Peter Steinbach

Peter Steinbach, Felicita Gernhardt, Mahnoor Tanveer et al.

With the availability of data, hardware, software ecosystem and relevant skill sets, the machine learning community is undergoing a rapid development with new architectures and approaches appearing at high frequency every year. In this article, we conduct an exemplary image classification study in order to demonstrate how confidence intervals around accuracy measurements can greatly enhance the communication of research results as well as impact the reviewing process. In addition, we explore the hallmarks and limitations of this approximation. We discuss the relevance of this approach reflecting on a spotlight publication of ICLR22. A reproducible workflow is made available as an open-source adjoint to this publication. Based on our discussion, we make suggestions for improving the authoring and reviewing process of machine learning articles.

André Homeyer, Christian Geißler, Lars Ole Schwen et al.

Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological diagnosis. Prior to routine use, it is important to evaluate their predictive performance and obtain regulatory approval. This assessment requires appropriate test datasets. However, compiling such datasets is challenging and specific recommendations are missing. A committee of various stakeholders, including commercial AI developers, pathologists, and researchers, discussed key aspects and conducted extensive literature reviews on test datasets in pathology. Here, we summarize the results and derive general recommendations for the collection of test datasets. We address several questions: Which and how many images are needed? How to deal with low-prevalence subsets? How can potential bias be detected? How should datasets be reported? What are the regulatory requirements in different countries? The recommendations are intended to help AI developers demonstrate the utility of their products and to help regulatory agencies and end users verify reported performance measures. Further research is needed to formulate criteria for sufficiently representative test datasets so that AI solutions can operate with less user intervention and better support diagnostic workflows in the future.

Danush Kumar Venkatesh, Peter Steinbach

Many deep learning methods have successfully solved complex tasks in computer vision and speech recognition applications. Nonetheless, the robustness of these models has been found to be vulnerable to perturbed inputs or adversarial examples, which are imperceptible to the human eye, but lead the model to erroneous output decisions. In this study, we adapt and introduce two geometric metrics, density and coverage, and evaluate their use in detecting adversarial samples in batches of unseen data. We empirically study these metrics using MNIST and two real-world biomedical datasets from MedMNIST, subjected to two different adversarial attacks. Our experiments show promising results for both metrics to detect adversarial examples. We believe that his work can lay the ground for further study on these metrics' use in deployed machine learning systems to monitor for possible attacks by adversarial examples or related pathologies such as dataset shift.

Qasim M. K. Siddiqui, Sebastian Starke, Peter Steinbach

Instance segmentation has witnessed promising advancements through deep neural network-based algorithms. However, these models often exhibit incorrect predictions with unwarranted confidence levels. Consequently, evaluating prediction uncertainty becomes critical for informed decision-making. Existing methods primarily focus on quantifying uncertainty in classification or regression tasks, lacking emphasis on instance segmentation. Our research addresses the challenge of estimating spatial certainty associated with the location of instances with star-convex shapes. Two distinct clustering approaches are evaluated which compute spatial and fractional certainty per instance employing samples by the Monte-Carlo Dropout or Deep Ensemble technique. Our study demonstrates that combining spatial and fractional certainty scores yields improved calibrated estimation over individual certainty scores. Notably, our experimental results show that the Deep Ensemble technique alongside our novel radial clustering approach proves to be an effective strategy. Our findings emphasize the significance of evaluating the calibration of estimated certainties for model reliability and decision-making.

Jan Boelts, Michael Deistler, Manuel Gloeckler et al.

Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challenge. Simulation-based inference (SBI) addresses this by enabling Bayesian inference for simulators, identifying parameters that match observed data and align with prior knowledge. Unlike traditional Bayesian inference, SBI only needs access to simulations from the model and does not require evaluations of the likelihood function. In addition, SBI algorithms do not require gradients through the simulator, allow for massive parallelization of simulations, and can perform inference for different observations without further simulations or training, thereby amortizing inference. Over the past years, we have developed, maintained, and extended sbi, a PyTorch-based package that implements Bayesian SBI algorithms based on neural networks. The sbi toolkit implements a wide range of inference methods, neural network architectures, sampling methods, and diagnostic tools. In addition, it provides well-tested default settings, but also offers flexibility to fully customize every step of the simulation-based inference workflow. Taken together, the sbi toolkit enables scientists and engineers to apply state-of-the-art SBI methods to black-box simulators, opening up new possibilities for aligning simulations with empirically observed data.

Michael Deistler, Jan Boelts, Peter Steinbach et al.

A central challenge in many areas of science and engineering is to identify model parameters that are consistent with prior knowledge and empirical data. Bayesian inference offers a principled framework for this task, but can be computationally prohibitive when models are defined by stochastic simulators. Simulation-based Inference (SBI) is a suite of methods developed to overcome this limitation, which has enabled scientific discoveries in fields such as particle physics, astrophysics, and neuroscience. The core idea of SBI is to train neural networks on data generated by a simulator, without requiring access to likelihood evaluations. Once trained, inference is amortized: The neural network can rapidly perform Bayesian inference on empirical observations without requiring additional training or simulations. In this tutorial, we provide a practical guide for practitioners aiming to apply SBI methods. We outline a structured SBI workflow and offer practical guidelines and diagnostic tools for every stage of the process -- from setting up the simulator and prior, choosing and training inference networks, to performing inference and validating the results. We illustrate these steps through examples from astrophysics, psychophysics, and neuroscience. This tutorial empowers researchers to apply state-of-the-art SBI methods, facilitating efficient parameter inference for scientific discovery.

Israt Jahan Tulin, Sebastian Starke, Dominic Windisch et al.

Ultrafast electron beam X-ray computed tomography produces noisy data due to short measurement times, causing reconstruction artifacts and limiting overall image quality. To counteract these issues, two self-supervised deep learning methods for denoising of raw detector data were investigated and compared against a non-learning based denoising method. We found that the application of the deep-learning-based methods was able to enhance signal-to-noise ratios in the detector data and also led to consistent improvements of the reconstructed images, outperforming the non-learning based method.

Stefan Kluth, Maria Grazia Pia, Thomas Schoerner-Sadenius et al.

The ability to read, use and develop code efficiently and successfully is a key ingredient in modern particle physics. We report the experience of a training program, identified as "Advanced Programming Concepts", that introduces software concepts, methods and techniques to work effectively on a daily basis in a HEP experiment or other programming intensive fields. This paper illustrates the principles, motivations and methods that shape the "Advanced Computing Concepts" training program, the knowledge base that it conveys, an analysis of the feedback received so far, and the integration of these concepts in the software development process of the experiments as well as its applicability to a wider audience.