Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.

2,095 rows · 907 KB · fasta, tsv

A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.

Robert Koch-Institut · AKTIN-Notaufnahmeregister

5 files · 10 KB · pdf, tsv, zip

Der Datensatz "Daten der Notaufnahmesurveillance" wird durch das Robert Koch-Institut und das AKTIN-Notaufnahmeregister bei Krankenhausaufnahmen bereitgestellt. Der Datensatz beinhaltet aggregierte Routinedaten aus deutschen Notaufnahmen zur syndromischen Überwachung von akuten Erkrankungen. Dazu zählen grippeähnliche Erkrankungen (ILI), Coronavirus-Erkrankungen (COVID-19), akute respiratorische Erkrankungen (ARE), gastrointestinale Infektionen (GI) und schwere akute respiratorische Infektionen (SARI). Dabei wird der relative Anteil dieser Erkrankungen an der Gesamtzahl der Notaufnahmevorstellungen sowie die berechneten Erwartungswerte und Prädiktionsintervalle ausgewiesen. Die Daten sind nach Notaufnahmetypen und Altersgruppen aggregiert. Damit bietet der Datensatz eine wertvolle Ressource für die Forschung im Bereich der Notfallmedizin und der Überwachung akuter Gesundheitsereignisse in Deutschland.

Kędziora, Mateusz

49 files · 1.8 MB · npy

Dataset for figures in the Article: Chiral polariton transport enabled by optical spin Hall effect in perovskite waveguides

González-González, Pablo

24 files · 776 KB · npz

Vectorial representations for common image datasets: CIFAR10, CIFAR100, CIFAR100coarse MNIST, FashionMNIST SVHN Extracted using the scripts in this repo, where more details of the extraction can be consulted. The embeddings are provided in different modalities: features: the next-to-last representation of the network logits: the pre-softmax values predictions: the post-softmax values (posterior probabilities) targets: the true labels Each file is stored in format npz (dictionary-like) and contains the numpy representations for the keys "train", "val", and "test" partitions for each dataset. The "train" partition was used to train the corresponding neural model, "val" was used for training monitoring, and "test" was not used during training. The name of the file uses the format <dataset>_<neural-model>_<modality>.npz; for example: "svhn_resnet18_logits.npz". See reference list for publications related to each dataset.

guo, na · pan, jiachen · li, tiantian · et al.

14 files · 100 MB · csv, rar, tsv

ADM_LSIR is a physics-inspired laparoscopic aerosol degradation dataset for aerosol-aware surgical image analysis and image restoration. The v1.0.0 release contains: - 21,916 clean clinical laparoscopic frames (clean/) - 9,562 real intraoperative aerosol-degraded frames (degraded/) - 36,052 simulated aerosol masks, including 19,701 smoke-like masks and 16,351 trajectory masks (mask/) - Blender simulation/cache materials (ADM_LSIR_Blender_simulation_files_v1.0.rar) - metadata_quality_report_v1.0.csv - recommended_splits_v1.0.csv - video_mapping_v1.0.csv - parts_manifest.txt - checksums_v1.0.tsv - release_manifest_v1.0.json All released clinical frames are de-identified and stored as lossless PNG files. Filenames use anonymized video identifiers, e.g., C-V##-####.png for clean frames and D-V##-####.png for degraded frames. The recommended split is defined at the source_video_id/public_video_label level to reduce leakage across frames from the same source video. The public video labels in video_mapping_v1.0.csv provide privacy-safe source-video identifiers (video1-video19). The Blender archive documents the smoke and trajectory mask simulation setup and supports reuse, but it is not a guaranteed exact per-mask reproduction package. The released pre-rendered mask library is the primary reusable dataset component. Source code for synthesis and quality screening is available at: https://github.com/SweetDeathh/ADM_LSIR

Manghi, Paolo

2 files · 8.0 MB · gzip, tsv

Using gene-level and species-level shotgun metagenomics, we provide the first characterization of the rural, Bolivian microbiome; we identified microbial genes which strongly correlate (rho>0.45) with arsenic in urine, and that overall contribute to substantiate that the gut microbiome helps tolerate arsenic via a evict-out-of-house mechanism. Mediation analysis, followed by phylogenetic investigation of metagenomic-assembled genomes, further strengthens this observation. This study elucidates the role of the microbiome in helping to tolerate arsenic-rich environments, and paves the way for probiotic interventions that may mitigate the effects of this toxic metal. This repository contains 2,478 HQ MAGs from the MicroToxBol cohort in fasta format and a descriptive table comprising taxonomic annotation, quality-checks, and coverage estimation.

Bar, Ido

9 files · 8.0 MB · gff, gzip

These files are downsampled WGS fastq files (250k paired-end reads each) of a fungal pathogen ( Ascochyta rabiei ), generated on MGI DNSeq-T7. The files are intended to be used directly as test datasets in PopFun - a Nextflow pipeline for variant calling in fungal genomes.

Kovaliov, Michael

1 files · 100 MB · parquet

Cai

12 files · 8.0 MB · npy

Madhusudan, Gujral

6 files · 29 MB · parquetdeclared

Large language models (LLMs) are trained on massive, publicly available text datasets comprising trillions of tokens, enabling them to excel at general language tasks like next-token prediction. However, LLMs often struggle with domain-specific prompts, exhibiting reduced accuracy or generating inaccurate information (hallucinations). This is because they lack sufficient subject matter expertise. Two primary approaches exist to address this limitation for augmenting LLMs knowledge: Retrieval-Augmented Generation (RAG) and fine-tuning. This presentation focuses on fine-tuning smaller LLMs with domain-specific instruct datasets using the LoRA (Low-Rank Adaptation) technique on Gaudi hardware. We will leverage publicly available LLMs and datasets from the Hugging Face Hub for this demonstration. Though it is possible to fine tune LLMs with plain text data - sourced from documents, articles, and other materials.

Hackl, Jürgen

6 files · 132 MB · parquet, tiffdeclared

EuroFlood is an open, cloud-native index over the JRC/Copernicus CEMS-EFAS Satellite-Derived Flood Depth Maps for Europe (Betterle & Salamon, 2025; CC-BY-4.0) - ~3,280 satellite-derived observed flood-depth maps across Europe, 2015-2024. The bundle is a sparse Cloud-Optimized GeoTIFF encoding, per pixel, the set of flood events that inundated it, plus a combo_id -sorted GeoParquet dictionary and a small events table. Query by region and time via HTTP range reads (GDAL /vsicurl + DuckDB) to retrieve matching events, then fetch only the source depth rasters needed. Built with the open-source EuroFlood Python package ( pip install euroflood ).

Petitpierre, Remi · di Lenardo, Isabella · Hudson, Polly · et al.

4 files · 1.4 GB · geopackage, zipdeclared

The dataset provides a large-scale vector layer of historical building footprints for the Greater London area at the end of the 19th century. It comprises 1,299,029 individual building footprints, extracted automatically from the Ordnance Survey five-feet-to-the-mile (1:1,056) map. The original maps were surveyed between 1891 and 1895 and published between 1893 and 1896, covering approximately 450 km² of urban and suburban London. The dataset was produced using a deep learning-based semantic segmentation pipeline, achieving approximately 97% precision and 95% recall in building detection. Source The source maps were digitised by the National Library of Scotland at 400 ppi and manually georeferenced in collaboration with the David Rumsey Map Collection. The extraction relies on 753 georeferenced map sheets, provided that six sheets are missing from the original archive. Extraction methodology The dataset was generated through an automated workflow: 262 image patches were annotated manually with three classes: (i) regular buildings; (ii) compound buildings; (iii) building boundaries A Mask2Former [1] semantic segmentation model is used. For training and inference, we followed the approach described by [2]. At inference time, boundary predictions are supplemented by the predictions of a specialist model, trained on cadastral plans [3]. Polygon geometries are extracted, based on predicted building contours, and vectorised. Compound buildings components are merged. Content Two versions of the dataset are provided: london_buildings_1891-96_raw.gpkg Raw output from the automated extraction pipeline (after vectorisation and merging) london_buildings_1891-96_corr_v1.gpkg Minimally corrected version including manual adjustments for major structures (e.g. railway stations, monuments, large buildings) Each geometry has a field buil_class , taking values in ['regular','compound'] , relative to the cartographic representation of building classes and the associated processing approach. In corr_v1, manually added geometries take the value NULL . In addition, we relase the labeled images used for training the segmentation model: annotations.zip ZIP folders containing the training and validation data The archive contains subfolders images , containing the tif image samples and labels , corresponding to the semantic class indexes, in png format. labelmap.txt details the class index codes. Data format Format: Geopackage Coordinate reference system: WGS 84 / Pseudo-Mercator (EPSG:3857) Temporal coverage Survey period: 1891-1895 Publication period: 1893-1896 Data creation: 2024-2026 Descriptive statistics Number of building footprints: 1,300,831 (raw), 1,299,040 (corr_v1) Coverage area: 450 km² Detection performance (raw): Precision: 97% Recall: 95% Use and reuse potential This dataset supports research in: urban history historical GIS urban morphology economic and social history It is particularly suited for studying long-term urban change and fine-grained spatial patterns in industrial-era cities. Related publication This dataset is described in a data paper submitted to the Journal of Open Humanities Data Corresponding author Remi Petitpierre Email: remi.petitpierre@epfl.ch Funding The research was supported by the College of Humanities at EPFL and the European Union Horizon Europe Programme (Grant No. 101233051). License This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Citation If you use this dataset, please cite: @misc{london_footprints_petitpierre_2026, author = {Petitpierre, R{\'{e}}mi and di Lenardo, Isabella and Hudson, Polly and Herold Hendrik and McDonough, Katherine and Hecht, Robert and Vaienti, Beatrice and Fleet, Christopher}, title = {{A Layer of Late Victorian London: The Building Footprints from the 1:1,056 Ordnance Survey Map (1891-1896)}}, year = {2026}, publisher = {EPFL}, url = {https://doi.org/10.5281/zenodo.19497434}} Limitations Lower accuracy for very small buildings Occasional segmentation errors in dense or complex areas Minor inconsistencies near map sheet boundaries Liability The authors assume no liability for the use of this dataset. References Cheng, B., Misra, I., Schwing, A. G., Kirillov, A., & Girdhar, R. (2022). Masked-attention Mask Transformer for Universal Image Segmentation . arXiv. https://doi.org/10.48550/arXiv.2112.01527 Petitpierre R. (2026) Generalizable Multiscale Segmentation of Heterogeneous Map Collections . arXiv. https://doi.org/10.48550/arXiv.2603.05037 Petitpierre, R., di Lenardo, I., & Rappo, L. (2024). Revealing the Structure of Land Ownership through the Automatic Vectorisation of Swiss Cadastral Plans . Digital History Switzerland. https://doi.org/10.13140/RG.2.2.26632.33281

Walsh, Calum · Srinivas, Meghana · Stinear, Timothy · et al.

100 files · 2.7 GB · gzip, tsvdeclared

GROND (Genome-derived Ribosomal OperoN Database) A quality-checked and publicly-available database of 16S-ITS-23S RRNA operon sequences and their constituent 16S and 23S genes. Based on GTDB release R232.

Robert Koch-Institut · AKTIN-Notaufnahmeregister

5 files · 24 MB · pdf, tsv, zipdeclared

Der Datensatz "Daten der Notaufnahmesurveillance" wird durch das Robert Koch-Institut und das AKTIN-Notaufnahmeregister bei Krankenhausaufnahmen bereitgestellt. Der Datensatz beinhaltet aggregierte Routinedaten aus deutschen Notaufnahmen zur syndromischen Überwachung von akuten Erkrankungen. Dazu zählen grippeähnliche Erkrankungen (ILI), Coronavirus-Erkrankungen (COVID-19), akute respiratorische Erkrankungen (ARE), gastrointestinale Infektionen (GI) und schwere akute respiratorische Infektionen (SARI). Dabei wird der relative Anteil dieser Erkrankungen an der Gesamtzahl der Notaufnahmevorstellungen sowie die berechneten Erwartungswerte und Prädiktionsintervalle ausgewiesen. Die Daten sind nach Notaufnahmetypen und Altersgruppen aggregiert. Damit bietet der Datensatz eine wertvolle Ressource für die Forschung im Bereich der Notfallmedizin und der Überwachung akuter Gesundheitsereignisse in Deutschland.

Tiskus, Edvinas · Tiškuvienė, Rūta · Bučas, Martynas · et al.

37 files · 1.6 GB · hdf5, tiff, torchdeclared

This record contains the labeled data, trained models, and analysis code supporting the article "Comparing a Vision Foundation Model (DINOv3) and a Task-Specific U-Net for Mapping Emergent Aquatic Vegetation from Fused UAV Multispectral and LiDAR Data" (Remote Sensing in Ecology and Conservation). Contents: - masks/ : georeferenced ground-truth segmentation masks (five classes: aquatic vegetation, water, sand, other objects, background), aligned to the fused UAV orthomosaics and spanning 13 sites across nine Lithuanian waterbodies surveyed between May and August 2024. - models/ : the two final trained segmentation models, a Keras/HDF5 U-Net and a PyTorch DINOv3 model. - code/ : Python scripts for training, evaluation, the label-efficiency experiment, and full-scene prediction. The fused 9-band orthomosaics (five-band multispectral, RGB, and a LiDAR canopy height model; approximately 62 GB) are archived separately because of their size and are available from the corresponding author on request. The DINOv3 SAT-493M pretrained backbone is distributed by Meta under its own license and is not redistributed here; obtain it from the official DINOv3 release.

Filippova, Nina · Bulyonkova, Tatiana · Zvyagina, Elena · et al.

1 files · 1.4 MB · tsvdeclared

Best hit results with analytical parameters

Tolksdorf, Kristin · Goerlitz, Luise · Staat, Doreen · et al.

4 files · 309 KB · pdf, tsv, zipdeclared

Im Datensatz "SARI-Hospitalisierungsinzidenz" des Robert Koch-Instituts werden die wöchentlichen Inzidenzen schwerer akuter respiratorischer Infektionen (SARI) auf Bundesebene in Deutschland bereitgestellt. Die Daten stammen aus der syndromischen Krankenhaussurveillance ICOSARI, die auf ICD-10-Diagnosecodes aus etwa 70 Sentinelkliniken basiert. Der Datensatz umfasst Hospitalisierungsinzidenzen pro 100.000 Einwohner, aufgeschlüsselt nach Altersgruppen, Saison und Kalenderwoche. Neben der Gesamtheit aller SARI-Fälle werden auch Fälle mit zusätzlicher COVID-19-, Influenza- oder RSV-Diagnose separat erfasst. Die Surveillance liefert entscheidende Informationen zur Krankheitslast akuter respiratorischer Erkrankungen und dient als Grundlage für epidemiologische Bewertungen und Empfehlungen für gesundheitspolitische Maßnahmen.

Buchholz, Udo · Lehfeld, Ann-Sophie · Loenenbach, Anna · et al.

5 files · 953 KB · pdf, tsv, zipdeclared

Im Datensatz "GrippeWeb - Daten des Wochenberichts" des Robert Koch-Instituts werden wöchentliche, bevölkerungsbasierte Schätzungen zur Inzidenz akuter respiratorischer Erkrankungen (ARE) und grippeähnlicher Erkrankungen (ILI) in Deutschland bereitgestellt. GrippeWeb als Online-Portal zur partizipativen syndromischen Surveillance nutzt Selbstauskünfte freiwilliger, pseudonym registrierter Teilnehmender ab 16 Jahren zu Symptomen wie Husten, Fieber und Halsschmerzen. Daraus werden Inzidenzen nach Altersgruppen und Regionen errechnet. Die erhobenen Daten unterstützen die Überwachung saisonaler Infektionen und dienen der Risikobewertung in Pandemien wie COVID-19.

Goerlitz, Luise · Tolksdorf, Kristin · Prahm, Kerstin · et al.

4 files · 1.0 MB · pdf, tsv, zipdeclared

Im Datensatz "ARE-Konsultationsinzidenz" des Robert Koch-Instituts werden wöchentliche Inzidenzen von ambulanten Konsultationen mit akuter respiratorischer Erkrankung (ARE) in Deutschland bereitgestellt. Die Daten stammen vom ARE-Praxis-Sentinel des RKI. Hier werden aus Sentinelpraxen Daten von gesetzlich versicherten Patientinnen und Patienten mit einer akuten Atemwegserkrankung entweder einzelfallbasiert anhand von ICD-10-Diagnosecodes mit dem SEED/ARE-Modul oder aggregiert nach Altersgruppen über eine Online-Eingabemaske erfasst. Die ARE-Konsultationsinzidenz wird pro 100.000 Einwohner und nach Altersgruppen und Bundesländern ausgewiesen. Ziel ist es, die Krankheitslast und den saisonalen Verlauf von Atemwegserkrankungen wie Influenza, COVID-19 und RSV-Erkrankungen zu bewerten sowie epidemiologische Entwicklungen frühzeitig zu erkennen