arXiv subjects

Hanno Scharr

Publications and source records attributed to Hanno Scharr.

At least 19 recordsLinked to original sources

arXiv2026

Least but not Last: Fine-tuning Intermediate Principal Components for Better Performance-Forgetting Trade-Offs

Low-Rank Adaptation (LoRA) methods have emerged as crucial techniques for adapting large pre-trained models to downstream tasks under computational and memory constraints. However, they face a fundamental challenge in balancing task-specific performance gains against catastrophic forgetting of pre-trained knowledge, where existing methods provide inconsistent recommendations. This paper presents a comprehensive analysis of the performance-forgetting trade-offs inherent in low-rank adaptation using principal components of weight matrices as initialization. Our investigation reveals that fine-tuning intermediate components leads to better balance and robustness to high learning rates than first (PiSSA) and last (MiLoRA) components in existing work. Building on these findings, we provide practical guidelines for initialization of LoRA methods to balance the performance-forgetting trade-off. In a thorough empirical study on a variety of computer vision and NLP tasks we confirm that these guidelines achieve high accuracy and reduced forgetting.

cs.LG↗

arXiv2026

Using Channel Representations in Regularization Terms: A Case Study on Image Diffusion

In this work we propose a novel non-linear diffusion filtering approach for images based on their channel representation. To derive the diffusion update scheme we formulate a novel energy functional using a soft-histogram representation of image pixel neighborhoods obtained from the channel encoding. The resulting Euler-Lagrange equation yields a non-linear robust diffusion scheme with additional weighting terms stemming from the channel representation which steer the diffusion process. We apply this novel energy formulation to image reconstruction problems, showing good performance in the presence of mixtures of Gaussian and impulse-like noise, e.g. missing data. In denoising experiments of common scalar-valued images our approach performs competitive compared to other diffusion schemes as well as state-of-the-art denoising methods for the considered noise types.

cs.CV↗

arXiv2026

Higher-Order Hit-&-Run Samplers for Linearly Constrained Densities

Markov chain Monte Carlo (MCMC) sampling of densities restricted to linearly constrained domains is an important task arising in Bayesian treatment of inverse problems in the natural sciences. While efficient algorithms for uniform polytope sampling exist, much less work has dealt with more complex constrained densities. In particular, gradient information as used in unconstrained MCMC is not necessarily helpful in the constrained case, where the gradient may push the proposal's density out of the polytope. In this work, we propose a novel constrained sampling algorithm, which combines strengths of higher-order information, like the target's log-density's gradients and curvature, with the Hit-&-Run proposal, a simple mechanism which guarantees the generation of feasible proposals, fulfilling the linear constraints. Our extensive experiments demonstrate improved sampling efficiency on complex constrained densities over various constrained and unconstrained samplers.

stat.CO↗

arXiv2026

RECAST: Model Reconstruction via Counterfactual-Aware Wasserstein Geometry under Limited Data

Counterfactual explanations (CFs) help understand machine learning models by identifying minimal input changes that would lead to alternative model outcomes. Recent work demonstrates their utility for reconstructing black-box models, enabling third-party auditing of opaque decision systems for fairness and accountability. Still, CF-based reconstruction may suffer from decision boundary shifts, overfitting, and restrictive assumptions requiring online query access to target platforms. We propose REconstruction via Counterfactual-Aware waSserstein opTimization (RECAST) under limited data and restricted access, a behavioral surrogate model based on Wasserstein barycentric prototypes. Our approach addresses decision boundary shifts by incorporating CFs as informative, though less representative, samples for both classes, maintaining high surrogate fidelity in low-sample regimes without requiring online access during reconstruction. To enhance fairness auditing, our method enables systematic group fairness diagnostics. Experiments on real-world datasets and various setups show that RECAST effectively achieves high fidelity and query efficiency, as well as stable results even when the access is limited and noisy.

cs.LG↗

arXiv2026

Residual-Space Evolutionary Optimization via Flow-based Generative Models

Data editing with generative methods typically requires differentiable objectives and gradient-based search. However, these assumptions break down in flow-based settings, where edits are performed through forward and backward integration and often involve non-differentiable or black-box objectives. We introduce residual-space evolutionary optimization, a model-agnostic framework that addresses this gap by combining flow-based generative editing with evolutionary algorithms. Building on the observation that conditional flow matching (CFM) can disentangle condition-controlled factors from instance-specific residuals, our framework directly operates in residual space and separates two complementary search regimes: self-pollination performs local exploitation through feature-preserving residual refinement, and cross-pollination promotes broader exploration by recombining residuals across heterogeneous samples. As a proof of concept, we validate on MorphoMNIST, a benchmark dataset for counterfactual generation, and on crystal data, demonstrating that this exploration--exploitation decomposition provides a useful mechanism for balancing target alignment, instance preservation, and diversity, and extends beyond images to real-world scientific domains.

cs.AI↗

arXiv2026

DART: A design-aware microfluidic chip paradigm for real-time live-cell image analysis

High-throughput microfluidic live-cell imaging generates rich single-cell data. Yet semi-automated procedures for locating regions of interest (RoIs), each containing one cell population, and removing surrounding microfluidic structures from recorded images, scale with the number of RoIs. This prevents real-time image analysis and delays time-to-insight by hours to days. We introduce the Design-Aware and Real-Time capable (DART) paradigm for microfluidic cultivation chips, which aligns the CAD blueprint with the physical chip and thereby enables throughput-independent localization of all RoIs and fully automated image processing across diverse RoI geometries and chip layouts. DART establishes this alignment through embedded fiducial markers and deep-learning-based marker detection. We validate DART using the Swiss Army Knife chip, which combines eight structurally distinct RoI designs across 1164 RoI locations. DART localizes all RoIs in five minutes, removes microfluidic structures from raw microscopy images in 40 ms, and performs fully automated image analysis, including cell segmentation, in under 1.1 s per image. Together, these capabilities establish DART as an end-to-end hardware-software paradigm with real-time-capable analysis that paves the way toward closed-loop and outcome-driven smart microscopy.

q-bio.QM↗

arXiv2026

Counterfactual Transport Flows for Offline Conservative Trajectory Refinement

Offline reinforcement learning (RL) offers a path to policy improvement from logged data alone, using historical returns or other measurable outcomes as world feedback. A key difficulty is improving observed behavior without extrapolating beyond what the offline data supports. We propose \emph{counterfactual transport flows}, a source-conditioned trajectory refinement framework for offline decision-making guided by world feedback. Given a low-feedback candidate trajectory, we construct local preference pairs from offline data by retrieving nearby trajectories in latent trajectory space with higher task-specific feedback, and use them as weak supervision for conservative refinement. The framework learns instance-specific refinement directions: at inference time, a refinement strength parameter controls how far the candidate trajectory is transported, enabling a trade-off between preserving the original behavior and applying stronger improvement. Experiments on D4RL benchmarks, including AntMaze and MuJoCo tasks, show that our method improves behavior from historical returns as world feedback, while providing interpretable trajectory-level refinement paths.

cs.LG↗

arXiv2026

Self-Supervised Learning Based on Transformed Image Reconstruction for Equivariance-Coherent Feature Representation

Self-supervised learning (SSL) methods have achieved remarkable success in learning image representations allowing invariances in them - but therefore discarding transformation information that some computer vision tasks actually require. While recent approaches attempt to address this limitation by learning equivariant features using linear operators in feature space, they impose restrictive assumptions that constrain flexibility and generalization. We introduce a weaker definition for the transformation relation between image and feature space denoted as equivariance-coherence. We propose a novel SSL auxiliary task that learns equivariance-coherent representations through intermediate transformation reconstruction, which can be integrated with existing joint embedding SSL methods. Our key idea is to reconstruct images at intermediate points along transformation paths, e.g. when training on 30-degree rotations, we reconstruct the 10-degree and 20-degree rotation states. Reconstructing intermediate states requires the transformation information used in augmentations, rather than suppressing it, and therefore fosters features containing the augmented transformation information. Our method decomposes feature vectors into invariant and equivariant parts, training them with standard SSL losses and reconstruction losses, respectively. We demonstrate substantial improvements on synthetic equivariance benchmarks while maintaining competitive performance on downstream tasks requiring invariant representations. The approach seamlessly integrates with existing SSL methods (iBOT, DINOv2) and consistently enhances performance across diverse tasks, including segmentation, detection, depth estimation, and video dense prediction. Our framework provides a practical way for augmenting SSL methods with equivariant capabilities while preserving invariant performance.

cs.CV↗

arXiv2025

Classifier Reconstruction Through Counterfactual-Aware Wasserstein Prototypes

Counterfactual explanations provide actionable insights by identifying minimal input changes required to achieve a desired model prediction. Beyond their interpretability benefits, counterfactuals can also be leveraged for model reconstruction, where a surrogate model is trained to replicate the behavior of a target model. In this work, we demonstrate that model reconstruction can be significantly improved by recognizing that counterfactuals, which typically lie close to the decision boundary, can serve as informative though less representative samples for both classes. This is particularly beneficial in settings with limited access to labeled data. We propose a method that integrates original data samples with counterfactuals to approximate class prototypes using the Wasserstein barycenter, thereby preserving the underlying distributional structure of each class. This approach enhances the quality of the surrogate model and mitigates the issue of decision boundary shift, which commonly arises when counterfactuals are naively treated as ordinary training instances. Empirical results across multiple datasets show that our method improves fidelity between the surrogate and target models, validating its effectiveness.

cs.LG↗

arXiv2025

Physics-Guided Diffusion Priors for Multi-Slice Reconstruction in Scientific Imaging

Accurate multi-slice reconstruction from limited measurement data is crucial to speed up the acquisition process in medical and scientific imaging. However, it remains challenging due to the ill-posed nature of the problem and the high computational and memory demands. We propose a framework that addresses these challenges by integrating partitioned diffusion priors with physics-based constraints. By doing so, we substantially reduce memory usage per GPU while preserving high reconstruction quality, outperforming both physics-only and full multi-slice reconstruction baselines for different modalities, namely Magnetic Resonance Imaging (MRI) and four-dimensional Scanning Transmission Electron Microscopy (4D-STEM). Additionally, we show that the proposed method improves in-distribution accuracy as well as strong generalization to out-of-distribution datasets.

eess.IV↗

arXiv2025

FlowTIE: Flow-based Transport of Intensity Equation for Phase Gradient Estimation from 4D-STEM Data

We introduce FlowTIE, a neural-network-based framework for phase reconstruction from 4D-Scanning Transmission Electron Microscopy (STEM) data, which integrates the Transport of Intensity Equation (TIE) with a flow-based representation of the phase gradient. This formulation allows the model to bridge data-driven learning with physics-based priors, improving robustness under dynamical scattering conditions for thick specimen. The validation on simulated datasets of crystalline materials, benchmarking to classical TIE and gradient-based optimization methods are presented. The results demonstrate that FlowTIE improves phase reconstruction accuracy, fast, and can be integrated with a thick specimen model, namely multislice method.

cs.LG↗

arXiv2025

LeapFactual: Reliable Visual Counterfactual Explanation Using Conditional Flow Matching

The growing integration of machine learning (ML) and artificial intelligence (AI) models into high-stakes domains such as healthcare and scientific research calls for models that are not only accurate but also interpretable. Among the existing explainable methods, counterfactual explanations offer interpretability by identifying minimal changes to inputs that would alter a model's prediction, thus providing deeper insights. However, current counterfactual generation methods suffer from critical limitations, including gradient vanishing, discontinuous latent spaces, and an overreliance on the alignment between learned and true decision boundaries. To overcome these limitations, we propose LeapFactual, a novel counterfactual explanation algorithm based on conditional flow matching. LeapFactual generates reliable and informative counterfactuals, even when true and learned decision boundaries diverge. Following a model-agnostic approach, LeapFactual is not limited to models with differentiable loss functions. It can even handle human-in-the-loop systems, expanding the scope of counterfactual explanations to domains that require the participation of human annotators, such as citizen science. We provide extensive experiments on benchmark and real-world datasets showing that LeapFactual generates accurate and in-distribution counterfactual explanations that offer actionable insights. We observe, for instance, that our reliable counterfactual samples with labels aligning to ground truth can be beneficially used as new training data to enhance the model. The proposed method is broadly applicable and enhances both scientific knowledge discovery and non-expert interpretability.

cs.LG↗

arXiv2025

Galaxy Morphology Classification with Counterfactual Explanation

Galaxy morphologies play an essential role in the study of the evolution of galaxies. The determination of morphologies is laborious for a large amount of data giving rise to machine learning-based approaches. Unfortunately, most of these approaches offer no insight into how the model works and make the results difficult to understand and explain. We here propose to extend a classical encoder-decoder architecture with invertible flow, allowing us to not only obtain a good predictive performance but also provide additional information about the decision process with counterfactual explanations.

cs.LG↗

arXiv2025

EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis

Microfluidic Live-Cell Imaging (MLCI) yields data on microbial cell factories. However, continuous acquisition is challenging as high-throughput experiments often lack real-time insights, delaying responses to stochastic events. We introduce three components in the Experiment Automation Pipeline for Event-Driven Microscopy to Smart Microfluidic Single-Cell Analysis (EAP4EMSIG): a fast, accurate Multi-Layer Perceptron (MLP)-based autofocusing method predicting the focus offset, an evaluation of real-time segmentation methods and a real-time data analysis dashboard. Our MLP-based autofocusing achieves a Mean Absolute Error (MAE) of 0.105 $μ$m with inference times from 87 ms. Among eleven evaluated Deep Learning (DL) segmentation methods, Cellpose reached a Panoptic Quality (PQ) of 93.36 %, while a distance-based method was fastest (121 ms, Panoptic Quality 93.02 %).

q-bio.QM↗

arXiv2025

Efficient Epistemic Uncertainty Estimation in Cerebrovascular Segmentation

Brain vessel segmentation of MR scans is a critical step in the diagnosis of cerebrovascular diseases. Due to the fine vessel structure, manual vessel segmentation is time consuming. Therefore, automatic deep learning (DL) based segmentation techniques are intensively investigated. As conventional DL models yield a high complexity and lack an indication of decision reliability, they are often considered as not trustworthy. This work aims to increase trust in DL based models by incorporating epistemic uncertainty quantification into cerebrovascular segmentation models for the first time. By implementing an efficient ensemble model combining the advantages of Bayesian Approximation and Deep Ensembles, we aim to overcome the high computational costs of conventional probabilistic networks. Areas of high model uncertainty and erroneous predictions are aligned which demonstrates the effectiveness and reliability of the approach. We perform extensive experiments applying the ensemble model on out-of-distribution (OOD) data. We demonstrate that for OOD-images, the estimated uncertainty increases. Additionally, omitting highly uncertain areas improves the segmentation quality, both for in- and out-of-distribution data. The ensemble model explains its limitations in a reliable manner and can maintain trustworthiness also for OOD data and could be considered in clinical applications

eess.IV↗

arXiv2025

How To Make Your Cell Tracker Say "I dunno!"

Cell tracking is a key computational task in live-cell microscopy, but fully automated analysis of high-throughput imaging requires reliable and, thus, uncertainty-aware data analysis tools, as the amount of data recorded within a single experiment exceeds what humans are able to overlook. We here propose and benchmark various methods to reason about and quantify uncertainty in linear assignment-based cell tracking algorithms. Our methods take inspiration from statistics and machine learning, leveraging two perspectives on the cell tracking problem explored throughout this work: Considering it as a Bayesian inference problem and as a classification problem. Our methods admit a framework-like character in that they equip any frame-to-frame tracking method with uncertainty quantification. We demonstrate this by applying it to various existing tracking algorithms including the recently presented Transformer-based trackers. We demonstrate empirically that our methods yield useful and well-calibrated tracking uncertainties.

cs.CV↗

arXiv2025

1LoRA: Summation Compression for Very Low-Rank Adaptation

Parameter-Efficient Fine-Tuning (PEFT) methods have transformed the approach to fine-tuning large models for downstream tasks by enabling the adjustment of significantly fewer parameters than those in the original model matrices. In this work, we study the "very low rank regime", where we fine-tune the lowest amount of parameters per linear layer for each considered PEFT method. We propose 1LoRA (Summation Low-Rank Adaptation), a compute, parameter and memory efficient fine-tuning method which uses the feature sum as fixed compression and a single trainable vector as decompression. Differently from state-of-the-art PEFT methods like LoRA, VeRA, and the recent MoRA, 1LoRA uses fewer parameters per layer, reducing the memory footprint and the computational cost. We extensively evaluate our method against state-of-the-art PEFT methods on multiple fine-tuning tasks, and show that our method not only outperforms them, but is also more parameter, memory and computationally efficient. Moreover, thanks to its memory efficiency, 1LoRA allows to fine-tune more evenly across layers, instead of focusing on specific ones (e.g. attention layers), improving performance further.

cs.CV↗

arXiv2025

Enhancing Monocular Depth Estimation with Multi-Source Auxiliary Tasks

Monocular depth estimation (MDE) is a challenging task in computer vision, often hindered by the cost and scarcity of high-quality labeled datasets. We tackle this challenge using auxiliary datasets from related vision tasks for an alternating training scheme with a shared decoder built on top of a pre-trained vision foundation model, while giving a higher weight to MDE. Through extensive experiments we demonstrate the benefits of incorporating various in-domain auxiliary datasets and tasks to improve MDE quality on average by ~11%. Our experimental analysis shows that auxiliary tasks have different impacts, confirming the importance of task selection, highlighting that quality gains are not achieved by merely adding data. Remarkably, our study reveals that using semantic segmentation datasets as Multi-Label Dense Classification (MLDC) often results in additional quality gains. Lastly, our method significantly improves the data efficiency for the considered MDE datasets, enhancing their quality while reducing their size by at least 80%. This paves the way for using auxiliary data from related tasks to improve MDE quality despite limited availability of high-quality labeled data. Code is available at https://jugit.fz-juelich.de/ias-8/mdeaux.

cs.CV↗