Andreas Müller

Lukas Johanns, Marilin Moor, Davide Panzeri et al.

Biological image analysis increasingly demands integration across heterogeneous tools, programming environments, and domain knowledge that few researchers can command simultaneously. We present Agentic-J, a containerised, multi-agent AI assistant, primarily for ImageJ/Fiji that enables biologists to specify analysis tasks in natural language, from nuclei segmentation and cell tracking to multi-condition quantification. The agent generates executable scripts organised into a documented project structure, so every analysis decision is traceable and the workflow can be reproduced or shared. The specialised sub-agents handle plugin management, code generation, debugging, quality assurance, and statistical reporting. In this paper we introduce the system's design, demonstrate real biological microscopy image analysis workflows, and detailed the technical implementation.

Andreas Müller, Deborah Schmidt, Lucas Rieckert et al.

Volume electron microscopy is the method of choice for the in-situ interrogation of cellular ultrastructure at the nanometer scale. Recent technical advances have led to a rapid increase in large raw image datasets that require computational strategies for segmentation and spatial analysis. In this protocol, we describe a practical and annotation-efficient pipeline for organelle-specific segmentation, spatial analysis, and visualization of large volume electron microscopy datasets using freely available, user-friendly software tools that can be run on a single standard workstation. We specifically target researchers in the life sciences with limited computational expertise, who face the following tasks within their volume electron microscopy projects: i) How to generate 3D segmentation labels for different types of cell organelles while minimizing manual annotation efforts, ii) how to analyze the spatial interactions between organelle instances, and iii) how to best visualize the 3D segmentation results. To meet these demands we give detailed guidelines for choosing the most efficient segmentation tools for the specific cell organelle. We furthermore provide easily executable components for spatial analysis and 3D rendering and bridge compatibility issues between freely available open-source tools, such that others can replicate our full pipeline starting from a raw dataset up to the final plots and rendered images. We believe that our detailed description can serve as a valuable reference for similar projects requiring special strategies for single- or multiple organelle analysis which can be achieved with computational resources commonly available to single-user setups.

Andreas Müller, Denis Lukovnikov, Shingo Kodama et al.

The proliferation of autoregressive (AR) image generators demands reliable detection and attribution of their outputs to mitigate misinformation, and to filter synthetic images from training data to prevent model collapse. To address this need, watermarking techniques, specifically designed for AR models, embed a subtle signal at generation time, enabling downstream verification through a corresponding watermark detector. In this work, we study these schemes and demonstrate their vulnerability to both watermark removal and forgery attacks. We assess existing attacks and further introduce three new attacks: (i) a vector-quantized regeneration removal attack, (ii) adversarial optimization-based attack, and (iii) a frequency injection attack. Our evaluation reveals that removal and forgery attacks can be effective with access to a single watermarked reference image and without access to original model parameters or watermarking secrets. Our findings indicate that existing watermarking schemes for AR image generation do not reliably support synthetic content detection for dataset filtering. Moreover, they enable Watermark Mimicry, whereby authentic images can be manipulated to imitate a generator's watermark and trigger false detection to prevent their inclusion in future model training.

Erwin Quiring, Andreas Müller, Konrad Rieck

Image scaling is an integral part of machine learning and computer vision systems. Unfortunately, this preprocessing step is vulnerable to so-called image-scaling attacks where an attacker makes unnoticeable changes to an image so that it becomes a new image after scaling. This opens up new ways for attackers to control the prediction or to improve poisoning and backdoor attacks. While effective techniques exist to prevent scaling attacks, their detection has not been rigorously studied yet. Consequently, it is currently not possible to reliably spot these attacks in practice. This paper presents the first in-depth systematization and analysis of detection methods for image-scaling attacks. We identify two general detection paradigms and derive novel methods from them that are simple in design yet significantly outperform previous work. We demonstrate the efficacy of these methods in a comprehensive evaluation with all major learning platforms and scaling algorithms. First, we show that image-scaling attacks modifying the entire scaled image can be reliably detected even under an adaptive adversary. Second, we find that our methods provide strong detection performance even if only minor parts of the image are manipulated. As a result, we can introduce a novel protection layer against image-scaling attacks.

Matthias Feurer, Jan N. van Rijn, Arlind Kadra et al.

OpenML is an online platform for open science collaboration in machine learning, used to share datasets and results of machine learning experiments. In this paper we introduce OpenML-Python, a client API for Python, opening up the OpenML platform for a wide range of Python-based tools. It provides easy access to all datasets, tasks and experiments on OpenML from within Python. It also provides functionality to conduct machine learning experiments, upload the results to OpenML, and reproduce results which are stored on OpenML. Furthermore, it comes with a scikit-learn plugin and a plugin mechanism to easily integrate other machine learning libraries written in Python into the OpenML ecosystem. Source code and documentation is available at https://github.com/openml/openml-python/.

Marcel Moravek, Alexander Zender, Andreas Müller

Transformer architectures and models have made significant progress in language-based tasks. In this area, is BERT one of the most widely used and freely available transformer architecture. In our work, we use BERT for context-based phrase recognition of magic spells in the Harry Potter novel series. Spells are a common part of active magic in fantasy novels. Typically, spells are used in a specific context to achieve a supernatural effect. A series of investigations were conducted to see if a Transformer architecture could recognize such phrases based on their context in the Harry Potter saga. For our studies a pre-trained BERT model was used and fine-tuned utilising different datasets and training methods to identify the searched context. By considering different approaches for sequence classification as well as token classification, it is shown that the context of spells can be recognised. According to our investigations, the examined sequence length for fine-tuning and validation of the model plays a significant role in context recognition. Based on this, we have investigated whether spells have overarching properties that allow a transfer of the neural network models to other fantasy universes as well. The application of our model showed promising results and is worth to be deepened in subsequent studies.

Andreas Müller, Denis Lukovnikov, Jonas Thietke et al.

Integrating watermarking into the generation process of latent diffusion models (LDMs) simplifies detection and attribution of generated content. Semantic watermarks, such as Tree-Rings and Gaussian Shading, represent a novel class of watermarking techniques that are easy to implement and highly robust against various perturbations. However, our work demonstrates a fundamental security vulnerability of semantic watermarks. We show that attackers can leverage unrelated models, even with different latent spaces and architectures (UNet vs DiT), to perform powerful and realistic forgery attacks. Specifically, we design two watermark forgery attacks. The first imprints a targeted watermark into real images by manipulating the latent representation of an arbitrary image in an unrelated LDM to get closer to the latent representation of a watermarked image. We also show that this technique can be used for watermark removal. The second attack generates new images with the target watermark by inverting a watermarked image and re-generating it with an arbitrary prompt. Both attacks just need a single reference image with the target watermark. Overall, our findings question the applicability of semantic watermarks by revealing that attackers can easily forge or remove these watermarks under realistic conditions.

Andreas Müller, Carlo Curino, Raghu Ramakrishnan

Foundation models are transforming machine learning across many modalities, with in-context learning replacing classical model training. Recent work on tabular data hints at a similar opportunity to build foundation models for classification for numerical data. However, existing meta-learning approaches can not compete with tree-based methods in terms of inference time. In this paper, we propose MotherNet, a hypernetwork architecture trained on synthetic classification tasks that, once prompted with a never-seen-before training set generates the weights of a trained ``child'' neural-network by in-context learning using a single forward pass. In contrast to most existing hypernetworks that are usually trained for relatively constrained multi-task settings, MotherNet can create models for multiclass classification on arbitrary tabular datasets without any dataset specific gradient descent. The child network generated by MotherNet outperforms neural networks trained using gradient descent on small datasets, and is comparable to predictions by TabPFN and standard ML methods like Gradient Boosting. Unlike a direct application of TabPFN, MotherNet generated networks are highly efficient at inference time. We also demonstrate that HyperFast is unable to perform effective in-context learning on small datasets, and heavily relies on dataset specific fine-tuning and hyper-parameter tuning, while MotherNet requires no fine-tuning or per-dataset hyper-parameters.

Michael Döll, Markus Döhring, Andreas Müller

Gender bias in artificial intelligence has become an important issue, particularly in the context of language models used in communication-oriented applications. This study examines the extent to which Large Language Models (LLMs) exhibit gender bias in pronoun selection in occupational contexts. The analysis evaluates the models GPT-4, GPT-4o, PaLM 2 Text Bison and Gemini 1.0 Pro using a self-generated dataset. The jobs considered include a range of occupations, from those with a significant male presence to those with a notable female concentration, as well as jobs with a relatively equal gender distribution. Three different sentence processing methods were used to assess potential gender bias: masked tokens, unmasked sentences, and sentence completion. In addition, the LLMs suggested names of individuals in specific occupations, which were then examined for gender distribution. The results show a positive correlation between the models' pronoun choices and the gender distribution present in U.S. labor force data. Female pronouns were more often associated with female-dominated occupations, while male pronouns were more often associated with male-dominated occupations. Sentence completion showed the strongest correlation with actual gender distribution, while name generation resulted in a more balanced 'politically correct' gender distribution, albeit with notable variations in predominantly male or female occupations. Overall, the prompting method had a greater impact on gender distribution than the model selection itself, highlighting the complexity of addressing gender bias in LLMs. The findings highlight the importance of prompting in gender mapping.

Andreas Müller, Erwin Quiring

Resource efficiency plays an important role for machine learning nowadays. The energy and decision latency are two critical aspects to ensure a sustainable and practical application. Unfortunately, the energy consumption and decision latency are not robust against adversaries. Researchers have recently demonstrated that attackers can compute and submit so-called sponge examples at inference time to increase the energy consumption and decision latency of neural networks. In computer vision, the proposed strategy crafts inputs with less activation sparsity which could otherwise be used to accelerate the computation. In this paper, we analyze the mechanism how these energy-latency attacks reduce activation sparsity. In particular, we find that input uniformity is a key enabler. A uniform image, that is, an image with mostly flat, uniformly colored surfaces, triggers more activations due to a specific interplay of convolution, batch normalization, and ReLU activation. Based on these insights, we propose two new simple, yet effective strategies for crafting sponge examples: sampling images from a probability distribution and identifying dense, yet inconspicuous inputs in natural datasets. We empirically examine our findings in a comprehensive evaluation with multiple image classification models and show that our attack achieves the same sparsity effect as prior sponge-example methods, but at a fraction of computation effort. We also show that our sponge examples transfer between different neural networks. Finally, we discuss applications of our findings for the good by improving efficiency by increasing sparsity.

Jonas Thietke, Andreas Müller, Denis Lukovnikov et al.

Semantic watermarking methods enable the direct integration of watermarks into the generation process of latent diffusion models by only modifying the initial latent noise. One line of approaches building on Gaussian Shading relies on cryptographic primitives to steer the sampling process of the latent noise. However, we identify several issues in the usage of cryptographic techniques in Gaussian Shading, particularly in its proof of lossless performance and key management, causing ambiguity in follow-up works, too. In this work, we therefore revisit the cryptographic primitives for semantic watermarking. We introduce a novel, general proof of lossless performance based on IND\$-CPA security for semantic watermarks. We then discuss the configuration of the cryptographic primitives in semantic watermarks with respect to security, efficiency, and generation quality.

Michael Döll, Andreas Müller, Bernd Ulmann

Memristor-based in-memory computing has emerged as a promising paradigm to overcome the constraints of the von Neumann bottleneck and the memory wall by enabling fully parallelisable and energy-efficient vector-matrix multiplications. We investigate the effect of nonlinear, memristor-driven weight updates on the convergence behaviour of neural networks trained with equilibrium propagation (EqProp). Six memristor models were characterised by their voltage-current hysteresis and integrated into the EBANA framework for evaluation on two benchmark classification tasks. EqProp can achieve robust convergence under nonlinear weight updates, provided that memristors exhibit a sufficiently wide resistance range of at least an order of magnitude.

Denis Lukovnikov, Andreas Müller, Erwin Quiring et al.

In-generation watermarking for detecting and attributing generated content has recently been explored for latent diffusion models (LDMs), demonstrating high robustness. However, the use of in-generation watermarks in autoregressive (AR) image models has not been explored yet. AR models generate images by autoregressively predicting a sequence of visual tokens that are then decoded into pixels using a vector-quantized decoder. Inspired by red-green watermarks for large language models, we examine token-level watermarking schemes that bias the next-token prediction based on prior tokens. We find that a direct transfer of these schemes works in principle, but the detectability of the watermarks decreases considerably under common image perturbations. As a remedy, we propose two novel watermarking methods that rely on visual token clustering to assign similar tokens to the same set. Firstly, we investigate a training-free approach that relies on a cluster lookup table, and secondly, we finetune VAE encoders to predict token clusters directly from perturbed images. Overall, our experiments show that cluster-level watermarks improve robustness against perturbations and regeneration attacks while preserving image quality. Cluster classification further boosts watermark detectability, outperforming a set of baselines. Moreover, our methods offer fast verification runtime, comparable to lightweight post-hoc watermarking methods.

Christoph Stoeffler, Shivesh Kumar, Andreas Müller

Based on the idea of variable stiffness mechanisms, a variety of such mechanisms is shown in this work. Specifically, 2-DOF parallel kinematic machines equipped with redundant actuators and non-linear springs in the actuated joints are presented and a comparative overview is drawn. Accordingly, a general stiffness formulation in task space of all mechanisms is given. Under fixed geometric parameters, optimization of task space stiffness is carried out on the designs comprising all kinematic solutions. Finally, a stiffness metric is introduced that allows a quantitative comparison of the given mechanism designs. This gives rise to design guidelines for engineers but also shows an interesting outline for future applications of variable stiffness mechanisms.

Zijia Li, Andreas Müller

It has become obvious that certain singular phenomena cannot be explained by a mere investigation of the configuration space, defined as the solution set of the loop closure equations. For example, it was observed that a particular 6R linkage, constructed by a combination of two Goldberg 5R linkages, exhibits kinematic singularities at a smooth point in its configuration space. Such problems are addressed in this paper. To this end, an algebraic framework is used in which the constraints are formulated as polynomial equations using Study parameters. The algebraic object of study is the ideal generated by the constraint equations (the constraint ideal). Using basic tools from commutative algebra and algebraic geometry (primary decomposition, Hilbert's Nullstellensatz), the special phenomenon is related to the fact that the constraint ideal is not a radical ideal. With a primary decomposition of the constraint ideal, the associated prime ideal of one primary ideal contains strictly into the associated prime ideal of another primary ideal which also gives the smooth configuration curve. This analysis is extended to shaky and kinematotropic linkages, for which examples are presented.

Florian Pfisterer, Jan N. van Rijn, Philipp Probst et al.

The performance of modern machine learning methods highly depends on their hyperparameter configurations. One simple way of selecting a configuration is to use default settings, often proposed along with the publication and implementation of a new algorithm. Those default values are usually chosen in an ad-hoc manner to work good enough on a wide variety of datasets. To address this problem, different automatic hyperparameter configuration algorithms have been proposed, which select an optimal configuration per dataset. This principled approach usually improves performance but adds additional algorithmic complexity and computational costs to the training procedure. As an alternative to this, we propose learning a set of complementary default values from a large database of prior empirical results. Selecting an appropriate configuration on a new dataset then requires only a simple, efficient and embarrassingly parallel search over this set. We demonstrate the effectiveness and efficiency of the approach we propose in comparison to random search and Bayesian Optimization.

Andreas Müller, Michal A. Kopera, Simone Marras et al.

Numerical weather prediction (NWP) has proven to be computationally challenging due to its inherent multiscale nature. Currently, the highest resolution NWP models use a horizontal resolution of about 10km. In order to increase the resolution of NWP models highly scalable atmospheric models are needed. The Non-hydrostatic Unified Model of the Atmosphere (NUMA), developed by the authors at the Naval Postgraduate School, was designed to achieve this purpose. NUMA is used by the Naval Research Laboratory, Monterey as the engine inside its next generation weather prediction system NEPTUNE. NUMA solves the fully compressible Navier-Stokes equations by means of high-order Galerkin methods (both spectral element as well as discontinuous Galerkin methods can be used). Mesh generation is done using the p4est library. NUMA is capable of running middle and upper atmosphere simulations since it does not make use of the shallow-atmosphere approximation. This paper presents the performance analysis and optimization of the spectral element version of NUMA. The performance at different optimization stages is analyzed using a theoretical performance model as well as measurements via hardware counters. Machine independent optimization is compared to machine specific optimization using BG/Q vector intrinsics. By using vector intrinsics the main computations reach 1.2 PFlops on the entire machine Mira (12% of the theoretical peak performance). The paper also presents scalability studies for two idealized test cases that are relevant for NWP applications. The atmospheric model NUMA delivers an excellent strong scaling efficiency of 99% on the entire supercomputer Mira using a mesh with 1.8 billion grid points. This allows to run a global forecast of a baroclinic wave test case at 3km uniform horizontal resolution and double precision within the time frame required for operational weather prediction.

Fabian Pedregosa, Gaël Varoquaux, Alexandre Gramfort et al.

Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.org.