Hecht M, Blümle A, Binder H, Schumacher M, Binder N. Investigator-initiated versus industry-sponsored trials – visibility and relevance of randomized controlled trials in clinical practice guidelines (IMPACT), BMC Med Res Methodol. Mar 2025.

Ziemann M, Mitrofanov A, Stöckl R, Alkhnbashi OS, Backofen R, Hess WR. Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems, bioRxiv. Mar 2025.

Fässler D, Heinken A, Hertel J. Characterising Measures of Functional Redundancy in, Microbiome Communities via Relative Entropy, Comput Struct Biotechnol J. Mar 2025.

Hindel J, Mohan R, Bratulic J, Cattaneo D, Brox T, Valada A. Label-Efficient LiDAR Semantic Segmentation with 2D-3D Vision Transformer Adapters, arxiv. Mar 2025.

Giuliani C, Benadi G, Engel F, […], Binder H, Kaier K. Identifying biomedical entities for datasets in scientific articles – A 4-step cache-augmented generation approach using GPT-4o and PubTator 3.0, medRxiv. Mar 2025.

Schramm E, Elsaesser M, Müller J, Kwarteng NA, Evrenoglou T, Cuijpers P, Orestis E, Klein DN, Keller MB, Furukawa TA, Nikolakopoulou A. Efficacy of psychotherapy versus pharmacotherapy, or their combination, in chronic depression: study protocol for a systematic review and network meta-analysis using aggregated and individual patient data, BMJ Open 2025;15(2):e089356. Feb 2025.

Kempf E, Schrodi S, Argus M, Brox T. When and How Does CLIP Enable Domain and Compositional Generalization? arxiv. Feb 2025.

Hackenberg M, Canal Guitart L, Backofen R, Binder H. Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data, bioRxiv. Feb 2025.

Heinzel CS, Purucker L, Hutter F, Pfaffelhuber P. Advancing biogeographical ancestry predictions through machine learning, bioRxiv. Feb 2025.

Stadelmaier J, […], Nikolakopoulou A, Schwingshackl L. Evaluating agreement between individual nutrition randomised controlled trials and cohort studies-a meta-epidemiological study, BMC medicine. Jan 2025.

Wigle A, […], Nikolakopoulou A. Precision of Treatment Hierarchy: A Metric for Quantifying Certainty in Treatment Hierarchies from Network Meta-Analysis, arXiv. Jan 2025.

Pfaffenlehner M, Behrens M, Zoeller D, […], Scherag A, Binder H, Binder N for the EVA4MII project. Methodological challenges using routine clinical care data for real-world evidence: a rapid review utilizing a systematic literature search and focus group discussion, BMC Med Res Methodol. Jan 2025.

Bratulić J, Mittal S, Rupprecht C, Brox T. What Matters for In-Context Learning: A Balancing Act of Look-up and In-Weight Learning, arxiv. Jan 2025.

Siemens W, Elm E von, Binder H, […], Meerpohl J. Opportunities, challenges and risks of using artificial intelligence for evidence synthesis, BMJ Evid Based Med. Jan 2025

Hollmann N, Müller S, Purucker L, […], Hutter F. Accurate predictions on small data with a tabular foundation model, Nature. Jan 2025

Scherer N, Fässler D, Borisov O, Cheng Y, Schlosser P, […], Schmidts M, […], Hertel J, Köttgen A. Coupling of metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and resulting traits and diseases, Nat Genet. Jan 2025

Hindel J, Cattaneo D, Valada A. Taxonomy-Aware Continual Semantic Segmentation in Hyperbolic Spaces for Open-World Perception, IEEE Robot Autom Lett. Dec 2024

Ma J, Li F, Kim S, […], Purucker L, […], Wang B. Efficient MedSAMs: Segment Anything in Medical Images on Laptop, arXiv. Dec 2024

Sukthanker RS, […], Purucker L, Franke JK, Hutter F. HW-GPT-Bench: Hardware-Aware Architecture Benchmark for Language Models. In NeurIPS 2024: Track Datasets and Benchmarks Poster. Dec 2024.

Mallik N, Janowski M, Hog J, Rakotoarison H, Klein A, Grabocka J, Hutter F. Warmstarting for Scaling Language Models. In NeurIPS 2024: Workshop on Adaptive Foundation Models. Dec 2024.

Brunn N, Hackenberg M, Vogel T, Binder H. Sparse dimensionality reduction for analyzing single-cell-resolved interactions, biorxiv. Dec 2024.

Heiss J, Krach F, Schmidt T, Tambe-Ndonfack FB. Nonparametric Filtering, Estimation and Classification using Neural Jump ODEs, arXiv. Dec 2024.

Fichtner UA, Knaus J, Graf E, […], Binder H, Weber S. Exploring the potential of large language models for integration into an academic statistical consulting service–the EXPOLS study protocol, PLoS One. Dec 2024.

Wesselkamp M, Moser N, Kalweit M, Boedecker J, Dormann CF. Process-Informed Neural Networks: A Hybrid Modelling Approach to Improve Predictive Performance and Inference of Neural Networks in Ecology and Beyond, Ecol Lett. Dec 2024.

Curteis T, Wigle A, Michaels CJ, Nikolakopoulou A. Ranking of Treatments in Network Meta-Analysis: Incorporating Minimally Important Differences, Res Sq. Nov 2024

Arango SP, Janowski M, Purucker L, Zela A, Hutter F, Grabocka J. Ensembling Finetuned Language Models for Text Classification, arXiv. Oct 2024.

Strangmann T, Purucker L, Franke JK, Rapant I, Ferreira F, Hutter F. Transfer Learning for Finetuning Large Language Models, arXiv. Nov 2024.

Heinzel CS, Baumdicker F, Pfafffelhuber P. Revealing the range of maximum likelihood estimates in the admixture model, bioRxiv. Oct 2024

Robertson J, Schmidt T, Hutter F, Awad N. A Human-in-the-Loop Fairness-Aware Model Selection Framework for Complex Fairness Objective Landscapes, arXiv. Oct 2024.

Möllenhoff K, Binder N, Dette H. Testing Similarity of Parametric Competing Risks Models for Identifying Potentially Similar Pathways in Healthcare, Stat. Med. Oct 2024.

Küken J, Purucker L, Hutter F. Large Language Models Engineer Too Many Simple Features for Tabular Data. InNeurIPS 2024: Third Table Representation Learning Workshop. Oct 2024.

Arango SP, Janowski M, Purucker L, Zela A, Hutter F, Grabocka J. Dynamic Post-Hoc Neural Ensemblers, arXiv. Oct 2024.

Runge F, Hutter F. Machine Learning for RNA Design: LEARNA. In RNA Design: Methods and Protocols (pp. 63-93). Sep 2024.

Marquart KF, […], Kaufmann MM, Matsushita M, Haenggi T, Cathomen T, […], Schwank G. Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs, Nature Methods. Sep 2024.

Schoenthaler M, […], Behrens M, Binder H, Binder N. A case is not a case is not a case – challenges and solutions in determining urolithiasis caseloads using the digital infrastructure of a clinical data warehouse, medRxiv. Sept 2024.

Farhadyar K, Bonofiglio F, Hackenberg M, Zoeller D, Binder H. Combining propensity score methods with variational autoencoders for generating synthetic data in presence of latent sub-groups, BMC Med. Res. Methodol. Sept 2024

Maier J, Möller F, Purucker L. Hardware Aware Ensemble Selection for Balancing Predictive Accuracy and Cost. In AutoML 2024: Workshop Track. Sept 2024

Rapant I, Purucker L, Ferreira F, Arango SP, Kadra A, Grabocka J, Hutter F. Quick-Tune-Tool: A Practical Tool and its User Guide for Automatically Finetuning Pretrained Models. In AutoML 2024: Workshop Track. Sept 2024

Schmidts M, Qader MA. The Many Faces of Congenital Anomalies of the Kidney and Urinary Tract. In Kidney International Reports; Volume 9, Issue 9 (pp. 2594-2595). Sep 2024.

Schaechter C, Treppner M, Hackenberg M, Raum H, Boedecker J, Binder H. Enhancement of network architecture alignment in comparative single-cell studies, bioRxiv. Aug 2024.

Iruzubieta P, Alves CA, Al Shamsi AM, […], Schmidts M, […], Maroofian R. Clinical and neuroradiological spectrum of biallelic variants in NOTCH3, EBioMedicine. Aug 2024.

Jobson Pargeter W, Backofen R, Tran VD. CRISPert: A Transformer-Based Model for CRISPR-Cas Off-Target Prediction. In ECML 2024: Machine Learning and Knowledge Discovery in Databases, Research Track. Aug 2024.

Bergman E, […], Purucker L, Segel S, Lindauer M, Hutter F, Eggensperger K. AMLTK: A Modular AutoML Toolkit in Python, JOSS. Aug 2024.

Patil S, Schirrmeister RT, Hutter F, Ball T. CoordConformer: Heterogenous EEG datasets decoding using Transformers. In ICML 2024: Workshop on Geometry-grounded Representation Learning and Generative Modeling. Jul 2024

Hoffmann DT, Schrodi S, Bratulić J, Behrmann N, Fischer V, Brox T. Eureka-Moments in Transformers: Multi-Step Tasks Reveal Softmax Induced Optimization Problems. In ICML 2024: Proceedings of Machine Learning Research. Jul 2024

Bordne P, Hasan MA, Bergman E, Awad N, Biedenkapp A. CANDID DAC: Leveraging Coupled Action Dimensions with Importance Differences in DAC, arXiv. Jul 2024.

Schrodi S, Schur J, Argus M, Brox T. Concept Bottleneck Models Without Predefined Concepts, arXiv. Jul 2024.

Pfefferle AT, Purucker L, Hutter F. DAFT: Data-Aware Fine-Tuning of Foundation Models for Efficient and Effective Medical Image Segmentation. In CVPR 2024: Segment Anything In Medical Images On Laptop. Jun 2024

Brutsche J, Rohde A. Sharp adaptive and pathwise stable similarity testing for scalar ergodic diffusions, Ann. Stat. Jun 2024

Behrens M, Farhadizadeh M, Rohde A, Rühle A, Nicolay NH, Binder H, Zöller D. Improving prediction models by incorporating external data with weights based on similarity, arXiv. May 2024.

Bergman E, Purucker L, Hutter F. Don’t Waste Your Time: Early Stopping Cross-Validation, arXiv. May 2024.

Dette H, Koletzko L, Bretz F. Testing for similarity of dose response in multi-regional clinical trials, arXiv. Apr 2024.

Reimer‐Taschenbrecker A, Hess M, […], Has C. IL‐6 levels dominate the serum cytokine signature of severe epidermolysis bullosa: A prospective cohort study, J Eur Acad Dermatol Venereol. Feb 2024.

Hackenberg M, Brunn N, Vogel T, Binder H. Infusing structural assumptions into dimension reduction for single-cell RNA sequencing data to identify small gene sets, bioRxiv. Feb 2024.

Franke JK, Runge F, Koeksal R, Backofen R, Hutter F. RNAformer: A Simple Yet Effective Deep Learning Model for RNA Secondary Structure Prediction, bioRxiv. Feb 2024.

Ging S, Bravo MA, Brox T. Open-ended VQA benchmarking of Vision-Language models by exploiting Classification datasets and their semantic hierarchy, arXiv. Feb 2024.

Hackenberg M, Pfaffenlehner M, Behrens M, Pechmann A, Kirschner J, Binder H. Investigating a Domain Adaptation Approach for Integrating Different Measurement Instruments in a Longitudinal Clinical Registry, Biom J. Dec 2023.

Hackenberg M, Pechmann A, Kreutz C, Kirschner J, Binder H. A statistical approach to latent dynamic modeling with differential equations. arXiv. Nov 2023.