# tSNE and clustering

tSNE can give really nice results when we want to visualize many groups of multi-dimensional points. Once the 2D graph is done we might want to identify which points cluster in the tSNE blobs.

Using simulated and real data, I’ll try different methods:

• Hierarchical clustering
• K-means
• Gaussian mixture
• Density-based clustering
• Louvain community detection.

TL;DR If <30K points, hierarchical clustering is robust, easy to use and with reasonable computing time. KNN + Louvain is fast and works well in general.

library(ggplot2)
library(dplyr)
library(magrittr)
library(ggrepel)

## Data

### Normally distributed points

First, I’ll simulate an easy situation with 10 different groups. 5,000 points are distributed following Gaussian distributions in 100 dimensions. Points are randomly assigned a group. For each group, 3 dimensions are randomly selected and the points shifted.

Because there are 10 groups that differ in different dimensions, a PCA shouldn’t be able to separate all the groups with the first two components. That’s when the tSNE comes in to do its magic (easily).

set.seed(123456)
N = 5000
D = 100
data.norm = matrix(rnorm(N * D, 2), N)
groups.probs = runif(10)
groups = sample(1:10, N, TRUE, groups.probs/sum(groups.probs))
for (gp in unique(groups)) {
dev = rep(1, D)
dev[sample.int(D, 3)] = runif(3, -10, 10)
data.norm[which(groups == gp), ] = data.norm[which(groups ==
gp), ] %*% diag(dev)
}
info.norm = tibble(truth = factor(groups))

The PCA and tSNE look like this:

pca.norm = prcomp(data.norm)
info.norm %<>% cbind(pca.norm$x[, 1:4]) ggplot(info.norm, aes(x = PC1, y = PC2, colour = truth)) + geom_point(alpha = 0.3) + theme_bw() ggplot(info.norm, aes(x = PC3, y = PC4, colour = truth)) + geom_point(alpha = 0.3) + theme_bw() We see something but it’s not so clear, let’s run the tSNE. library(Rtsne) tsne.norm = Rtsne(pca.norm$x, pca = FALSE)
info.norm %<>% mutate(tsne1 = tsne.norm$Y[, 1], tsne2 = tsne.norm$Y[,
2])
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = truth)) +
geom_point(alpha = 0.3) + theme_bw() Time for this code chunk: 83.76 s

### Real data

As a real-life example, I use the data that motivated this exploration. It contains a bit more than 26K points and the tSNE looks like that:

tsne.real = read.csv("https://docs.google.com/uc?id=1KArwfOd5smzuCsrpgW9Xpf9I06VOW4ga&export=download")
info.real = tsne.real
ggplot(tsne.real, aes(x = tsne1, y = tsne2)) + geom_point(alpha = 0.1) +
theme_bw() ## Hierarchical clustering

• + Once built, it’s fast to try different number clusters.
• + Different linkage criteria to match the behavior we want.
• - Doesn’t scale well. High memory usage and computation time when >30K.
hc.norm = hclust(dist(tsne.norm$Y)) info.norm$hclust = factor(cutree(hc.norm, 9))
hc.norm.cent = info.norm %>% group_by(hclust) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = hclust)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = hclust),
data = hc.norm.cent) + guides(colour = FALSE) +
ggtitle("Linkage criterion: Complete") hc.norm = hclust(dist(tsne.norm$Y), method = "ward.D") info.norm$hclust = factor(cutree(hc.norm, 9))
hc.norm.cent = info.norm %>% group_by(hclust) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = hclust)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = hclust),
data = hc.norm.cent) + guides(colour = FALSE) +
ggtitle("Linkage criterion: Ward") Now on real data:

hc.real = hclust(dist(tsne.real))
info.real$hclust = factor(cutree(hc.real, 18)) hc.real.cent = info.real %>% group_by(hclust) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.real, aes(x = tsne1, y = tsne2, colour = hclust)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = hclust), data = hc.real.cent) + guides(colour = FALSE) + ggtitle("Linkage criterion: Complete") hc.real = hclust(dist(tsne.real), method = "ward.D") info.real$hclust = factor(cutree(hc.real, 18))
hc.real.cent = info.real %>% group_by(hclust) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.real, aes(x = tsne1, y = tsne2, colour = hclust)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = hclust),
data = hc.real.cent) + guides(colour = FALSE) +
ggtitle("Linkage criterion: Ward") Time for this code chunk: 38.01 s

For both data, Ward gives the best clusters. For example it splits the top-left clusters better in the real data.

## Kmeans

• + Very fast.
• - Simple.
km.norm = kmeans(tsne.norm$Y, 9, nstart = 100) info.norm$kmeans = factor(km.norm$cluster) km.cent = info.norm %>% group_by(kmeans) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = kmeans)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = kmeans), data = km.cent) + guides(colour = FALSE) + ggtitle("9 clusters") km.norm = kmeans(tsne.norm$Y, 10, nstart = 100)
info.norm$kmeans = factor(km.norm$cluster)
km.cent = info.norm %>% group_by(kmeans) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = kmeans)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = kmeans),
data = km.cent) + guides(colour = FALSE) + ggtitle("10 clusters") Because it’s not working well for cluster that are not “round”, we need to ask for more clusters. In practice we’ll need to merge back together the clusters that were fragmented.

set.seed(123456)
km.real = kmeans(tsne.real, 24, nstart = 200, iter.max = 100)
info.real$kmeans = factor(km.real$cluster)
km.cent = info.real %>% group_by(kmeans) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.real, aes(x = tsne1, y = tsne2, colour = kmeans)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = kmeans),
data = km.cent) + guides(colour = FALSE) Not perfect in the middle-left big cluster: cluster 11 is grabbing points from the bottom blob. Maybe increasing the number of clusters could fix this?

set.seed(123456)
km.real = kmeans(tsne.real, 25, nstart = 200, iter.max = 100)
info.real$kmeans = factor(km.real$cluster)
km.cent = info.real %>% group_by(kmeans) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.real, aes(x = tsne1, y = tsne2, colour = kmeans)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = kmeans),
data = km.cent) + guides(colour = FALSE) Time for this code chunk: 15.48 s

Better. Same as with the other methods: we need to manually tweak the parameters to obtain the clustering we want…

Note: using several starting points help getting more robust results (nstart=). Increasing the number of iterations helps too (iter.max=).

## Mclust

• + Better clusters.
• + Can find the best K (number of clusters (although slowly).
• - Slow.
• - Need to be recomputed for each choice of K (number of clusters).
library(mclust)
mc.norm = Mclust(tsne.norm$Y, 9) info.norm$mclust = factor(mc.norm$classification) mc.cent = info.norm %>% group_by(mclust) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = mclust)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = mclust), data = mc.cent) + guides(colour = FALSE) Even the elongated cluster is nicely identified and we don’t need to split it. set.seed(123456) mc.real = Mclust(tsne.real, 20, initialization = list(subset = sample.int(nrow(tsne.real), 1000))) info.real$mclust = factor(mc.real$classification) mc.cent = info.real %>% group_by(mclust) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.real, aes(x = tsne1, y = tsne2, colour = mclust)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = mclust), data = mc.cent) + guides(colour = FALSE) Sometimes the results are a bit surprising. For example, points are assigned to cluster far away or there is another cluster in between (e.g. clusters 6 and 17). As usual changing the number of clusters helps. set.seed(123456) mc.real = Mclust(tsne.real, 24, initialization = list(subset = sample.int(nrow(tsne.real), 1000))) info.real$mclust = factor(mc.real$classification) mc.cent = info.real %>% group_by(mclust) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.real, aes(x = tsne1, y = tsne2, colour = mclust)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = mclust), data = mc.cent) + guides(colour = FALSE) Time for this code chunk: 90.61 s Note: I had to use the sub-sampling trick to speed up the process, otherwise it was taking too long. Using initialization=list(subset=sample.int(nrow(tsne.real), 1000)), only a thousand points are used for the EM (but all the points are assigned to a cluster at the end). ## Density-based clustering • + Can find clusters with different “shapes”. • - Bad on real/noisy data. • - Slow when many points. library(fpc) ds.norm = dbscan(tsne.norm$Y, 2)
info.norm$density = factor(ds.norm$cluster)
ds.cent = info.norm %>% group_by(density) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = density)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = density),
data = ds.cent) + guides(colour = FALSE) Woah, it found the small cluster !

ds.real = dbscan(tsne.real, 1)
info.real$density = factor(ds.real$cluster)
ds.cent = info.real %>% group_by(density) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.real, aes(x = tsne1, y = tsne2, colour = density)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = density),
data = ds.cent) + guides(colour = FALSE) Time for this code chunk: 100.98 s

Ouch…

## KNN graph and Louvain community detection

library(igraph)
library(FNN)
k = 100
knn.norm = get.knn(as.matrix(tsne.norm$Y), k = k) knn.norm = data.frame(from = rep(1:nrow(knn.norm$nn.index),
k), to = as.vector(knn.norm$nn.index), weight = 1/(1 + as.vector(knn.norm$nn.dist)))
nw.norm = graph_from_data_frame(knn.norm, directed = FALSE)
nw.norm = simplify(nw.norm)
lc.norm = cluster_louvain(nw.norm)
info.norm$louvain = as.factor(membership(lc.norm)) lc.cent = info.norm %>% group_by(louvain) %>% select(tsne1, tsne2) %>% summarize_all(mean) ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = louvain)) + geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = louvain), data = lc.cent) + guides(colour = FALSE) Playing with the resolution parameter we can get more/less communities. For gamma=.3: lc.norm = cluster_louvain(nw.norm, gamma = 0.3) info.norm$louvain = as.factor(membership(lc.norm))
lc.cent = info.norm %>% group_by(louvain) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.norm, aes(x = tsne1, y = tsne2, colour = louvain)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = louvain),
data = lc.cent) + guides(colour = FALSE) On real data and using gamma=.1:

k = 100
knn.real = get.knn(as.matrix(tsne.real), k = k)
knn.real = data.frame(from = rep(1:nrow(knn.real$nn.index), k), to = as.vector(knn.real$nn.index), weight = 1/(1 +
as.vector(knn.real$nn.dist))) nw.real = graph_from_data_frame(knn.real, directed = FALSE) nw.real = simplify(nw.real) lc.real = cluster_louvain(nw.real, gamma = 0.1) info.real$louvain = as.factor(membership(lc.real))
lc.cent = info.real %>% group_by(louvain) %>% select(tsne1,
tsne2) %>% summarize_all(mean)
ggplot(info.real, aes(x = tsne1, y = tsne2, colour = louvain)) +
geom_point(alpha = 0.3) + theme_bw() + geom_label_repel(aes(label = louvain),
data = lc.cent) + guides(colour = FALSE) Time for this code chunk: 18.86 s

Pretty good.

PS: I added the resolution parameter gamma in the igraph function for the Louvain clustering. While it was easy to change in the C code, compiling igraph from source was a pain. I couldn’t get it to work on OSX but I managed to install this modified version of igraph on Linux (see instructions).

## Conclusions

If not too many points or too many groups, hierarchical clustering might be enough. Especially with the Ward criterion, it worked well for both simulated and real data. Once the hierarchy is built, it’s fast to try different values for the number of clusters. Also, in the real data, I could get satisfactory results using a lower number of clusters than for the K-means (18 vs 25).

If there are too many points (e.g. >30K), hierarchical clustering might be too demanding and I would fall back to KNN+Louvain. It’s fast enough and the results are pretty good.

The more advanced methods are good to keep in mind if the points ever form diverse or unusual shapes.

I learned two tricks to improve the performance of the methods: increasing the number of iterations and starting points for the K-means, and sub-sampling for the EM clustering.

Clustering points from the tSNE is good to explore the groups that we visually see in the tSNE but if we want more meaningful clusters we could run these methods in the PC space directly. The KNN + Louvain community clustering, for example, is used in single cell sequencing analysis.