arXiv subjects

Thomas Kirste

Publications and source records attributed to Thomas Kirste.

14 recordsLinked to original sources

arXiv2026

CytoBERT: A Foundation Model for Cytometry Data

Cytometry measures the complex characteristics of single cells (e.g., counts and protein expression of immune cells) and is widely used across immunological research and clinical settings. However, cytometry data is highly heterogeneous and unstandardized due to experimental protocols and the choice of measured features. While machine learning methods hold the potential to gain deeper insights into cell biology, these challenges make them difficult to apply and transfer across studies. Recent advances in foundation models can alleviate these issues, but corresponding approaches are still scarce in this field. To address this, we provide CytoBERT, a publicly available, open-source, open-weight foundation model for single-cell cytometry data with variable marker panels. CytoBERT is pretrained in a self-supervised manner on a large-scale cytometry corpus (15 human datasets with heterogeneous marker panels and more than 50 million cells) curated through marker standardization, enabling it to learn transferable inter-marker relationships within cells. Fine-tuning CytoBERT for sample-level classification demonstrates that transfer learning across heterogeneous cytometry datasets is feasible, providing a starting point for scalable, generalizable cytometry analysis. Code is available at GitHub.

cs.LG↗

arXiv2025

Towards representation agnostic probabilistic programming

Current probabilistic programming languages and tools tightly couple model representations with specific inference algorithms, preventing experimentation with novel representations or mixed discrete-continuous models. We introduce a factor abstraction with five fundamental operations that serve as a universal interface for manipulating factors regardless of their underlying representation. This enables representation-agnostic probabilistic programming where users can freely mix different representations (e.g. discrete tables, Gaussians distributions, sample-based approaches) within a single unified framework, allowing practical inference in complex hybrid models that current toolkits cannot adequately express.

cs.PL↗

arXiv2025

Towards Training-Free Underwater 3D Object Detection from Sonar Point Clouds: A Comparison of Traditional and Deep Learning Approaches

Underwater 3D object detection remains one of the most challenging frontiers in computer vision, where traditional approaches struggle with the harsh acoustic environment and scarcity of training data. While deep learning has revolutionized terrestrial 3D detection, its application underwater faces a critical bottleneck: obtaining sufficient annotated sonar data is prohibitively expensive and logistically complex, often requiring specialized vessels, expert surveyors, and favorable weather conditions. This work addresses a fundamental question: Can we achieve reliable underwater 3D object detection without real-world training data? We tackle this challenge by developing and comparing two paradigms for training-free detection of artificial structures in multibeam echo-sounder point clouds. Our dual approach combines a physics-based sonar simulation pipeline that generates synthetic training data for state-of-the-art neural networks, with a robust model-based template matching system that leverages geometric priors of target objects. Evaluation on real bathymetry surveys from the Baltic Sea reveals surprising insights: while neural networks trained on synthetic data achieve 98% mean Average Precision (mAP) on simulated scenes, they drop to 40% mAP on real sonar data due to domain shift. Conversely, our template matching approach maintains 83% mAP on real data without requiring any training, demonstrating remarkable robustness to acoustic noise and environmental variations. Our findings challenge conventional wisdom about data-hungry deep learning in underwater domains and establish the first large-scale benchmark for training-free underwater 3D detection. This work opens new possibilities for autonomous underwater vehicle navigation, marine archaeology, and offshore infrastructure monitoring in data-scarce environments where traditional machine learning approaches fail.

cs.CV↗

arXiv2024

Neuro-Symbolic Artificial Intelligence for Patient Monitoring

In this paper we argue that Neuro-Symbolic AI (NeSy-AI) should be applied for patient monitoring. In this context, we introduce patient monitoring as a special case of Human Activity Recognition and derive concrete requirements for this application area. We then present a process architecture and discuss why NeSy-AI should be applied for patient monitoring. To further support our argumentation, we show how NeSy-AI can help to overcome certain technical challenges that arise from this application area.

cs.HC↗

arXiv2023

AI-Assisted Ethics? Considerations of AI Simulation for the Ethical Assessment and Design of Assistive Technologies

Current ethical debates on the use of artificial intelligence (AI) in health care treat AI as a product of technology in three ways: First, by assessing risks and potential benefits of currently developed AI-enabled products with ethical checklists; second, by proposing ex ante lists of ethical values seen as relevant for the design and development of assisting technology, and third, by promoting AI technology to use moral reasoning as part of the automation process. Subsequently, we propose a fourth approach to AI, namely as a methodological tool to assist ethical reflection. We provide a concept of an AI-simulation informed by three separate elements: 1) stochastic human behavior models based on behavioral data for simulating realistic settings, 2) qualitative empirical data on value statements regarding internal policy, and 3) visualization components that aid in understanding the impact of changes in these variables. The potential of this approach is to inform an interdisciplinary field about anticipated ethical challenges or ethical trade-offs in concrete settings and, hence, to spark a re-evaluation of design and implementation plans. This may be particularly useful for applications that deal with extremely complex values and behavior or with limitations on the communication resources of affected persons (e.g., persons with dementia care or for care of persons with cognitive impairment). Simulation does not replace ethical reflection but does allow for detailed, context-sensitive analysis during the design process and prior to implementation. Finally, we discuss the inherently quantitative methods of analysis afforded by stochastic simulations as well as the potential for ethical discussions and how simulations with AI can improve traditional forms of thought experiments and future-oriented technology assessment.

cs.MA↗

arXiv2023

Towards Measuring Ethicality of an Intelligent Assistive System

Artificial intelligence (AI) based assistive systems, so called intelligent assistive technology (IAT) are becoming increasingly ubiquitous by each day. IAT helps people in improving their quality of life by providing intelligent assistance based on the provided data. A few examples of such IATs include self-driving cars, robot assistants and smart-health management solutions. However, the presence of such autonomous entities poses ethical challenges concerning the stakeholders involved in using these systems. There is a lack of research when it comes to analysing how such IAT adheres to provided ethical regulations due to ethical, logistic and cost issues associated with such an analysis. In the light of the above-mentioned problem statement and issues, we present a method to measure the ethicality of an assistive system. To perform this task, we utilised our simulation tool that focuses on modelling navigation and assistance of Persons with Dementia (PwD) in indoor environments. By utilising this tool, we analyse how well different assistive strategies adhere to provided ethical regulations such as autonomy, justice and beneficence of the stakeholders.

cs.CY↗

arXiv2022

Discovering Behavioral Predispositions in Data to Improve Human Activity Recognition

The automatic, sensor-based assessment of challenging behavior of persons with dementia is an important task to support the selection of interventions. However, predicting behaviors like apathy and agitation is challenging due to the large inter- and intra-patient variability. Goal of this paper is to improve the recognition performance by making use of the observation that patients tend to show specific behaviors at certain times of the day or week. We propose to identify such segments of similar behavior via clustering the distributions of annotations of the time segments. All time segments within a cluster then consist of similar behaviors and thus indicate a behavioral predisposition (BPD). We utilize BPDs by training a classifier for each BPD. Empirically, we demonstrate that when the BPD per time segment is known, activity recognition performance can be substantially improved.

cs.LG↗

arXiv2022

Activity Recognition in Assembly Tasks by Bayesian Filtering in Multi-Hypergraphs

We study sensor-based human activity recognition in manual work processes like assembly tasks. In such processes, the system states often have a rich structure, involving object properties and relations. Thus, estimating the hidden system state from sensor observations by recursive Bayesian filtering can be very challenging, due to the combinatorial explosion in the number of system states. To alleviate this problem, we propose an efficient Bayesian filtering model for such processes. In our approach, system states are represented by multi-hypergraphs, and the system dynamics is modeled by graph rewriting rules. We show a preliminary concept that allows to represent distributions over multi-hypergraphs more compactly than by full enumeration, and present an inference algorithm that works directly on this compact representation. We demonstrate the applicability of the algorithm on a real dataset.

cs.AI↗

arXiv2021

Human Activity Recognition using Attribute-Based Neural Networks and Context Information

We consider human activity recognition (HAR) from wearable sensor data in manual-work processes, like warehouse order-picking. Such structured domains can often be partitioned into distinct process steps, e.g., packaging or transporting. Each process step can have a different prior distribution over activity classes, e.g., standing or walking, and different system dynamics. Here, we show how such context information can be integrated systematically into a deep neural network-based HAR system. Specifically, we propose a hybrid architecture that combines a deep neural network-that estimates high-level movement descriptors, attributes, from the raw-sensor data-and a shallow classifier, which predicts activity classes from the estimated attributes and (optional) context information, like the currently executed process step. We empirically show that our proposed architecture increases HAR performance, compared to state-of-the-art methods. Additionally, we show that HAR performance can be further increased when information about process steps is incorporated, even when that information is only partially correct.

eess.SP↗

arXiv2021

SimDem A Multi-agent Simulation Environment to Model Persons with Dementia and their Assistance

Developing artificial intelligence based assistive systems to aid Persons with Dementia (PwD) requires large amounts of training data. However, data collection poses ethical, legal, economic, and logistic issues. Synthetic data generation tools, in this regard, provide a potential solution. However, we believe that already available such tools do not adequately reflect cognitive deficiencies in behavior simulation. To counter these issues we propose a simulation model (SimDem ) that primarily focuses on cognitive impairments suffered by PwD and can be easily configured and adapted by the users to model and evaluate assistive solutions.

cs.AI↗

arXiv2020

Gaussian graphical models reveal inter-modal and inter-regional conditional dependencies of brain alterations in Alzheimer's disease

Alzheimer's disease (AD) is characterized by a sequence of pathological changes, which are commonly assessed in vivo using MRI and PET. Currently, the most approaches to analyze statistical associations between brain regions rely on Pearson correlation. However, these are prone to spurious correlations arising from uninformative shared variance. Notably, there are no appropriate multivariate statistical models available that can easily integrate dozens of variables derived from such data, being able to use the additional information provided from the combination of data sources. Gaussian graphical models (GGMs) can estimate the conditional dependency from given data, which is expected to reflect the underlying causal relationships. We applied GGMs to assess multimodal regional brain alterations in AD. We obtained data from N=972 subjects from the Alzheimer's Disease Neuroimaging Initiative. The mean amyloid load (AV45-PET), glucose metabolism (FDG-PET), and gray matter volume (MRI) were calculated. GGMs were estimated using a Bayesian framework for the combined multimodal data to obtain conditional dependency networks. Conditional dependency matrices were much sparser (10% density) than Pearson correlation matrices (50% density). Within modalities, conditional dependency networks yielded clusters connecting anatomically adjacent regions. For associations between different modalities, only few region-specific connections remained. Graph-theoretical network statistics were significantly altered between groups, with a biphasic u-shape trajectory. GGMs removed shared variance among multimodal measures of regional brain alterations in MCI and AD, and yielded sparser matrices compared to Pearson correlation networks. Therefore, GGMs may be used as alternative to thresholding-approaches typically applied to correlation networks to obtain the most informative relations between variables.

q-bio.NC↗

arXiv2018

State-Space Abstractions for Probabilistic Inference: A Systematic Review

Tasks such as social network analysis, human behavior recognition, or modeling biochemical reactions, can be solved elegantly by using the probabilistic inference framework. However, standard probabilistic inference algorithms work at a propositional level, and thus cannot capture the symmetries and redundancies that are present in these tasks. Algorithms that exploit those symmetries have been devised in different research fields, for example by the lifted inference-, multiple object tracking-, and modeling and simulation-communities. The common idea, that we call state space abstraction, is to perform inference over compact representations of sets of symmetric states. Although they are concerned with a similar topic, the relationship between these approaches has not been investigated systematically. This survey provides the following contributions. We perform a systematic literature review to outline the state of the art in probabilistic inference methods exploiting symmetries. From an initial set of more than 4,000 papers, we identify 116 relevant papers. Furthermore, we provide new high-level categories that classify the approaches, based on common properties of the approaches. The research areas underlying each of the categories are introduced concisely. Researchers from different fields that are confronted with a state space explosion problem in a probabilistic system can use this classification to identify possible solutions. Finally, based on this conceptualization, we identify potentials for future research, as some relevant application domains are not addressed by current approaches.

cs.AI↗

arXiv2018

Lifted Filtering via Exchangeable Decomposition

We present a model for exact recursive Bayesian filtering based on lifted multiset states. Combining multisets with lifting makes it possible to simultaneously exploit multiple strategies for reducing inference complexity when compared to list-based grounded state representations. The core idea is to borrow the concept of Maximally Parallel Multiset Rewriting Systems and to enhance it by concepts from Rao-Blackwellization and Lifted Inference, giving a representation of state distributions that enables efficient inference. In worlds where the random variables that define the system state are exchangeable -- where the identity of entities does not matter -- it automatically uses a representation that abstracts from ordering (achieving an exponential reduction in complexity) -- and it automatically adapts when observations or system dynamics destroy exchangeability by breaking symmetry.

cs.AI↗

arXiv2017

Sequential Lifted Bayesian Filtering in Multiset Rewriting Systems

Bayesian Filtering for plan and activity recognition is challenging for scenarios that contain many observation equivalent entities (i.e. entities that produce the same observations). This is due to the combinatorial explosion in the number of hypotheses that need to be tracked. However, this class of problems exhibits a certain symmetry that can be exploited for state space representation and inference. We analyze current state of the art methods and find that none of them completely fits the requirements arising in this problem class. We sketch a novel inference algorithm that provides a solution by incorporating concepts from Lifted Inference algorithms, Probabilistic Multiset Rewriting Systems, and Computational State Space Models. Two experiments confirm that this novel algorithm has the potential to perform efficient probabilistic inference on this problem class.

cs.AI↗