Acta Neurochirurgica. Supplement

Not only the time-dependent varying of signal intensity (i.e. haematoma evolution) characteristics of the intracranial blood in computed tomography images, but also the fluctuating image quality, the distortions introduced after medical interventions, and the brain deformations and intensity profile variations due to underlying pathologies make the segmentation of intracranial blood a challenging task. In addition to describing various challenges with blood segmentation, this chapter also reviews the following: (1) the general concept of segmentation-explaining why a proper segmentation is a critical step when creating machine learning algorithms for image detection purposes, (2) the different segmentation types and how different medical conditions and technical issues can further complicate this task, (3) how to choose a proper software to facilitate the segmentation task, and (4) useful tips that may be applied before launching a similar segmentation project...

In the last decades, modern medicine has evolved into a data-centered discipline, generating massive amounts of granular high-dimensional data exceeding human comprehension. With improved computational methods, machine learning and artificial intelligence (AI) as tools for data processing and analysis are becoming more and more important. At the forefront of neuro-oncology and AI-research, the field of radiomics has emerged. Non-invasive assessments of quantitative radiological biomarkers mined from complex imaging characteristics across various applications are used to predict survival, discriminate between primary and secondary tumors, as well as between progression and pseudo-progression...

Machine learning (ML) and artificial intelligence (AI) applications in the field of neuroimaging have been on the rise in recent years, and their clinical adoption is increasing worldwide. Deep learning (DL) is a field of ML that can be defined as a set of algorithms enabling a computer to be fed with raw data and progressively discover-through multiple layers of representation-more complex and abstract patterns in large data sets. The combination of ML and radiomics, namely the extraction of features from medical images, has proven valuable, too: Radiomic information can be used for enhanced image characterization and prognosis or outcome prediction...

Advancements in neuroimaging and the availability of large-scale datasets enable the use of more sophisticated machine learning algorithms. In this chapter, we non-exhaustively discuss relevant analytical steps for the analysis of neuroimaging data using machine learning (ML), while the field of radiomics will be addressed separately (c.f., Chap. 18 -Radiomics). Broadly classified into supervised and unsupervised approaches, we discuss the encoding/decoding framework, which is often applied in cognitive neuroscience, and the use of ML for the analysis of unlabeled data using clustering...

Decision curve analysis is an increasingly popular method to assess the impact of a prediction model on medical decision making. The analysis provides a graphical summary. A basic understanding of a decision curve is needed to interpret these graphics. This short introduction addresses the common features of a decision curve. Furthermore, using a glioblastoma patient set provided by the Machine Intelligence in Clinical Neuroscience Lab from the Department of Neurosurgery and Clinical Neuroscience Center, University Hospital Zurich a decision curve is plotted for two prediction models...

The performance of clinical prediction models tends to deteriorate over time. Researchers often develop a new prediction if an existing model performs poorly at external validation. Model updating is an efficient technique and promising alternative to the de novo development of clinical prediction models. Model updating has been recommended by the TRIPOD guidelines. To illustrate several model updating techniques, a case study is provided for the development and updating of a clinical prediction model assessing postoperative anxiety in data coming from two double-blinded placebo-controlled randomized controlled trials with a very similar methodological framework...

The use of predictive models within neurosurgery is increasing and many models described in published journal articles are made available to readers in formats such as nomograms and online calculators. The present chapter details a step-by-step methodology with accompanying R code that may be used to implement models both in the form of traditional nomograms and as open-access, online calculators through RStudio's Shinyapps. The chapter assumes a basic understanding of predictive modeling in R and utilizes open-access files created by the Machine Intelligence in Clinical Neuroscience (MICN) Lab (Department of Neurosurgery and the Clinical Neuroscience Center of the University Hospital Zurich)...

Unsupervised learning, the task of clustering observations in such a way that observations within cluster are more similar than those assigned to other clusters is one the central tasks of data science. Its exploratory and descriptive nature make it one of the most underused and underappreciated methods. In the present chapter we describe its core function with applied examples, explore different approaches, and discuss meaningful applications of the approach for the practicing researcher.

The use of deep learning (DL) is rapidly increasing in clinical neuroscience. The term denotes models with multiple sequential layers of learning algorithms, architecturally similar to neural networks of the brain. We provide examples of DL in analyzing MRI data and discuss potential applications and methodological caveats.Important aspects are data pre-processing, volumetric segmentation, and specific task-performing DL methods, such as CNNs and AEs. Additionally, GAN-expansion and domain mapping are useful DL techniques for generating artificial data and combining several smaller datasets...

There is an increasing interest in using prediction models to forecast clinical outcomes within the fields of neurosurgery and clinical neuroscience. The present chapter outlines the foundations of Bayesian learning and introduces Bayes theorem and its use in machine learning methodology. The use of Bayesian networks to structure and define associations between outcome predictors and final outcomes is highlighted and Naïve Bayes classifiers are outlined for use in predicting neurosurgical outcomes, where the understanding of underlying causes is less important...

While machine learning has occupied a niche in clinical medicine for decades, continued method development and increased accessibility of medical data have led to broad diversification of approaches. These range from humble regression-based models to more complex artificial neural networks; yet, despite heterogeneity in foundational principles and architecture, the spectrum of machine learning approaches to clinical prediction modeling have invariably led to the development of algorithms advancing our ability to provide optimal care for our patients...

Advancements in population neuroscience are spurred by the availability of large scale, open datasets, such as the Human Connectome Project or recently introduced UK Biobank. With the increasing data availability, analyses of brain imaging data employ more and more sophisticated machine learning algorithms. However, all machine learning algorithms must balance generalization and complexity. As the detail of neuroimaging data leads to high-dimensional data spaces, model complexity and hence the chance of overfitting increases...

Selecting a set of features to include in a clinical prediction model is not always a simple task. The goals of creating parsimonious models with low complexity while, at the same time, upholding predictive performance by explaining a large proportion of the variance within the dependent variable must be balanced. With this aim, one must consider the clinical setting and what data are readily available to clinicians at specific timepoints, as well as more obvious aspects such as the availability of computational power and size of the training dataset...

This chapter goes through the steps required to train and validate a simple, machine learning-based clinical prediction model for any continuous outcome. We supply fully structured code for the readers to download and execute in parallel to this section, as well as a simulated database of 10,000 glioblastoma patients who underwent microsurgery, and predict survival from diagnosis in months. We walk the reader through each step, including import, checking, splitting of data. In terms of pre-processing, we focus on how to practically implement imputation using a k-nearest neighbor algorithm...

We illustrate the steps required to train and validate a simple, machine learning-based clinical prediction model for any binary outcome, such as, for example, the occurrence of a complication, in the statistical programming language R. To illustrate the methods applied, we supply a simulated database of 10,000 glioblastoma patients who underwent microsurgery, and predict the occurrence of 12-month survival. We walk the reader through each step, including import, checking, and splitting of datasets. In terms of pre-processing, we focus on how to practically implement imputation using a k-nearest neighbor algorithm, and how to perform feature selection using recursive feature elimination...

Various available metrics to describe model performance in terms of discrimination (area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value, negative predictive value, F1 Score) and calibration (slope, intercept, Brier score, expected/observed ratio, Estimated Calibration Index, Hosmer-Lemeshow goodness-of-fit) are presented. Recalibration is introduced, with Platt scaling and Isotonic regression as proposed methods. We also discuss considerations regarding the sample size required for optimal training of clinical prediction models-explaining why low sample sizes lead to unstable models, and offering the common rule of thumb of at least ten patients per class per input feature, as well as some more nuanced approaches...

We review the concept of overfitting, which is a well-known concern within the machine learning community, but less established in the clinical community. Overfitted models may lead to inadequate conclusions that may wrongly or even harmfully shape clinical decision-making. Overfitting can be defined as the difference among discriminatory training and testing performance, while it is normal that out-of-sample performance is equal to or ever so slightly worse than training performance for any adequately fitted model, a massively worse out-of-sample performance suggests relevant overfitting...

We provide explanations on the general principles of machine learning, as well as analytical steps required for successful machine learning-based predictive modeling, which is the focus of this series. In particular, we define the terms machine learning, artificial intelligence, as well as supervised and unsupervised learning, continuing by introducing optimization, thus, the minimization of an objective error function as the central dogma of machine learning. In addition, we discuss why it is important to separate predictive and explanatory modeling, and most importantly state that a prediction model should not be used to make inferences...

The democratization of machine learning (ML) through availability of open-source learning libraries, the availability of datasets in the "big data" era, increasing computing power even on mobile devices, and online training resources have both led to an explosion in applications and publications of ML in the clinical neurosciences, but has also enabled a dangerous amount of flawed analyses and cardinal methodological errors committed by benevolent authors. While powerful ML methods are nowadays available to almost anyone and can be applied after just few minutes of familiarizing oneself with these methods, that does not imply that one has mastered these techniques...

No abstract text is available yet for this article.