Multiplexed imaging technologies provide insights into complex tissue architectures. However, challenges arise due to software fragmentation with cumbersome data handoffs, inefficiencies in processing large images (8 to 40 gigabytes per image), and limited spatial analysis capabilities. To efficiently analyze multiplexed imaging data, we developed SPACEc, a scalable end-to-end Python solution, that handles image extraction, cell segmentation, and data preprocessing and incorporates machine-learning-enabled, multi-scaled, spatial analysis, operated through a user-friendly and interactive interface. The demonstration dataset was derived from a previous analysis and contains TMA cores from a human tonsil and tonsillitis sample that were acquired with the Akoya PhenocyclerFusion platform. The dataset can be used to test the workflow and establish it on a user’s system or to familiarize oneself with the pipeline. Methods Tissue samples: Tonsil cores were extracted from a larger multi-tumor tissue microarray (TMA), which included a total of 66 unique tissues (51 malignant and semi-malignant tissues, as well as 15 non-malignant tissues). Representative tissue regions were annotated on corresponding hematoxylin and eosin (H&E)-stained sections by a board-certified surgical pathologist (S.Z.). Annotations were used to generate the 66 cores each with cores of 1mm diameter. FFPE tissue blocks were retrieved from the tissue archives of the Institute of Pathology, University Medical Center Mainz, Germany, and the Department of Dermatology, University Medical Center Mainz, Germany. The multi-tumor-TMA block was sectioned at 3µm thickness onto SuperFrost Plus microscopy slides before being processed for CODEX multiplex imaging as previously described. CODEX multiplexed imaging and processing To run the CODEX machine, the slide was taken from the storage buffer and placed in PBS for 10 minutes to equilibrate. After drying the PBS with a tissue, a flow cell was sealed onto the tissue slide. The assembled slide and flow cell were then placed in a PhenoCycler Buffer made from 10X PhenoCycler Buffer & Additive for at least 10 minutes before starting the experiment. A 96-well reporter plate was prepared with each reporter corresponding to the correct barcoded antibody for each cycle, with up to 3 reporters per cycle per well. The fluorescence reporters were mixed with 1X PhenoCycler Buffer, Additive, nuclear-staining reagent, and assay reagent according to the manufacturer's instructions. With the reporter plate and assembled slide and flow cell placed into the CODEX machine, the automated multiplexed imaging experiment was initiated. Each imaging cycle included steps for reporter binding, imaging of three fluorescent channels, and reporter stripping to prepare for the next cycle and set of markers. This was repeated until all markers were imaged. After the experiment, a .qptiff image file containing individual antibody channels and the DAPI channel was obtained. Image stitching, drift compensation, deconvolution, and cycle concatenation are performed within the Akoya PhenoCycler software. The raw imaging data output (tiff, 377.442nm per pixel for 20x CODEX) is first examined with QuPath software (https://qupath.github.io/) for inspection of staining quality. Any markers that produce unexpected patterns or low signal-to-noise ratios should be excluded from the ensuing analysis. The qptiff files must be converted into tiff files for input into SPACEc. Data preprocessing includes image stitching, drift compensation, deconvolution, and cycle concatenation performed using the Akoya Phenocycler software. The raw imaging data (qptiff, 377.442 nm/pixel for 20x CODEX) files from the Akoya PhenoCycler technology were first examined with QuPath software (https://qupath.github.io/) to inspect staining qualities. Markers with untenable patterns or low signal-to-noise ratios were excluded from further analysis. A custom CODEX analysis pipeline was used to process all acquired CODEX data (scripts available upon request). The qptiff files were converted into tiff files for tissue detection (watershed algorithm) and cell segmentation.

Please also see the latest version of the repository: https://doi.org/10.5281/zenodo.6374011 and our website: https://ilandavis.com/jcb2023-yfp

The explosion in the volume of biological imaging data challenges the available technologies for data interrogation and its intersection with related published bioinformatics data sets. Moreover, intersection of highly rich and complex datasets from different sources provided as flat csv files requires advanced informatics skills, which is time consuming and not accessible to all. Here, we provide a “user manual” to our new paradigm for systematically filtering and analysing a dataset with more than 1300 microscopy data figures using Multi-Dimensional Viewer (MDV) -link, a solution for interactive multimodal data visualisation and exploration. The primary data we use are derived from our published systematic analysis of 200 YFP traps reveals common discordance between mRNA and protein across the nervous system (eprint link). This manual provides the raw image data together with the expert annotations of the mRNA and protein distribution as well as associated bioinformatics data. We provide an explanation, with specific examples, of how to use MDV to make the multiple data types interoperable and explore them together. We also provide the open-source python code (github link) used to annotate the figures, which could be adapted to any other kind of data annotation task.

The self-documenting aspects and the ability to reproduce results have been touted as significant benefits of Jupyter Notebooks. At the same time, there has been growing criticism that the way notebooks are being used leads to unexpected behavior, encourage poor coding practices and that their results can be hard to reproduce. To understand good and bad practices used in the development of real notebooks, we analyzed 1.4 million notebooks from GitHub.

Paper: https://2019.msrconf.org/event/msr-2019-papers-a-large-scale-study-about-quality-and-reproducibility-of-jupyter-notebooks

This repository contains two files:

• dump.tar.bz2
• jupyter_reproducibility.tar.bz2

The dump.tar.bz2 file contains a PostgreSQL dump of the database, with all the data we extracted from the notebooks.

The jupyter_reproducibility.tar.bz2 file contains all the scripts we used to query and download Jupyter Notebooks, extract data from them, and analyze the data. It is organized as follows:

• analyses: this folder has all the notebooks we use to analyze the data in the PostgreSQL database.
• archaeology: this folder has all the scripts we use to query, download, and extract data from GitHub notebooks.
• paper: empty. The notebook analyses/N12.To.Paper.ipynb moves data to it

In the remaining of this text, we give instructions for reproducing the analyses, by using the data provided in the dump and reproducing the collection, by collecting data from GitHub again.

Reproducing the Analysis

This section shows how to load the data in the database and run the analyses notebooks. In the analysis, we used the following environment:

Ubuntu 18.04.1 LTS
PostgreSQL 10.6
Conda 4.5.11
Python 3.7.2
PdfCrop 2012/11/02 v1.38

First, download dump.tar.bz2 and extract it:

tar -xjf dump.tar.bz2

It extracts the file db2019-03-13.dump. Create a database in PostgreSQL (we call it "jupyter"), and use psql to restore the dump:

psql jupyter < db2019-03-13.dump

It populates the database with the dump. Now, configure the connection string for sqlalchemy by setting the environment variable JUP_DB_CONNECTTION:

export JUP_DB_CONNECTION="postgresql://user:password@hostname/jupyter";

Download and extract jupyter_reproducibility.tar.bz2:

tar -xjf jupyter_reproducibility.tar.bz2

Create a conda environment with Python 3.7:

conda create -n analyses python=3.7
conda activate analyses

Go to the analyses folder and install all the dependencies of the requirements.txt

cd jupyter_reproducibility/analyses
pip install -r requirements.txt

For reproducing the analyses, run jupyter on this folder:

jupyter notebook

Execute the notebooks on this order:

• Index.ipynb
• N0.Repository.ipynb
• N1.Skip.Notebook.ipynb
• N2.Notebook.ipynb
• N3.Cell.ipynb
• N4.Features.ipynb
• N5.Modules.ipynb
• N6.AST.ipynb
• N7.Name.ipynb
• N8.Execution.ipynb
• N9.Cell.Execution.Order.ipynb
• N10.Markdown.ipynb
• N11.Repository.With.Notebook.Restriction.ipynb
• N12.To.Paper.ipynb

Reproducing or Expanding the Collection

The collection demands more steps to reproduce and takes much longer to run (months). It also involves running arbitrary code on your machine. Proceed with caution.

Requirements

This time, we have extra requirements:

All the analysis requirements
lbzip2 2.5
gcc 7.3.0
Github account
Gmail account

Environment

First, set the following environment variables:

export JUP_MACHINE="db"; # machine identifier
export JUP_BASE_DIR="/mnt/jupyter/github"; # place to store the repositories
export JUP_LOGS_DIR="/home/jupyter/logs"; # log files
export JUP_COMPRESSION="lbzip2"; # compression program
export JUP_VERBOSE="5"; # verbose level
export JUP_DB_CONNECTION="postgresql://user:password@hostname/jupyter"; # sqlchemy connection
export JUP_GITHUB_USERNAME="github_username"; # your github username
export JUP_GITHUB_PASSWORD="github_password"; # your github password
export JUP_MAX_SIZE="8000.0"; # maximum size of the repositories directory (in GB)
export JUP_FIRST_DATE="2013-01-01"; # initial date to query github
export JUP_EMAIL_LOGIN="gmail@gmail.com"; # your gmail address
export JUP_EMAIL_TO="target@email.com"; # email that receives notifications
export JUP_OAUTH_FILE="~/oauth2_creds.json" # oauth2 auhentication file
export JUP_NOTEBOOK_INTERVAL=""; # notebook id interval for this machine. Leave it in blank
export JUP_REPOSITORY_INTERVAL=""; # repository id interval for this machine. Leave it in blank
export JUP_WITH_EXECUTION="1"; # run execute python notebooks
export JUP_WITH_DEPENDENCY="0"; # run notebooks with and without declared dependnecies
export JUP_EXECUTION_MODE="-1"; # run following the execution order
export JUP_EXECUTION_DIR="/home/jupyter/execution"; # temporary directory for running notebooks
export JUP_ANACONDA_PATH="~/anaconda3"; # conda installation path
export JUP_MOUNT_BASE="/home/jupyter/mount_ghstudy.sh"; # bash script to mount base dir
export JUP_UMOUNT_BASE="/home/jupyter/umount_ghstudy.sh"; # bash script to umount base dir
export JUP_NOTEBOOK_TIMEOUT="300"; # timeout the extraction


# Frequenci of log report
export JUP_ASTROID_FREQUENCY="5";
export JUP_IPYTHON_FREQUENCY="5";
export JUP_NOTEBOOKS_FREQUENCY="5";
export JUP_REQUIREMENT_FREQUENCY="5";
export JUP_CRAWLER_FREQUENCY="1";
export JUP_CLONE_FREQUENCY="1";
export JUP_COMPRESS_FREQUENCY="5";

export JUP_DB_IP="localhost"; # postgres database IP

Then, configure the file ~/oauth2_creds.json, according to yagmail documentation: https://media.readthedocs.org/pdf/yagmail/latest/yagmail.pdf

Configure the mount_ghstudy.sh and umount_ghstudy.sh scripts. The first one should mount the folder that stores the directories. The second one should umount it. You can leave the scripts in blank, but it is not advisable, as the reproducibility study runs arbitrary code on your machine and you may lose your data.

Scripts

Download and extract jupyter_reproducibility.tar.bz2:

tar -xjf jupyter_reproducibility.tar.bz2

Install 5 conda environments and 5 anaconda environments, for each python version. In each of them, upgrade pip, install pipenv, and install the archaeology package (Note that it is a local package that has not been published to pypi. Make sure to use the -e option):

Conda 2.7

conda create -n raw27 python=2.7 -y
conda activate raw27
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Anaconda 2.7

conda create -n py27 python=2.7 anaconda -y
conda activate py27
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Conda 3.4

It requires a manual jupyter and pathlib2 installation due to some incompatibilities found on the default installation.

conda create -n raw34 python=3.4 -y
conda activate raw34
conda install jupyter -c conda-forge -y
conda uninstall jupyter -y
pip install --upgrade pip
pip install jupyter
pip install pipenv
pip install -e jupyter_reproducibility/archaeology
pip install pathlib2

Anaconda 3.4

conda create -n py34 python=3.4 anaconda -y
conda activate py34
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Conda 3.5

conda create -n raw35 python=3.5 -y
conda activate raw35
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Anaconda 3.5

It requires the manual installation of other anaconda packages.

conda create -n py35 python=3.5 anaconda -y
conda install -y appdirs atomicwrites keyring secretstorage libuuid navigator-updater prometheus_client pyasn1 pyasn1-modules spyder-kernels tqdm jeepney automat constantly anaconda-navigator
conda activate py35
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Conda 3.6

conda create -n raw36 python=3.6 -y
conda activate raw36
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Anaconda 3.6

conda create -n py36 python=3.6 anaconda -y
conda activate py36
conda install -y anaconda-navigator jupyterlab_server navigator-updater
pip install --upgrade pip
pip install pipenv
pip install -e jupyter_reproducibility/archaeology

Conda 3.7

<code

This research study was conducted to analyze the (potential) relationship between hardware and data set sizes. 100 data scientists from France between Jan-2016 and Aug-2016 were interviewed in order to have exploitable data. Therefore, this sample might not be representative of the true population.

What can you do with the data?

• Look up whether Kagglers has "stronger" hardware than non-Kagglers
• Whether there is a correlation between a preferred data set size and hardware
• Is proficiency a predictor of specific preferences?
• Are data scientists more Intel or AMD?
• How spread is GPU computing, and is there any relationship with Kaggling?
• Are you able to predict the amount of euros a data scientist might invest, provided their current workstation details?

I did not find any past research on a similar scale. You are free to play with this data set. For re-usage of this data set out of Kaggle, please contact the author directly on Kaggle (use "Contact User"). Please mention:

• Your intended usage (research? business use? blogging?...)
• Your first/last name

Arbitrarily, we chose characteristics to describe Data Scientists and data set sizes.

Data set size:

• Small: under 1 million values
• Medium: between 1 million and 1 billion values
• Large: over 1 billion values

For the data, it uses the following fields (DS = Data Scientist, W = Workstation):

• DS_1 = Are you working with "large" data sets at work? (large = over 1 billion values) => Yes or No
• DS_2 = Do you enjoy working with large data sets? => Yes or No
• DS_3 = Would you rather have small, medium, or large data sets for work? => Small, Medium, or Large
• DS_4 = Do you have any presence at Kaggle or any other Data Science platforms? => Yes or No
• DS_5 = Do you view yourself proficient at working in Data Science? => Yes, A bit, or No
• W_1 = What is your CPU brand? => Intel or AMD
• W_2 = Do you have access to a remote server to perform large workloads? => Yes or No
• W_3 = How much Euros would you invest in Data Science brand new hardware? => numeric output, rounded by 100s
• W_4 = How many cores do you have to work with data sets? => numeric output
• W_5 = How much RAM (in GB) do you have to work with data sets? => numeric output
• W_6 = Do you do GPU computing? => Yes or No
• W_7 = What programming languages do you use for Data Science? => R or Python (any other answer accepted)
• W_8 = What programming languages do you use for pure statistical analysis? => R or Python (any other answer accepted)
• W_9 = What programming languages do you use for training models? => R or Python (any other answer accepted)

You should expect potential noise in the data set. It might not be "free" of internal contradictions, as with all researches.

The first benchmark of Python projects that is large-scale, diverse, ready-to-run (i.e., with fully configured and prepared test suites), and ready-to-analyze (i.e., using an integrated Python dynamic analysis framework). The benchmark encompasses 50 popular open-source projects from various application domains, with a total of 681K lines of Python code, and 30K test cases.

Mass spectrometry-based proteomics is increasingly employed in biology and medicine. To generate reliable information from large data sets and ensure comparability of results it is crucial to implement and standardize the quality control of the raw data, the data processing steps and the statistical analyses. The MSPypeline provides a platform for the import of MaxQuant output tables, the generation of quality control reports, the preprocessing of data including normalization and exploratory analyses by statistical inference plots. These standardized steps assess data quality, provide customizable figures and enable the identification of differentially expressed proteins to reach biologically relevant conclusions.

This repository contains the code, data, and models of the paper titled "BᴀɴɢʟᴀBᴏᴏᴋ: A Large-scale Bangla Dataset for Sentiment Analysis from Book Reviews" published in the Findings of the Association for Computational Linguistics: ACL 2023.

License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

Data Format Each row consists of a book review sample. The table below describes what each column signifies.

Column Title	Description
id	The unique identification number of the sample
Book_Name	The title of the book that has been evaluated by the review
Writer_Name	The name of the book's author
Category	The genre to which the book belongs
Rating	A numerical value $r$ such that $1\leq r \leq 5$ A score reflecting the reviewer's subjective assessment of the book's quality
Review	The review text written by the reviewer
Site	The name of the online bookshop
sentiment	The conveyed sentiment and class label of the review For a review sample $i$ with rating $r_i$, the sentiment label $S_i$ is, $S_i =\begin{cases}Negative, & \text{if $r_i \leq 2$}\Neutral, & \text{if $r_i = 3$}\Positive, & \text{if $r_i \geq 4$}\end{cases}$
label	The numerical representation of the sentiment label For a review sample $i$ with sentiment label $S_i$, the numerical label is, $label_i =\begin{cases}0, & \text{if $S_i = Negative$}\1, & \text{if $S_i = Neutral$}\2, & \text{if $S_i = Positive$}\end{cases}$

Data Construction Data Collection Process For the data collection and preparation process of the BᴀɴɢʟᴀBᴏᴏᴋ dataset, we first compile a list of URLs for authors from online bookstores. From there, we procure URLs for the books. We meticulously scrape information such as book titles, author names, book categories, review texts, reviewer names, review dates, and ratings by utilizing these book URLs. https://github.com/mohsinulkabir14/BanglaBook/raw/main/images/banglabookgithub1.png" alt="drawing" style="width:1000px;"/>

Labeling, Translation, and Validation of the Curated Samples If a review does not have a rating, we deem it unannotated. Reviews with a rating of 1 or 2 are classified as negative, a rating of 3 is considered neutral, and a rating of 4 or 5 is classified as positive. After discarding the unannotated reviews, we curate a final dataset of 158,065 annotated reviews. Of these, 89,371 are written entirely in Bangla. The remaining 68,694 reviews were written in Romanized Bangla, English, or a mix of languages. They are translated into Bangla with Google Translator and a custom Python program using the googletrans library. The translations are subsequently subjected to manual review and scrutiny to confirm their accuracy. https://github.com/mohsinulkabir14/BanglaBook/raw/main/images/banglabookgithub2.png" alt="drawing" style="width:1000px;"/>

Results https://github.com/mohsinulkabir14/BanglaBook/raw/main/images/banglabookgithub3.png" alt="drawing" style="width:1000px;"/>

Citation If you find this work useful, please cite our paper: bib @inproceedings{kabir-etal-2023-banglabook, title = "{B}angla{B}ook: A Large-scale {B}angla Dataset for Sentiment Analysis from Book Reviews", author = "Kabir, Mohsinul and Bin Mahfuz, Obayed and Raiyan, Syed Rifat and Mahmud, Hasan and Hasan, Md Kamrul", booktitle = "Findings of the Association for Computational Linguistics: ACL 2023", month = jul, year = "2023", address = "Toronto, Canada", publisher = "Association for Computational Linguistics", url = "https://aclanthology.org/2023.findings-acl.80", pages = "1237--1247", abstract = "The analysis of consumer sentiment, as expressed through reviews, can provide a wealth of insight regarding the quality of a product. While the study of sentiment analysis has been widely explored in many popular languages, relatively less attention has been given to the Bangla language, mostly due to a lack of relevant data and cross-domain adaptability. To address this limitation, we present BanglaBook, a large-scale dataset of Bangla book reviews consisting of 158,065 samples classified into three broad categories: positive, negative, and neutral. We provide a detailed statistical analysis of the dataset and employ a range of machine learning models to establish baselines including SVM, LSTM, and Bangla-BERT. Our findings demonstrate a substantial performance advantage of pre-trained models over models that rely on manually crafted features, emphasizing the necessity for additional training resources in this domain. Additionally, we conduct an in-depth error analysis by examining sentiment unigrams, which may provide insight into common classification errors in under-resourced languages like Bangla. Our codes and data are publicly available at https://github.com/mohsinulkabir14/BanglaBook.", }

GitHub is how people build software and is home to the largest community of open source developers in the world, with over 12 million people contributing to 31 million projects on GitHub since 2008.

This 3TB+ dataset comprises the largest released source of GitHub activity to date. It contains a full snapshot of the content of more than 2.8 million open source GitHub repositories including more than 145 million unique commits, over 2 billion different file paths, and the contents of the latest revision for 163 million files, all of which are searchable with regular expressions.

Querying BigQuery tables

You can use the BigQuery Python client library to query tables in this dataset in Kernels. Note that methods available in Kernels are limited to querying data. Tables are at bigquery-public-data.github_repos.[TABLENAME]. Fork this kernel to get started to learn how to safely manage analyzing large BigQuery datasets.

Acknowledgements

This dataset was made available per GitHub's terms of service. This dataset is available via Google Cloud Platform's Marketplace, GitHub Activity Data, as part of GCP Public Datasets.

Inspiration

• This is the perfect dataset for fighting language wars.
• Can you identify any signals that predict which packages or languages will become popular, in advance of their mass adoption?

This file set includes the final paper, original data, python scripts, and output logs for my term project in Introduction to Digital Scholarship at the University of Tennessee to assess the utility of a computational analytic technique called probabilistic topic modeling to identify latent topics or themes present in a large corpus of textual information. I set out to accomplish this goal by performing a topic modeling text analysis on a corpus of 622 key U.S. presidential speeches identified by the University of Virginia Miller Center and archived on their web site at http://millercenter.org/president/speeches.The results of this project, together with a review of the available literature on topic modeling, suggest that this technique is an effective tool for mining large data sets to identify latent themes or topics. The results of the topic modeling analysis of the presidential speeches suggest that the technique accurately identified latent themes or discourses across different presidential speeches over time. The results also suggest that it is an effective tool for producing new insights into the history of presidential speeches, including finding similarities between speeches that otherwise might not be apparent.

Python is a free computer language that prioritizes readability for humans and general application. It is one of the easier computer languages to learn and start especially with no prior programming knowledge. I have been using Python for Excel spreadsheet automation, data analysis, and data visualization. It has allowed me to better focus on learning how to automate my data analysis workload. I am currently examining the North Carolina Department of Environmental Quality (NCDEQ) database for water quality sampling for the Town of Nags Head, NC. It spans over 26 years (1997-2023) and lists a total of currently 41 different testing site locations. You can see at the bottom of image 2 below that I have 148,204 testing data points for the entirety of the NCDEQ testing for the state. From this large dataset 34,759 data points are from Dare County (Nags Head) specifically with this subdivided into testing sites.

The modeled data in these archives are in the NetCDF format (https://www.unidata.ucar.edu/software/netcdf/). NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. It is also a community standard for sharing scientific data. The Unidata Program Center supports and maintains netCDF programming interfaces for C, C++, Java, and Fortran. Programming interfaces are also available for Python, IDL, MATLAB, R, Ruby, and Perl. Data in netCDF format is: • Self-Describing. A netCDF file includes information about the data it contains. • Portable. A netCDF file can be accessed by computers with different ways of storing integers, characters, and floating-point numbers. • Scalable. Small subsets of large datasets in various formats may be accessed efficiently through netCDF interfaces, even from remote servers. • Appendable. Data may be appended to a properly structured netCDF file without copying the dataset or redefining its structure. • Sharable. One writer and multiple readers may simultaneously access the same netCDF file. • Archivable. Access to all earlier forms of netCDF data will be supported by current and future versions of the software. Pub_figures.tar.zip Contains the NCL scripts for figures 1-5 and Chesapeake Bay Airshed shapefile. The directory structure of the archive is ./Pub_figures/Fig#_data. Where # is the figure number from 1-5. EMISS.data.tar.zip This archive contains two NetCDF files that contain the emission totals for 2011ec and 2040ei emission inventories. The name of the files contain the year of the inventory and the file header contains a description of each variable and the variable units. EPIC.data.tar.zip contains the monthly mean EPIC data in NetCDF format for ammonium fertilizer application (files with ANH3 in the name) and soil ammonium concentration (files with NH3 in the name) for historical (Hist directory) and future (RCP-4.5 directory) simulations. WRF.data.tar.zip contains mean monthly and seasonal data from the 36km downscaled WRF simulations in the NetCDF format for the historical (Hist directory) and future (RCP-4.5 directory) simulations. CMAQ.data.tar.zip contains the mean monthly and seasonal data in NetCDF format from the 36km CMAQ simulations for the historical (Hist directory), future (RCP-4.5 directory) and future with historical emissions (RCP-4.5-hist-emiss directory). This dataset is associated with the following publication: Campbell, P., J. Bash, C. Nolte, T. Spero, E. Cooter, K. Hinson, and L. Linker. Projections of Atmospheric Nitrogen Deposition to the Chesapeake Bay Watershed. Journal of Geophysical Research - Biogeosciences. American Geophysical Union, Washington, DC, USA, 12(11): 3307-3326, (2019).

Part of the dissertation Pitch of Voiced Speech in the Short-Time Fourier Transform: Algorithms, Ground Truths, and Evaluation Methods.© 2020, Bastian Bechtold. All rights reserved. Estimating the fundamental frequency of speech remains an active area of research, with varied applications in speech recognition, speaker identification, and speech compression. A vast number of algorithms for estimatimating this quantity have been proposed over the years, and a number of speech and noise corpora have been developed for evaluating their performance. The present dataset contains estimated fundamental frequency tracks of 25 algorithms, six speech corpora, two noise corpora, at nine signal-to-noise ratios between -20 and 20 dB SNR, as well as an additional evaluation of synthetic harmonic tone complexes in white noise.The dataset also contains pre-calculated performance measures both novel and traditional, in reference to each speech corpus’ ground truth, the algorithms’ own clean-speech estimate, and our own consensus truth. It can thus serve as the basis for a comparison study, or to replicate existing studies from a larger dataset, or as a reference for developing new fundamental frequency estimation algorithms. All source code and data is available to download, and entirely reproducible, albeit requiring about one year of processor-time.Included Code and Data

ground truth data.zip is a JBOF dataset of fundamental frequency estimates and ground truths of all speech files in the following corpora:

CMU-ARCTIC (consensus truth) [1]FDA (corpus truth and consensus truth) [2]KEELE (corpus truth and consensus truth) [3]MOCHA-TIMIT (consensus truth) [4]PTDB-TUG (corpus truth and consensus truth) [5]TIMIT (consensus truth) [6]

noisy speech data.zip is a JBOF datasets of fundamental frequency estimates of speech files mixed with noise from the following corpora:NOISEX [7]QUT-NOISE [8]

synthetic speech data.zip is a JBOF dataset of fundamental frequency estimates of synthetic harmonic tone complexes in white noise.noisy_speech.pkl and synthetic_speech.pkl are pickled Pandas dataframes of performance metrics derived from the above data for the following list of fundamental frequency estimation algorithms:AUTOC [9]AMDF [10]BANA [11]CEP [12]CREPE [13]DIO [14]DNN [15]KALDI [16]MAPSMBSC [17]NLS [18]PEFAC [19]PRAAT [20]RAPT [21]SACC [22]SAFE [23]SHR [24]SIFT [25]SRH [26]STRAIGHT [27]SWIPE [28]YAAPT [29]YIN [30]

noisy speech evaluation.py and synthetic speech evaluation.py are Python programs to calculate the above Pandas dataframes from the above JBOF datasets. They calculate the following performance measures:Gross Pitch Error (GPE), the percentage of pitches where the estimated pitch deviates from the true pitch by more than 20%.Fine Pitch Error (FPE), the mean error of grossly correct estimates.High/Low Octave Pitch Error (OPE), the percentage pitches that are GPEs and happens to be at an integer multiple of the true pitch.Gross Remaining Error (GRE), the percentage of pitches that are GPEs but not OPEs.Fine Remaining Bias (FRB), the median error of GREs.True Positive Rate (TPR), the percentage of true positive voicing estimates.False Positive Rate (FPR), the percentage of false positive voicing estimates.False Negative Rate (FNR), the percentage of false negative voicing estimates.F₁, the harmonic mean of precision and recall of the voicing decision.

Pipfile is a pipenv-compatible pipfile for installing all prerequisites necessary for running the above Python programs.

The Python programs take about an hour to compute on a fast 2019 computer, and require at least 32 Gb of memory.References:

John Kominek and Alan W Black. CMU ARCTIC database for speech synthesis, 2003.Paul C Bagshaw, Steven Hiller, and Mervyn A Jack. Enhanced Pitch Tracking and the Processing of F0 Contours for Computer Aided Intonation Teaching. In EUROSPEECH, 1993.F Plante, Georg F Meyer, and William A Ainsworth. A Pitch Extraction Reference Database. In Fourth European Conference on Speech Communication and Technology, pages 837–840, Madrid, Spain, 1995.Alan Wrench. MOCHA MultiCHannel Articulatory database: English, November 1999.Gregor Pirker, Michael Wohlmayr, Stefan Petrik, and Franz Pernkopf. A Pitch Tracking Corpus with Evaluation on Multipitch Tracking Scenario. page 4, 2011.John S. Garofolo, Lori F. Lamel, William M. Fisher, Jonathan G. Fiscus, David S. Pallett, Nancy L. Dahlgren, and Victor Zue. TIMIT Acoustic-Phonetic Continuous Speech Corpus, 1993.Andrew Varga and Herman J.M. Steeneken. Assessment for automatic speech recognition: II. NOISEX-92: A database and an experiment to study the effect of additive noise on speech recog- nition systems. Speech Communication, 12(3):247–251, July 1993.David B. Dean, Sridha Sridharan, Robert J. Vogt, and Michael W. Mason. The QUT-NOISE-TIMIT corpus for the evaluation of voice activity detection algorithms. Proceedings of Interspeech 2010, 2010.Man Mohan Sondhi. New methods of pitch extraction. Audio and Electroacoustics, IEEE Transactions on, 16(2):262—266, 1968.Myron J. Ross, Harry L. Shaffer, Asaf Cohen, Richard Freudberg, and Harold J. Manley. Average magnitude difference function pitch extractor. Acoustics, Speech and Signal Processing, IEEE Transactions on, 22(5):353—362, 1974.Na Yang, He Ba, Weiyang Cai, Ilker Demirkol, and Wendi Heinzelman. BaNa: A Noise Resilient Fundamental Frequency Detection Algorithm for Speech and Music. IEEE/ACM Transactions on Audio, Speech, and Language Processing, 22(12):1833–1848, December 2014.Michael Noll. Cepstrum Pitch Determination. The Journal of the Acoustical Society of America, 41(2):293–309, 1967.Jong Wook Kim, Justin Salamon, Peter Li, and Juan Pablo Bello. CREPE: A Convolutional Representation for Pitch Estimation. arXiv:1802.06182 [cs, eess, stat], February 2018. arXiv: 1802.06182.Masanori Morise, Fumiya Yokomori, and Kenji Ozawa. WORLD: A Vocoder-Based High-Quality Speech Synthesis System for Real-Time Applications. IEICE Transactions on Information and Systems, E99.D(7):1877–1884, 2016.Kun Han and DeLiang Wang. Neural Network Based Pitch Tracking in Very Noisy Speech. IEEE/ACM Transactions on Audio, Speech, and Language Processing, 22(12):2158–2168, Decem- ber 2014.Pegah Ghahremani, Bagher BabaAli, Daniel Povey, Korbinian Riedhammer, Jan Trmal, and Sanjeev Khudanpur. A pitch extraction algorithm tuned for automatic speech recognition. In Acoustics, Speech and Signal Processing (ICASSP), 2014 IEEE International Conference on, pages 2494–2498. IEEE, 2014.Lee Ngee Tan and Abeer Alwan. Multi-band summary correlogram-based pitch detection for noisy speech. Speech Communication, 55(7-8):841–856, September 2013.Jesper Kjær Nielsen, Tobias Lindstrøm Jensen, Jesper Rindom Jensen, Mads Græsbøll Christensen, and Søren Holdt Jensen. Fast fundamental frequency estimation: Making a statistically efficient estimator computationally efficient. Signal Processing, 135:188–197, June 2017.Sira Gonzalez and Mike Brookes. PEFAC - A Pitch Estimation Algorithm Robust to High Levels of Noise. IEEE/ACM Transactions on Audio, Speech, and Language Processing, 22(2):518—530, February 2014.Paul Boersma. Accurate short-term analysis of the fundamental frequency and the harmonics-to-noise ratio of a sampled sound. In Proceedings of the institute of phonetic sciences, volume 17, page 97—110. Amsterdam, 1993.David Talkin. A robust algorithm for pitch tracking (RAPT). Speech coding and synthesis, 495:518, 1995.Byung Suk Lee and Daniel PW Ellis. Noise robust pitch tracking by subband autocorrelation classification. In Interspeech, pages 707–710, 2012.Wei Chu and Abeer Alwan. SAFE: a statistical algorithm for F0 estimation for both clean and noisy speech. In INTERSPEECH, pages 2590–2593, 2010.Xuejing Sun. Pitch determination and voice quality analysis using subharmonic-to-harmonic ratio. In Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on, volume 1, page I—333. IEEE, 2002.Markel. The SIFT algorithm for fundamental frequency estimation. IEEE Transactions on Audio and Electroacoustics, 20(5):367—377, December 1972.Thomas Drugman and Abeer Alwan. Joint Robust Voicing Detection and Pitch Estimation Based on Residual Harmonics. In Interspeech, page 1973—1976, 2011.Hideki Kawahara, Masanori Morise, Toru Takahashi, Ryuichi Nisimura, Toshio Irino, and Hideki Banno. TANDEM-STRAIGHT: A temporally stable power spectral representation for periodic signals and applications to interference-free spectrum, F0, and aperiodicity estimation. In Acous- tics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on, pages 3933–3936. IEEE, 2008.Arturo Camacho. SWIPE: A sawtooth waveform inspired pitch estimator for speech and music. PhD thesis, University of Florida, 2007.Kavita Kasi and Stephen A. Zahorian. Yet Another Algorithm for Pitch Tracking. In IEEE International Conference on Acoustics Speech and Signal Processing, pages I–361–I–364, Orlando, FL, USA, May 2002. IEEE.Alain de Cheveigné and Hideki Kawahara. YIN, a fundamental frequency estimator for speech and music. The Journal of the Acoustical Society of America, 111(4):1917, 2002.

Heterogenous Big dataset is presented in this proposed work: electrocardiogram (ECG) signal, blood pressure signal, oxygen saturation (SpO2) signal, and the text input. This work is an extension version for our relevant formulating of dataset that presented in [1] and a trustworthy and relevant medical dataset library (PhysioNet [2]) was used to acquire these signals. The dataset includes medical features from heterogenous sources (sensory data and non-sensory). Firstly, ECG sensor’s signals which contains QRS width, ST elevation, peak numbers, and cycle interval. Secondly: SpO2 level from SpO2 sensor’s signals. Third, blood pressure sensors’ signals which contain high (systolic) and low (diastolic) values and finally text input which consider non-sensory data. The text inputs were formulated based on doctors diagnosing procedures for heart chronic diseases. Python software environment was used, and the simulated big data is presented along with analyses.

This dataset was created to simulate a market basket dataset, providing insights into customer purchasing behavior and store operations. The dataset facilitates market basket analysis, customer segmentation, and other retail analytics tasks. Here's more information about the context and inspiration behind this dataset:

Context:

Retail businesses, from supermarkets to convenience stores, are constantly seeking ways to better understand their customers and improve their operations. Market basket analysis, a technique used in retail analytics, explores customer purchase patterns to uncover associations between products, identify trends, and optimize pricing and promotions. Customer segmentation allows businesses to tailor their offerings to specific groups, enhancing the customer experience.

Inspiration:

The inspiration for this dataset comes from the need for accessible and customizable market basket datasets. While real-world retail data is sensitive and often restricted, synthetic datasets offer a safe and versatile alternative. Researchers, data scientists, and analysts can use this dataset to develop and test algorithms, models, and analytical tools.

Dataset Information:

The columns provide information about the transactions, customers, products, and purchasing behavior, making the dataset suitable for various analyses, including market basket analysis and customer segmentation. Here's a brief explanation of each column in the Dataset:

• Transaction_ID: A unique identifier for each transaction, represented as a 10-digit number. This column is used to uniquely identify each purchase.
• Date: The date and time when the transaction occurred. It records the timestamp of each purchase.
• Customer_Name: The name of the customer who made the purchase. It provides information about the customer's identity.
• Product: A list of products purchased in the transaction. It includes the names of the products bought.
• Total_Items: The total number of items purchased in the transaction. It represents the quantity of products bought.
• Total_Cost: The total cost of the purchase, in currency. It represents the financial value of the transaction.
• Payment_Method: The method used for payment in the transaction, such as credit card, debit card, cash, or mobile payment.
• City: The city where the purchase took place. It indicates the location of the transaction.
• Store_Type: The type of store where the purchase was made, such as a supermarket, convenience store, department store, etc.
• Discount_Applied: A binary indicator (True/False) representing whether a discount was applied to the transaction.
• Customer_Category: A category representing the customer's background or age group.
• Season: The season in which the purchase occurred, such as spring, summer, fall, or winter.
• Promotion: The type of promotion applied to the transaction, such as "None," "BOGO (Buy One Get One)," or "Discount on Selected Items."

Use Cases:

• Market Basket Analysis: Discover associations between products and uncover buying patterns.
• Customer Segmentation: Group customers based on purchasing behavior.
• Pricing Optimization: Optimize pricing strategies and identify opportunities for discounts and promotions.
• Retail Analytics: Analyze store performance and customer trends.

Note: This dataset is entirely synthetic and was generated using the Python Faker library, which means it doesn't contain real customer data. It's designed for educational and research purposes.

This item contains data and code used in experiments that produced the results for Sadler et. al (2022) (see below for full reference). We ran five experiments for the analysis, Experiment A, Experiment B, Experiment C, Experiment D, and Experiment AuxIn. Experiment A tested multi-task learning for predicting streamflow with 25 years of training data and using a different model for each of 101 sites. Experiment B tested multi-task learning for predicting streamflow with 25 years of training data and using a single model for all 101 sites. Experiment C tested multi-task learning for predicting streamflow with just 2 years of training data. Experiment D tested multi-task learning for predicting water temperature with over 25 years of training data. Experiment AuxIn used water temperature as an input variable for predicting streamflow. These experiments and their results are described in detail in the WRR paper. Data from a total of 101 sites across the US was used for the experiments. The model input data and streamflow data were from the Catchment Attributes and Meteorology for Large-sample Studies (CAMELS) dataset (Newman et. al 2014, Addor et. al 2017). The water temperature data were gathered from the National Water Information System (NWIS) (U.S. Geological Survey, 2016). The contents of this item are broken into 13 files or groups of files aggregated into zip files:

1. input_data_processing.zip: A zip file containing the scripts used to collate the observations, input weather drivers, and catchment attributes for the multi-task modeling experiments
2. flow_observations.zip: A zip file containing collated daily streamflow data for the sites used in multi-task modeling experiments. The streamflow data were originally accessed from the CAMELs dataset. The data are stored in csv and Zarr formats.
3. temperature_observations.zip: A zip file containing collated daily water temperature data for the sites used in multi-task modeling experiments. The data were originally accessed via NWIS. The data are stored in csv and Zarr formats.
4. temperature_sites.geojson: Geojson file of the locations of the water temperature and streamflow sites used in the analysis.
5. model_drivers.zip: A zip file containing the daily input weather driver data for the multi-task deep learning models. These data are from the Daymet drivers and were collated from the CAMELS dataset. The data are stored in csv and Zarr formats.
6. catchment_attrs.csv: Catchment attributes collatted from the CAMELS dataset. These data are used for the Random Forest modeling. For full metadata regarding these data see CAMELS dataset.
7. experiment_workflow_files.zip: A zip file containing workflow definitions used to run multi-task deep learning experiments. These are Snakemake workflows. To run a given experiment, one would run (for experiment A) 'snakemake -s expA_Snakefile --configfile expA_config.yml'
8. river-dl-paper_v0.zip: A zip file containing python code used to run multi-task deep learning experiments. This code was called by the Snakemake workflows contained in 'experiment_workflow_files.zip'.
9. random_forest_scripts.zip: A zip file containing Python code and a Python Jupyter Notebook used to prepare data for, train, and visualize feature importance of a Random Forest model.
10. plotting_code.zip: A zip file containing python code and Snakemake workflow used to produce figures showing the results of multi-task deep learning experiments.
11. results.zip: A zip file containing results of multi-task deep learning experiments. The results are stored in csv and netcdf formats. The netcdf files were used by the plotting libraries in 'plotting_code.zip'. These files are for five experiments, 'A', 'B', 'C', 'D', and 'AuxIn'. These experiment names are shown in the file name.
12. sample_scripts.zip: A zip file containing scripts for creating sample output to demonstrate how the modeling workflow was executed.
13. sample_output.zip: A zip file containing sample output data. Similar files are created by running the sample scripts provided.

A. Newman; K. Sampson; M. P. Clark; A. Bock; R. J. Viger; D. Blodgett, 2014. A large-sample watershed-scale hydrometeorological dataset for the contiguous USA. Boulder, CO: UCAR/NCAR. https://dx.doi.org/10.5065/D6MW2F4D

N. Addor, A. Newman, M. Mizukami, and M. P. Clark, 2017. Catchment attributes for large-sample studies. Boulder, CO: UCAR/NCAR. https://doi.org/10.5065/D6G73C3Q

Sadler, J. M., Appling, A. P., Read, J. S., Oliver, S. K., Jia, X., Zwart, J. A., & Kumar, V. (2022). Multi-Task Deep Learning of Daily Streamflow and Water Temperature. Water Resources Research, 58(4), e2021WR030138. https://doi.org/10.1029/2021WR030138

U.S. Geological Survey, 2016, National Water Information System data available on the World Wide Web (USGS Water Data for the Nation), accessed Dec. 2020.

Large go-around, also referred to as missed approach, data set. The data set is in support of the paper presented at the OpenSky Symposium on November the 10th.

If you use this data for a scientific publication, please consider citing our paper.

The data set contains landings from 176 (mostly) large airports from 44 different countries. The landings are labelled as performing a go-around (GA) or not. In total, the data set contains almost 9 million landings with more than 33000 GAs. The data was collected from OpenSky Network's historical data base for the year 2019. The published data set contains multiple files:

go_arounds_minimal.csv.gz

Compressed CSV containing the minimal data set. It contains a row for each landing and a minimal amount of information about the landing, and if it was a GA. The data is structured in the following way:

    Column name
    Type
    Description




    time
    date time
    UTC time of landing or first GA attempt


    icao24
    string
    Unique 24-bit (hexadecimal number) ICAO identifier of the aircraft concerned


    callsign
    string
    Aircraft identifier in air-ground communications


    airport
    string
    ICAO airport code where the aircraft is landing


    runway
    string
    Runway designator on which the aircraft landed


    has_ga
    string
    "True" if at least one GA was performed, otherwise "False"


    n_approaches
    integer
    Number of approaches identified for this flight


    n_rwy_approached
    integer
    Number of unique runways approached by this flight

The last two columns, n_approaches and n_rwy_approached, are useful to filter out training and calibration flight. These have usually a large number of n_approaches, so an easy way to exclude them is to filter by n_approaches > 2.

go_arounds_augmented.csv.gz

Compressed CSV containing the augmented data set. It contains a row for each landing and additional information about the landing, and if it was a GA. The data is structured in the following way:

    Column name
    Type
    Description




    time
    date time
    UTC time of landing or first GA attempt


    icao24
    string
    Unique 24-bit (hexadecimal number) ICAO identifier of the aircraft concerned


    callsign
    string
    Aircraft identifier in air-ground communications


    airport
    string
    ICAO airport code where the aircraft is landing


    runway
    string
    Runway designator on which the aircraft landed


    has_ga
    string
    "True" if at least one GA was performed, otherwise "False"


    n_approaches
    integer
    Number of approaches identified for this flight


    n_rwy_approached
    integer
    Number of unique runways approached by this flight


    registration
    string
    Aircraft registration


    typecode
    string
    Aircraft ICAO typecode


    icaoaircrafttype
    string
    ICAO aircraft type


    wtc
    string
    ICAO wake turbulence category


    glide_slope_angle
    float
    Angle of the ILS glide slope in degrees


    has_intersection

string

    Boolean that is true if the runway has an other runway intersecting it, otherwise false


    rwy_length
    float
    Length of the runway in kilometre


    airport_country
    string
    ISO Alpha-3 country code of the airport


    airport_region
    string
    Geographical region of the airport (either Europe, North America, South America, Asia, Africa, or Oceania)


    operator_country
    string
    ISO Alpha-3 country code of the operator


    operator_region
    string
    Geographical region of the operator of the aircraft (either Europe, North America, South America, Asia, Africa, or Oceania)


    wind_speed_knts
    integer
    METAR, surface wind speed in knots


    wind_dir_deg
    integer
    METAR, surface wind direction in degrees


    wind_gust_knts
    integer
    METAR, surface wind gust speed in knots


    visibility_m
    float
    METAR, visibility in m


    temperature_deg
    integer
    METAR, temperature in degrees Celsius


    press_sea_level_p
    float
    METAR, sea level pressure in hPa


    press_p
    float
    METAR, QNH in hPA


    weather_intensity
    list
    METAR, list of present weather codes: qualifier - intensity


    weather_precipitation
    list
    METAR, list of present weather codes: weather phenomena - precipitation


    weather_desc
    list
    METAR, list of present weather codes: qualifier - descriptor


    weather_obscuration
    list
    METAR, list of present weather codes: weather phenomena - obscuration


    weather_other
    list
    METAR, list of present weather codes: weather phenomena - other

This data set is augmented with data from various public data sources. Aircraft related data is mostly from the OpenSky Network's aircraft data base, the METAR information is from the Iowa State University, and the rest is mostly scraped from different web sites. If you need help with the METAR information, you can consult the WMO's Aerodrom Reports and Forecasts handbook.

go_arounds_agg.csv.gz

Compressed CSV containing the aggregated data set. It contains a row for each airport-runway, i.e. every runway at every airport for which data is available. The data is structured in the following way:

    Column name
    Type
    Description




    airport
    string
    ICAO airport code where the aircraft is landing


    runway
    string
    Runway designator on which the aircraft landed


    n_landings
    integer
    Total number of landings observed on this runway in 2019


    ga_rate
    float
    Go-around rate, per 1000 landings


    glide_slope_angle
    float
    Angle of the ILS glide slope in degrees


    has_intersection
    string
    Boolean that is true if the runway has an other runway intersecting it, otherwise false


    rwy_length
    float
    Length of the runway in kilometres


    airport_country
    string
    ISO Alpha-3 country code of the airport


    airport_region
    string
    Geographical region of the airport (either Europe, North America, South America, Asia, Africa, or Oceania)

This aggregated data set is used in the paper for the generalized linear regression model.

Downloading the trajectories

Users of this data set with access to OpenSky Network's Impala shell can download the historical trajectories from the historical data base with a few lines of Python code. For example, you want to get all the go-arounds of the 4th of January 2019 at London City Airport (EGLC). You can use the Traffic library for easy access to the database:

import datetime from tqdm.auto import tqdm import pandas as pd from traffic.data import opensky from traffic.core import Traffic

load minimum data set

df = pd.read_csv("go_arounds_minimal.csv.gz", low_memory=False) df["time"] = pd.to_datetime(df["time"])

select London City Airport, go-arounds, and 2019-01-04

airport = "EGLC" start = datetime.datetime(year=2019, month=1, day=4).replace( tzinfo=datetime.timezone.utc ) stop = datetime.datetime(year=2019, month=1, day=5).replace( tzinfo=datetime.timezone.utc )

df_selection = df.query("airport==@airport & has_ga & (@start <= time <= @stop)")

iterate over flights and pull the data from OpenSky Network

flights = [] delta_time = pd.Timedelta(minutes=10) for _, row in tqdm(df_selection.iterrows(), total=df_selection.shape[0]): # take at most 10 minutes before and 10 minutes after the landing or go-around start_time = row["time"] - delta_time stop_time = row["time"] + delta_time

# fetch the data from OpenSky Network
flights.append(
  opensky.history(
    start=start_time.strftime("%Y-%m-%d %H:%M:%S"),
    stop=stop_time.strftime("%Y-%m-%d %H:%M:%S"),
    callsign=row["callsign"],
    return_flight=True,
  )
)

The flights can be converted into a Traffic object

Traffic.from_flights(flights)

Additional files

Additional files are available to check the quality of the classification into GA/not GA and the selection of the landing runway. These are:

validation_table.xlsx: This Excel sheet was manually completed during the review of the samples for each runway in the data set. It provides an estimate of the false positive and false negative rate of the go-around classification. It also provides an estimate of the runway misclassification rate when the airport has two or more parallel runways. The columns with the headers highlighted in red were filled in manually, the rest is generated automatically.

validation_sample.zip: For each runway, 8 batches of 500 randomly selected trajectories (or as many as available, if fewer than 4000) classified as not having a GA and up to 8 batches of 10 random landings, classified as GA, are plotted. This allows the interested user to visually inspect a random sample of the landings and go-arounds easily.

Bluesky Social Dataset Pollution of online social spaces caused by rampaging d/misinformation is a growing societal concern. However, recent decisions to reduce access to social media APIs are causing a shortage of publicly available, recent, social media data, thus hindering the advancement of computational social science as a whole. To address this pressing issue, we present a large, high-coverage dataset of social interactions and user-generated content from Bluesky Social.

The dataset contains the complete post history of over 4M users (81% of all registered accounts), totaling 235M posts. We also make available social data covering follow, comment, repost, and quote interactions.

Since Bluesky allows users to create and bookmark feed generators (i.e., content recommendation algorithms), we also release the full output of several popular algorithms available on the platform, along with their timestamped “like” interactions and time of bookmarking.

This dataset allows unprecedented analysis of online behavior and human-machine engagement patterns. Notably, it provides ground-truth data for studying the effects of content exposure and self-selection, and performing content virality and diffusion analysis.

Dataset Here is a description of the dataset files.

followers.csv.gz. This compressed file contains the anonymized follower edge list. Once decompressed, each row consists of two comma-separated integers u, v, representing a directed following relation (i.e., user u follows user v). posts.tar.gz. This compressed folder contains data on the individual posts collected. Decompressing this file results in 100 files, each containing the full posts of up to 50,000 users. Each post is stored as a JSON-formatted line. interactions.csv.gz. This compressed file contains the anonymized interactions edge list. Once decompressed, each row consists of six comma-separated integers, and represents a comment, repost, or quote interaction. These integers correspond to the following fields, in this order: user_id, replied_author, thread_root_author, reposted_author ,quoted_author, and date. graphs.tar.gz. This compressed folder contains edge list files for the graphs emerging from reposts, quotes, and replies. Each interaction is timestamped. The folder also contains timestamped higher-order interactions emerging from discussion threads, each containing all users participating in a thread. feed_posts.tar.gz. This compressed folder contains posts that appear in 11 thematic feeds. Decompressing this folder results in 11 files containing posts from one feed each. Posts are stored as a JSON-formatted line. Fields are correspond to those in posts.tar.gz, except for those related to sentiment analysis (sent_label, sent_score), and reposts (repost_from, reposted_author); feed_bookmarks.csv. This file contains users who bookmarked any of the collected feeds. Each record contains three comma-separated values, namely the feed name, the user id, and the timestamp. feed_post_likes.tar.gz. This compressed folder contains data on likes to posts appearing in the feeds, one file per feed. Each record in the files contains the following information, in this order: the id of the ``liker'', the id of the post's author, the id of the liked post, and the like timestamp; scripts.tar.gz. A collection of Python scripts, including the ones originally used to crawl the data, and to perform experiments. These scripts are detailed in a document released within the folder.

Citation If used for research purposes, please cite the following paper describing the dataset details:

Andrea Failla and Giulio Rossetti. "I'm in the Bluesky Tonight": Insights from a Year Worth of Social Data. (2024) arXiv:2404.18984

Acknowledgments: This work is supported by :

the European Union – Horizon 2020 Program under the scheme “INFRAIA-01-2018-2019 – Integrating Activities for Advanced Communities”, Grant Agreement n.871042, “SoBigData++: European Integrated Infrastructure for Social Mining and Big Data Analytics” (http://www.sobigdata.eu); SoBigData.it which receives funding from the European Union – NextGenerationEU – National Recovery and Resilience Plan (Piano Nazionale di Ripresa e Resilienza, PNRR) – Project: “SoBigData.it – Strengthening the Italian RI for Social Mining and Big Data Analytics” – Prot. IR0000013 – Avviso n. 3264 del 28/12/2021; EU NextGenerationEU programme under the funding schemes PNRR-PE-AI FAIR (Future Artificial Intelligence Research).

We release two tomographic scans with two levels of radiation dosage of two measured objects for noise-level comparative studies in data analysis, reconstruction or segmentation methods. The objects are referred to as apple and pebbles (more specific, hydrograins), respectively. The dataset collected with higher dosage is referred to as the "good" dataset; and the other as the "noisy" dataset, as a way to distinguish between the two dosage levels.

The dataset are acquired using the custom built and highly flexible CT scanner, FlexRay Lab, developed by XRE NV and located at CWI. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1943-by-1535 pixels, 14-bit, flat detector panel.

Both dataset were collected over a 360 degrees in circular and continuous motion with 2001 projections distributed evenly over the full circle for the good dataset and 501 projections distributed evenly over the full circle for the noisy dataset. The uploaded dataset are not binned or normalized; a single dark and two (pre- and post-) flat fields are included for each scan. Projections for both sets were collected with 100 ms exposure time with the good data projections averaged over 5 takes, and no averaging was made for the noisy data. The tube settings for the good and noisy dataset were 70kV, 45W and 70kV, 20W, respectively. The total scanning time were 20 minutes for the good; 3 minutes for the noisy scan. Each dataset is packaged with the full list of data and scan settings files (in .txt format). These files contain the tube settings, scan geometry and full list of motor settings.

These dataset are produced by the Computational Imaging members at Centrum Wiskunde & Informatica (CI-CWI). For any useful Python/MATLAB scripts for FlexRay dataset, we refer the reader to our group's GitHub page.

For more information or guidance in using these dataset, please get in touch with

• s.b.coban [at] cwi.nl or
• m.j.lagerwerf [at] cwi.nl

What is IPGOD?\r

The Intellectual Property Government Open Data (IPGOD) includes over 100 years of registry data on all intellectual property (IP) rights administered by IP Australia. It also has derived information about the applicants who filed these IP rights, to allow for research and analysis at the regional, business and individual level. This is the 2019 release of IPGOD.\r \r \r

How do I use IPGOD?\r

IPGOD is large, with millions of data points across up to 40 tables, making them too large to open with Microsoft Excel. Furthermore, analysis often requires information from separate tables which would need specialised software for merging. We recommend that advanced users interact with the IPGOD data using the right tools with enough memory and compute power. This includes a wide range of programming and statistical software such as Tableau, Power BI, Stata, SAS, R, Python, and Scalar.\r \r \r

IP Data Platform\r

IP Australia is also providing free trials to a cloud-based analytics platform with the capabilities to enable working with large intellectual property datasets, such as the IPGOD, through the web browser, without any installation of software. IP Data Platform\r \r

References\r

\r The following pages can help you gain the understanding of the intellectual property administration and processes in Australia to help your analysis on the dataset.\r \r * Patents\r * Trade Marks\r * Designs\r * Plant Breeder’s Rights\r \r \r

Updates\r

\r

Tables and columns\r

\r Due to the changes in our systems, some tables have been affected.\r \r * We have added IPGOD 225 and IPGOD 325 to the dataset!\r * The IPGOD 206 table is not available this year.\r * Many tables have been re-built, and as a result may have different columns or different possible values. Please check the data dictionary for each table before use.\r \r

Data quality improvements\r

\r Data quality has been improved across all tables.\r \r * Null values are simply empty rather than '31/12/9999'.\r * All date columns are now in ISO format 'yyyy-mm-dd'.\r * All indicator columns have been converted to Boolean data type (True/False) rather than Yes/No, Y/N, or 1/0.\r * All tables are encoded in UTF-8.\r * All tables use the backslash \ as the escape character.\r * The applicant name cleaning and matching algorithms have been updated. We believe that this year's method improves the accuracy of the matches. Please note that the "ipa_id" generated in IPGOD 2019 will not match with those in previous releases of IPGOD.

Fingerprint methods applied to molecules have proven to be useful for similarity determination and as inputs to machine-learning models. Here, we present the development of a new fingerprint for chemical reactions and validate its usefulness in building machine-learning models and in similarity assessment. Our final fingerprint is constructed as the difference of the atom-pair fingerprints of products and reactants and includes agents via calculated physicochemical properties. We validated the fingerprints on a large data set of reactions text-mined from granted United States patents from the last 40 years that have been classified using a substructure-based expert system. We applied machine learning to build a 50-class predictive model for reaction-type classification that correctly predicts 97% of the reactions in an external test set. Impressive accuracies were also observed when applying the classifier to reactions from an in-house electronic laboratory notebook. The performance of the novel fingerprint for assessing reaction similarity was evaluated by a cluster analysis that recovered 48 out of 50 of the reaction classes with a median F-score of 0.63 for the clusters. The data sets used for training and primary validation as well as all python scripts required to reproduce the analysis are provided in the Supporting Information.