in the n samples.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 4/41
7. What are metagenomic data used for?
produce a profile of the diversity of a given sample ⇒ allows to
compare diversity between various conditions
used in various fields: environmental science, microbiote, ...
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 5/41
8. What are metagenomic data used for?
produce a profile of the diversity of a given sample ⇒ allows to
compare diversity between various conditions
used in various fields: environmental science, microbiote, ...
Processed by computing a relevant dissimilarity between samples
(standard Euclidean distance is not relevant) and by using this dissimilarity
in subsequent analyses.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 5/41
9. β-diversity data: dissimilarities between count data
Compositional dissimilarities: (nig) count of species g for sample i
Jaccard: the fraction of species specific of either sample i or j:
djac =
g I{nig>0,njg=0} + I{njg>0,nig=0}
j I{nig+njg>0}
Bray-Curtis: the fraction of the sample which is specific of either
sample i or j
dBC =
g |nig − njg|
g(nig + njg)
Other dissimilarities available in the R package philoseq, most of them
not Euclidean.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 6/41
11. β-diversity data: phylogenetic dissimilarities
Phylogenetic dissimilarities
For each branch e, note le its length and pei
the fraction of counts in sample i
corresponding to species below branch e.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 7/41
12. β-diversity data: phylogenetic dissimilarities
Phylogenetic dissimilarities
For each branch e, note le its length and pei
the fraction of counts in sample i
corresponding to species below branch e.
Unifrac: the fraction of the tree specific to
either sample i or sample j.
dUF =
e le(I{pei>0,pej=0} + I{pej>0,pei=0})
e leI{pei+pej>0}
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 7/41
13. β-diversity data: phylogenetic dissimilarities
Phylogenetic dissimilarities
For each branch e, note le its length and pei
the fraction of counts in sample i
corresponding to species below branch e.
Unifrac: the fraction of the tree specific to
either sample i or sample j.
dUF =
e le(I{pei>0,pej=0} + I{pej>0,pei=0})
e leI{pei+pej>0}
Weighted Unifrac: the fraction of the
diversity specific to sample i or to sample j.
dwUF =
e le|pei − pej|
e(pei + pej)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 7/41
14. Sommaire
1 Metagenomic datasets and associated questions
2 A typical (and rich) case study: TARA Oceans datasets
3 A UMKL framework for integrating multiple metagenomic data
4 Application to TARA Oceans datasets
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15. TARA Oceans datasets
The 2009-2013 expedition
Co-directed by Étienne Bourgois
and Éric Karsenti.
7,012 datasets collected from
35,000 samples of plankton and
water (11,535 Gb of data).
Study the plankton: bacteria,
protists, metazoans and viruses
representing more than 90% of the
biomass in the ocean.
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16. TARA Oceans datasets
Science (May 2015) - Studies on:
eukaryotic plankton diversity
[de Vargas et al., 2015],
ocean viral communities
[Brum et al., 2015],
global plankton interactome
[Lima-Mendez et al., 2015],
global ocean microbiome
[Sunagawa et al., 2015],
. . . .
→ datasets from different types and
different sources analyzed separately.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 10/41
17. Background of this talk
Objectives
Until now: many papers using many methods. No integrated analysis
performed.
What do the datasets reveal if integrated in a single analysis?
Our purpose: develop a generic method to integrate phylogenetic,
taxonomic and functional community composition together with
environmental factors.
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18. TARA Oceans datasets that we used
[Sunagawa et al., 2015]
Datasets used
environmental dataset: 22 numeric features (temperature, salinity, . . . ).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 12/41
19. TARA Oceans datasets that we used
[Sunagawa et al., 2015]
Datasets used
environmental dataset: 22 numeric features (temperature, salinity, . . . ).
bacteria phylogenomic tree: computed from ∼ 35,000 OTUs.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 12/41
20. TARA Oceans datasets that we used
[Sunagawa et al., 2015]
Datasets used
environmental dataset: 22 numeric features (temperature, salinity, . . . ).
bacteria phylogenomic tree: computed from ∼ 35,000 OTUs.
bacteria functional composition: ∼ 63,000 KEGG orthologous groups.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 12/41
21. TARA Oceans datasets that we used
[de Vargas et al., 2015]
Datasets used
environmental dataset: 22 numeric features (temperature, salinity, . . . ).
bacteria phylogenomic tree: computed from ∼ 35,000 OTUs.
bacteria functional composition: ∼ 63,000 KEGG orthologous groups.
eukaryotic plankton composition splited into 4 groups pico (0.8 − 5µm),
nano (5 − 20µm), micro (20 − 180µm) and meso (180 − 2000µm).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 12/41
22. TARA Oceans datasets that we used
[Brum et al., 2015]
Datasets used
environmental dataset: 22 numeric features (temperature, salinity, . . . ).
bacteria phylogenomic tree: computed from ∼ 35,000 OTUs.
bacteria functional composition: ∼ 63,000 KEGG orthologous groups.
eukaryotic plankton composition splited into 4 groups pico (0.8 − 5µm),
nano (5 − 20µm), micro (20 − 180µm) and meso (180 − 2000µm).
virus composition: ∼ 867 virus clusters based on shared gene content.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 12/41
23. TARA Oceans datasets that we used
Common samples
48 samples,
2 depth layers: surface
(SRF) and deep chlorophyll
maximum (DCM),
31 different sampling
stations.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 13/41
24. Sommaire
1 Metagenomic datasets and associated questions
2 A typical (and rich) case study: TARA Oceans datasets
3 A UMKL framework for integrating multiple metagenomic data
4 Application to TARA Oceans datasets
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 14/41
25. Kernel methods
Kernel viewed as the dot product in an implicit Hilbert space
K : X × X → R st: K(xi, xj) = K(xj, xi) and ∀ m ∈ N, ∀x1, ..., xm ∈ X,
∀ α1, ..., αm ∈ R, m
i,j=1 αiαjK(xi, xj) ≥ 0.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 15/41
26. Kernel methods
Kernel viewed as the dot product in an implicit Hilbert space
K : X × X → R st: K(xi, xj) = K(xj, xi) and ∀ m ∈ N, ∀x1, ..., xm ∈ X,
∀ α1, ..., αm ∈ R, m
i,j=1 αiαjK(xi, xj) ≥ 0.
⇒ [Aronszajn, 1950]
∃!(H, ., . ), φ : X → H st: K(xi, xj) = φ(xi), φ(xj)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 15/41
27. Exploratory analysis with kernels
A well know example: kernel PCA [Schölkopf et al., 1998]
PCA analysis performed in the feature space induced by the kernel K.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 16/41
28. Exploratory analysis with kernels
A well know example: kernel PCA [Schölkopf et al., 1998]
PCA analysis performed in the feature space induced by the kernel K.
In practice:
K is centered: K ← K − 1
N KIN + 1
N2 IN
KIN;
K-PCA is performed by the eigen-decomposition of (centered) K
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 16/41
29. Exploratory analysis with kernels
A well know example: kernel PCA [Schölkopf et al., 1998]
PCA analysis performed in the feature space induced by the kernel K.
In practice:
K is centered: K ← K − 1
N KIN + 1
N2 IN
KIN;
K-PCA is performed by the eigen-decomposition of (centered) K
If (αk )k=1,...,N ∈ RN
and (λk )k=1,...,N are the eigenvectors and eigenvalues,
PC axes are:
ak =
N
i=1
αkiφ(xi)
and ak = (aki)i=1,...,n are orthonormal in the feature space induced by the
kernel:
∀ k, k , ak , ak = αk Kαk = δkk with δkk =
0 if k k
1 otherwise
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 16/41
30. Exploratory analysis with kernels
A well know example: kernel PCA [Schölkopf et al., 1998]
PCA analysis performed in the feature space induced by the kernel K.
In practice:
K is centered: K ← K − 1
N KIN + 1
N2 IN
KIN;
K-PCA is performed by the eigen-decomposition of (centered) K
Coordinate of the projection of the observations (φ(xi))i:
ak , φ(xi) =
n
j=1
αkjKji = Ki.αk = λk αki,
where Ki. is the i-th row of K.
No representation for the variables (no real variables...).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 16/41
31. Exploratory analysis with kernels
A well know example: kernel PCA [Schölkopf et al., 1998]
PCA analysis performed in the feature space induced by the kernel K.
In practice:
K is centered: K ← K − 1
N KIN + 1
N2 IN
KIN;
K-PCA is performed by the eigen-decomposition of (centered) K
Other unsupervised kernel methods: kernel SOM
[Olteanu and Villa-Vialaneix, 2015, Mariette et al., 2017]
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 16/41
32. Usefulness of K-PCA
Non linear PCA
Source: By Petter Strandmark - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=3936753
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 17/41
33. Usefulness of K-PCA
[Mariette et al., 2017] K-PCA for non numeric datasets - here a
quantitative time series: job trajectories after graduation from the French
survey “Generation 98” [Cottrell and Letrémy, 2005]
color is the mode of the trajectories
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 17/41
34. From multiple dissimilarities to multiple kernels
1 several (non Euclidean) dissimilarities D1
, . . . , DM
, transformed into
similarities with [Lee and Verleysen, 2007]:
Km
(xi, xj) = −
1
2
Dm
(xi, xj) −
2
N
N
k=1
Dm
(xi, xk ) +
1
N2
N
k, k =1
Dm
(xk , xk )
2 if non positive, clipping or flipping (removing the negative part of the
eigenvalues decomposition or taking its opposite) produce kernels
[Chen et al., 2009].
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 18/41
35. From multiple kernels to an integrated kernel
How to combine multiple kernels?
naive approach: K∗ = 1
M m Km
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 19/41
36. From multiple kernels to an integrated kernel
How to combine multiple kernels?
naive approach: K∗ = 1
M m Km
supervised framework: K∗ = m βmKm
with βm ≥ 0 and m βm = 1
with βm chosen so as to minimize the prediction error
[Gönen and Alpaydin, 2011]
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 19/41
37. From multiple kernels to an integrated kernel
How to combine multiple kernels?
naive approach: K∗ = 1
M m Km
supervised framework: K∗ = m βmKm
with βm ≥ 0 and m βm = 1
with βm chosen so as to minimize the prediction error
[Gönen and Alpaydin, 2011]
unsupervised framework but input space is Rd
[Zhuang et al., 2011]
K∗ = m βmKm
with βm ≥ 0 and m βm = 1 with βm chosen so as to
minimize the distortion between all training data ij K∗
(xi, xj) xi − xj
2
;
AND minimize the approximation of the original data by the kernel
embedding i xi − j K∗
(xi, xj)xj
2
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 19/41
38. From multiple kernels to an integrated kernel
How to combine multiple kernels?
naive approach: K∗ = 1
M m Km
supervised framework: K∗ = m βmKm
with βm ≥ 0 and m βm = 1
with βm chosen so as to minimize the prediction error
[Gönen and Alpaydin, 2011]
unsupervised framework but input space is Rd
[Zhuang et al., 2011]
K∗ = m βmKm
with βm ≥ 0 and m βm = 1 with βm chosen so as to
minimize the distortion between all training data ij K∗
(xi, xj) xi − xj
2
;
AND minimize the approximation of the original data by the kernel
embedding i xi − j K∗
(xi, xj)xj
2
.
Our proposal: 2 UMKL frameworks which do not require data to have
values in Rd
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 19/41
39. STATIS like framework
[L’Hermier des Plantes, 1976, Lavit et al., 1994]
Similarities between kernels:
Cmm =
Km
, Km
F
Km
F Km
F
=
Trace(Km
Km
)
Trace((Km)2)Trace((Km )2)
.
(Cmm is an extension of the RV-coefficient [Robert and Escoufier, 1976] to
the kernel framework)
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40. STATIS like framework
[L’Hermier des Plantes, 1976, Lavit et al., 1994]
Similarities between kernels:
Cmm =
Km
, Km
F
Km
F Km
F
=
Trace(Km
Km
)
Trace((Km)2)Trace((Km )2)
.
(Cmm is an extension of the RV-coefficient [Robert and Escoufier, 1976] to
the kernel framework)
maximize
M
m=1
K∗
(v),
Km
Km
F F
= v Cv
for K∗
(v) =
M
m=1
vmKm
and v ∈ RM
such that v 2 = 1.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 20/41
41. STATIS like framework
[L’Hermier des Plantes, 1976, Lavit et al., 1994]
Similarities between kernels:
Cmm =
Km
, Km
F
Km
F Km
F
=
Trace(Km
Km
)
Trace((Km)2)Trace((Km )2)
.
(Cmm is an extension of the RV-coefficient [Robert and Escoufier, 1976] to
the kernel framework)
maximize
M
m=1
K∗
(v),
Km
Km
F F
= v Cv
for K∗
(v) =
M
m=1
vmKm
and v ∈ RM
such that v 2 = 1.
Solution: first eigenvector of C ⇒ Set β = v
M
m=1 vm
(consensual kernel).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 20/41
42. A kernel preserving the original topology of the data I
From an idea similar to that of [Lin et al., 2010], find a kernel such that the
local geometry of the data in the feature space is similar to that of the
original data.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 21/41
43. A kernel preserving the original topology of the data I
From an idea similar to that of [Lin et al., 2010], find a kernel such that the
local geometry of the data in the feature space is similar to that of the
original data.
Proxy of the local geometry
Km
−→ Gm
k
k−nearest neighbors graph
−→ Am
k
adjacency matrix
⇒ W = m I{Am
k
>0} or W = m Am
k
Adjacency matrix image from: By S. Mohammad H. Oloomi, CC BY-SA 3.0,
https://commons.wikimedia.org/w/index.php?curid=35313532
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 21/41
44. A kernel preserving the original topology of the data I
From an idea similar to that of [Lin et al., 2010], find a kernel such that the
local geometry of the data in the feature space is similar to that of the
original data.
Proxy of the local geometry
Km
−→ Gm
k
k−nearest neighbors graph
−→ Am
k
adjacency matrix
⇒ W = m I{Am
k
>0} or W = m Am
k
Feature space geometry measured by
∆i(β) = φ∗
β(xi),
φ∗
β(x1)
...
φ∗
β(xN)
=
K∗
β (xi, x1)
...
K∗
β (xi, xN)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 21/41
45. A kernel preserving the original topology of the data II
Sparse version
minimize
N
i,j=1
Wij ∆i(β) − ∆j(β)
2
for K∗
β =
M
m=1
βmKm
and β ∈ RM
st βm ≥ 0 and
M
m=1
βm = 1.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 22/41
46. A kernel preserving the original topology of the data II
Sparse version
minimize
N
i,j=1
Wij ∆i(β) − ∆j(β)
2
for K∗
β =
M
m=1
βmKm
and β ∈ RM
st βm ≥ 0 and
M
m=1
βm = 1.
⇔ minimize
M
m,m =1
βmβm Smm
β ∈ RM
such that βm ≥ 0 and
M
m=1
βm = 1,
for Smm = N
i,j=1 Wij ∆m
i
− ∆m
j
2
and ∆m
i
=
Km
(xi, x1)
...
Km
(xi, xN)
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 22/41
47. A kernel preserving the original topology of the data II
Non sparse version
minimize
N
i,j=1
Wij ∆i(β) − ∆j(β)
2
for K∗
v =
M
m=1
vmKm
and v ∈ RM
st vm ≥ 0 and v 2 = 1.
⇔ minimize
M
m,m =1
vmvm Smm
v ∈ RM
such that vm ≥ 0 and v 2 = 1,
for Smm = N
i,j=1 Wij ∆m
i
− ∆m
j
2
and ∆m
i
=
Km
(xi, x1)
...
Km
(xi, xN)
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 22/41
48. Optimization issues
Sparse version writes minβ βT
Sβ st β ≥ 0 and β 1 = m βm = 1 ⇒
standard QP problem with linear constrains (ex: package quadprog
in R).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 23/41
49. Optimization issues
Sparse version writes minβ βT
Sβ st β ≥ 0 and β 1 = m βm = 1 ⇒
standard QP problem with linear constrains (ex: package quadprog
in R).
Non sparse version writes minβ βT
Sβ st β ≥ 0 and β 2 = 1 ⇒ QPQC
problem (hard to solve).
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 23/41
50. Optimization issues
Sparse version writes minβ βT
Sβ st β ≥ 0 and β 1 = m βm = 1 ⇒
standard QP problem with linear constrains (ex: package quadprog
in R).
Non sparse version writes minβ βT
Sβ st β ≥ 0 and β 2 = 1 ⇒ QPQC
problem (hard to solve).
Solved using Alternating Direction Method of Multipliers (ADMM
[Boyd et al., 2011]) by replacing the previous optimization problem
with
min
x,z
x Sx + 1{x≥0}(x) + 1{ z 2
2
≥1}(z)
with the constraint x − z = 0.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 23/41
51. Optimization issues
Sparse version writes minβ βT
Sβ st β ≥ 0 and β 1 = m βm = 1 ⇒
standard QP problem with linear constrains (ex: package quadprog
in R).
Non sparse version writes minβ βT
Sβ st β ≥ 0 and β 2 = 1 ⇒ QPQC
problem (hard to solve).
Solved using Alternating Direction Method of Multipliers (ADMM
[Boyd et al., 2011])
1 minx x Sx + y (x − z) + λ
2
x − z 2
under the constraint x ≥ 0
(standard QP problem)
2 project on the unit ball z = x
min{ x 2,1}
3 update auxiliary variable y = y + λ(x − z)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 23/41
52. A proposal to improve interpretability of K-PCA in our
framework
Issue: How to assess the importance of a given species in the K-PCA?
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 24/41
53. A proposal to improve interpretability of K-PCA in our
framework
Issue: How to assess the importance of a given species in the K-PCA?
our datasets are either numeric (environmental) or are built from a
n × p count matrix
⇒ for a given species, randomly permute counts and re-do the
analysis (kernel computation - with the same optimized weights - and
K-PCA)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 24/41
54. A proposal to improve interpretability of K-PCA in our
framework
Issue: How to assess the importance of a given species in the K-PCA?
our datasets are either numeric (environmental) or are built from a
n × p count matrix
⇒ for a given species, randomly permute counts and re-do the
analysis (kernel computation - with the same optimized weights - and
K-PCA)
the influence of a given species in a given dataset on a given PC
subspace is accessed by computing the Crone-Crosby distance
between these two PCA subspaces [Crone and Crosby, 1995] (∼
Frobenius norm between the projectors)
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 24/41
55. Sommaire
1 Metagenomic datasets and associated questions
2 A typical (and rich) case study: TARA Oceans datasets
3 A UMKL framework for integrating multiple metagenomic data
4 Application to TARA Oceans datasets
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 25/41
56. Integrating ’omics data using kernels
M TARA Oceans datasets
(xm
i
)i=1,...,n,m=1,...,M measured on the same
ocean samples (1, . . . , N) which take
values in an arbitrary space (Xm
)m:
environmental dataset,
bacteria phylogenomic tree,
bacteria functional composition,
eukaryote pico-plankton composition,
. . .
virus composition.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
57. Integrating ’omics data using kernels
Environmental dataset: standard euclidean
distance, given by K(xi, xj) = xT
i
xj.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
58. Integrating ’omics data using kernels
Bacteria phylogenomic tree: the weighted
Unifrac distance, given by
dwUF (xi, xj) =
e le|pei − pej|
e pei + pej
.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
59. Integrating ’omics data using kernels
All composition based datasets: bacteria
functional composition, eukaryote (pico,
nano, micro, meso)-plankton composition
and virus composition calculated using the
Bray-Curtis dissimilarity,
dBC(xi, xj) =
g |nig − njg|
g nig + njg
,
nig: gene g abundances summarized at the
KEGG orthologous groups level in sample
i.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
60. Integrating ’omics data using kernels
Combinaison of M kernels by a weighted
sum
K∗
=
M
m=1
βmKm
,
where βm ≥ 0 and M
m=1 βm = 1.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
61. Integrating ’omics data using kernels
Apply standard data mining methods
(clustering, linear model, PCA, . . . ) in the
feature space.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 26/41
63. Correlation between kernels (STATIS)
Low correlations between the bacteria functional composition and
other datasets.
Nathalie Villa-Vialaneix | Unsupervised multiple kernel learning 27/41
64. Correlation between kernels (STATIS)
Low correlations between the bacteria functional composition and
other datasets.
Strong correlation between environmental variables and small
organisms (bacteria, eukarote pico-plankton and virus).
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65. Influence of k (nb of neighbors) on (βm)m
k ≥ 5 provides stable results
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66. (βm)m values returned by graph-MKL
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67. (βm)m values returned by graph-MKL
The dataset the less correlated to the others: the bacteria functional
composition has the highest coefficient.
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68. (βm)m values returned by graph-MKL
The dataset the less correlated to the others: the bacteria functional
composition has the highest coefficient.
Three kernels have a weight equal to 0 (sparse version).
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69. Proof of concept: using [Sunagawa et al., 2015]
Datasets
139 samples, 3 layers (SRF, DCM and MES)
kernels: phychem, pro-OTUs and pro-OGs
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70. Proof of concept: using [Sunagawa et al., 2015]
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71. Proof of concept: using [Sunagawa et al., 2015]
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72. Proof of concept: using [Sunagawa et al., 2015]
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73. Proof of concept: using [Sunagawa et al., 2015]
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74. Proof of concept: using [Sunagawa et al., 2015]
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75. Proof of concept: using [Sunagawa et al., 2015]
Proteobacteria (clade SAR11 (Alphaproteobacteria) and SAR86)
dominate the sampled areas of the ocean in term of relative
abundance and taxonomic richness.
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79. Conclusion et perspectives
Summary
an integrative exploratory method
... particularly well suited for multi metagenomic datasets
with enhanced interpretability
Perspectives
implement ADMM solution and test it
improve biological interpretation
soon-to-be-released R package
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