arXiv subjects

Nils Strodthoff

Publications and source records attributed to Nils Strodthoff.

At least 55 records · Page 3Linked to original sources

arXiv2024

Insights Into the Inner Workings of Transformer Models for Protein Function Prediction

Motivation: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent representations inside of transformer models, which were finetuned to Gene Ontology term and Enzyme Commission number prediction, can be inspected too. Results: The approach enabled us to identify amino acids in the sequences that the transformers pay particular attention to, and to show that these relevant sequence parts reflect expectations from biology and chemistry, both in the embedding layer and inside of the model, where we identified transformer heads with a statistically significant correspondence of attribution maps with ground truth sequence annotations (e.g. transmembrane regions, active sites) across many proteins. Availability and Implementation: Source code can be accessed at https://github.com/markuswenzel/xai-proteins .

cs.LG↗

arXiv2024

Decoupling Pixel Flipping and Occlusion Strategy for Consistent XAI Benchmarks

Feature removal is a central building block for eXplainable AI (XAI), both for occlusion-based explanations (Shapley values) as well as their evaluation (pixel flipping, PF). However, occlusion strategies can vary significantly from simple mean replacement up to inpainting with state-of-the-art diffusion models. This ambiguity limits the usefulness of occlusion-based approaches. For example, PF benchmarks lead to contradicting rankings. This is amplified by competing PF measures: Features are either removed starting with most influential first (MIF) or least influential first (LIF). This study proposes two complementary perspectives to resolve this disagreement problem. Firstly, we address the common criticism of occlusion-based XAI, that artificial samples lead to unreliable model evaluations. We propose to measure the reliability by the R(eference)-Out-of-Model-Scope (OMS) score. The R-OMS score enables a systematic comparison of occlusion strategies and resolves the disagreement problem by grouping consistent PF rankings. Secondly, we show that the insightfulness of MIF and LIF is conversely dependent on the R-OMS score. To leverage this, we combine the MIF and LIF measures into the symmetric relevance gain (SRG) measure. This breaks the inherent connection to the underlying occlusion strategy and leads to consistent rankings. This resolves the disagreement problem, which we verify for a set of 40 different occlusion strategies.

cs.CV↗

arXiv2023

Towards quantitative precision for ECG analysis: Leveraging state space models, self-supervision and patient metadata

Deep learning has emerged as the preferred modeling approach for automatic ECG analysis. In this study, we investigate three elements aimed at improving the quantitative accuracy of such systems. These components consistently enhance performance beyond the existing state-of-the-art, which is predominantly based on convolutional models. Firstly, we explore more expressive architectures by exploiting structured state space models (SSMs). These models have shown promise in capturing long-term dependencies in time series data. By incorporating SSMs into our approach, we not only achieve better performance, but also gain insights into long-standing questions in the field. Specifically, for standard diagnostic tasks, we find no advantage in using higher sampling rates such as 500Hz compared to 100Hz. Similarly, extending the input size of the model beyond 3 seconds does not lead to significant improvements. Secondly, we demonstrate that self-supervised learning using contrastive predictive coding can further improve the performance of SSMs. By leveraging self-supervision, we enable the model to learn more robust and representative features, leading to improved analysis accuracy. Lastly, we depart from synthetic benchmarking scenarios and incorporate basic demographic metadata alongside the ECG signal as input. This inclusion of patient metadata departs from the conventional practice of relying solely on the signal itself. Remarkably, this addition consistently yields positive effects on predictive performance. We firmly believe that all three components should be considered when developing next-generation ECG analysis algorithms.

eess.SP↗

arXiv2023

Multi-dimensional concept discovery (MCD): A unifying framework with completeness guarantees

The completeness axiom renders the explanation of a post-hoc XAI method only locally faithful to the model, i.e. for a single decision. For the trustworthy application of XAI, in particular for high-stake decisions, a more global model understanding is required. Recently, concept-based methods have been proposed, which are however not guaranteed to be bound to the actual model reasoning. To circumvent this problem, we propose Multi-dimensional Concept Discovery (MCD) as an extension of previous approaches that fulfills a completeness relation on the level of concepts. Our method starts from general linear subspaces as concepts and does neither require reinforcing concept interpretability nor re-training of model parts. We propose sparse subspace clustering to discover improved concepts and fully leverage the potential of multi-dimensional subspaces. MCD offers two complementary analysis tools for concepts in input space: (1) concept activation maps, that show where a concept is expressed within a sample, allowing for concept characterization through prototypical samples, and (2) concept relevance heatmaps, that decompose the model decision into concept contributions. Both tools together enable a detailed understanding of the model reasoning, which is guaranteed to relate to the model via a completeness relation. This paves the way towards more trustworthy concept-based XAI. We empirically demonstrate the superiority of MCD against more constrained concept definitions.

cs.LG↗

arXiv2023

Diffusion-based Conditional ECG Generation with Structured State Space Models

Synthetic data generation is a promising solution to address privacy issues with the distribution of sensitive health data. Recently, diffusion models have set new standards for generative models for different data modalities. Also very recently, structured state space models emerged as a powerful modeling paradigm to capture long-term dependencies in time series. We put forward SSSD-ECG, as the combination of these two technologies, for the generation of synthetic 12-lead electrocardiograms conditioned on more than 70 ECG statements. Due to a lack of reliable baselines, we also propose conditional variants of two state-of-the-art unconditional generative models. We thoroughly evaluate the quality of the generated samples, by evaluating pretrained classifiers on the generated data and by evaluating the performance of a classifier trained only on synthetic data, where SSSD-ECG clearly outperforms its GAN-based competitors. We demonstrate the soundness of our approach through further experiments, including conditional class interpolation and a clinical Turing test demonstrating the high quality of the SSSD-ECG samples across a wide range of conditions.

eess.SP↗

arXiv2023

From Modern CNNs to Vision Transformers: Assessing the Performance, Robustness, and Classification Strategies of Deep Learning Models in Histopathology

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

eess.IV↗

arXiv2023

Diffusion-based Time Series Imputation and Forecasting with Structured State Space Models

The imputation of missing values represents a significant obstacle for many real-world data analysis pipelines. Here, we focus on time series data and put forward SSSD, an imputation model that relies on two emerging technologies, (conditional) diffusion models as state-of-the-art generative models and structured state space models as internal model architecture, which are particularly suited to capture long-term dependencies in time series data. We demonstrate that SSSD matches or even exceeds state-of-the-art probabilistic imputation and forecasting performance on a broad range of data sets and different missingness scenarios, including the challenging blackout-missing scenarios, where prior approaches failed to provide meaningful results.

cs.LG↗

arXiv2023

ECG Feature Importance Rankings: Cardiologists vs. Algorithms

Feature importance methods promise to provide a ranking of features according to importance for a given classification task. A wide range of methods exist but their rankings often disagree and they are inherently difficult to evaluate due to a lack of ground truth beyond synthetic datasets. In this work, we put feature importance methods to the test on real-world data in the domain of cardiology, where we try to distinguish three specific pathologies from healthy subjects based on ECG features comparing to features used in cardiologists' decision rules as ground truth. Some methods generally performed well and others performed poorly, while some methods did well on some but not all of the problems considered.

physics.med-ph↗

arXiv2022

Advancing the State-of-the-Art for ECG Analysis through Structured State Space Models

The field of deep-learning-based ECG analysis has been largely dominated by convolutional architectures. This work explores the prospects of applying the recently introduced structured state space models (SSMs) as a particularly promising approach due to its ability to capture long-term dependencies in time series. We demonstrate that this approach leads to significant improvements over the current state-of-the-art for ECG classification, which we trace back to individual pathologies. Furthermore, the model's ability to capture long-term dependencies allows to shed light on long-standing questions in the literature such as the optimal sampling rate or window size to train classification models. Interestingly, we find no evidence for using data sampled at 500Hz as opposed to 100Hz and no advantages from extending the model's input size beyond 3s. Based on this very promising first assessment, SSMs could develop into a new modeling paradigm for ECG analysis.

cs.LG↗

arXiv2022

PredDiff: Explanations and Interactions from Conditional Expectations

PredDiff is a model-agnostic, local attribution method that is firmly rooted in probability theory. Its simple intuition is to measure prediction changes while marginalizing features. In this work, we clarify properties of PredDiff and its close connection to Shapley values. We stress important differences between classification and regression, which require a specific treatment within both formalisms. We extend PredDiff by introducing a new, well-founded measure for interaction effects between arbitrary feature subsets. The study of interaction effects represents an inevitable step towards a comprehensive understanding of black-box models and is particularly important for science applications. Equipped with our novel interaction measure, PredDiff is a promising model-agnostic approach for obtaining reliable, numerically inexpensive and theoretically sound attributions.

cs.LG↗

arXiv2022

Sparse Subspace Clustering for Concept Discovery (SSCCD)

Concepts are key building blocks of higher level human understanding. Explainable AI (XAI) methods have shown tremendous progress in recent years, however, local attribution methods do not allow to identify coherent model behavior across samples and therefore miss this essential component. In this work, we study concept-based explanations and put forward a new definition of concepts as low-dimensional subspaces of hidden feature layers. We novelly apply sparse subspace clustering to discover these concept subspaces. Moving forward, we derive insights from concept subspaces in terms of localized input (concept) maps, show how to quantify concept relevances and lastly, evaluate similarities and transferability between concepts. We empirically demonstrate the soundness of the proposed Sparse Subspace Clustering for Concept Discovery (SSCCD) method for a variety of different image classification tasks. This approach allows for deeper insights into the actual model behavior that would remain hidden from conventional input-level heatmaps.

cs.LG↗

arXiv2022

Self-supervised representation learning from 12-lead ECG data

Clinical 12-lead electrocardiography (ECG) is one of the most widely encountered kinds of biosignals. Despite the increased availability of public ECG datasets, label scarcity remains a central challenge in the field. Self-supervised learning represents a promising way to alleviate this issue. In this work, we put forward the first comprehensive assessment of self-supervised representation learning from clinical 12-lead ECG data. To this end, we adapt state-of-the-art self-supervised methods based on instance discrimination and latent forecasting to the ECG domain. In a first step, we learn contrastive representations and evaluate their quality based on linear evaluation performance on a recently established, comprehensive, clinical ECG classification task. In a second step, we analyze the impact of self-supervised pretraining on finetuned ECG classifiers as compared to purely supervised performance. For the best-performing method, an adaptation of contrastive predictive coding, we find a linear evaluation performance only 0.5% below supervised performance. For the finetuned models, we find improvements in downstream performance of roughly 1% compared to supervised performance, label efficiency, as well as robustness against physiological noise. This work clearly establishes the feasibility of extracting discriminative representations from ECG data via self-supervised learning and the numerous advantages when finetuning such representations on downstream tasks as compared to purely supervised training. As first comprehensive assessment of its kind in the ECG domain carried out exclusively on publicly available datasets, we hope to establish a first step towards reproducible progress in the rapidly evolving field of representation learning for biosignals.

eess.SP↗

arXiv2021

On the Robustness of Pretraining and Self-Supervision for a Deep Learning-based Analysis of Diabetic Retinopathy

There is an increasing number of medical use-cases where classification algorithms based on deep neural networks reach performance levels that are competitive with human medical experts. To alleviate the challenges of small dataset sizes, these systems often rely on pretraining. In this work, we aim to assess the broader implications of these approaches. For diabetic retinopathy grading as exemplary use case, we compare the impact of different training procedures including recently established self-supervised pretraining methods based on contrastive learning. To this end, we investigate different aspects such as quantitative performance, statistics of the learned feature representations, interpretability and robustness to image distortions. Our results indicate that models initialized from ImageNet pretraining report a significant increase in performance, generalization and robustness to image distortions. In particular, self-supervised models show further benefits to supervised models. Self-supervised models with initialization from ImageNet pretraining not only report higher performance, they also reduce overfitting to large lesions along with improvements in taking into account minute lesions indicative of the progression of the disease. Understanding the effects of pretraining in a broader sense that goes beyond simple performance comparisons is of crucial importance for the broader medical imaging community beyond the use-case considered in this work.

cs.CV↗

arXiv2021

Predicting the Binding of SARS-CoV-2 Peptides to the Major Histocompatibility Complex with Recurrent Neural Networks

Predicting the binding of viral peptides to the major histocompatibility complex with machine learning can potentially extend the computational immunology toolkit for vaccine development, and serve as a key component in the fight against a pandemic. In this work, we adapt and extend USMPep, a recently proposed, conceptually simple prediction algorithm based on recurrent neural networks. Most notably, we combine regressors (binding affinity data) and classifiers (mass spectrometry data) from qualitatively different data sources to obtain a more comprehensive prediction tool. We evaluate the performance on a recently released SARS-CoV-2 dataset with binding stability measurements. USMPep not only sets new benchmarks on selected single alleles, but consistently turns out to be among the best-performing methods or, for some metrics, to be even the overall best-performing method for this task.

q-bio.QM↗

arXiv2021

Emergent Hadrons and Diquarks

We discuss the emergence of a low-energy effective theory with quarks, mesons, diquarks and baryons at vanishing and finite baryon density from first principle QCD. The present work also includes an overview on diquarks at vanishing and finite density, and elucidates the physics of transitional changes from baryonic matter to quark matter including diquarks. This set-up is discussed within the functional renormalisation group approach with dynamical hadronisation. In this framework it is detailed how mesons, diquarks, and baryons emerge dynamically from the renormalisation flow of the QCD effective action. Moreover, the fundamental degrees of freedom of QCD, quarks and gluons, decouple from the dynamics of QCD below the respective mass gaps. The resulting global picture unifies the different low energy effective theories used for low and high densities within QCD, and allows for a determination of the respective low energy constants directly from QCD.

hep-ph↗

arXiv2020

Generative Neural Samplers for the Quantum Heisenberg Chain

Generative neural samplers offer a complementary approach to Monte Carlo methods for problems in statistical physics and quantum field theory. This work tests the ability of generative neural samplers to estimate observables for real-world low-dimensional spin systems. It maps out how autoregressive models can sample configurations of a quantum Heisenberg chain via a classical approximation based on the Suzuki-Trotter transformation. We present results for energy, specific heat and susceptibility for the isotropic XXX and the anisotropic XY chain that are in good agreement with Monte Carlo results within the same approximation scheme.

cond-mat.stat-mech↗

arXiv2020

Inferring respiratory and circulatory parameters from electrical impedance tomography with deep recurrent models

Electrical impedance tomography (EIT) is a noninvasive imaging modality that allows a continuous assessment of changes in regional bioimpedance of different organs. One of its most common biomedical applications is monitoring regional ventilation distribution in critically ill patients treated in intensive care units. In this work, we put forward a proof-of-principle study that demonstrates how one can reconstruct synchronously measured respiratory or circulatory parameters from the EIT image sequence using a deep learning model trained in an end-to-end fashion. We demonstrate that one can accurately infer absolute volume, absolute flow, normalized airway pressure and within certain limitations even the normalized arterial blood pressure from the EIT signal alone, in a way that generalizes to unseen patients without prior calibration. As an outlook with direct clinical relevance, we furthermore demonstrate the feasibility of reconstructing the absolute transpulmonary pressure from a combination of EIT and absolute airway pressure, as a way to potentially replace the invasive measurement of esophageal pressure. With these results, we hope to stimulate further studies building on the framework put forward in this work.

eess.IV↗

arXiv2020

Towards Novel Insights in Lattice Field Theory with Explainable Machine Learning

Machine learning has the potential to aid our understanding of phase structures in lattice quantum field theories through the statistical analysis of Monte Carlo samples. Available algorithms, in particular those based on deep learning, often demonstrate remarkable performance in the search for previously unidentified features, but tend to lack transparency if applied naively. To address these shortcomings, we propose representation learning in combination with interpretability methods as a framework for the identification of observables. More specifically, we investigate action parameter regression as a pretext task while using layer-wise relevance propagation (LRP) to identify the most important observables depending on the location in the phase diagram. The approach is put to work in the context of a scalar Yukawa model in (2+1)d. First, we investigate a multilayer perceptron to determine an importance hierarchy of several predefined, standard observables. The method is then applied directly to the raw field configurations using a convolutional network, demonstrating the ability to reconstruct all order parameters from the learned filter weights. Based on our results, we argue that due to its broad applicability, attribution methods such as LRP could prove a useful and versatile tool in our search for new physical insights. In the case of the Yukawa model, it facilitates the construction of an observable that characterises the symmetric phase.

hep-lat↗