Jan Klein

Etienne van de Bijl, Jan Klein, Joris Pries et al.

Novel prediction methods should always be compared to a baseline to know how well they perform. Without this frame of reference, the performance score of a model is basically meaningless. What does it mean when a model achieves an $F_1$ of 0.8 on a test set? A proper baseline is needed to evaluate the `goodness' of a performance score. Comparing with the latest state-of-the-art model is usually insightful. However, being state-of-the-art can change rapidly when newer models are developed. Contrary to an advanced model, a simple dummy classifier could be used. However, the latter could be beaten too easily, making the comparison less valuable. This paper presents a universal baseline method for all binary classification models, named the Dutch Draw (DD). This approach weighs simple classifiers and determines the best classifier to use as a baseline. We theoretically derive the DD baseline for many commonly used evaluation measures and show that in most situations it reduces to (almost) always predicting either zero or one. Summarizing, the DD baseline is: (1) general, as it is applicable to all binary classification problems; (2) simple, as it is quickly determined without training or parameter-tuning; (3) informative, as insightful conclusions can be drawn from the results. The DD baseline serves two purposes. First, to enable comparisons across research papers by this robust and universal baseline. Secondly, to provide a sanity check during the development process of a prediction model. It is a major warning sign when a model is outperformed by the DD baseline.

Luca Canalini, Jan Klein, Nuno Pedrosa de Barros et al.

In this work, we compare five deep learning solutions to automatically segment the resection cavity in postoperative MRI. The proposed methods are based on the same 3D U-Net architecture. We use a dataset of postoperative MRI volumes, each including four MRI sequences and the ground truth of the corresponding resection cavity. Four solutions are trained with a different MRI sequence. Besides, a method designed with all the available sequences is also presented. Our experiments show that the method trained only with the T1 weighted contrast-enhanced MRI sequence achieves the best results, with a median DICE index of 0.81.

Joris Pries, Etienne van de Bijl, Jan Klein et al.

Before any binary classification model is taken into practice, it is important to validate its performance on a proper test set. Without a frame of reference given by a baseline method, it is impossible to determine if a score is `good' or `bad'. The goal of this paper is to examine all baseline methods that are independent of feature values and determine which model is the `best' and why. By identifying which baseline models are optimal, a crucial selection decision in the evaluation process is simplified. We prove that the recently proposed Dutch Draw baseline is the best input-independent classifier (independent of feature values) for all positional-invariant measures (independent of sequence order) assuming that the samples are randomly shuffled. This means that the Dutch Draw baseline is the optimal baseline under these intuitive requirements and should therefore be used in practice.

Bhakti Baheti, Satrajit Chakrabarty, Hamed Akbari et al.

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

Jan Klein, Sandjai Bhulai, Mark Hoogendoorn et al.

Over the past decade, the advent of cybercrime has accelarated the research on cybersecurity. However, the deployment of intrusion detection methods falls short. One of the reasons for this is the lack of realistic evaluation datasets, which makes it a challenge to develop techniques and compare them. This is caused by the large amounts of effort it takes for a cyber analyst to classify network connections. This has raised the need for methods (i) that can learn from small sets of labeled data, (ii) that can make predictions on large sets of unlabeled data, and (iii) that request the label of only specially selected unlabeled data instances. Hence, Active Learning (AL) methods are of interest. These approaches choose specific unlabeled instances by a query function that are expected to improve overall classification performance. The resulting query observations are labeled by a human expert and added to the labeled set. In this paper, we propose a new hybrid AL method called Jasmine. Firstly, it determines how suitable each observation is for querying, i.e., how likely it is to enhance classification. These properties are the uncertainty score and anomaly score. Secondly, Jasmine introduces dynamic updating. This allows the model to adjust the balance between querying uncertain, anomalous and randomly selected observations. To this end, Jasmine is able to learn the best query strategy during the labeling process. This is in contrast to the other AL methods in cybersecurity that all have static, predetermined query functions. We show that dynamic updating, and therefore Jasmine, is able to consistently obtain good and more robust results than querying only uncertainties, only anomalies or a fixed combination of the two.

Miriam H. A. Bauer, Sebastiano Barbieri, Jan Klein et al.

Diffusion Tensor Imaging (DTI) is a non-invasive imaging technique that allows estimation of the location of white matter tracts in-vivo, based on the measurement of water diffusion properties. For each voxel, a second-order tensor can be calculated by using diffusion-weighted sequences (DWI) that are sensitive to the random motion of water molecules. Given at least 6 diffusion-weighted images with different gradients and one unweighted image, the coefficients of the symmetric diffusion tensor matrix can be calculated. Deriving the eigensystem of the tensor, the eigenvectors and eigenvalues can be calculated to describe the three main directions of diffusion and its magnitude. Using DTI data, fiber bundles can be determined, to gain information about eloquent brain structures. Especially in neurosurgery, information about location and dimension of eloquent structures like the corticospinal tract or the visual pathways is of major interest. Therefore, the fiber bundle boundary has to be determined. In this paper, a novel ray-based approach for boundary estimation of tubular structures is presented.