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Author

Philipp Seegerer

Bio: Philipp Seegerer is an academic researcher from Technical University of Berlin. The author has contributed to research in topics: Artificial neural network & Cardiac electrophysiology. The author has an hindex of 10, co-authored 15 publications receiving 626 citations. Previous affiliations of Philipp Seegerer include Siemens & Princeton University.

Papers
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Journal Article
TL;DR: iNNvestigate as mentioned in this paper provides a common interface and out-of-the-box implementation for many analysis methods, including the reference implementation for PatternNet and PatternAttribution as well as for LRP-methods.
Abstract: 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 pre- dictions, 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 short- coming 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-the- box 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.

211 citations

Journal ArticleDOI
TL;DR: This paper proposes a novel criterion for CNN pruning inspired by neural network interpretability: the most relevant elements, i.e. weights or filters, are automatically found using their relevance scores obtained from concepts of explainable AI (XAI).

131 citations

Journal ArticleDOI
TL;DR: Different automated TIL scoring approaches are discussed ranging from classical image segmentation, where cell boundaries are identified and the resulting objects classified according to shape properties, to machine learning-based approaches that directly classify cells without segmentation but rely on large amounts of training data.

114 citations

Journal ArticleDOI
TL;DR: In this paper, the authors investigate three types of biases: biases which affect the entire dataset, biases which are by chance correlated with class labels and sampling biases, and they advocate pixel-wise heatmaps, which offer a more precise and versatile diagnostic instrument.
Abstract: Deep learning has recently gained popularity in digital pathology due to its high prediction quality. However, the medical domain requires explanation and insight for a better understanding beyond standard quantitative performance evaluation. Recently, many explanation methods have emerged. This work shows how heatmaps generated by these explanation methods allow to resolve common challenges encountered in deep learning-based digital histopathology analyses. We elaborate on biases which are typically inherent in histopathological image data. In the binary classification task of tumour tissue discrimination in publicly available haematoxylin-eosin-stained images of various tumour entities, we investigate three types of biases: (1) biases which affect the entire dataset, (2) biases which are by chance correlated with class labels and (3) sampling biases. While standard analyses focus on patch-level evaluation, we advocate pixel-wise heatmaps, which offer a more precise and versatile diagnostic instrument. This insight is shown to not only be helpful to detect but also to remove the effects of common hidden biases, which improves generalisation within and across datasets. For example, we could see a trend of improved area under the receiver operating characteristic (ROC) curve by 5% when reducing a labelling bias. Explanation techniques are thus demonstrated to be a helpful and highly relevant tool for the development and the deployment phases within the life cycle of real-world applications in digital pathology.

107 citations

Journal ArticleDOI
TL;DR: A machine learning algorithm that exploits the differential DNA methylation observed in primary LUSC and metastasized HNSC tumors in the lung was able to discriminate between these two tumor types with high accuracy across multiple cohorts, suggesting its potential as a clinical diagnostic tool.
Abstract: 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.

85 citations


Cited by
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Journal Article
TL;DR: An efficient deep learning approach is developed that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems, and unifies concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate chemical space predictions.
Abstract: Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol−1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

570 citations

Journal ArticleDOI
TL;DR: In this paper, a deep multi-task artificial neural network is used to predict multiple electronic ground-and excited-state properties, such as atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity, and excitation energies.
Abstract: The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel, and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning (ML) model, trained on a data base of \textit{ab initio} calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity, and excitation energies. The ML model is based on a deep multi-task artificial neural network, exploiting underlying correlations between various molecular properties. The input is identical to \emph{ab initio} methods, \emph{i.e.} nuclear charges and Cartesian coordinates of all atoms. For small organic molecules the accuracy of such a "Quantum Machine" is similar, and sometimes superior, to modern quantum-chemical methods---at negligible computational cost.

456 citations

Book ChapterDOI
01 Jan 2019
TL;DR: This chapter gives a concise introduction to LRP with a discussion of how to implement propagation rules easily and efficiently, how the propagation procedure can be theoretically justified as a ‘deep Taylor decomposition’, how to choose the propagation rules at each layer to deliver high explanation quality, and how LRP can be extended to handle a variety of machine learning scenarios beyond deep neural networks.
Abstract: For a machine learning model to generalize well, one needs to ensure that its decisions are supported by meaningful patterns in the input data. A prerequisite is however for the model to be able to explain itself, e.g. by highlighting which input features it uses to support its prediction. Layer-wise Relevance Propagation (LRP) is a technique that brings such explainability and scales to potentially highly complex deep neural networks. It operates by propagating the prediction backward in the neural network, using a set of purposely designed propagation rules. In this chapter, we give a concise introduction to LRP with a discussion of (1) how to implement propagation rules easily and efficiently, (2) how the propagation procedure can be theoretically justified as a ‘deep Taylor decomposition’, (3) how to choose the propagation rules at each layer to deliver high explanation quality, and (4) how LRP can be extended to handle a variety of machine learning scenarios beyond deep neural networks.

428 citations

Journal ArticleDOI
TL;DR: In this paper, the authors provide a timely overview of explainable AI, with a focus on 'post-hoc' explanations, explain its theoretical foundations, and put interpretability algorithms to a test both from a theory and comparative evaluation perspective using extensive simulations.
Abstract: With the broader and highly successful usage of machine learning in industry and the sciences, there has been a growing demand for Explainable AI. Interpretability and explanation methods for gaining a better understanding about the problem solving abilities and strategies of nonlinear Machine Learning, in particular, deep neural networks, are therefore receiving increased attention. In this work we aim to (1) provide a timely overview of this active emerging field, with a focus on 'post-hoc' explanations, and explain its theoretical foundations, (2) put interpretability algorithms to a test both from a theory and comparative evaluation perspective using extensive simulations, (3) outline best practice aspects i.e. how to best include interpretation methods into the standard usage of machine learning and (4) demonstrate successful usage of explainable AI in a representative selection of application scenarios. Finally, we discuss challenges and possible future directions of this exciting foundational field of machine learning.

385 citations

Journal ArticleDOI
TL;DR: Recent promising applications of AI in cardiology and cardiac imaging, which potentially add value to patient care are summarized.

327 citations