Image classification in Galaxy with fruit 360 dataset

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# Image classification in Galaxy with fruit 360 dataset

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  <a href="/training-material/hall-of-fame/kxk302/" class="contributor-badge contributor-kxk302"><img src="https://avatars.githubusercontent.com/kxk302?s=36" alt="Kaivan Kamali avatar" width="36" class="avatar" />
    Kaivan Kamali</a>
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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

- [Statistics and machine learning](/training-material/topics/statistics)
    - Deep Learning (Part 3) - Convolutional neural networks (CNN): [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/statistics/tutorials/CNN/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/statistics/tutorials/CNN/tutorial.html)

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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- How to solve an image classification problem using convolutional neural network (CNN)?

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn how to create a CNN using Galaxy's deep learning tools

- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

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# What is a convolutional neural network (CNN)?

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What is a convolutional neural network (CNN)?

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# Convolutional Neural Network (CNN)

- Increasing popularity of social media in past decade
	- Image and video processing tasks have become very important
- FNN could not scale up to image and video processing tasks
- CNN specifically tailored for image and video processing tasks

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# Inspiration for CNN

- In 1959 Hubel & Wiesel did an experiment to understand how visual cortex of brain processes visual info
	- Recorded activity of neurons in visual cortex of a cat
	- While moving a bright line in front of the cat
- Some cells fired when bright line is shown at a particular angle/location
	- Called these *simple* cells
- Other cells fired when bright line was shown regardless of angle/location
	- Seemed to detect movement
	- Called these *complex* cells
- Seemed complex cells receive inputs from multiple simple cells
	- Have an hierarchical structure
- Hubel and Wiesel won Noble prize in 1981

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# Inspiration for CNN

- Inspired by complex/simple cells, Fukushima proposed *Neocognitron* (1980)
	- Hierarchical neural network used for handwritten Japanese character recognition
	- First CNN, had its own training algorithm
- In 1989, LeCun proposed CNN that was trained by backpropagation
- CNN got popular when outperformed other models at ImageNet Challenge
	- Competition in object classification/detection
	- On hundreds of object categories and millions of images
	- Run annually from 2010 to present
- Notable CNN architectures that won ImageNet challenge
	- AlexNet (2012), ZFNet (2013), GoogLeNet & VGG (2014), ResNet (2015)

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# Architecture of CNN

- A typical CNN has 4 layers
	- Input layer
	- Convolution layer
	- Pooling layer
	- Fully connected layer

- We will explain a 2D CNN here
	- Same concepts apply to a 1 (or 3) dimensional CNN

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# Input layer

- Example input a 28 pixel by 28 pixel grayscale image
- Unlike FNN, we do not “flatten” the input to a 1D vector
	- input is presented to network in 2D as 28 x 28 matrix
	- This makes capturing spatial relationships easier

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# Convolution layer

- Composed of multiple filters (kernels)
- Filters for 2D image are also 2D
- Suppose we have a 3 by 3 filter (9 values in total)
	- Values are randomly set to 0 or 1
- Convolution: placing 3 by 3 filter on the top left corner of image
	- Multiply filter values by pixel values, add the results
	- Move filter to right one pixel at a time, and repeat this process
	- When at top right corner, move filter down one pixel and repeat process
	- Process ends when we get to bottom right corner of image

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# 3 by 3 Filter

![A 3 by 3 filter applied to a 4 by 4 image, resulting in a 2 by 2 image](/training-material/topics/statistics/images/Conv_no_padding_no_strides.gif)

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# Convolution operator parameters

- Filter size
- Padding
- Stride
- Dilation
- Activation function

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# Filter size

- Filter size can be 5 by 5, 3 by 3, and so on
- Larger filter sizes should be avoided
	- As learning algorithm needs to learn filter values (weights)
- Odd sized filters are preferred to even sized filters
	- Nice geometric property of all input pixels being around output pixel

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# Padding

- After applying 3 by 3 filter to 4 by 4 image, we get a 2 by 2 image
	– Size of the image has gone down
- If we want to keep image size the same, we can use padding
	- We pad input in every direction with 0’s before applying filter
	- If padding is 1 by 1, then we add 1 zero in every direction
	- If padding is 2 by 2, then we add 2 zeros in every direction, and so on

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# 3 by 3 filter with padding of 1

![A 3 by 3 filter applied to a 5 by 5 image, with padding of 1, resulting in a 5 by 5 image](/training-material/topics/statistics/images/Conv_same_padding_no_strides.gif)

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# Stride

- How many pixels we move filter to the right/down is stride
- Stride 1: move filter one pixel to the right/down
- Stride 2: move filter two pixels to the right/down

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# 3 by 3 filter with stride of 2

![A 3 by 3 filter applied to a 5 by 5 image, with stride of 2, resulting in a 2 by 2 image](/training-material/topics/statistics/images/Conv_no_padding_strides.gif)

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# Dilation

- When we apply 3 by 3 filter, output affected by pixels in 3 by 3 subset of image
- Dilation: To have a larger receptive field (portion of image affecting filter’s output)
- If dilation set to 2, instead of contiguous 3 by 3 subset of image, every other pixel of a 5 by 5 subset of image affects output

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# 3 by 3 filter with dilation of 2

![A 3 by 3 filter applied to a 7 by 7 image, with dilation of 2, resulting in a 3 by 3 image](/training-material/topics/statistics/images/Conv_dilation.gif)

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# Activation function

- After filter applied to whole image, apply activation function to output to introduce non-linearity
- Preferred activation function in CNN is ReLU
- ReLU leaves outputs with positive values as is, replaces negative values with 0

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# Relu activation function

![Two matrices representing filter output before and after ReLU activation function is applied](/training-material/topics/statistics/images/Conv_ReLU.png)

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# Single channel 2D convolution

![One matrix representing an input vector and another matrix representing a filter, along with calculation for single input channel two dimensional convolution operation](/training-material/topics/statistics/images/Conv_single_input_channel.png)

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# Triple channel 2D convolution

![Three matrices representing an input vector and another three matrices representing a filter, along with calculation for multiple input channel two dimensional convolution operation](/training-material/topics/statistics/images/Conv_multiple_input_channel.png)

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# Triple channel 2D convolution in 3D

![Multiple cubes representing input vector, filter, and output in a 3 channel 2 dimensional convolution operation](/training-material/topics/statistics/images/Conv_multiple_channel_3d.gif)

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# Change channel size

- Output of a multi-channel 2D filter is a single channel 2D image
- Applying *multiple* filters results in a multi-channel 2D image
- E.g., if input image is 28 x 28 x 3 (rows x columns x channels)
	- We apply a 3 x 3 filter with 1 x 1 padding, we get a 28 x 28 x 1 image
	- If we apply 15 such filters, we get a 28 x 28 x 15
- Number of filters allows us to increase or decrease channel size

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# Pooling layer

- Pooling layer performs down sampling to reduce spatial dimensionality of input
- This decreases number of parameters
	- Reduces learning time/computation
	- Reduces likelihood of overfitting
- Most popular type is *max* pooling
	- Usually a 2 x 2 filter with a stride of 2 
	- Returns maximum value as it slides over input data

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# Fully connected layer

- Last layer in a CNN
- Connect all nodes from previous layer to this fully connected layer
	- Which is responsible for classification of the image

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# An example CNN

![A convolutional neural network with 3 convolution layers followed by 3 pooling layers](/training-material/topics/statistics/images/Conv_CNN.png)

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# An example CNN

- A typical CNN has several convolution plus pooling layers
	- Each responsible for feature extraction at different levels of abstraction
	- E.g., filters in first layer detect horizental, vertical, and diagonal edges
	- Filters in the next layer detect shapes
	- Filters in the last layer detect collection of shapes
- Filter values randomly initialized, learned by learning algorithm
- CNN not only do classification, but can also automatically do feature extraction
	- Distinguishes CNN from other classification techniques (like Support Vector Machines)

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# Fruit 360 dataset

- A dataset with 90,380 images of 131 fruits and vegetables
	- Images are 100 by 100 pixel and are color (RGB) images (3 values per pixel)
	- 67,692 images in training dataset and 22,688 images in test dataset
	- https://www.kaggle.com/moltean/fruits
- This tutorial's dataset is a subset of fruit 360 dataset
	- Containing only 10 fruits/vegetables 
	- Selected a subset of images, so dataset size is smaller and CNN trains faster 
	- 5,015 images in training dataset, and 1,679 images in test dataset
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# Utilities for creating a subset of fruit 360 dataset

- The utilities and instructions at https://github.com/kxk302/fruit_dataset_utilities
- First, creat feature vectors for each image 
	- Images are 100 by 100 pixel color (RGB) images
	- Each image represented by 30,000 values (100 X 100 X 3)
- Second, we selected a subset of 10 fruit/vegetable images
	- Training and test dataset sizes went from 7 GB and 2.5 GB to 500 MB and 177 MB
- Third, we created separate files for feature vectors and labels 
- Finally, mapped labels for 10 selected fruits/vegetables to a 0 to 9 range 
	- Full dataset labels are in the 0 to 130 range
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# Classification of fruit/vegetable images with CNN

- We define a CNN and train it using fruit 360 dataset training data
- Goal is to learn a model such that given image of a fruit/vegetable we predict its label (0 to 9)
- We then evaluate the trained CNN on test dataset and plot the confusion matrix
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# For references, please see tutorial's References section

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- Galaxy Training Materials ([training.galaxyproject.org](https://training.galaxyproject.org))

![Screenshot of the gtn stats page with 21 topics, 170 tutorials, 159 contributors, 16 scientific topics, and a growing community](/training-material/topics/introduction/images/gtn_stats.png)

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- If you would like to learn more about Galaxy, there are a large number of tutorials available.
- These tutorials cover a wide range of scientific domains.

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# Getting Help

- **Help Forum** ([help.galaxyproject.org](https://help.galaxyproject.org))

![Galaxy Help](/training-material/topics/introduction/images/galaxy_help.png)

- **Gitter Chat**
    - [Main Chat](https://gitter.im/galaxyproject/Lobby)
    - [Galaxy Training Chat](https://gitter.im/Galaxy-Training-Network/Lobby)
    - Many more channels (scientific domains, developers, admins)

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- If you get stuck, there are ways to get help.
- You can ask your questions on the help forum.
- Or you can chat with the community on Gitter.

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# Join an event

- Many Galaxy events across the globe
- Event Horizon: [galaxyproject.org/events](https://galaxyproject.org/events)

![Event schedule](/training-material/topics/introduction/images/event_horizon.png)

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- There are frequent Galaxy events all around the world.
- You can find upcoming events on the Galaxy Event Horizon.

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			
  <a href="/training-material/hall-of-fame/kxk302/" class="contributor-badge contributor-kxk302"><img src="https://avatars.githubusercontent.com/kxk302?s=36" alt="Kaivan Kamali avatar" width="36" class="avatar" />
    Kaivan Kamali</a>
  
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  <a href="/training-material/hall-of-fame/anuprulez/" class="contributor-badge contributor-anuprulez">
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    <img src="https://avatars.githubusercontent.com/kxk302?s=36" alt="Kaivan Kamali avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena">
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