@article{VegaSchuetteConrad2016, author = {Vega, Iliusi and Sch{\"u}tte, Christof and Conrad, Tim}, title = {Finding metastable states in real-world time series with recurrence networks}, volume = {445}, journal = {Physica A: Statistical Mechanics and its Applications}, doi = {10.1016/j.physa.2015.10.041}, pages = {1 -- 17}, year = {2016}, abstract = {In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we introduce a way to set the embedding parameters used to reconstruct the state space from the time series. We set them as the ones giving the maximum Shannon entropy of the diagonal line length distribution for the first simultaneous minima of recurrence rate and Shannon entropy. To identify metastable states, as well as the transitions between them, we use a soft partitioning algorithm for module finding which is specifically developed for the case in which a system shows metastability. We illustrate our method with a complex time series example. Finally, we show the robustness of our method for identifying metastable states. Our results suggest that our method is robust for identifying metastable states in complex time series, even when introducing considerable levels of noise and missing data points.}, language = {en} } @article{ConradGenzelCvetkovicetal.2017, author = {Conrad, Tim and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Leichtle, Alexander Benedikt and Vybiral, Jan and Kytyniok, Gitta and Sch{\"u}tte, Christof}, title = {Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data}, volume = {18}, journal = {BMC Bioinfomatics}, number = {160}, doi = {10.1186/s12859-017-1565-4}, year = {2017}, abstract = {Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust against noise and outliers, while the identified feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA),based on thet heory of compressed sensing that allows us to identify a minimal discriminating set of features from mass spectrometry data-sets. We show (1) how our method performs on artificial and real-world data-sets, (2) that its performance is competitive with standard (and widely used) algorithms for analyzing proteomics data, and (3) that it is robust against random and systematic noise. We further demonstrate the applicability of our algorithm to two previously published clinical data-sets.}, language = {en} } @misc{VegaSchuetteConrad2014, author = {Vega, Iliusi and Sch{\"u}tte, Christof and Conrad, Tim}, title = {SAIMeR: Self-adapted method for the identification of metastable states in real-world time series}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50130}, year = {2014}, abstract = {In the framework of time series analysis with recurrence networks, we introduce SAIMeR, a heuristic self-adapted method that determines the elusive recurrence threshold and identifies metastable states in complex time series. To identify metastable states as well as the transitions between them, we use graph theory concepts and a fuzzy partitioning clustering algorithm. We illustrate SAIMeR by applying it to three real-world time series and show that it is able to identify metastable states in real-world data with noise and missing data points. Finally, we suggest a way to choose the embedding parameters used to construct the state space in which this method is performed, based on the analysis of how the values of these parameters affect two recurrence quantitative measurements: recurrence rate and entropy.}, language = {en} } @misc{SchuetteConrad2014, author = {Sch{\"u}tte, Christof and Conrad, Tim}, title = {Showcase 3: Information-based medicine}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, pages = {66 -- 67}, year = {2014}, language = {en} } @article{MuellerPaltraRehmannetal.2023, author = {M{\"u}ller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, Tim}, title = {Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2}, volume = {26}, journal = {iScience}, number = {9}, doi = {10.1016/j.isci.2023.107554}, year = {2023}, abstract = {Measurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibody levels are dynamic: due to waning, antibody levels will drop over time. During the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to support the planning of public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects. This paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. The model was developed in response to the complexity of different immunization sequences and types and is based on neutralization titer studies. This approach allows complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases.}, language = {en} } @inproceedings{WeimannConrad2023, author = {Weimann, Kuba and Conrad, Tim}, title = {Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks}, volume = {50}, booktitle = {Computing in Cardiology (CinC) 2023}, publisher = {IEEE}, doi = {10.22489/CinC.2023.093}, year = {2023}, abstract = {Aims: Interpretation of continuous EEG is a demanding task that requires the expertise of trained neurologists. However, these experts are not always available in many medical centers. As part of the 2023 George B. Moody PhysioNet Challenge, we developed a deep learning based method for analyzing EEG data of comatose patients and predicting prognosis following cardiac arrest. Methods: Our approach is a two-step pipeline that consists of a prediction model and a decision-making strategy. The prediction model is a residual neural network (ResNet-18) that extracts features and makes a prediction based on a short 5-minute EEG recording. In the second step, a majority vote over multiple predictions made for several EEG recordings of a patient determines the final prognosis. Results: Based on 10-fold cross-validation on the training set, we achieved a true positive rate (TPR) of 0.41 for predicting poor outcome while keeping the false positive rate below 0.05 at 72 hours after recovery of spontaneous circulation. On the official challenge leaderboard, our team ZIB_Visual scored 0.426 TPR. Conclusion: Our approach, while simple to implement and execute, faced overfitting challenges during the official competition phase. In this paper, we discuss our implementation and potential improvements to address these issues.}, language = {de} } @article{BleichLinnemannJaidietal.2023, author = {Bleich, Amnon and Linnemann, Antje and Jaidi, Benjamin and Diem, Bjoern H and Conrad, Tim}, title = {Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification}, volume = {5}, journal = {Machine Learning and Knowledge Extraction}, number = {4}, publisher = {MDPI}, doi = {10.3390/make5040077}, year = {2023}, abstract = {Implantable Cardiac Monitor (ICM) devices are demonstrating as of today, the fastest-growing market for implantable cardiac devices. As such, they are becoming increasingly common in patients for measuring heart electrical activity. ICMs constantly monitor and record a patient's heart rhythm and when triggered - send it to a secure server where health care professionals (denote HCPs from here on) can review it. These devices employ a relatively simplistic rule-based algorithm (due to energy consumption constraints) to alert for abnormal heart rhythms. This algorithm is usually parameterized to an over-sensitive mode in order to not miss a case (resulting in a relatively high false-positive rate) and this, combined with the device's nature of constantly monitoring the heart rhythm and its growing popularity, results in HCPs having to analyze and diagnose an increasingly growing amount of data. In order to reduce the load on the latter, automated methods for ECG analysis are nowadays becoming a great tool to assist HCPs in their analysis. While state-of-the-art algorithms are data-driven rather than rule-based, training data for ICMs often consist of specific characteristics that make its analysis unique and particularly challenging. This study presents the challenges and solutions in automatically analyzing ICM data and introduces a method for its classification that outperforms existing methods on such data. It does so by combining high-frequency noise detection (which often occurs in ICM data) with a semi-supervised learning pipeline that allows for re-labeling of training episodes, and by using segmentation and dimension reduction techniques that are robust to morphology variations of the sECG signal (which are typical to ICM data). As a result, it performs better than state-of-the-art techniques on such data with e.g. F1 score of 0.51 vs. 0.38 of our baseline state-of-the-art technique in correctly calling Atrial Fibrilation in ICM data. As such, it could be used in numerous ways such as aiding HCPs in the analysis of ECGs originating from ICMs by, e.g., suggesting a rhythm type.}, language = {en} } @inproceedings{SchubotzFerrerStegmuelleretal.2023, author = {Schubotz, Moritz and Ferrer, Eloi and Stegm{\"u}ller, Johannes and Mietchen, Daniel and Teschke, Olaf and Pusch, Larissa and Conrad, Tim}, title = {Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics}, booktitle = {Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023)}, year = {2023}, abstract = {Mathematical world knowledge is a fundamental component of Wikidata. However, to date, no expertly curated knowledge graph has focused specifically on contemporary mathematics. Addressing this gap, the Mathematical Research Data Initiative (MaRDI) has developed a comprehensive knowledge graph that links multimodal research data in mathematics. This encompasses traditional research data items like datasets, software, and publications and includes semantically advanced objects such as mathematical formulae and hypotheses. This paper details the abilities of the MaRDI knowledge graph, which is based on Wikibase, leading up to its inaugural public release, codenamed Bravo, available on https://portal.mardi4nfdi.de.}, language = {de} } @article{PuschConrad2025, author = {Pusch, Larissa and Conrad, Tim}, title = {Combining LLMs and Knowledge Graphs to Reduce Hallucinations in Biomedical Question Answering}, volume = {5}, journal = {BioMedInformatics}, doi = {10.3390/biomedinformatics5040070}, year = {2025}, abstract = {Advancements in natural language processing (NLP), particularly Large Language Models (LLMs), have greatly improved how we access knowledge. However, in critical domains like biomedicine, challenges like hallucinations—where language models generate infor- mation not grounded in data—can lead to dangerous misinformation. This paper presents a hybrid approach that combines LLMs with Knowledge Graphs (KGs) to improve the accuracy and reliability of question-answering systems in the biomedical field. Our method, implemented using the LangChain framework, includes a query-checking algorithm that checks and, where possible, corrects LLM-generated Cypher queries, which are then exe- cuted on the Knowledge Graph, grounding answers in the KG and reducing hallucinations in the evaluated cases. We evaluated several LLMs, including several GPT models and Llama 3.3:70b, on a custom benchmark dataset of 50 biomedical questions. GPT-4 Turbo achieved 90\% query accuracy, outperforming most other models. We also evaluated prompt engineering, but found little statistically significant improvement compared to the standard prompt, except for Llama 3:70b, which improved with few-shot prompting. To enhance usability, we developed a web-based interface that allows users to input natural language queries, view generated and corrected Cypher queries, and inspect results for accuracy. This framework improves reliability and accessibility by accepting natural language questions and returning verifiable answers directly from the knowledge graph, enabling inspection and reproducibility. The source code for generating the results of this paper and for the user- interface can be found in our Git repository: https://git.zib.de/lpusch/cyphergenkg-gui, accessed on 1 November 2025.}, language = {en} } @article{ConradFerrerMietchenetal.2024, author = {Conrad, Tim and Ferrer, Eloi and Mietchen, Daniel and Pusch, Larissa and Stegmuller, Johannes and Schubotz, Moritz}, title = {Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing}, volume = {11}, journal = {Scientific Data}, doi = {10.1038/s41597-024-03480-0}, year = {2024}, language = {en} } @article{FuerstConradJaegeretal.2024, author = {F{\"u}rst, Steffen and Conrad, Tim and Jaeger, Carlo and Wolf, Sarah}, title = {Vahana.jl - A framework (not only) for large-scale agent-based models}, journal = {Proceedings of Social Simulation Conference 2024 (SSC24)}, year = {2024}, language = {en} } @article{WeimannConrad2024, author = {Weimann, Kuba and Conrad, Tim}, title = {Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification}, volume = {28}, journal = {IEEE Journal of Biomedical and Health Informatics}, number = {11}, doi = {10.1109/JBHI.2024.3427787}, year = {2024}, language = {en} } @article{MaierWeiserConrad2025, author = {Maier, Kristina and Weiser, Martin and Conrad, Tim}, title = {Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology}, volume = {481}, journal = {Proceedings of the Royal Society A}, number = {2306}, publisher = {Royal Society}, arxiv = {http://arxiv.org/abs/2405.12938}, doi = {10.1098/rspa.2024.0421}, year = {2025}, abstract = {This paper introduces a novel hybrid model combining Partial Differential Equations (PDEs) and Ordinary Differential Equations (ODEs) to simulate infectious disease dynamics across geographic regions. By leveraging the spatial detail of PDEs and the computational efficiency of ODEs, the model enables rapid evaluation of public health interventions. Applied to synthetic environments and real-world scenarios in Lombardy, Italy, and Berlin, Germany, the model highlights how interactions between PDE and ODE regions affect infection dynamics, especially in high-density areas. Key findings reveal that the placement of model boundaries in densely populated regions can lead to inaccuracies in infection spread, suggesting that boundaries should be positioned in areas of lower population density to better reflect transmission dynamics. Additionally, regions with low population density hinder infection flow, indicating a need for incorporating, e.g., jumps in the model to enhance its predictive capabilities. Results indicate that the hybrid model achieves a balance between computational speed and accuracy, making it a valuable tool for policymakers in real-time decision-making and scenario analysis in epidemiology and potentially in other fields requiring similar modeling approaches.}, language = {en} } @article{WeimannConrad2024, author = {Weimann, Kuba and Conrad, Tim}, title = {FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems}, journal = {International Journal of Data Science and Analytics}, number = {2024}, publisher = {Springer Nature}, doi = {10.1007/s41060-024-00635-5}, year = {2024}, language = {en} } @article{BostanciConrad2025, author = {Bostanci, Inan and Conrad, Tim}, title = {Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach}, volume = {28}, journal = {Journal of Artificial Societies and Social Simulation}, number = {1}, doi = {10.18564/jasss.5567}, year = {2025}, abstract = {This study investigates the spatial integration of agent-based models (ABMs) and compartmental models for infectious disease modeling, presenting a novel hybrid approach and examining its implications. ABMs offer detailed insights by simulating interactions and decisions among individuals but are computationally expensive for large populations. Compartmental models capture population-level dynamics more efficiently but lack granular detail. We developed a hybrid model that aims to balance the granularity of ABMs with the computational efficiency of compartmental models, offering a more nuanced understanding of disease spread in diverse scenarios, including large populations. This model spatially couples discrete and continuous populations by integrating an ordinary differential equation model with a spatially explicit ABM. Our key objectives were to systematically assess the consistency of disease dynamics and the computational efficiency across various configurations. For this, we evaluated two experimental scenarios and varied the influence of each sub-model via spatial distribution. In the first, the ABM component modeled a homogeneous population; in the second, it simulated a heterogeneous population with landscape-driven movement. Results show that the hybrid model can significantly reduce computational costs but is sensitive to between-model differences, highlighting the importance of model equivalence in hybrid approaches. The code is available at: git.zib.de/ibostanc/hybrid_abm_ode.}, language = {en} } @article{PaltraConrad2024, author = {Paltra, Sydney and Conrad, Tim}, title = {Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review}, volume = {92}, journal = {Advances in Respiratory Medicine}, number = {1}, doi = {10.3390/arm92010009}, year = {2024}, abstract = {Nirmatrelvir/Ritonavir is an oral treatment for mild to moderate COVID-19 cases with a high risk for a severe course of the disease. For this paper, a comprehensive literature review was performed, leading to a summary of currently available data on Nirmatrelvir/Ritonavir's ability to reduce the risk of progressing to a severe disease state. Herein, the focus lies on publications that include comparisons between patients receiving Nirmatrelvir/Ritonavir and a control group. The findings can be summarized as follows: Data from the time when the Delta-variant was dominant show that Nirmatrelvir/Ritonavir reduced the risk of hospitalization or death by 88.9\% for unvaccinated, non-hospitalized high-risk individuals. Data from the time when the Omicron variant was dominant found decreased relative risk reductions for various vaccination statuses: between 26\% and 65\% for hospitalization. The presented papers that differentiate between unvaccinated and vaccinated individuals agree that unvaccinated patients benefit more from treatment with Nirmatrelvir/Ritonavir. However, when it comes to the dependency of potential on age and comorbidities, further studies are necessary. From the available data, one can conclude that Nirmatrelvir/Ritonavir cannot substitute vaccinations; however, its low manufacturing cost and easy administration make it a valuable tool in fighting COVID-19, especially for countries with low vaccination rates.}, language = {de} }