26. But we don’t have to measure gene
expression in order to say that these cells
are different…
Neuron White blood cell
Red blood cell
Bone cell
Egg cell
Cancer cell
47. Mitotic Cells
Breast cancer diagnostics
Mitotic cell count is
one of the key
diagnostic markers of
the diseaseHistology images
Breast cancer is the second
most common cancer in the
world with an estimated 1.67
million new cancer cases
annually
93. Training set
Empty
Empty
Empty
NucleiN
E
Compare predictions
with true labels
Validation set
Train the network using extracted patches from training set.
Predictions generated by the network should be consistent
with true labels
After network has been trained, evaluate
its performance on unseen validation set
patches
Validation set
104. Convolutional Neural Network
Convolutional layer works as a
filter applied to the original image
There are many filters in the
convolutional layer, they detect
different patterns
4 filters
105. Convolutional Neural Network
4 filters
Each filter applied to all possible
2x2 patches of the original image
produces one output value
106. Convolutional Neural Network
4 filters
Each filter applied to all possible
2x2 patches of the original image
produces one output value
107. Convolutional Neural Network
4 filters
Each filter applied to all possible
2x2 patches of the original image
produces one output value
108. Convolutional Neural Network
4 filters
Each filter applied to all possible
2x2 patches of the original image
produces one output value
109. Convolutional Neural Network
Each filter applied to all possible
2x2 patches of the original image
produces one output value
Repeat this process for all filters in
this layer
110. Convolutional Neural Network
Each filter applied to all possible
2x2 patches of the original image
produces one output value
Repeat this process for all filters in
this layer and the next
111. Flattening
The output of the last
convolutional layer is flattened into
a single vector (like we did with
images)
Convolutional Neural Network
112. Flattening
The output of the last
convolutional layer is flattened into
a single vector (like we did with
images)
Convolutional Neural Network
0
1
2
7
8
9
This vector is fed into fully
connected layer with as many
neutrons as possible classes
113. Flattening
The output of the last
convolutional layer is flattened into
a single vector (like we did with
images)
Convolutional Neural Network
0
1
2
8
9
This vector is fed into fully
connected layer with as many
neutrons as possible classes
Each neuron
outputs
probabilities
7
148. Something important that we learnt today
Difference in gene expression profile
causes cells to be different
149. Something important that we learnt today
Difference in gene expression profile
causes cells to be different
t = 0
t = 1
t = 2
Effective cell detection can help
develop better and cheaper drugs
150. Something important that we learnt today
t = 0
t = 1
t = 2
Thresholding
Difference in gene expression profile
causes cells to be different
Classical image analysis pipeline
includes manual parameter tuning
Effective cell detection can help
develop better and cheaper drugs
151. Something important that we learnt today
t = 0
t = 1
t = 2
Thresholding
There are ways in which Deep
Learning can make a difference
Difference in gene expression profile
causes cells to be different
Classical image analysis pipeline
includes manual parameter tuning
Effective cell detection can help
develop better and cheaper drugs
152. Something important that we learnt today
t = 0
t = 1
t = 2
Thresholding
Classical image analysis pipeline
includes manual parameter tuning
There are ways in which Deep
Learning can make a difference
Dude is hard to beat (human is still
superior when it comes to cell detection)
Difference in gene expression profile
causes cells to be different
Effective cell detection can help
develop better and cheaper drugs
153. Something important that we learnt today
t = 0
t = 1
t = 2
Thresholding
There are ways in which Deep
Learning can make a difference
Dude is hard to beat (human is still
superior when it comes to cell detection)
and last but not least…
Difference in gene expression profile
causes cells to be different
Classical image analysis pipeline
includes manual parameter tuning
Effective cell detection can help
develop better and cheaper drugs