A curated evaluation dataset for end-to-end Relation Extraction of relationships between organisms and natural-products.
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Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental de
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We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement.
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The CheXmask Database presents a comprehensive, uniformly annotated collection of chest radiographs, constructed from five public databases: ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest and VinDr-CXR. The database aggregates 657,566 anatomical segmentation masks derived from images which have been processed using the HybridGNet model to ensure consistent, high-quality segmentation. To confirm the quality of the segmentations, we include in this database individual Reverse Classification Accuracy (RCA) scores for each of the segmentation masks. This dataset is intended to catalyze further innovation and refinement in the field of semantic chest X-ray analysis, offering a significant resource for researchers in the medical imaging domain.
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This dataset is a collection of fluorescent images from mice in order to test an automatic cell counting tool that we developed. 62 images viewed from 2 or 3 different fields of views are shown. In brief, the dataset was derived from brain sections of a model for HIV-induced brain injury (HIVgp120tg), which expresses soluble gp120 envelope protein in astrocytes under the control of a modified GFAP promoter. The mice were in a mixed C57BL/6.129/SJL genetic background, and two genotypes of 9 month old male mice were selected: wild type controls (Resting, n = 3) and transgenic littermates (HIVgp120tg, Activated, n = 3). No randomization was performed. HIVgp120tg mice show among other hallmarks of human HIV neuropathology an increase in microglia numbers which indicates activation of the cells compared to non-transgenic littermate controls.
PubMedCite is a domain-specific dataset with about 192K biomedical scientific papers and a large citation graph preserving 917K citation relationships between them. It is characterized by preserving the salient contents extracted from full texts of references, and the weighted correlation between the salient.
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The Fraunhofer Portugal AICOS EDoF Dataset was produced within the TAMI project and is composed of images of microscopic fields of view (FOV) of Liquid-based Cervical Cytology (LBC) samples. A total of 15 LBC samples were supplied by the Pathology Services from Hospital Fernando Fonseca and the Portuguese Oncology Institute of Porto. For each LBC sample, a set of images were obtained using a version of µSmartScope [1,2] prototype adapted to the cervical cytology use case [3,4].
The National Health and Nutrition Examination Survey (NHANES) provides data on the health and environmental exposure of the non-institutionalized US population. Such data have considerable potential to understand how the environment and behaviors impact human health. These data are also currently leveraged to answer public health questions such as prevalence of disease. However, these data need to first be processed before new insights can be derived through large-scale analyses. NHANES data are stored across hundreds of files with multiple inconsistencies. Correcting such inconsistencies takes systematic cross examination and considerable efforts but is required for accurately and reproducibly characterizing the associations between the exposome and diseases (e.g., cancer mortality outcomes). Thus, we developed a set of curated and unified datasets and accompanied code by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-20
Plain Language Adaptation of Biomedical Abstracts (PLABA) is a dataset designed for automatic adaptation that is both document- and sentence-aligned. The dataset contains 750 adapted abstracts, totaling 7643 sentence pairs.
CheXlocalize is a radiologist-annotated segmentation dataset on chest X-rays. The dataset consists of two types of radiologist annotations for the localization of 10 pathologies: pixel-level segmentations and most-representative points. Annotations were drawn on images from the CheXpert validation and test sets. The dataset also consists of two separate sets of radiologist annotations: (1) ground-truth pixel-level segmentations on the validation and test sets, drawn by two board-certified radiologists, and (2) benchmark pixel-level segmentations and most-representative points on the test set, drawn by a separate group of three board-certified radiologists.
The MIMIC PERform Testing dataset contains the following physiological signals recorded from 200 critically-ill patients during routine clinical care:
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Audiogram data based on a "gold standard" audiometer and the uHear iOS application of 163 participants
FHRMA is an open-source project for Fetal Heart Rate Morphological Analysis containing Matlab source code and datasets. As a sub-project, it includes a deep learning method and dataset for automatic identification of the maternal heart rate (MHR) and, more generally, false signals (FSs) on fetal heart rate (FHR) recordings. The challenge concerns particularly the FHR signal recorded with Doppler sensors, on which MHR interference and other FSs are particularly common, but the dataset also includes FHR recorded with scalp-ECG. The training and validation dataset contained 1030 expert-annotated periods (mean duration: 36 min) from 635 recordings. Labels consist of annotating each time sample as either 1: False signal; 0: True signal, or -1: do not know or irrelevant.
Abstract The Norwegian Endurance Athlete ECG Database contains 12-lead ECG recordings from 28 elite athletes from various sports in Norway. All recordings are 10 seconds resting ECGs recorded with a General Electric (GE) MAC VUE 360 electrocardiograph. All ECGs are interpreted with both the GE Marquette SL12 algorithm (version 23 (v243)) and one cardiologist with training in interpretation of athlete's ECG. The data was collected at the University of Oslo in February and March 2020.
Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge. Through FetReg2021 challenge, we released the first large-scale multi-centre dataset of fetoscopy laser photocoagulation procedure. The dataset contains 2,718 pixel-wise annotated images (for background, vessel, fetus, tool classes) from 24 different in vivo TTTS fetoscopic surgeries and 24 unannotated video clips video clips containing 9,616 frames for training and testing. The dataset is useful for the development of generalized and robust semantic segmentation and video mosaicking algorithms for long duration fetoscopy videos.
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Accurate lesion segmentation is critical in stroke rehabilitation research for the quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted (T1w) MRIs, commonly used in rehabilitation research, lack accuracy and reliability. Manual segmentation remains the gold standard, but it is time-consuming, subjective, and requires significant neuroanatomical expertise. However, many methods developed with ATLAS v1.2 report low accuracy, are not publicly accessible or are improperly validated, limiting their utility to the field. Here we present ATLAS v2.0 (N=1271), a larger dataset of T1w stroke MRIs and manually segmented lesion masks that includes training (public. n=655), test (masks hidden, n=300), and generalizability (completely hidden, n=316) data. Algorithm development using this larger sample should lead to more robust solutions, and the hidden test and generalizability datasets allow for unbiased performance evaluation
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The MS-CXR dataset provides 1162 image–sentence pairs of bounding boxes and corresponding phrases, collected across eight different cardiopulmonary radiological findings, with an approximately equal number of pairs for each finding. This dataset complements the existing MIMIC-CXR v.2 dataset and comprises: 1. Reviewed and edited bounding boxes and phrases (1026 pairs of bounding box/sentence); and 2. Manual bounding box labels from scratch (136 pairs of bounding box/sentence).e
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CoVERT is a fact-checked corpus of tweets with a focus on the domain of biomedicine and COVID-19-related (mis)information. The corpus consists of 300 tweets, each annotated with medical named entities and relations. Employs a novel crowdsourcing methodology to annotate all tweets with fact-checking labels and supporting evidence, which crowdworkers search for online. This methodology results in moderate inter-annotator agreement.
The evaluation of human epidermal growth factor receptor 2 (HER2) expression is essential to formulate a precise treatment for breast cancer. The routine evaluation of HER2 is conducted with immunohistochemical techniques (IHC), which is very expensive. Therefore, we propose a breast cancer immunohistochemical (BCI) benchmark attempting to synthesize IHC data directly with the paired hematoxylin and eosin (HE) stained images. The dataset contains 4870 registered image pairs, covering a variety of HER2 expression levels (0, 1+, 2+, 3+).
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The LIMUC dataset is the largest publicly available labeled ulcerative colitis dataset that compromises 11276 images from 564 patients and 1043 colonoscopy procedures. Three experienced gastroenterologists were involved in the annotation process, and all images are labeled according to the Mayo endoscopic score (MES).
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The dataset contains full-spectral autofluorescence lifetime microscopic images (FS-FLIM) acquired on unstained ex-vivo human lung tissue, where 100 4D hypercubes of 256x256 (spatial resolution) x 32 (time bins) x 512 (spectral channels from 500nm to 780nm). This dataset associates with our paper "Deep Learning-Assisted Co-registration of Full-Spectral Autofluorescence Lifetime Microscopic Images with H&E-Stained Histology Images" (https://arxiv.org/abs/2202.07755) and "Full spectrum fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution" (https://doi.org/10.1038/s41467-021-26837-0). The FS-FLIM images provide transformative insights into human lung cancer with extra-dimensional information. This will enable visual and precise detection of early lung cancer. With the methodology in our co-registration paper, FS-FLIM images can be registered with H&E-stained histology images, allowing characterisation of tumour and surrounding cells at a celluar level with abs
PETRAW data set was composed of 150 sequences of peg transfer training sessions. The objective of the peg transfer session is to transfer 6 blocks from the left to the right and back. Each block must be extracted from a peg with one hand, transferred to the other hand, and inserted in a peg at the other side of the board. All cases were acquired by a non-medical expert on the LTSI Laboratory from the University of Rennes. The data set was divided into a training data set composed of 90 cases and a test data set composed of 60 cases. A case was composed of kinematic data, a video, semantic segmentation of each frame, and workflow annotation.
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The dataset X of this work is an extension of the heartSeg dataset. Each sample x ∈ X is an RGB image capturing the heart region of Medaka (Oryzias latipes) hatchlings from a constant ventral view. Since the body of Medaka is see-through, noninvasive studies regarding the internal organs and the whole circulatory system are practicable. A Medaka’s heart contains three parts: the atrium, the ventricle, and the bulbus. The atrium receives deoxygenated blood from the circulatory system and delivers it to the ventricle, which forwards it into the bulbus. The bulbus is the heart’s exit chamber and provides the gill arches with a constant blood flow. The blood flow through these three chambers was captured in 63 short recordings (around 11 seconds with 24 frames per second each) in total, from which the single image samples x ∈ X are extracted. The dataset is split into training and test data following the heartSeg dataset with ntrain = 565 samples in the training set Xtrain and ntest = 165
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
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:
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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.
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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.
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SinGAN-Seg-polyps is a synthetic dataset for polyp segmentation consisting of 10,000 synthetic polyps and masks.
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
The dataset contains a Video capsule endoscopy dataset for polyp segmentation.
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Full-text chemical identification and indexing in PubMed articles.
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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.
Data The data for this Challenge are from multiple sources: CPSC Database and CPSC-Extra Database INCART Database PTB and PTB-XL Database The Georgia 12-lead ECG Challenge (G12EC) Database Undisclosed Database The first source is the public (CPSC Database) and unused data (CPSC-Extra Database) from the China Physiological Signal Challenge in 2018 (CPSC2018), held during the 7th International Conference on Biomedical Engineering and Biotechnology in Nanjing, China. The unused data from the CPSC2018 is NOT the test data from the CPSC2018. The test data of the CPSC2018 is included in the final private database that has been sequestered. This training set consists of two sets of 6,877 (male: 3,699; female: 3,178) and 3,453 (male: 1,843; female: 1,610) of 12-ECG recordings lasting from 6 seconds to 60 seconds. Each recording was sampled at 500 Hz.
A public open dataset of synthetic chest X-ray images of COVID-19.
Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present the real results severity (BIRADS) and pathology (post-report) classifications provided by the Radiologist Director from the Radiology Department of Hospital Fernando Fonseca while diagnosing several patients (see dataset-uta4-dicom) from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset for the measurements of both severity (BIRADS) and pathology classifications concerning the patient diagnostic. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted from our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these t
Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present our medical imaging DICOM files of patients from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset of the used medical images during the UTA4 tasks. This repository and respective dataset should be paired with the dataset-uta4-rates repository dataset. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted on our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby dataset repres
Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present our severity rates (BIRADS) of clinicians while diagnosing several patients from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset for the measurements of severity rates (BIRADS) concerning the patient diagnostic. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted from our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby dataset represents the pieces of information of bot
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.
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Data Description The training data contains twelve-lead ECGs. The validation and test data contains twelve-lead, six-lead, four-lead, three-lead, and two-lead ECGs:
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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.
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.
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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.
Electrophysiological data from implanted electrodes in the human brain are rare, and therefore scientific access to it has remained somewhat exclusive. Here we present a freely-available curated library of implanted electrocorticographic (ECoG) data and analyses for 16 benchmark behavioral experiments, with 204 individual datasets from 34 patients made with the same amplifiers (at the same sampling rate and filter settings). In every case, electrode positions have been carefully registered to brain anatomy. A large set of fully-commented analysis scripts to interpret these data using modern techniques is embedded in the library alongside the data. All data, anatomic correlations, and analysis files (MATLAB code) are in a common, intuitive file structure at https://searchworks.stanford.edu/view/zk881ps0522. The library may be used as course material or serve as a starter package for researchers early in their career or for established groups, to modify the analyses and re-apply them in
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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.
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).
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.
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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!
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This mouse cerebellar atlas can be used for mouse cerebellar morphometry.