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Sebastian Lobentanzer

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2 published item(s)

preprint2026arXiv

Croissant Baker: Metadata Generation for Discoverable, Governable, and Reusable ML Datasets

Croissant has emerged as the metadata standard for machine learning datasets, providing a structured, JSON-LD-based format that makes dataset discovery, automated ingestion, and reproducible analysis machine-checkable across ML platforms. Adoption has accelerated, and NeurIPS now requires Croissant metadata in every submission to its dataset tracks. Yet in practice Croissant generation usually starts with uploading data to a public platform, a path infeasible for governed and large local repositories that hold much of the high-value data ML increasingly relies on. We release Croissant Baker, a local-first, open-source command-line tool that generates validated Croissant metadata directly from a dataset directory through a modular handler registry. We evaluate Croissant Baker on over 140 datasets, scaling to MIMIC-IV at 886 million rows and 374 Parquet files. On held-out comparisons against producer-authored or standards-derived ground truth, Croissant Baker reaches 97-100% agreement across multiple domains.

preprint2023arXiv

Democratising Knowledge Representation with BioCypher

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community.