Artificial Intelligence in Digital Pathology Flashcards

1
Q

What does artificial intelligence aim to teach machines?

A
Decision making
Reasoning
Computer Vision
Natural language processing
Knowledge representation
Motion and manipulation
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2
Q

What are two types of AI?

A

Artificial general intelligence:
Perform across several domains of human intelligence
Turing test

Narrow (weak) AI:
Perform single task as well as humans
Alpha go

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3
Q

What are subsets of AI?

A

Machine learning:
Algorithms that learn to act from data without being explicitly programmed

Deep learning:
Subset of machine learning based on neural network models

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4
Q

What does machine learning use?

A

Data to detect patterns

“a set of methods that can automatically detect patterns in data, and then use the . . . patterns to predict future data, or to perform other kinds of decision making. . . ” – Kevin Murphy

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5
Q

How does traditional programme differ to machine learning?

A

In traditional programming input and program lead to computation and result

In machine learning input and a desired result lead to computation and result

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6
Q

What three categorised is machine learning divided into?

A

Supervised: Data modelled using label . Used to cluster data

Unsupervised: Data modelled without labels.

Used to cluster data

Reinforcement: Learn from experience. Model uses trial and error to learn from experience. A reward function is used to measure how good each action taken was

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7
Q

Supervised learning techniques include classification and regression

How do both differ?

A

Classification-
Discrete or categorical labels
Separate observations into categories
Classifier finds mapping between features and classes (categories) that can can predict category for future observations
Logistic regression and random forests common classifiers

Regression-
Numerical or continuous output variables
Explanatory variables (features)
Try to predict a dependent variable
Finds function that maps between dependent variable and  explanatory variables (features) which can be used to predict a  real value for future observations
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8
Q

What does deep learning use?

A

Neural networks based on biological neurons networks

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9
Q
  1. Deep learning is based upon what?

2. Why is this powerful?

A
  1. Computational networks which are loosely based upon biological neural networks.
  2. As known as universal function approximates meaning can model complex functions.
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10
Q

What are features of the deep learning model?

A

Input layer: features for each observation enter the network

Hidden layers: the neurons perform feature extraction and learning task

Output = prediction

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11
Q

In deep learning what is making decisions about its inputs based on the weights it tries to learn during training?

A

A single neuron

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12
Q

In supervised deep learning a loss function evaluates…

A

what predictions adjusts the parameters of the network based

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13
Q

What are the two phases within neural networks?

A

Training and Inference.

During training learning most important features and weights to produce accurate prediction of the weights. Weights extremely important as informing of which features are significant in forming final prediction. This is achieved through an iterative process using two segments: Forward pass and backward pass. Forward pass: Learn which features are important through process using calculation for each neuron to form a decision about its input based upon the weights it tries to learn during training, use features to form a prediction at end of network. Backward pass: Compare prediction to ground truth label using function we defined and adjust weights in the network using an optimisation algorithm - this adjusts the weights proportional to the loss calculated such that can improve on this in next iteration.

Inference: Only single forward pass here whereby weights are static and set at level learnt during training phase. Use this to predict data, extract learnt features and form prediction at end of network

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14
Q

Computer vision is the area teaching machines to understand visual data

What are 4 main tasks often performed using computer vision?

A

Classification– Correctly label image

Classification and Localization- Correctly label and locate image

Object Detection- Localising all objects of interest in the image

Instance Segmentation- Classification task attempting to apply to all images

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15
Q

In computer vision image date is?

How does this differ to machine learning?

A

Unstructured and features are learned or engineered from raw pixel values

In machine learning must engineer features manually, whereas here this is not needed

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16
Q

Computer vision in histopathology focuses upon what tasks?

A

Classification and Segmentation

17
Q

Computer vision is a form of deep learning

True or false

A

True

18
Q

What are applications of AI in digital pathology?

A

Detect or grade cancer
Identify metastases
Prognosis prediction
Personalised care plans

Aid pathologist in decision making which could lead to
Improved efficiency
Improved workflow
More advanced diagnostics

19
Q

Whole-slide scanners are used digitize glass slides containing tissue specimens at high resolution.

Why is this beneficial?

A

High resolution- Typical resolutions of 100,000×100,000

Images are stored at different magnifications – generally up to 40x

20
Q

How do pathologists annotate whole slider scanner images (WSIs)?

What is a limitation of this?

How can this be overcome and what are the advantages of this?

A

Manually annotate images using programs designed to deal with these images – Qupath

Annotating single lymph node extremely time consuming – estimated max 30-40 lymph nodes a day!

Given WSIs are a large source of information images can be analysed using AI techniques

Automation beneficial because

  • Free up pathologist time
  • Improve accuracy, reproducibility and reduce potential errors
  • Improve inter-pathologist agreement

Automation order of magnitude quicker once models are trained!

21
Q

How is machine learning used to analyse whole slider scanner images (WSIs)?

A

Split the WSI images into a train and test dataset

Automate annotation of lymph nodes for histological features using a deep learning segmentation pipeline

Compare network predictions with pathologist ground truth annotation

Stitch patches back together to create entire segmented whole slide image

22
Q

What is the Camelyon16/17 challenge?

A

Goal: evaluate algorithms for automated detection of metastases in H&E whole-slide images of lymph node sections.

400 whole-slide images (WSIs) of sentinel lymph nodes

1st Task:
Whole slide level prediction
Binary classification problem
Assign metastatic or not metastatic to each image

2nd Task
Find metastasis location
Segmentation problem
Assign metastatic or not metastatic to each pixel

23
Q

What are the current challenges of AI and digital pathology?

A

Lack of labelled data
AI requires large set of training images – ideally labelled

Extreme variability
Large variation in tissue type
Extreme polymorphism

Dimensionality obstacle
Gigapixel digital images
Memory intensive
Down-sampling my result in loss of crucial information

Computationally intensive
Large data requirements
GPUs required for training (otherwise patience required!)

Narrow AI
Deep NNs are belong to weak AI
Train multiple AI solutions for different tasks

Lack of transparency
Black box
No obvious rationale behind decisions
Unacceptable in medical discipline
Decision making process behind diagnosis needs to be clear
Transparency key for regulatory approval

Adversarial attacks
DNNs can be easily fooled
Noise or artifacts skew output – mistakenly diagnose as cancer or vice versa

AI in practice
Buy in from pathologists
Ease of use
Scalable
Trust
understandable
24
Q

What are ethical considerations in AI ?

A

Bias
Natural bias in society can bias data

Biased data can lead to biased decisions and results

Shared prosperity in AI

Automation revolution
Job displacement
Effects on skill requirements

Transparency
Builds public trust in system
Important to explain why decisions are being made
Safety certification

Data protection
protection of sensitive or individual data

Security
Can the AI be hacked or used for malicious
purposes

Accountability
Erroneous decisions
Who is responsible if machines make mistake or mis-diagnosis

25
Q

Cathy O’Neil coined weapons of math destruction

What does this refer to?

A

ML models have the capacity to create great damage to
society.

Weapons of math destruction models:
Opacity, Black box models: cannot easily be interrogated. Especially by the subjects.

Scale: Can the effects of the model extend beyond the decision that it helps to make.

Damage: The model causes damage. Could cause harm
to people, especially members of vulnerable groups.