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Making the Role of AI in Breast Cancer Explainable

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March 22, 2021 — Researchers at Charité – Universitätsmedizin Berlin and TU Berlin as well as the University of Oslo have developed a new tissue-section analysis system for diagnosing breast cancer based on artificial intelligence (AI). Two further developments make this system unique: For the first time, morphological, molecular and histological data are integrated in a single analysis. Secondly, the system provides a clarification of the AI decision process in the form of heatmaps. Pixel by pixel, these heatmaps show which visual information influenced the AI decision process and to what extent, thus enabling doctors to understand and assess the plausibility of the results of the AI analysis. This represents a decisive and essential step forward for the future regular use of AI systems in hospitals. The results of this research have now been published in Nature Machine Intelligence.

Cancer treatment is increasingly concerned with the molecular characterization of tumor tissue samples. Studies are conducted to determine whether and/or how the DNA has changed in the tumor tissue as well as the gene and protein expression in the tissue sample. At the same time, researchers are becoming increasingly aware that cancer progression is closely related to intercellular cross-talk and the interaction of neoplastic cells with the surrounding tissue – including the immune system.

Although microscopic techniques enable biological processes to be studied with high spatial detail, they only permit a limited measurement of molecular markers. These are rather determined using proteins or DNA taken from tissue. As a result, spatial detail is not possible and the relationship between these markers and the microscopic structures is typically unclear. “We know that in the case of breast cancer, the number of immigrated immune cells, known as lymphocytes, in tumor tissue has an influence on the patient’s prognosis. There are also discussions as to whether this number has a predictive value – in other words if it enables us to say how effective a particular therapy is,” said Prof. Frederick Klauschen, M.D., of Charité’s Institute of Pathology.

“The problem we have is the following: We have good and reliable molecular data and we have good histological data with high spatial detail. What we don’t have as yet is the decisive link between imaging data and high-dimensional molecular data,” added Prof. Klaus-Robert Müller, M.D., professor of machine learning at TU Berlin. Both researchers have been working together for a number of years now at the national AI center of excellence the Berlin Institute for the Foundations of Learning and Data (BIFOLD) located at TU Berlin.

It is precisely this symbiosis which the newly published approach makes possible. “Our system facilitates the detection of pathological alterations in microscopic images. Parallel to this, we are able to provide precise heatmap visualizations showing which pixel in the microscopic image contributed to the diagnostic algorithm and to what extent,” explained Müller. The research team has also succeeded in significantly further developing this process: “Our analysis system has been trained using machine learning processes so that it can also predict various molecular characteristics, including the condition of the DNA, the gene expression as well as the protein expression in specific areas of the tissue, on the basis of the histological images.

Next on the agenda are certification and further clinical validations – including tests in tumor routine diagnostics. However, Klauschen is already convinced of the value of the research: “The methods we have developed will make it possible in the future to make histopathological tumor diagnostics more precise, more standardized and qualitatively better.”

For more information: www.charite.de

Related Breast Cancer/AI Workflow Content:

VIDEO: Integrating Artificial Intelligence Into Radiologists Workflow

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Understanding dimensionality reduction in machine learning models

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Machine learning algorithms have gained fame for being able to ferret out relevant information from datasets with many features, such as tables with dozens of rows and images with millions of pixels. Thanks to advances in cloud computing, you can often run very large machine learning models without noticing how much computational power works behind the scenes.

But every new feature that you add to your problem adds to its complexity, making it harder to solve it with machine learning algorithms. Data scientists use dimensionality reduction, a set of techniques that remove excessive and irrelevant features from their machine learning models.

Dimensionality reduction slashes the costs of machine learning and sometimes makes it possible to solve complicated problems with simpler models.

The curse of dimensionality

Machine learning models map features to outcomes. For instance, say you want to create a model that predicts the amount of rainfall in one month. You have a dataset of different information collected from different cities in separate months. The data points include temperature, humidity, city population, traffic, number of concerts held in the city, wind speed, wind direction, air pressure, number of bus tickets purchased, and the amount of rainfall. Obviously, not all this information is relevant to rainfall prediction.

Some of the features might have nothing to do with the target variable. Evidently, population and number of bus tickets purchased do not affect rainfall. Other features might be correlated to the target variable, but not have a causal relation to it. For instance, the number of outdoor concerts might be correlated to the volume of rainfall, but it is not a good predictor for rain. In other cases, such as carbon emission, there might be a link between the feature and the target variable, but the effect will be negligible.

In this example, it is evident which features are valuable and which are useless. in other problems, the excessive features might not be obvious and need further data analysis.

But why bother to remove the extra dimensions? When you have too many features, you’ll also need a more complex model. A more complex model means you’ll need a lot more training data and more compute power to train your model to an acceptable level.

And since machine learning has no understanding of causality, models try to map any feature included in their dataset to the target variable, even if there’s no causal relation. This can lead to models that are imprecise and erroneous.

On the other hand, reducing the number of features can make your machine learning model simpler, more efficient, and less data-hungry.

The problems caused by too many features are often referred to as the “curse of dimensionality,” and they’re not limited to tabular data. Consider a machine learning model that classifies images. If your dataset is composed of 100×100-pixel images, then your problem space has 10,000 features, one per pixel. However, even in image classification problems, some of the features are excessive and can be removed.

Dimensionality reduction identifies and removes the features that are hurting the machine learning model’s performance or aren’t contributing to its accuracy. There are several dimensionality techniques, each of which is useful for certain situations.

Feature selection

Feature selection

A basic and very efficient dimensionality reduction method is to identify and select a subset of the features that are most relevant to target variable. This technique is called “feature selection.” Feature selection is especially effective when you’re dealing with tabular data in which each column represents a specific kind of information.

When doing feature selection, data scientists do two things: keep features that are highly correlated with the target variable and contribute the most to the dataset’s variance. Libraries such as Python’s Scikit-learn have plenty of good functions to analyze, visualize, and select the right features for machine learning models.

For instance, a data scientist can use scatter plots and heatmaps to visualize the covariance of different features. If two features are highly correlated to each other, then they will have a similar effect on the target variable, and including both in the machine learning model will be unnecessary. Therefore, you can remove one of them without causing a negative impact on the model’s performance.

Heatmap

Above: Heatmaps illustrate the covariance between different features. They are a good guide to finding and culling features that are excessive.

The same tools can help visualize the correlations between the features and the target variable. This helps remove variables that do not affect the target. For instance, you might find out that out of 25 features in your dataset, seven of them account for 95 percent of the effect on the target variable. This will enable you to shave off 18 features and make your machine learning model a lot simpler without suffering a significant penalty to your model’s accuracy.

Projection techniques

Sometimes, you don’t have the option to remove individual features. But this doesn’t mean that you can’t simplify your machine learning model. Projection techniques, also known as “feature extraction,” simplify a model by compressing several features into a lower-dimensional space.

A common example used to represent projection techniques is the “swiss roll” (pictured below), a set of data points that swirl around a focal point in three dimensions. This dataset has three features. The value of each point (the target variable) is measured based on how close it is along the convoluted path to the center of the swiss roll. In the picture below, red points are closer to the center and the yellow points are farther along the roll.

Swiss roll

In its current state, creating a machine learning model that maps the features of the swiss roll points to their value is a difficult task and would require a complex model with many parameters. But with the help of dimensionality reduction techniques, the points can be projected to a lower-dimension space that can be learned with a simple machine learning model.

There are various projection techniques. In the case of the above example, we used “locally-linear embedding,” an algorithm that reduces the dimension of the problem space while preserving the key elements that separate the values of data points. When our data is processed with the LLE, the result looks like the following image, which is like an unrolled version of the swiss roll. As you can see, points of each color remain together. In fact, this problem can still be simplified into a single feature and modeled with linear regression, the simplest machine learning algorithm.

Swiss roll, projected

While this example is hypothetical, you’ll often face problems that can be simplified if you project the features to a lower-dimensional space. For instance, “principal component analysis” (PCA), a popular dimensionality reduction algorithm, has found many useful applications to simplify machine learning problems.

In the excellent book Hands-on Machine Learning with Python, data scientist Aurelien Geron shows how you can use PCA to reduce the MNIST dataset from 784 features (28×28 pixels) to 150 features while preserving 95 percent of the variance. This level of dimensionality reduction has a huge impact on the costs of training and running artificial neural networks.

dimensionality reduction mnist dataset

There are a few caveats to consider about projection techniques. Once you develop a projection technique, you must transform new data points to the lower dimension space before running them through your machine learning model. However, the costs of this preprocessing step are not comparable to the gains of having a lighter model. A second consideration is that transformed data points are not directly representative of their original features and transforming them back to the original space can be tricky and in some cases impossible. This might make it difficult to interpret the inferences made by your model.

Dimensionality reduction in the machine learning toolbox

Having too many features will make your model inefficient. But cutting removing too many features will not help either. Dimensionality reduction is one among many tools data scientists can use to make better machine learning models. And as with every tool, they must be used with caution and care.

Ben Dickson is a software engineer and the founder of TechTalks, a blog that explores the ways technology is solving and creating problems.

This story originally appeared on Bdtechtalks.com. Copyright 2021

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Bitcoin Mining Company Vows to be Carbon Neutral Following Tesla’s Recent Statement

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Last week, Elon Musk and Tesla shocked the entire crypto industry following an announcement that the electric car company will no longer accept bitcoin payments for “environmental reasons.”

A Hard Pill For Bitcoin Maximalists

Giving its reasons, Tesla argued that Bitcoin mining operation requires massive energy consumption, which is generated from fossil fuel, especially coal, and as such, causes environmental pollution.

The announcement caused a market dip which saw over $4 billion of both short and long positions liquidated as the entire capitalization lost almost $400 billion in a day.

For Bitcoin maximalists and proponents, Tesla’s decision was a hard pill to swallow, and that was evident in their responses to the electric car company and its CEO.

While the likes of Max Keiser lambasted Musk for his company’s move, noting that it was due to political pressure, others like popular YouTuber Chris Dunn were seen canceling their Tesla Cybertruck orders.


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Adding more fuel to the fire, Musk also responded to a long Twitter thread by Peter McCormack, implying that Bitcoin is not actually decentralized.

Musk Working With Dogecoin Devs

Elon Musk, who named himself the “Dogefather” on SNL, created a Twitter poll, asking his nearly 55 million followers if they want Tesla to integrate DOGE as a payment option.

The poll, which had almost 4 million votes, was favorable for Dogecoin, as more than 75% of the community voted “Yes.”

Following Tesla’s announcement, the billionaire tweeted that he is working closely with Dogecoin developers to improve transaction efficiency, saying that it is “potentially promising.”

Tesla dropping bitcoin as a payment instrument over energy concerns, with the possibility of integrating dogecoin payments, comes as a surprise to bitcoiners since the two cryptocurrencies use a Proof-of-Work (PoW) consensus algorithm and, as such, face the same underlying energy problem.

Elon Musk: Dogecoin Wins Bitcoin

Despite using a PoW algorithm, Elon Musk continues to favor Dogecoin over Bitcoin. Responding to a tweet that covered some of the reasons why Musk easily chose DOGE over BTC, the billionaire CEO agreed that Dogecoin wins Bitcoin in many ways.

Comparing DOGE to BTC, Musk noted that “DOGE speeds up block time 10X, increases block size 10X & drops fee 100X. Then it wins hands down.”

Max Keiser: Who’s The Bigger Idiot?

As Elon Musk continues his lovey-dovey affair with Dogecoin, Bitcoin proponents continue to criticize the Dogefather.

Following Musk’s comments on Dogecoin today, popular Bitcoin advocate Max Keiser took to his Twitter page to ridicule the Tesla boss while recalling when gold bug Peter Schiff described Bitcoin as “intrinsically worthless” after he lost access to his BTC wallet.

“Who’s the bigger idiot?” Keiser asked.

Aside from Keiser, other Bitcoin proponents such as Michael Saylor replied to Tesla’s CEO:

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Bitcoin Proponents Against Elon Musk Following Heated Dogecoin vs Bitcoin Tweets

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Last week, Elon Musk and Tesla shocked the entire crypto industry following an announcement that the electric car company will no longer accept bitcoin payments for “environmental reasons.”

A Hard Pill For Bitcoin Maximalists

Giving its reasons, Tesla argued that Bitcoin mining operation requires massive energy consumption, which is generated from fossil fuel, especially coal, and as such, causes environmental pollution.

The announcement caused a market dip which saw over $4 billion of both short and long positions liquidated as the entire capitalization lost almost $400 billion in a day.

For Bitcoin maximalists and proponents, Tesla’s decision was a hard pill to swallow, and that was evident in their responses to the electric car company and its CEO.

While the likes of Max Keiser lambasted Musk for his company’s move, noting that it was due to political pressure, others like popular YouTuber Chris Dunn were seen canceling their Tesla Cybertruck orders.


ADVERTISEMENT

Adding more fuel to the fire, Musk also responded to a long Twitter thread by Peter McCormack, implying that Bitcoin is not actually decentralized.

Musk Working With Dogecoin Devs

Elon Musk, who named himself the “Dogefather” on SNL, created a Twitter poll, asking his nearly 55 million followers if they want Tesla to integrate DOGE as a payment option.

The poll, which had almost 4 million votes, was favorable for Dogecoin, as more than 75% of the community voted “Yes.”

Following Tesla’s announcement, the billionaire tweeted that he is working closely with Dogecoin developers to improve transaction efficiency, saying that it is “potentially promising.”

Tesla dropping bitcoin as a payment instrument over energy concerns, with the possibility of integrating dogecoin payments, comes as a surprise to bitcoiners since the two cryptocurrencies use a Proof-of-Work (PoW) consensus algorithm and, as such, face the same underlying energy problem.

Elon Musk: Dogecoin Wins Bitcoin

Despite using a PoW algorithm, Elon Musk continues to favor Dogecoin over Bitcoin. Responding to a tweet that covered some of the reasons why Musk easily chose DOGE over BTC, the billionaire CEO agreed that Dogecoin wins Bitcoin in many ways.

Comparing DOGE to BTC, Musk noted that “DOGE speeds up block time 10X, increases block size 10X & drops fee 100X. Then it wins hands down.”

Max Keiser: Who’s The Bigger Idiot?

As Elon Musk continues his lovey-dovey affair with Dogecoin, Bitcoin proponents continue to criticize the Dogefather.

Following Musk’s comments on Dogecoin today, popular Bitcoin advocate Max Keiser took to his Twitter page to ridicule the Tesla boss while recalling when gold bug Peter Schiff described Bitcoin as “intrinsically worthless” after he lost access to his BTC wallet.

“Who’s the bigger idiot?” Keiser asked.

Aside from Keiser, other Bitcoin proponents such as Michael Saylor replied to Tesla’s CEO:

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PlotX v2 Mainnet Launch: DeFi Prediction Markets

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In early Sunday trading, BTC prices had fallen to their lowest levels for over 11 weeks, hitting $46,700 before a minor recovery.

The last time Bitcoin dropped to these levels was at the end of February during the second major correction of this ongoing rally. A rebound off that bottom sent prices above $60K for the first time in the two weeks that followed.

Later today, Bitcoin is going to close another weekly candle. In case the candle closes at those levels, this will become the worst weekly close since February 22nd, when BTC ended the week at $45,240, according to Bitstamp. Two weeks ago the weekly candle closed at $49,200, which the current lowest week close since February.

Second ‘Lower Low’ For Bitcoin

This time around, things feel slightly different and the bearish sentiment is returning to crypto-asset markets. Since its all-time high of $65K on April 14, Bitcoin has made a lower high and has now formed a second lower low on the daily chart, which is indicative of a larger downtrend developing.

Analyst ‘CryptoFibonacci’ has been eyeing the weekly chart which also suggests the bulls could be running out of steam.


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The move appears to have been driven by Elon Musk again with a tweet about Bitcoin’s energy consumption on May 13. Bitcoin’s fear and greed index has dropped to 20 – ‘extreme fear’ – its lowest level since the March 2020 market crash. At the time of press, BTC was trading at just under $48,000, down 4% over the past 24 hours.

Market Cap Shrinks by $150B

As usual, the move has initiated a selloff for the majority of other cryptocurrencies resulting in around $150 billion exiting the markets over the past day or so.

The total market cap has declined to $2.3 trillion after an all-time high of $2.5 trillion on May 12. Things are still high on the long term view but losses could accelerate rapidly if the bearish sentiment increases.

Not all crypto assets are correcting this weekend, and some have been building on recent gains to push even higher – although they are few in number.

Those weekend warriors include Cardano which has added 4.8% on the day to trade at $2.27 according to Coingecko. ADA hit an all-time high on Saturday, May 15 reaching $2.36, a gain of 54% over the past 30 days.

Ripple’s XRP is also seeing a resurgence with a 13% pump on the day to flip Cardano for the fourth spot. XRP is currently trading at $1.58 with a market cap of $73 billion. The only other two cryptocurrencies in the green at the time of writing are Stellar and Solana, gaining 3.7% and 12% respectively.

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