The BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora. These tasks cover a diverse range of text genres (biomedical literature and clinical notes), dataset sizes, and degrees of difficulty and, more importantly, highlight common biomedicine text-mining challenges.

51 PAPERS • NO BENCHMARKS YET

Kvasir-SEG is an open-access dataset of gastrointestinal polyp images and corresponding segmentation masks, manually annotated by a medical doctor and then verified by an experienced gastroenterologist.

35 PAPERS • 3 BENCHMARKS

BioGRID is a biomedical interaction repository with data compiled through comprehensive curation efforts. The current index is version 4.2.192 and searches 75,868 publications for 1,997,840 protein and genetic interactions, 29,093 chemical interactions and 959,750 post translational modifications from major model organism species.

31 PAPERS • 2 BENCHMARKS

Contains hundreds of frontal view X-rays and is the largest public resource for COVID-19 image and prognostic data, making it a necessary resource to develop and evaluate tools to aid in the treatment of COVID-19.

28 PAPERS • NO BENCHMARKS YET

The goal of the Automated Cardiac Diagnosis Challenge (ACDC) challenge is to:

13 PAPERS • 3 BENCHMARKS

ChemProt consists of 1,820 PubMed abstracts with chemical-protein interactions annotated by domain experts and was used in the BioCreative VI text mining chemical-protein interactions shared task.

12 PAPERS • 1 BENCHMARK

The National Institutes of Health’s Clinical Center has made a large-scale dataset of CT images publicly available to help the scientific community improve detection accuracy of lesions. While most publicly available medical image datasets have less than a thousand lesions, this dataset, named DeepLesion, has over 32,000 annotated lesions (220GB) identified on CT images. DeepLesion, a dataset with 32,735 lesions in 32,120 CT slices from 10,594 studies of 4,427 unique patients. There are a variety of lesion types in this dataset, such as lung nodules, liver tumors, enlarged lymph nodes, and so on. It has the potential to be used in various medical image applications

10 PAPERS • 1 BENCHMARK

BLURB is a collection of resources for biomedical natural language processing. In general domains such as newswire and the Web, comprehensive benchmarks and leaderboards such as GLUE have greatly accelerated progress in open-domain NLP. In biomedicine, however, such resources are ostensibly scarce. In the past, there have been a plethora of shared tasks in biomedical NLP, such as BioCreative, BioNLP Shared Tasks, SemEval, and BioASQ, to name just a few. These efforts have played a significant role in fueling interest and progress by the research community, but they typically focus on individual tasks. The advent of neural language models such as BERTs provides a unifying foundation to leverage transfer learning from unlabeled text to support a wide range of NLP applications. To accelerate progress in biomedical pretraining strategies and task-specific methods, it is thus imperative to create a broad-coverage benchmark encompassing diverse biomedical tasks.

7 PAPERS • NO BENCHMARKS YET

Consists of annotated frames containing GI procedure tools such as snares, balloons and biopsy forceps, etc. Beside of the images, the dataset includes ground truth masks and bounding boxes and has been verified by two expert GI endoscopists.

5 PAPERS • 2 BENCHMARKS

Diabetic retinopathy is the leading cause of blindness in the working-age population of the developed world. It is estimated to affect over 93 million people.

4 PAPERS • 1 BENCHMARK

SICAPv2 is a database containing prostate histology whole slide images with both annotations of global Gleason scores and path-level Gleason grades.

4 PAPERS • NO BENCHMARKS YET

BioLAMA is a benchmark comprised of 49K biomedical factual knowledge triples for probing biomedical Language Models. It is used to assess the capabilities of Language Models for being valid biomedical knowledge bases.

3 PAPERS • NO BENCHMARKS YET

CHAOS challenge aims the segmentation of abdominal organs (liver, kidneys and spleen) from CT and MRI data. ONsite section of the CHAOS was held in The IEEE International Symposium on Biomedical Imaging (ISBI) on April 11, 2019, Venice, ITALY. Online submissions are still welcome!

3 PAPERS • NO BENCHMARKS YET

How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly sought after as they could yield significant advances in drug discovery and design as well as protein function analysis. However, the traditional benchmark dataset for this task, Docking Benchmark 5 (DB5), contains only a paltry 230 complexes for training, validating, and testing different machine learning algorithms. In this work, we expand on a dataset recently introduced for this task, the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for geometric deep learning of protein interfaces. The previous version of DIPS contains only the Cartesian coordinates and types of the atoms comprising a given protein complex, whereas DIPS-Plus now includes a plethora of new residue-level

3 PAPERS • NO BENCHMARKS YET

EHR-RelB is a benchmark dataset for biomedical concept relatedness, consisting of 3630 concept pairs sampled from electronic health records (EHRs). EHR-RelA is a smaller dataset of 111 concept pairs, which are mainly unrelated.

3 PAPERS • NO BENCHMARKS YET

Indian Diabetic Retinopathy Image Dataset (IDRiD) dataset consists of typical diabetic retinopathy lesions and normal retinal structures annotated at a pixel level. This dataset also provides information on the disease severity of diabetic retinopathy and diabetic macular edema for each image. This dataset is perfect for the development and evaluation of image analysis algorithms for early detection of diabetic retinopathy.

3 PAPERS • NO BENCHMARKS YET

The Kvasir-SEG dataset includes 196 polyps smaller than 10 mm classified as Paris class 1 sessile or Paris class IIa. We have selected it with the help of expert gastroenterologists. We have released this dataset separately as a subset of Kvasir-SEG. We call this subset Kvasir-Sessile.

3 PAPERS • 1 BENCHMARK

The “Medico automatic polyp segmentation challenge” aims to develop computer-aided diagnosis systems for automatic polyp segmentation to detect all types of polyps (for example, irregular polyp, smaller or flat polyps) with high efficiency and accuracy. The main goal of the challenge is to benchmark semantic segmentation algorithms on a publicly available dataset, emphasizing robustness, speed, and generalization.

3 PAPERS • 1 BENCHMARK

MICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images.

2 PAPERS • 1 BENCHMARK

The dataset contains a Video capsule endoscopy dataset for polyp segmentation.

2 PAPERS • 1 BENCHMARK

The NuCLS dataset contains over 220,000 labeled nuclei from breast cancer images from TCGA. These nuclei were annotated through the collaborative effort of pathologists, pathology residents, and medical students using the Digital Slide Archive. These data can be used in several ways to develop and validate algorithms for nuclear detection, classification, and segmentation, or as a resource to develop and evaluate methods for interrater analysis.

2 PAPERS • NO BENCHMARKS YET

Overview This database of simulated arterial pulse waves is designed to be representative of a sample of pulse waves measured from healthy adults. It contains pulse waves for 4,374 virtual subjects, aged from 25-75 years old (in 10 year increments). The database contains a baseline set of pulse waves for each of the six age groups, created using cardiovascular properties (such as heart rate and arterial stiffness) which are representative of healthy subjects at each age group. It also contains 728 further virtual subjects at each age group, in which each of the cardiovascular properties are varied within normal ranges. This allows for extensive in silico analyses of haemodynamics and the performance of pulse wave analysis algorithms.

2 PAPERS • NO BENCHMARKS YET

This mouse cerebellar atlas can be used for mouse cerebellar morphometry.

2 PAPERS • NO BENCHMARKS YET

UI-PRMD is a data set of movements related to common exercises performed by patients in physical therapy and rehabilitation programs. The data set consists of 10 rehabilitation exercises. A sample of 10 healthy individuals repeated each exercise 10 times in front of two sensory systems for motion capturing: a Vicon optical tracker, and a Kinect camera. The data is presented as positions and angles of the body joints in the skeletal models provided by the Vicon and Kinect mocap systems.

2 PAPERS • 1 BENCHMARK

The eSports Sensors dataset contains sensor data collected from 10 players in 22 matches in League of Legends. The sensor data collected includes:

2 PAPERS • 2 BENCHMARKS

By releasing this dataset, we aim at providing a new testbed for computer vision techniques using Deep Learning. The main peculiarity is the shift from the domain of "natural images" proper of common benchmark dataset to biological imaging. We anticipate that the advantages of doing so could be two-fold: i) fostering research in biomedical-related fields - for which popular pre-trained models perform typically poorly - and ii) promoting methodological research in deep learning by addressing peculiar requirements of these images. Possible applications include but are not limited to semantic segmentation, object detection and object counting. The data consist of 283 high-resolution pictures (1600x1200 pixels) of mice brain slices acquired through a fluorescence microscope. The final goal is to individuate and count neurons highlighted in the pictures by means of a marker, so to assess the result of a biological experiment. The corresponding ground-truth labels were generated through a hy

2 PAPERS • NO BENCHMARKS YET

The 2017 PhysioNet/CinC Challenge aims to encourage the development of algorithms to classify, from a single short ECG lead recording (between 30 s and 60 s in length), whether the recording shows normal sinus rhythm, atrial fibrillation (AF), an alternative rhythm, or is too noisy to be classified.

1 PAPER • NO BENCHMARKS YET

The BCSS dataset contains over 20,000 segmentation annotations of tissue regions from breast cancer images from The Cancer Genome Atlas (TCGA). This large-scale dataset was annotated through the collaborative effort of pathologists, pathology residents, and medical students using the Digital Slide Archive. It enables the generation of highly accurate machine-learning models for tissue segmentation.

1 PAPER • NO BENCHMARKS YET

BioLeaflets is a biomedical dataset for Data2Text generation. It is a corpus of 1,336 package leaflets of medicines authorised in Europe, which were obtained by scraping the European Medicines Agency (EMA) website. Package leaflets are included in the packaging of medicinal products and contain information to help patients use the product safely and appropriately, under the guidance of their healthcare professional. Each document contains six sections: 1) What is the product and what is it used for 2) What you need to know before you take the product 3) product usage instructions 4) possible side effects, 5) product storage conditions 6) other information.

1 PAPER • NO BENCHMARKS YET

The complete blood count (CBC) dataset contains 360 blood smear images along with their annotation files splitting into Training, Testing, and Validation sets. The training folder contains 300 images with annotations. The testing and validation folder both contain 60 images with annotations. We have done some modifications over the original dataset to prepare this CBC dataset where some of the image annotation files contain very low red blood cells (RBCs) than actual and one annotation file does not include any RBC at all although the cell smear image contains RBCs. So, we clear up all the fallacious files and split the dataset into three parts. Among the 360 smear images, 300 blood cell images with annotations are used as the training set first, and then the rest of the 60 images with annotations are used as the testing set. Due to the shortage of data, a subset of the training set is used to prepare the validation set which contains 60 images with annotations.

1 PAPER • NO BENCHMARKS YET

Dataset contains 33,010 molecule-description pairs split into 80\%/10\%/10\% train/val/test splits. The goal of the task is to retrieve the relevant molecule for a natural language description. It is defined as follows:

1 PAPER • 1 BENCHMARK

This collection contains data and code associated with the IPCAI/IJCARS 2020 paper “Automatic Annotation of Hip Anatomy in Fluoroscopy for Robust and Efficient 2D/3D Registration.” The data hosted here consists of annotated datasets of actual hip fluoroscopy, CT and derived data from six lower torso cadaveric specimens. Documentation and examples for using the dataset and Python code for training and testing the proposed models are also included. Higher-level information, including clinical motivations, prior works, algorithmic details, applications to 2D/3D registration, and experimental details, may be found in the companion paper which is available at https://arxiv.org/abs/1911.07042 or https://doi.org/10.1007/s11548-020-02162-7. We hope that this code and data will be useful in the development of new computer-assisted capabilities that leverage fluoroscopy.

1 PAPER • NO BENCHMARKS YET

The data presented here was extracted from a larger dataset collected through a collaboration between the Embedded Systems Laboratory (ESL) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland and the Institute of Sports Sciences of the University of Lausanne (ISSUL). In this dataset, we report the extracted segments used for an analysis of R peak detection algorithms during high intensity exercise.

1 PAPER • NO BENCHMARKS YET

A challenge that consists of three tasks, each targeting a different requirement for in-clinic use. The first task involves classifying images from the GI tract into 23 distinct classes. The second task focuses on efficiant classification measured by the amount of time spent processing each image. The last task relates to automatcially segmenting polyps.

1 PAPER • 1 BENCHMARK

This is the supplemental data for our paper on how to benchmark registrations of serial sections with ground truths. There are three main modalities and one further, as a reference.

1 PAPER • NO BENCHMARKS YET

The LIVECell (Label-free In Vitro image Examples of Cells) dataset is a large-scale microscopic image dataset for instance-segmentation of individual cells in 2D cell cultures.

1 PAPER • 1 BENCHMARK

Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the original webpage)

1 PAPER • NO BENCHMARKS YET

The second Ninapro database includes 40 intact subjects and it is thoroughly described in the paper: "Manfredo Atzori, Arjan Gijsberts, Claudio Castellini, Barbara Caputo, Anne-Gabrielle Mittaz Hager, Simone Elsig, Giorgio Giatsidis, Franco Bassetto & Henning Müller. Electromyography data for non-invasive naturally-controlled robotic hand prostheses. Scientific Data, 2014" (http://www.nature.com/articles/sdata201453). Please, cite this paper for any work related to the Ninapro database. Please, use also the paper by Gijsberts et al., 2014 (http://publications.hevs.ch/index.php/publications/show/1629) for more information about the database.

1 PAPER • NO BENCHMARKS YET

SinGAN-Seg-polyps is a synthetic dataset for polyp segmentation consisting of 10,000 synthetic polyps and masks.

1 PAPER • NO BENCHMARKS YET

A public open dataset of synthetic chest X-ray images of COVID-19.

1 PAPER • NO BENCHMARKS YET

We've made available several genome-wide datasets, which can be used for training microRNA (miRNA) classifiers. The hairpin sequences available are from the genomes of: Homo sapiens, Arabidopsis thaliana, Anopheles gambiae, Caenorhabditis elegans and Drosophila melanogaster. Hairpin.s are small RNA sequences that naturaly folds into a hairpin-structure. However, not all hairpins have clear function (they are not miRNAs).

0 PAPER • NO BENCHMARKS YET

The medaka (Oryzias latipes) and the zebrafish (Danio rerio) are used as a model organism for a variety of subjects in biomedical research. The presented work aims to study the potential of automated ventricular dimension estimation through heart segmentation in medaka. For more on this, it's time for a closer look on our paper and the supplementary materials.

0 PAPER • NO BENCHMARKS YET

HyperKvasir dataset contains 110,079 images and 374 videos where it captures anatomical landmarks and pathological and normal findings. A total of around 1 million images and video frames altogether.

0 PAPER • NO BENCHMARKS YET

Kvasir-Capsule dataset is the largest publicly released VCE dataset. In total, the dataset contains 47,238 labeled images and 117 videos, where it captures anatomical landmarks and pathological and normal findings. The results is more than 4,741,621 images and video frames altogether.

0 PAPER • NO BENCHMARKS YET

The RSNA Pulmonary Embolism CT (RSPECT) Dataset is composed of CT pulmonary angiogram images and annotations related to pulmonary embolism. It's part of the 2020 RSNA Pulmonary Embolism Detection Challenge which invited researchers to develop machine-learning algorithms to detect and characterize instances of pulmonary embolism (PE) on chest CT studies. The competition, conducted in collaboration with the Society of Thoracic Radiology (STR), involved creating the largest publicly available annotated PE dataset, comprised of more than 12,000 CT studies. Imaging data was contributed by five international research centers and labeled with detailed clinical annotations by a group of more than 80 expert thoracic radiologists. For the first time in an RSNA data challenge, the rules required competitors to submit and run their code in a standard shared environment, producing simpler, more readily usable models.

0 PAPER • NO BENCHMARKS YET