Introduction

Deep learning and neural networks

Deep learning, a branch of artificial intelligence, provides a collection of learning methods to model data with complex architectures to perform different non-linear transformations of data. Using these transformations, patterns are recognised in large volumes of data and new data can be categorised using these patterns extracted on existing data. These patterns are learned by computational models devised using different architectures of neural networks. In the recent years, the neural network architectures such as convolutional, long short-term memory networks, deep belief networks have become increasingly popular as machine learning tools in the fields of computer vision, image analysis, bioinformatics, speech recognition, natural language processing and so on achieving state-of-the-art performance, sometimes exceeding human performance. The availability of greater computational resources, more data, new algorithms for training deep models and easy to use libraries for implementation and training of neural networks are the drivers of this development. Deep learning works by approximating the mathematical function which maps data to its output and it has been shown that it can approximate any function making it widely popular across multiple fields to analyse data. A neural network is a web of artificial neurons which are also called processing units. The idea of a neural network is inspired by biological neural networks where neuronal circuits are used to process information and learn. An artificial neural network is structured into multiple layers where each layer contains several neurons. The neurons from adjacent layers are interconnected (feed-forward neural network) allowing the exchange of information between layers of neurons.

An artificial neuron is shown in Figure 1. The neuron, shown in orange, takes input x (only x1 and x2 are shown for simplicity) and computes output y. The entities w1, w2 are the weights of the connections (between inputs and neuron). The weights and inputs are combined following the basic principles of mathematics to produce output y (shown in Figures 2, 3 and 4).

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Weights denote the significance of a particular input to produce the observed output. When it is large, the input is significant and when small, the input is less significant to produce the output. These weights can be initialised randomly and they are modified throughout the learning by a neural network. Using the updated inputs (as shown in the above equations), the output is computed:

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where f is an activation function. An activation function is a mathematical function which translates the combination of inputs to an output. The choices of these functions are many - sigmoid, linear, tanh, ReLU and so on. For example, sigmoid is:

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The above equation will return a real number between 0 and 1.

Rectified exponential linear unit (ReLU) is given by:

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As discussed earlier, neurons make the building blocks of a neural network and are arranged in several layers and a usual neural network looks like as shown in Figure 7.

Input layer

In the neural network (Figure 7), the input layer is shown in green. This layer receives input data and passes it on to the next layer. The number of neurons in this layer depends on the number of dimensions of input data. For example, if input data (matrix) is of size (500, 10), 500 rows (samples) and 10 columns (features), then the number of neurons in the input layer should be 10. Each neuron in input layer is connected to all neurons in the next layer. All these connections have a separate weight (denoted by w).

Hidden layer

The next two layers after the input layer are called hidden layers. In the first hidden layer too, all the neurons are connected to all other neurons in the adjacent (hidden) layer. The number of hidden layers determines if the resulting neural network is deep (2 or more hidden layers) or shallow. When the number of hidden layers is 2 or more, the structure or architecture of the neural network is deep and overall learning is called deep learning. More the number of hidden layers, the more complex the architecture is. A complex architecture is beneficial for learning unique patterns from big data. But, complex architecture is prone to overfitting when a neural network starts memorising data without learning unique and general patterns.

The number of hidden layers and the size of each hidden layer is not fixed as it completely depends on the data. If the dataset is small (say only 1,000 samples), then it is sufficient to choose a less complex architecture (fewer hidden layers) to avoid the danger of overfitting. However, if the dataset is large (say > 100,000 samples), more complex architecture can be chosen. In short, the architecture of the hidden layer is completely dependent on the nature and size of data.

Output layer

This layer collects output computed using input data and weights which are optimised during learning. An activation function is chosen to transform the combination of input and weight to an output. Some examples of activation functions have been discussed above.

Optimisation

Compted or predicted output, collected at the output layer, and the actual output are compared to find error (or loss). Neural network learning aims is to minimise this error so that the predicted output gets as close to the actual output as possible. This process of minimising error between predicted and actual output is called optimisation. There are several optimisers such as gradient descent, root mean square propagation (RMSProp), adadelta and so on are available. These optimisers work by primarily adjusting the weights of connections so that the error is minimised. Once, a set of weights are achieved which provides the best accuracy or minimum error, the learning is terminated because the weights cannot be updated anymore which can further minimise the error.

Neural network training

Training is a process where input data is passed to a neural network at input layer and when finished, a trained model is created containing all the learned parameters such as weights of all connections in the neural network. Usually, a portion of data is extracted and saved as test data which is not used for training. It is used only for evaluating the trained model to get an unbiased estimate of learning and prediction strength. The partitioning of data into training and test can be set by deep learning practitioners. An example of partition can be - 70% training and 30% test data.

Batch and Epoch

While training a neural network, input data is passed in small batches. A batch is a subset of training data. An epoch is one iteration when all the training data is used for training in multiple batches. For example, if there is training data of size (500, 10) and batch size is fixed at 50, then there would be 10 batches (50 * 10 = 500) in each epoch. Each batch will have 50 samples and they are passed to the input layer of neural network. The loss computed at the output layer is propagated back and the weights are adjusted. The newly adjusted weights are used for the second batch of samples and so on. When all batches are finished, then one epoch of learning is done. The number of epochs and the size of a batch are parameters to be set by deep learning practitioners. These parameters depend on the size of data and should be tuned according to the data for optimum results.

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Loss function

The error between the computed and actual output is calculated using a loss function which is necessary to evaluate the strength of learning. Learning is good when loss decreases with training epochs otherwise, training should be stopped and the architecture should be carefully adjusted. There are several choices of loss functions too. Functions such as root mean squared error (RMSE) and absolute error (AE) are used for regression problems while cross-entropy error functions such as binary cross-entropy and categorical cross-entropy are used in classification problems. An example of loss function is shown in Figure 8.

Question

1. What do you understand by an architecture of a neural network?
2. How does a neural network learn?

Solution

1. Architecture of a neural network consists of multiple layers such as input, hidden, convolutional, output and their number of respective neurons, optimiser, loss and activation functions etc.
2. The learning happens by minimising the loss between the computed and actual output. The weights of all neuronal connections are adjusted (increased or decreased) to achieve the minimum loss. To ascertain the amount of change for weights, a technique known as backpropagation is used. Using this technique, the loss computed at the output layer is “propagated” back in the neural network (from output to input layer) and each neuronal connection is assigned a share of the total loss. In other words, how much each neuron is contributing to the total accumulated loss. For example, w1 is adjusted according to equation:

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In the above equation, L is the total loss, w1 is the weight of a connection between an input neuron and a hidden neuron. Similarly, all weights are adjusted and in the subsequent iteration, the updated weights are used to compute loss at the output layer. Parameter n is the learning rate which determines how small or big changes are needed in weights. It can either be a fixed quantity or a variable one. In case of a variable learning rate, it usually starts with a large number (say 1.0) and subsequently decays to a small number (say 0.001) as the training epochs proceed because initially a large learning rate helps to reach close to the minimum error quickly and then it is decayed to slow down the learning so that it stabilises at the minimum. More on backpropagation can be read here.

Relevance of deep learning in Bioinformatics

Deep learning is an established tool in finding patterns in big data for multiple fields of research such as computer vision, image analysis, drug response prediction, protein structure prediction and so on. Different research areas use different architectures of neural network which are suitable to their respective data. For example - in computer vision and image analysis, convolutional neural network (CNN) is popular, graph convolutional neural network is often used for drug response prediction, recurrent neural network is useful for identifying motifs in protein sequences and so on. The table below shows more examples of neural networks which are popular with different fields of bioinformatics. These use-cases of deep learning in bioinformatics prove that it is essential to explore deep learning algorithms to find patterns in big data in biology. More details can be found in Deep learning in bioinformatics: Introduction, application, and perspective in the big data era.

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Get training and test datasets

The datasets used for this tutorial contain gene expression profiles of humans suffering from two types of cancer - acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). The tutorial aims to differentiate between these two cancer types, predicting a cancer type for each patient, by learning unique patterns in gene expression profiles of patients. The data is divided into 2 parts - one for training and another for prediction. Each part contains two datasets - one has the gene expression profiles and another has labels (the types of cancer). The size of the training data (X_train) is (38, 7129) where 38 is the number of patients and 7129 is the number of genes. The label dataset (y_train) is of size (38, 1) and contains the information of the type of cancer for each patient (label encoding is 0 for ALL and 1 for AML). The test dataset (X_test) is of size (34, 7129) and contains the same genes for 34 different patients. The label dataset for test is y_test and is of size (34, 1). The neural network, which will be formulated in the remaining part of the tutorial, learns on the training data and its labels to create a trained model. The prediction ability of this model is evaluated on the test data (which is unseen during training to get an unbiased estimate of prediction ability). These datasets are uploaded to Galaxy by following the steps defined below:

Hands-on: Data upload

1. Create a new history for this tutorial

   Tip: Creating a new history

   To create a new history simply click the new-history icon at the top of the history panel:

   

2. Import the files from Zenodo

   https://zenodo.org/record/3706539/files/X_test.tsv
   https://zenodo.org/record/3706539/files/X_train.tsv
   https://zenodo.org/record/3706539/files/y_test.tsv
   https://zenodo.org/record/3706539/files/y_train.tsv
   

3. Rename the datasets as X_test, X_train, y_test and y_train respectively.

   Tip: Renaming a dataset

   • Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
   • In the central panel, change the Name field
   • Click the Save button

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

4. Check that the datatype is tabular.

   Tip: Changing the datatype

   • Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
   • In the central panel, click galaxy-chart-select-data Datatypes tab on the top
   • In the galaxy-chart-select-data Assign Datatype, select datatypes from “New type” dropdown
     • Tip: you can start typing the datatype into the field to filter the dropdown menu
   • Click the Save button

Neural network architecture

Defining a neural network architecture needs to ascertain the types and number of layers, the number of neurons for each layer, activation functions for all layers, type of optimiser and loss function. Choosing these parameters may require many experiments with data as there is no golden rule to choose the best combination of these parameters. The neural network used in this tutorial has an input layer, 2 hidden layers and one output layer. The input layer has a parameter input_shape which is set according to the number of dimensions of data. It is set to (7129,) which is the number of genes present in data. The hidden layers have 16 neurons (units) each and the output layer has only one because a scalar output is expected (0 or 1). This partial architecture (having input shape, types and size of layers, and activation functions) of the neural network is defined as follows:

Create architecture: Choose layers

Hands-on: Create a deep learning model architecture using Keras

1. Create a deep learning model architecture using Keras tool with the following parameters:
   • “Select keras model type”: Sequential

   • “input_shape”: (7129, )

   • In “LAYER”:
     • param-repeat “1: LAYER”:
       • “Choose the type of layer”: Core -- Dense
         • “units”: 16
         • “Activation function”: elu
     • param-repeat “2: LAYER”:
       • “Choose the type of layer”: Core -- Dense
         • “units”: 16
         • “Activation function”: elu
     • param-repeat “3: LAYER”:
       • “Choose the type of layer”: Core -- Dense
         • “units”: 1
         • “Activation function”: sigmoid

The tool returns a JSON output file containing data about the neural network layers and their attributes like their types, number of units they have and their activation functions. This file is used as an input to the next step where the architecture of the neural network is completed by adding optimiser, loss function, and training parameters such as the number of epochs and batch size. The loss function is chosen as binary_crossentropy as the learning task is the classification of two labels (0 and 1).

Create architecture: Add training parameters

Hands-on: Create deep learning model with an optimizer, loss function and fit parameters

1. Create deep learning model with an optimizer, loss function and fit parameters tool with the following parameters:
   • “Choose a building mode”: Build a training model
   • “Select the dataset containing model configurations (JSON)”: Keras model config (output of Create a deep learning model architecture using Keras tool)
   • “Do classification or regression?”: KerasGClassifier

   KerasGClassifier is chosen because the learning task is classfication i.e. assigning each patient a type of cancer.

   • In “Compile Parameters”:
     • “Select a loss function”: binary_crossentropy

     The loss function is binary_crossentropy because the labels are discrete and binary (0 and 1).

     • “Select an optimizer”: RMSprop - RMSProp optimizer
   • In “Fit Parameters”:
     • “epochs”: 10
     • “batch_size”: 4

     The training data is small (only 38 patients). Therefore the number of epochs and batch size are also small.

The tool returns a zipped file containing an object of the neural network architecture (define in the last two steps) which is used as a classifier to train it on data. Once the architecture is finalised, its associated object is used for training combining it with the training data as follows:

Deep learning training

A neural network is trained on training data to learn hidden representations and mapping from features (genes) to both the types of cancer. As discussed earlier, the neural network minimises the error, which is given by the loss function, between actual and predicted labels while adjusting the weights of connections among neurons in multiple layers. Once the training is finished, the architecture and learned weights are saved. They are used to predict labels in test data. The deep learning training is set up as follows:

Hands-on: Deep learning training and evaluation conduct deep training and evaluation either implicitly or explicitly

1. Deep learning training and evaluation conduct deep training and evaluation tool with the following parameters:
   • “Select a scheme”: Train and validate
   • “Choose the dataset containing pipeline/estimator object”: Keras model builder (output of Create deep learning model tool)
   • “Select input type”: tabular data
   • “Training samples dataset”: X_train
     • “Does the dataset contain header”: Yes
     • “Choose how to select data by column”: All columns
   • “Dataset containing class labels or target values”: y_train
     • “Does the dataset contain header”: Yes
     • “Choose how to select data by column”: All columns

The tool gives 3 files as output - a tabular file containing output (accuracy of cross-validation) of training, a zipped file with the trained model (fitted estimator) and an H5 (HDF5) file containing the weights of neural network layers. The files containing the fitted estimator and weights are used to recreate the model and this recreated model is used to predict labels in test data.

Prediction on test data

After training, the saved architecture (fitted estimator) and weights are used to predict labels for the test data. For each patient in the test data, a type of cancer is predicted using the trained model learned in the previous step.

Hands-on: Model Prediction predicts on new data using a preffited model

1. Model Prediction predicts on new data using a preffited model tool with the following parameters:
   • “Choose the dataset containing pipeline/estimator object”: Fitted estimator or estimator skeleton (output of Deep learning training and evaluation tool)
   • “Choose the dataset containing weights for the estimator above”: Weights trained (output of Create deep learning model tool)
   • “Select invocation method”: predict
   • “Select input data type for prediction”: tabular data
     • “Training samples dataset”: X_test
     • “Does the dataset contain header”: Yes
     • “Choose how to select data by column”: All columns

The tool returns the predicted labels (0 for ALL and 1 AML) for test data in a tabular format. The size of this data is (34,1) where 34 is the number of cancer patients in test data.

Visualisation

Visualising the results is important to ascertain the generalisation ability of the trained model on an unseen dataset. Using a dataset with the actual labels for the test data, the performance of the trained model is estimated by comparing the actual labels against the predicted labels using a confusion matrix plot.

Hands-on: Machine Learning Visualization Extension includes several types of plotting for machine learning

1. Machine Learning Visualization Extension includes several types of plotting for machine learning tool with the following parameters:
   • “Select a plotting type”: Confusion matrix for classes
   • “Select dataset containing true labels”: y_test
   • “Does the dataset contain header”: Yes
   • “Choose how to select data by column”: All columns
   • “Select dataset containing predicted labels”: Model prediction (output of Model Prediction predicts on new data using a preffited model tool)
   • “Does the dataset contain header”: Yes

Comment

Please note that your predictions could be different from the plot shown in Figure 11 because the training data is small and the predictions may vary. Stability in predictions can be achieved if the deep learning model is trained on large data. But, for this tutorial, it is kept small to reduce the training time as the aim is to showcase how to create a pipeline for deep learning training. Generally, deep learning models are trained on large data and may keep running for a few hours to a few days.

The image below shows confusion matrix which is a square matrix. It contains actual labels on the y-axis and predicted labels on the x-axis. Each cell in the matrix plot gives the number of cancer patients who got predicted correctly or incorrectly. For example, the number in the top-left cell (0, 0) denotes how many of these patients are predicted correctly for ALL (17/20). The higher the number in this cell, the better is the model for this cell. In the top-right cell, 3 patients who have ALL but they are predicted having AML. Similarly, the bottom-right cell denotes how many patients are predicted correctly for AML (10/14). In the bottom-left cell, 4 patients have AML but are predicted as ALL.

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Conclusion

The tutorial presents a case-study to predict labels (ALL and AML) of 34 new cancer patients after learning gene expression profiles of 38 cancer patients through multiple steps of a deep learning pipeline. All these steps show how to create a neural network architecture using Galaxy’s deep learning tools and analyse results using a confusion matrix visualisation. Similarly, multiple different architectures of neural networks can be created well-suited to datasets and aim of particular experiments. Moreover, it should be noted that one architecture of neural network giving promising results on a dataset may not work at all with another dataset. It is essential to perform multiple experiments with a dataset to formulate an optimal neural network architecture.

You've Finished the Tutorial

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Key points

• Multiple tools to constitute a neural network architecture

• Interpretation of predictions using visualisation tools

Frequently Asked Questions

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Citing this Tutorial

1. Anup Kumar, Alireza Khanteymoori, Introduction to deep learning (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{statistics-intro_deep_learning,
author = "Anup Kumar and Alireza Khanteymoori",
	title = "Introduction to deep learning (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools:
- name: keras_model_builder
  owner: bgruening
  revisions: 772e0e89fc68
  tool_panel_section_label: Machine Learning
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: keras_model_config
  owner: bgruening
  revisions: 8a794e6d3388
  tool_panel_section_label: Machine Learning
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: keras_train_and_eval
  owner: bgruening
  revisions: f1b9a42d6809
  tool_panel_section_label: Machine Learning
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: ml_visualization_ex
  owner: bgruening
  revisions: 05143043ca13
  tool_panel_section_label: Machine Learning
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: model_prediction
  owner: bgruening
  revisions: 83228baae3c5
  tool_panel_section_label: Machine Learning
  tool_shed_url: https://toolshed.g2.bx.psu.edu/

Feedback

5 stars	3
4 stars	2

May 2024

• 5 stars: Liked: detailing of neural network Disliked: coding explanation

April 2023

• 4 stars: Liked: How it explained each feature of the model. Disliked: Providing more links to resources for further reading (e.g., on how to select models or various aspects of them) would be nice!

February 2021

• 5 stars: Liked: Very easy and simple to understand

April 2020

• 4 stars: Liked: Exhaustive and extensive introductory chapter, easing readers into complex concepts without the need for in-depth prior knowledge. Disliked: The English used in the introductory section is spotty, containing grammatical errors and incorrect use of prepositions in many places. It misattributes terminology to mathematics when said terms more properly belong to neural networks or programming. The text contains types, such as Figure 1 being referred to as Figure 3 in at least one place.