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Machine learning has become an essential tool for extracting regularities in the data and for making inferences. Neural networks, in particular, provide the scalability and flexibility that is needed to convert complex datasets into structured and well-generalizing models. Pretrained models have strongly facilitated the application of neural networks to images and text data. Application to other types of data, e.g., in physics, remains more challenging and often requires ad-hoc approaches. In this chapter, we give an introduction to neural networks with a focus on the latter applications. We present practical steps that ease training of neural networks, and then review simple approaches to introduce prior knowledge into the model. The discussion is supported by theoretical arguments as well as examples showing how well-performing neural networks can be implemented easily in modern neural network frameworks. [ABSTRACT FROM AUTHOR]

Discriminating lung primary tumors and metastases: Pulmonary metastases of head and neck squamous cell carcinoma (HNSC) are currently difficult to distinguish from primary lung squamous cell carcinomas (LUSCs). Differentiating these tumor types has important clinical implications, as whether the lung tumor is primary or has spread can affect the treatment options offered to a patient. Here, Jurmeister et al. developed a machine learning algorithm that exploits the differential DNA methylation observed in primary LUSC and metastasized HNSC tumors in the lung. Their method was able to discriminate between these two tumor types with high accuracy across multiple cohorts, suggesting its potential as a clinical diagnostic tool. Head and neck squamous cell carcinoma (HNSC) patients are at risk of suffering from both pulmonary metastases or a second squamous cell carcinoma of the lung (LUSC). Differentiating pulmonary metastases from primary lung cancers is of high clinical importance, but not possible in most cases with current diagnostics. To address this, we performed DNA methylation profiling of primary tumors and trained three different machine learning methods to distinguish metastatic HNSC from primary LUSC. We developed an artificial neural network that correctly classified 96.4% of the cases in a validation cohort of 279 patients with HNSC and LUSC as well as normal lung controls, outperforming support vector machines (95.7%) and random forests (87.8%). Prediction accuracies of more than 99% were achieved for 92.1% (neural network), 90% (support vector machine), and 43% (random forest) of these cases by applying thresholds to the resulting probability scores and excluding samples with low confidence. As independent clinical validation of the approach, we analyzed a series of 51 patients with a history of HNSC and a second lung tumor, demonstrating the correct classifications based on clinicopathological properties. In summary, our approach may facilitate the reliable diagnostic differentiation of pulmonary metastases of HNSC from primary LUSC to guide therapeutic decisions. [ABSTRACT FROM AUTHOR]

Text documents can be described by a number of abstract concepts such as semantic category, writing style, or sentiment. Machine learning (ML) models have been trained to automatically map documents to these abstract concepts, allowing to annotate very large text collections, more than could be processed by a human in a lifetime. Besides predicting the text’s category very accurately, it is also highly desirable to understand how and why the categorization process takes place. In this paper, we demonstrate that such understanding can be achieved by tracing the classification decision back to individual words using layer-wise relevance propagation (LRP), a recently developed technique for explaining predictions of complex non-linear classifiers. We train two word-based ML models, a convolutional neural network (CNN) and a bag-of-words SVM classifier, on a topic categorization task and adapt the LRP method to decompose the predictions of these models onto words. Resulting scores indicate how much individual words contribute to the overall classification decision. This enables one to distill relevant information from text documents without an explicit semantic information extraction step. We further use the word-wise relevance scores for generating novel vector-based document representations which capture semantic information. Based on these document vectors, we introduce a measure of model explanatory power and show that, although the SVM and CNN models perform similarly in terms of classification accuracy, the latter exhibits a higher level of explainability which makes it more comprehensible for humans and potentially more useful for other applications. [ABSTRACT FROM AUTHOR]

Understanding and interpreting classification decisions of automated image classification systems is of high value in many applications, as it allows to verify the reasoning of the system and provides additional information to the human expert. Although machine learning methods are solving very successfully a plethora of tasks, they have in most cases the disadvantage of acting as a black box, not providing any information about what made them arrive at a particular decision. This work proposes a general solution to the problem of understanding classification decisions by pixel-wise decomposition of nonlinear classifiers. We introduce a methodology that allows to visualize the contributions of single pixels to predictions for kernel-based classifiers over Bag of Words features and for multilayered neural networks. These pixel contributions can be visualized as heatmaps and are provided to a human expert who can intuitively not only verify the validity of the classification decision, but also focus further analysis on regions of potential interest. We evaluate our method for classifiers trained on PASCAL VOC 2009 images, synthetic image data containing geometric shapes, the MNIST handwritten digits data set and for the pre-trained ImageNet model available as part of the Caffe open source package. [ABSTRACT FROM AUTHOR]

When training deep networks it is common knowledge that an efficient and well generalizing representation of the problem is formed. In this paper we aim to elucidate what makes the emerging representation successful. We analyze the layer-wise evolution of the representation in a deep network by building a sequence of deeper and deeper kernels that subsume the mapping performed by more and more layers of the deep network and measuring how these increasingly complex kernels fit the learning problem. We observe that deep networks create increasingly better representations of the learning problem and that the structure of the deep network controls how fast the representation of the task is formed layer after layer. [ABSTRACT FROM AUTHOR]

When training deep networks it is common knowledge that an efficient and well generalizing representation of the problem is formed. In this paper we aim to elucidate what makes the emerging representation successful. We analyze the layer-wise evolution of the representation in a deep network by building a sequence of deeper and deeper kernels that subsume the mapping performed by more and more layers of the deep network and measuring how these increasingly complex kernels fit the learning problem. We observe that deep networks create increasingly better representations of the learning problem and that the structure of the deep network controls how fast the representation of the task is formed layer after layer. [ABSTRACT FROM AUTHOR]

In recent years, deep neural networks have revolutionized many application domains of machine learning and are key components of many critical decision or predictive processes. Therefore, it is crucial that domain specialists can understand and analyze actions and predictions, even of the most complex neural network architectures. Despite these arguments neural networks are often treated as black boxes. In the attempt to alleviate this shortcoming many analysis methods were proposed, yet the lack of reference implementations often makes a systematic comparison between the methods a major effort. The presented library iNNvestigate addresses this by providing a common interface and out-of-thebox implementation for many analysis methods, including the reference implementation for PatternNet and PatternAttribution as well as for LRP-methods. To demonstrate the versatility of iNNvestigate, we provide an analysis of image classifications for variety of state-of-the-art neural network architectures. [ABSTRACT FROM AUTHOR]