SmallData Symposium 2024

Prof. Dr.  

Harald Binder

Institute of Medical Biometry and Statistics (IMBI), Medical Faculty and Medical Center, University of Freiburg
Stefan-Meier-Str. 26, 79104 Freiburg

Projects

Publications

Schönthaler M, [...], Behrens M, Binder H, Binder N. Challenges and solutions in determining urolithiasis caseloads using the digital infrastructure of a clinical data warehouse, PLOS ONE. Jan 2026
Watter M, Giuliani C, Benadi G, Engel F, Binder H, Kaier K. Automated identification of contextually relevant biomedical entities with grounded LLMs, Scientific Reports. Jan 2026
Kaier K, [...], Binder H. Identification of biomedical entities from multiple repositories using a specialized metadata schema and search-augmented large language models, BMC Research Notes. Jan 2026
Giuliani C, [...], Binder H, Kaier K. Identifying Biomedical Entities for Datasets in Scientific Articles: 4-Step Cache-Augmented Generation Approach Using GPT-4o and PubTator 3.0, JMIR Formative Research. Nov 2025
Dobler D, Binder H, [...], Weber S. ChatGPT as a Tool for Biostatisticians: A Tutorial on Applications, Opportunities, and Limitations, Statistics in Medicine. Oct 2025
Kaier K, Benadi G, Connor SG, Tagle Ludwig C, Giuliani C, Engel F, Watter M, Binder H. Development and automated deployment of a specialised machine learning schema within a collaborative research centre: an explorative approach using large language models, medRxiv. Oct 2025
Hackenberg M, Pechmann A, Kreutz C, Kirschner J, Binder H. A Statistical Approach to Latent Dynamic Modeling with Differential Equations, The American Statistician. Sep 2025
Brunn N, Hackenberg M, Fullio CL, Vogel T, Binder H. Sparse dimensionality reduction for analyzing single-cell-resolved interactions, Bioinformatics Advances. Sep 2025
Krißmer SM, Menger J, Rollin J, Vogel T, Binder H, Hackenberg M. Adding layers of information to scRNA-seq data using pre-trained language models, bioRxiv. Aug 2025
Frosch M, [...], Binder H, [...], Prinz M. Microglia–neuron crosstalk through Hex–GM2–MGL2 maintains brain homeostasis, Nature. Aug 2025
Hackenberg M, Connor SG, Kabus F, [...], Backofen R, Köttgen A, Rohde A, Binder N, Binder H, the Collaborative Research Center 1597 SmallData. Small Data Explainer -- The impact of small data methods in everyday life, arXiv. Jul 2025
Farhadizadeh M, [...], Walter S, Hempen N, Binder H, Binder N. Challenges and proposed solutions in modeling multimodal medical data: A systematic review, arXiv. May 2025
Hackenberg M, Canal Guitart L, Backofen R, Binder H. Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data, Briefings in Bioinformatics. May 2025
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 Medical Research Methodology. Mar 2025
Hackenberg M, Brunn N, Vogel T, Binder H. Infusing structural assumptions into dimensionality reduction for single-cell RNA sequencing data to identify small gene sets, Communications Biology. Mar 2025
Pfaffenlehner M, Behrens M, [...], 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 Medical Research Methodology. Jan 2025
Siemens W, von Elm E, Binder H, [...], Meerpohl JJ. Opportunities, challenges and risks of using artificial intelligence for evidence synthesis, BMJ Evidence-Based Medicine. Jan 2025
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, Biometrical Journal. Dec 2024
Fichtner UA, [...], Wolkewitz M, 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
Farhadyar K, Bonofiglio F, Hackenberg M, Behrens M, Zöller D, Binder H. Combining propensity score methods with variational autoencoders for generating synthetic data in presence of latent sub-groups, BMC Medical Research Methodology. Sep 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

Related Resources in the Small Data Companion

Binder H, et al. (2025) Sparse dimensionality reduction for analyzing single-cell-resolved interactions
Model, algorithm or code
Binder H, et al. (2025) Single-Cell ALRA-imputed Rat Lung Data
Dataset
Binder H, et al. (2025) Sparse dimensionality reduction for analyzing single-cell-resolved interactions
Original Preprint
Benadi G, et al. (2025) 4-step cache-augmented generation approach for biomedical entity identification
Model, algorithm or code
Benadi G, et al. (2025) Biomedical entity annotation predictions and author validation data for 23 OncoEscape articles Contact for access
Dataset
Benadi G, et al. (2025) SFB1479 Metadata schema
Tutorial
Amann L, et al. (2025) Microglia–neuron crosstalk through Hex–GM2–MGL2 maintains brain homeostasis
Dataset
Amann L, et al. (2025) snRNA-seq of Hexb-deficient brain cells
Dataset
Amann L, et al. (2025) snRNA-seq of Sandhoff disease brain cells
Dataset
Amann L, et al. (2025) snRNA-seq of Hexb-deficient brain cells upon microglia replacement
Dataset
Amann L, et al. (2025) bulk RNA-seq of Hexb-deficient microglia
Dataset
Binder H, et al. (2025) BoostingAutoencoder
Model, algorithm or code
Binder H, et al. (2025) Tasic data: dataset of adult mouse cortical cells
Dataset
Binder H, et al. (2025) Embryoid Body data for PHATE
Dataset
Binder H, et al. (2025) Infusing structural assumptions into dimension reduction for single-cell RNA sequencing data to identify small gene sets
Original Preprint
Al Tawil A, et al. (2025) ChatGPT-as-a-Tool-for-Biostatisticians
Model, algorithm or code
Backofen R, et al. (2025) scManifoldDynamics
Model, algorithm or code
Backofen R, et al. (2025) Embryoid Body data for PHATE
Dataset
Backofen R, et al. (2025) PBMC dataset
Dataset
Backofen R, et al. (2025) Zeisel dataset
Dataset
Backofen R, et al. (2025) scVI.jl
Programming package
Backofen R, et al. (2025) Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data
Original Preprint
Benadi G, et al. (2026) llm-metadata-annotation
Model, algorithm or code
Benadi G, et al. (2026) Identification of biomedical entities from multiple repositories using a specialized metadata schema and search-augmented large language models
Original Preprint
Benadi G, et al. (2025) machine learning schema Contact for access
Model, algorithm or code
Binder H, et al. (2025) LatentDynamics.jl: a Julia package for learning dynamics based on ODEs in the latent space of a VAE
Model, algorithm or code
Binder H, et al. (2025) SMArtCARE dataset
Dataset
Binder H, et al. (2025) LatentDynamics.jl
Tutorial
Binder H, et al. (2025) A statistical approach to latent dynamic modeling with differential equations
Original Preprint
Binder H, et al. (2025) Human Immune Health Atlas: dataset
Dataset
Binder H, et al. (2025) Developing mouse brain dataset (LaManno et al. 2016)
Dataset
Binder H, et al. (2025) Python package "alias"
Model, algorithm or code
Benadi G, et al. (2026) llm-metadata-annotation
Model, algorithm or code
Benadi G, et al. (2026) PubTator3
Website
Benadi G, et al. (2026) LLM Metadata Annoatation Example
Use case scenario
Behrens M, et al. (2024) simcow code/method implementation
Model, algorithm or code
Behrens M, et al. (2024) LatentSubgroups
Model, algorithm or code
Behrens M, et al. (2024) Modified ART study - Simulation design for an artifical but realistic human study dataset
Dataset
Behrens M, et al. (2024) The International Stroke Trial database
Dataset
Behrens M, et al. (2024) IntegratingMeasurementInstruments
Model, algorithm or code
Behrens M, et al. (2024) SMArtCARE registry - spinal muscular atrophy (SMA) patient registry Contact for access
Dataset
Behrens M, et al. (2024) Investigating a domain adaptation approach for integrating different measurement instruments in a longitudinal clinical registry
Binder H, et al. (2025) IMPACT study dataset Contact for access
Dataset

Administrative Manager

Marc Schumacher

Institute of Medical Biometry and Statistics,
Faculty of Medicine and Medical Center –
University of Freiburg