Entropy primarily based Uncertainty Prediction | by François Porcher | Sep, 2023



This text explores how Entropy might be employed as a device for uncertainty estimation in picture segmentation duties. We’ll stroll by what Entropy is, and tips on how to implement it with Python.

François PorcherTowards Data SciencePicture by Michael Dziedzic on Unsplash

Whereas working at Cambridge College as a Analysis Scientist in Neuroimaging and AI, I confronted the problem of performing picture segmentation on intricate mind datasets utilizing the newest Deep Studying methods, particularly the nnU-Web. Throughout this endeavor, I noticed a major hole: the overlooking of uncertainty estimation. But, uncertainty is essential for dependable decision-making.

Earlier than delving into the specifics, be happy to take a look at my Github repository which comprises all of the code snippets mentioned on this article.

On the earth of pc imaginative and prescient and machine studying, picture segmentation is a central downside. Whether or not it’s in medical imaging, self-driving automobiles, or robotics, correct segmentation are important for efficient decision-making. Nonetheless, one usually missed side is the measure of uncertainty related to these segmentations.

Why ought to we care about uncertainty in picture segmentation?

In lots of real-world purposes, an incorrect segmentation may end in dire penalties. For instance, if a self-driving automobile misidentifies an object or a medical imaging system incorrectly labels a tumor, the results could possibly be catastrophic. Uncertainty estimation provides us a measure of how ‘positive’ the mannequin is about its prediction, permitting for better-informed choices.

We will additionally use Entropy as a measure of uncertainty to enhance the educational of our neural networks. This space is is aware of as ‘energetic studying’. This concept might be explored in additional articles however the primary concept is to establish the zones on which the fashions are probably the most unsure to concentrate on them. For instance we may have a CNN performing medical picture segmentation on the mind, however performing very poorly on topics with tumours. Then we may focus our efforts to accumulate extra labels of this kind.

Entropy is an idea borrowed from thermodynamics and knowledge principle, which quantifies the quantity of uncertainty or randomness in a system. Within the context of machine studying, entropy can be utilized to measure the uncertainty of mannequin predictions.

Mathematically, for a discrete random variable X with likelihood mass operate P(x), the entropy H(X) is outlined as:

Or within the continous case:

The upper the entropy, the higher the uncertainty, and vice versa.

A traditional instance to totally grasp the idea:

Scenario 1: A biased coin

Picture by Jizhidexiaohailang on Unsplash

Think about a biased coin, which lands on head with a likelihood p=0.9, and tail with a likelihood 1-p=0.1.

Its entropy is

Scenario 2: Balanced coin

Now let’s think about a balanced coin which lands on head and tail with likelihood p=0.5

Its entropy is:

The entropy is bigger, which is coherent with what we mentioned earlier than: extra uncertainty = extra entropy.

Really it’s attention-grabbing to notice that p=0.5 corresponds to the utmost entropy:

Entropy visualisation, Picture by creator

Intuitively, do not forget that a uniform distribution is the case with maximal entropy. If each final result is equally possible, then this corresponds to the maximal uncertainty.

To hyperlink this to picture segmentation, take into account that in deep studying, the ultimate softmax layer often gives the category possibilities for every pixel. One can simply compute the entropy for every pixel primarily based on these softmax outputs.

However How does it work?

When a mannequin is assured a few specific pixel belonging to a particular class, the softmax layer reveals excessive likelihood (~1) for that class, and really small possibilities (~0) for the opposite courses.

Softmax layer, assured case, Picture by creator

Conversely, when the mannequin is unsure, the softmax output is extra evenly unfold throughout a number of courses.

Softmax layer, unsure case, Picture by creator

The possibilities are far more diffuse, near the uniform case for those who bear in mind, as a result of the mannequin can not determine which class is related to the pixel.

When you have made it till now, nice! You must have an important instinct of how entropy works.

Let’s illustrate this with a hands-on instance utilizing medical imaging, particularly T1 Mind scans of fetuses. All codes and pictures for this case research can be found in my Github repository.

1. Computing Entropy with Python

As we mentioned earlier than, we’re working with the softmax output tensor, given by our Neural Community. This method is model-free, it solely makes use of the chances of every class.

Let’s make clear one thing vital in regards to the dimensions of the tensors we’re working with.

If you’re working with 2D Photos, the form of your softmax layer ought to be:

That means that for every pixel (or voxel), we’ve a vector of dimension Lessons, which supplies us the chances of a pixel to belong to every of the courses we’ve.

Due to this fact the entropy ought to be pc alongside the primary dimension:

def compute_entropy_4D(tensor):
Compute the entropy on a 4D tensor with form (number_of_classes, 256, 256, 256).

tensor (np.ndarray): 4D tensor of form (number_of_classes, 256, 256, 256)

np.ndarray: 3D tensor of form (256, 256, 256) with entropy values for every pixel.

# First, normalize the tensor alongside the category axis in order that it represents possibilities
sum_tensor = np.sum(tensor, axis=0, keepdims=True)
tensor_normalized = tensor / sum_tensor

# Calculate entropy
entropy_elements = -tensor_normalized * np.log2(tensor_normalized + 1e-12) # Added a small worth to keep away from log(0)
entropy = np.sum(entropy_elements, axis=0)

entropy = np.transpose(entropy, (2,1,0))

total_entropy = np.sum(entropy)

return entropy, total_entropy

2. Visualizing Entropy-based Uncertainty

Now let’s visualize the uncertainties by utilizing a heatmap, on every slice of our picture segmentation.

T1 scan (left), Segmentation (center), Entropy (Proper), Picture by creator

Let’s have a look at an different instance:

T1 scan (left), Segmentation (center), Entropy (Proper), Picture by creator

The outcomes look nice! Certainly we will see that that is coherent as a result of the zones of excessive entropy are on the contour of the shapes. That is regular as a result of the mannequin does probably not doubt the factors on the center of every zone, however its quite the delimitation or contour that’s tough to identify.

This uncertainty can be utilized in loads of alternative ways:

As medical consultants work increasingly with AI as a device, being conscious of the uncertainty of the mannequin is essential. This imply that medical consultants may spend extra instances on the zone the place extra fine-grained consideration is required.

2. Within the context of Energetic Studying or Semi-Supervised Studying, we will leverage Entropy primarily based Uncertainty to concentrate on the examples with maximal uncertainty, and enhance the effectivity of studying (extra about this in coming articles).

Entropy is a particularly highly effective idea to measure the randomness or uncertainty of a system.It’s doable to leverage Entropy in Picture Segmentation. This method is mannequin free and solely makes use of the softmax output tensor.Uncertainty estimation is missed, however it’s essential. Good Data Scientists know tips on how to make good fashions. Nice Data Scientists know the place their mannequin fail and use this to enhance studying.


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