Sample data set used in an introductory course on Programming in Python

Description: - This dataset includes all 22 built-in datasets from the Seaborn library, a widely used Python data visualization tool. Seaborn's built-in datasets are essential resources for anyone interested in practicing data analysis, visualization, and machine learning. They span a wide range of topics, from classic datasets like the Iris flower classification to real-world data such as Titanic survival records and diamond characteristics.

• Included Datasets:
  • Anagrams: Analysis of word anagram patterns.
  • Anscombe: Anscombe's quartet demonstrating the importance of data visualization.
  • Attention: Data on attention span variations in different scenarios.
  • Brain Networks: Connectivity data within brain networks.
  • Car Crashes: US car crash statistics.
  • Diamonds: Data on diamond properties including price, cut, and clarity.
  • Dots: Randomly generated data for scatter plot visualization.
  • Dow Jones: Historical records of the Dow Jones Industrial Average.
  • Exercise: The relationship between exercise and health metrics.
  • Flights: Monthly passenger numbers on flights.
  • FMRI: Functional MRI data capturing brain activity.
  • Geyser: Eruption times of the Old Faithful geyser.
  • Glue: Strength of glue under different conditions.
  • Health Expenditure: Health expenditure statistics across countries.
  • Iris: Famous dataset for classifying Iris species.
  • MPG: Miles per gallon for various vehicles.
  • Penguins: Data on penguin species and their features.
  • Planets: Characteristics of discovered exoplanets.
  • Sea Ice: Measurements of sea ice extent.
  • Taxis: Taxi trips data in a city.
  • Tips: Tipping data collected from a restaurant.
  • Titanic: Survival data from the Titanic disaster.

This complete collection serves as an excellent starting point for anyone looking to improve their data science skills, offering a wide array of datasets suitable for both beginners and advanced users.

We present Code4ML: a Large-scale Dataset of annotated Machine Learning Code, a corpus of Python code snippets, competition summaries, and data descriptions from Kaggle.

The data is organized in a table structure. Code4ML includes several main objects: competitions information, raw code blocks collected form Kaggle and manually marked up snippets. Each table has a .csv format.

Each competition has the text description and metadata, reflecting competition and used dataset characteristics as well as evaluation metrics (competitions.csv). The corresponding datasets can be loaded using Kaggle API and data sources.

The code blocks themselves and their metadata are collected to the data frames concerning the publishing year of the initial kernels. The current version of the corpus includes two code blocks files: snippets from kernels up to the 2020 year (сode_blocks_upto_20.csv) and those from the 2021 year (сode_blocks_21.csv) with corresponding metadata. The corpus consists of 2 743 615 ML code blocks collected from 107 524 Jupyter notebooks.

Marked up code blocks have the following metadata: anonymized id, the format of the used data (for example, table or audio), the id of the semantic type, a flag for the code errors, the estimated relevance to the semantic class (from 1 to 5), the id of the parent notebook, and the name of the competition. The current version of the corpus has ~12 000 labeled snippets (markup_data_20220415.csv).

As marked up code blocks data contains the numeric id of the code block semantic type, we also provide a mapping from this number to semantic type and subclass (actual_graph_2022-06-01.csv).

The dataset can help solve various problems, including code synthesis from a prompt in natural language, code autocompletion, and semantic code classification.

Dataset

This dataset was created by Toxirmalik

Released under MIT

Contents

This resource contains a Jupyter notebook that demonstrates how someone can query the I-GUIDE data catalog, retrieve data, and execute a code workflow.

This dataset contains 55,000 entries of synthetic customer transactions, generated using Python's Faker library. The goal behind creating this dataset was to provide a resource for learners like myself to explore, analyze, and apply various data analysis techniques in a context that closely mimics real-world data.

About the Dataset: - CID (Customer ID): A unique identifier for each customer. - TID (Transaction ID): A unique identifier for each transaction. - Gender: The gender of the customer, categorized as Male or Female. - Age Group: Age group of the customer, divided into several ranges. - Purchase Date: The timestamp of when the transaction took place. - Product Category: The category of the product purchased, such as Electronics, Apparel, etc. - Discount Availed: Indicates whether the customer availed any discount (Yes/No). - Discount Name: Name of the discount applied (e.g., FESTIVE50). - Discount Amount (INR): The amount of discount availed by the customer. - Gross Amount: The total amount before applying any discount. - Net Amount: The final amount after applying the discount. - Purchase Method: The payment method used (e.g., Credit Card, Debit Card, etc.). - Location: The city where the purchase took place.

Use Cases: 1. Exploratory Data Analysis (EDA): This dataset is ideal for conducting EDA, allowing users to practice techniques such as summary statistics, visualizations, and identifying patterns within the data. 2. Data Preprocessing and Cleaning: Learners can work on handling missing data, encoding categorical variables, and normalizing numerical values to prepare the dataset for analysis. 3. Data Visualization: Use tools like Python’s Matplotlib, Seaborn, or Power BI to visualize purchasing trends, customer demographics, or the impact of discounts on purchase amounts. 4. Machine Learning Applications: After applying feature engineering, this dataset is suitable for supervised learning models, such as predicting whether a customer will avail a discount or forecasting purchase amounts based on the input features.

This dataset provides an excellent sandbox for honing skills in data analysis, machine learning, and visualization in a structured but flexible manner.

This is not a real dataset. This dataset was generated using Python's Faker library for the sole purpose of learning

Evol-Instruct-Python-1k

Subset of the mlabonne/Evol-Instruct-Python-26k dataset with only 1000 samples. It was made by filtering out a few rows (instruction + output) with more than 2048 tokens, and then by keeping the 1000 longest samples. Here is the distribution of the number of tokens in each row using Llama's tokenizer:

example dataset with Python files

This resource contains Jupyter Notebooks with examples that illustrate how to work with SQLite databases in Python including database creation and viewing and querying with SQL. The resource is part of set of materials for hydroinformatics and water data science instruction. Complete learning module materials are found in HydroLearn: Jones, A.S., Horsburgh, J.S., Bastidas Pacheco, C.J. (2022). Hydroinformatics and Water Data Science. HydroLearn. https://edx.hydrolearn.org/courses/course-v1:USU+CEE6110+2022/about..

This resources consists of 3 example notebooks and a SQLite database.

Notebooks: 1. Example 1: Querying databases using SQL in Python 2. Example 2: Python functions to query SQLite databases 3. Example 3: SQL join, aggregate, and subquery functions

Data files: These examples use a SQLite database that uses the Observations Data Model structure and is pre-populated with Logan River temperature data.

Dataset to run Example.py script of the Valparaíso Stacking Analysis Tool (VSAT-3D). The Valparaíso Stacking Analysis Tool (VSAT-3D) provides a series of tools for selecting, stacking, and analyzing 3D spectra. It is intended for stacking samples of datacubes extracted from interferometric datasets, belonging to large extragalactic catalogs by selecting subsamples of galaxies defined by their available properties (e.g. redshift, stellar mass, star formation rate) being possible to generate diverse (e.g. median, average, weighted average, histogram) composite spectra. However, it is possible to also use VSAT-3D on smaller datasets containing any type of astronomical object.

VSAT-3D can be downloaded from the github repository link.

Dataset to run Example.py script of the Valparaíso Stacking Analysis Tool (VSAT-2D). The Valparaíso Stacking Analysis Tool (VSAT-2D) provides a series of tools for selecting, stacking, and analyzing moment-0 intensity maps from interferometric datasets. It is intended for stacking samples of moment-0 extracted from interferometric datasets, belonging to large extragalactic catalogs by selecting subsamples of galaxies defined by their available properties (e.g. redshift, stellar mass, star formation rate) being possible to generate diverse (e.g. median, average, weighted average, histogram) composite spectra. However, it is possible to also use VSAT-2D on smaller datasets containing any type of astronomical object.

VSAT-2D can be downloaded from the github repository link.

Attention: This dataset is a summary and reformat pulled from github code.

You should make your own assumptions based on this. In fact, there is another dataset I formed through parsing that addresses several points:

out of 500k python related items, most of them are python-ish, not pythonic the majority of the items here contain excessive licensing inclusion of original code the items here are sometimes not even python but have references There's a whole lot of gpl summaries… See the full description on the dataset page: https://huggingface.co/datasets/jtatman/python-code-dataset-500k.

ieadoboe/python-function-examples dataset hosted on Hugging Face and contributed by the HF Datasets community

This dataset is about book subjects. It has 2 rows and is filtered where the books is Scientific computing with Python 3 : an example-rich, comprehensive guide for all of your Python computational needs. It features 10 columns including number of authors, number of books, earliest publication date, and latest publication date.

Vezora/Tested-188k-Python-Alpaca: Functional Python Code Dataset

188k Functional Python Code Samples

By Vezora (From Huggingface) [source]

About this dataset

The Vezora/Tested-188k-Python-Alpaca dataset is a comprehensive collection of functional Python code samples, specifically designed for training and analysis purposes. With 188,000 samples, this dataset offers an extensive range of examples that cater to the research needs of Python programming enthusiasts.

This valuable resource consists of various columns, including input, which represents the input or parameters required for executing the Python code sample. The instruction column describes the task or objective that the Python code sample aims to solve. Additionally, there is an output column that showcases the resulting output generated by running the respective Python code.

By utilizing this dataset, researchers can effectively study and analyze real-world scenarios and applications of Python programming. Whether for educational purposes or development projects, this dataset serves as a reliable reference for individuals seeking practical examples and solutions using Python

How to use the dataset

The Vezora/Tested-188k-Python-Alpaca dataset is a comprehensive collection of functional Python code samples, containing 188,000 samples in total. This dataset can be a valuable resource for researchers and programmers interested in exploring various aspects of Python programming.

Contents of the Dataset

The dataset consists of several columns:

• output: This column represents the expected output or result that is obtained when executing the corresponding Python code sample.
• instruction: It provides information about the task or instruction that each Python code sample is intended to solve.
• input: The input parameters or values required to execute each Python code sample.

Exploring the Dataset

To make effective use of this dataset, it is essential to understand its structure and content properly. Here are some steps you can follow:

• Importing Data: Load the dataset into your preferred environment for data analysis using appropriate tools like pandas in Python.

import pandas as pd

# Load the dataset
df = pd.read_csv('train.csv')

• Understanding Column Names: Familiarize yourself with the column names and their meanings by referring to the provided description.

# Display column names
print(df.columns)

• Sample Exploration: Get an initial understanding of the data structure by examining a few random samples from different columns.

# Display random samples from 'output' column
print(df['output'].sample(5))

• Analyzing Instructions: Analyze different instructions or tasks present in the 'instruction' column to identify specific areas you are interested in studying or learning about.

# Count unique instructions and display top ones with highest occurrences
instruction_counts = df['instruction'].value_counts()
print(instruction_counts.head(10))

Potential Use Cases

The Vezora/Tested-188k-Python-Alpaca dataset can be utilized in various ways:

• Code Analysis: Analyze the code samples to understand common programming patterns and best practices.
• Code Debugging: Use code samples with known outputs to test and debug your own Python programs.
• Educational Purposes: Utilize the dataset as a teaching tool for Python programming classes or tutorials.
• Machine Learning Applications: Train machine learning models to predict outputs based on given inputs.

Remember that this dataset provides a plethora of diverse Python coding examples, allowing you to explore different

Research Ideas

• Code analysis: Researchers and developers can use this dataset to analyze various Python code samples and identify patterns, best practices, and common mistakes. This can help in improving code quality and optimizing performance.
• Language understanding: Natural language processing techniques can be applied to the instruction column of this dataset to develop models that can understand and interpret natural language instructions for programming tasks.
• Code generation: The input column of this dataset contains the required inputs for executing each Python code sample. Researchers can build models that generate Python code based on specific inputs or task requirements using the examples provided in this dataset. This can be useful in automating repetitive programming tasks o...

Objectives: In quantitative research, understanding basic parameters of the study population is key for interpretation of the results. As a result, it is typical for the first table (“Table 1”) of a research paper to include summary statistics for the study data. Our objectives are 2-fold. First, we seek to provide a simple, reproducible method for providing summary statistics for research papers in the Python programming language. Second, we seek to use the package to improve the quality of summary statistics reported in research papers.

Materials and Methods: The tableone package is developed following good practice guidelines for scientific computing and all code is made available under a permissive MIT License. A testing framework runs on a continuous integration server, helping to maintain code stability. Issues are tracked openly and public contributions are encouraged.

Results: The tableone software package automatically compiles summary statistics into publishable formats such...

These four labeled data sets are targeted at ordinal quantification. The goal of quantification is not to predict the label of each individual instance, but the distribution of labels in unlabeled sets of data.

With the scripts provided, you can extract CSV files from the UCI machine learning repository and from OpenML. The ordinal class labels stem from a binning of a continuous regression label.

We complement this data set with the indices of data items that appear in each sample of our evaluation. Hence, you can precisely replicate our samples by drawing the specified data items. The indices stem from two evaluation protocols that are well suited for ordinal quantification. To this end, each row in the files app_val_indices.csv, app_tst_indices.csv, app-oq_val_indices.csv, and app-oq_tst_indices.csv represents one sample.

Our first protocol is the artificial prevalence protocol (APP), where all possible distributions of labels are drawn with an equal probability. The second protocol, APP-OQ, is a variant thereof, where only the smoothest 20% of all APP samples are considered. This variant is targeted at ordinal quantification tasks, where classes are ordered and a similarity of neighboring classes can be assumed.

Usage

You can extract four CSV files through the provided script extract-oq.jl, which is conveniently wrapped in a Makefile. The Project.toml and Manifest.toml specify the Julia package dependencies, similar to a requirements file in Python.

Preliminaries: You have to have a working Julia installation. We have used Julia v1.6.5 in our experiments.

Data Extraction: In your terminal, you can call either

make

(recommended), or

julia --project="." --eval "using Pkg; Pkg.instantiate()"
julia --project="." extract-oq.jl

Outcome: The first row in each CSV file is the header. The first column, named "class_label", is the ordinal class.

Further Reading

Implementation of our experiments: https://github.com/mirkobunse/regularized-oq

Dataset overview

This dataset provides data and images of snowflakes in free fall collected with a Multi-Angle Snowflake Camera (MASC) The dataset includes, for each recorded snowflakes:

A triplet of gray-scale images corresponding to the three cameras of the MASC

A large quantity of geometrical, textural descriptors and the pre-compiled output of published retrieval algorithms as well as basic environmental information at the location and time of each measurement.

The pre-computed descriptors and retrievals are available either individually for each camera view or, some of them, available as descriptors of the triplet as a whole. A non exhaustive list of precomputed quantities includes for example:

Textural and geometrical descriptors as in Praz et al 2017

Hydrometeor classification, riming degree estimation, melting identification, as in Praz et al 2017

Blowing snow identification, as in Schaer et al 2020

Mass, volume, gyration estimation, as in Leinonen et al 2021

Data format and structure

The dataset is divided into four .parquet file (for scalar descriptors) and a Zarr database (for the images). A detailed description of the data content and of the data records is available here.

Supporting code

A python-based API is available to manipulate, display and organize the data of our dataset. It can be found on GitHub. See also the code documentation on ReadTheDocs.

Download notes

All files available here for download should be stored in the same folder, if the python-based API is used

MASCdb.zarr.zip must be unzipped after download

Field campaigns

A list of campaigns included in the dataset, with a minimal description is given in the following table

    Campaign_name
    Information

Shielded / Not shielded

DFIR = Double Fence Intercomparison Reference

APRES3-2016 & APRES3-2017

    Instrument installed in Antarctica in the context of the APRES3 project. See for example Genthon et al, 2018 or Grazioli et al 2017
    Not shielded


    Davos-2015
    Instrument installed in the Swiss Alps within the context of SPICE (Solid Precipitation InterComparison Experiment)
    Shielded (DFIR)


    Davos-2019
    Instrument installed in the Swiss Alps within the context of RACLETS (Role of Aerosols and CLouds Enhanced by Topography on Snow)
    Not shielded


    ICEGENESIS-2021
    Instrument installed in the Swiss Jura in a MeteoSwiss ground measurement site, within the context of ICE-GENESIS. See for example Billault-Roux et al, 2023
    Not shielded


    ICEPOP-2018
    Instrument installed in Korea, in the context of ICEPOP. See for example Gehring et al 2021.
    Shielded (DFIR)


    Jura-2019 & Jura-2023
    Instrument installed in the Swiss Jura within a MeteoSwiss measurement site
    Not shielded


    Norway-2016
    Instrument installed in Norway during the High-Latitude Measurement of Snowfall (HiLaMS). See for example Cooper et al, 2022.
    Not shielded


    PLATO-2019
    Instrument installed in the "Davis" Antarctic base during the PLATO field campaign
    Not shielded


    POPE-2020
    Instrument installed in the "Princess Elizabeth Antarctica" base during the POPE campaign. See for example Ferrone et al, 2023.
    Not shielded


    Remoray-2022
    Instrument installed in the French Jura.
    Not shielded


    Valais-2016
    Instrument installed in the Swiss Alps in a ski resort.
    Not shielded

Version

1.0 - Two new campaigns ("Jura-2023", "Norway-2016") added. Added references and list of campaigns.

0.3 - a new campaign is added to the dataset ("Remoray-2022")

0.2 - rename of variables. Variable precision (digits) standardized

0.1 - first upload

General

For more details and the most up-to-date information please consult our project page: https://kainmueller-lab.github.io/fisbe.

Summary

A new dataset for neuron instance segmentation in 3d multicolor light microscopy data of fruit fly brains

30 completely labeled (segmented) images

71 partly labeled images

altogether comprising ∼600 expert-labeled neuron instances (labeling a single neuron takes between 30-60 min on average, yet a difficult one can take up to 4 hours)

To the best of our knowledge, the first real-world benchmark dataset for instance segmentation of long thin filamentous objects

A set of metrics and a novel ranking score for respective meaningful method benchmarking

An evaluation of three baseline methods in terms of the above metrics and score

Abstract

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

Dataset documentation:

We provide a detailed documentation of our dataset, following the Datasheet for Datasets questionnaire:

FISBe Datasheet

Our dataset originates from the FlyLight project, where the authors released a large image collection of nervous systems of ~74,000 flies, available for download under CC BY 4.0 license.

Files

fisbe_v1.0_{completely,partly}.zip

contains the image and ground truth segmentation data; there is one zarr file per sample, see below for more information on how to access zarr files.

fisbe_v1.0_mips.zip

maximum intensity projections of all samples, for convenience.

sample_list_per_split.txt

a simple list of all samples and the subset they are in, for convenience.

view_data.py

a simple python script to visualize samples, see below for more information on how to use it.

dim_neurons_val_and_test_sets.json

a list of instance ids per sample that are considered to be of low intensity/dim; can be used for extended evaluation.

Readme.md

general information

How to work with the image files

Each sample consists of a single 3d MCFO image of neurons of the fruit fly.For each image, we provide a pixel-wise instance segmentation for all separable neurons.Each sample is stored as a separate zarr file (zarr is a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.").The image data ("raw") and the segmentation ("gt_instances") are stored as two arrays within a single zarr file.The segmentation mask for each neuron is stored in a separate channel.The order of dimensions is CZYX.

We recommend to work in a virtual environment, e.g., by using conda:

conda create -y -n flylight-env -c conda-forge python=3.9conda activate flylight-env

How to open zarr files

Install the python zarr package:

pip install zarr

Opened a zarr file with:

import zarrraw = zarr.open(, mode='r', path="volumes/raw")seg = zarr.open(, mode='r', path="volumes/gt_instances")

optional:import numpy as npraw_np = np.array(raw)

Zarr arrays are read lazily on-demand.Many functions that expect numpy arrays also work with zarr arrays.Optionally, the arrays can also explicitly be converted to numpy arrays.

How to view zarr image files

We recommend to use napari to view the image data.

Install napari:

pip install "napari[all]"

Save the following Python script:

import zarr, sys, napari

raw = zarr.load(sys.argv[1], mode='r', path="volumes/raw")gts = zarr.load(sys.argv[1], mode='r', path="volumes/gt_instances")

viewer = napari.Viewer(ndisplay=3)for idx, gt in enumerate(gts): viewer.add_labels( gt, rendering='translucent', blending='additive', name=f'gt_{idx}')viewer.add_image(raw[0], colormap="red", name='raw_r', blending='additive')viewer.add_image(raw[1], colormap="green", name='raw_g', blending='additive')viewer.add_image(raw[2], colormap="blue", name='raw_b', blending='additive')napari.run()

Execute:

python view_data.py /R9F03-20181030_62_B5.zarr

Metrics

S: Average of avF1 and C

avF1: Average F1 Score

C: Average ground truth coverage

clDice_TP: Average true positives clDice

FS: Number of false splits

FM: Number of false merges

tp: Relative number of true positives

For more information on our selected metrics and formal definitions please see our paper.

Baseline

To showcase the FISBe dataset together with our selection of metrics, we provide evaluation results for three baseline methods, namely PatchPerPix (ppp), Flood Filling Networks (FFN) and a non-learnt application-specific color clustering from Duan et al..For detailed information on the methods and the quantitative results please see our paper.

License

The FlyLight Instance Segmentation Benchmark (FISBe) dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Citation

If you use FISBe in your research, please use the following BibTeX entry:

@misc{mais2024fisbe, title = {FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures}, author = {Lisa Mais and Peter Hirsch and Claire Managan and Ramya Kandarpa and Josef Lorenz Rumberger and Annika Reinke and Lena Maier-Hein and Gudrun Ihrke and Dagmar Kainmueller}, year = 2024, eprint = {2404.00130}, archivePrefix ={arXiv}, primaryClass = {cs.CV} }

Acknowledgments

We thank Aljoscha Nern for providing unpublished MCFO images as well as Geoffrey W. Meissner and the entire FlyLight Project Team for valuablediscussions.P.H., L.M. and D.K. were supported by the HHMI Janelia Visiting Scientist Program.This work was co-funded by Helmholtz Imaging.

Changelog

There have been no changes to the dataset so far.All future change will be listed on the changelog page.

Contributing

If you would like to contribute, have encountered any issues or have any suggestions, please open an issue for the FISBe dataset in the accompanying github repository.

All contributions are welcome!

This dataset contains a collection of medical imaging files for use in the "Medical Image Processing with Python" lesson, developed by the Netherlands eScience Center.

The dataset includes:

1. SimpleITK compatible files: MRI T1 and CT scans (training_001_mr_T1.mha, training_001_ct.mha), digital X-ray (digital_xray.dcm in DICOM format), neuroimaging data (A1_grayT1.nrrd, A1_grayT2.nrrd). Data have been downloaded from here.
2. MRI data: a T2-weighted image (OBJECT_phantom_T2W_TSE_Cor_14_1.nii in NIfTI-1 format). Data have been downloaded from here.
3. Example images for the machine learning lesson: chest X-rays (rotatechest.png, other_op.png), cardiomegaly example (cardiomegaly_cc0.png).
4. Additional anonymized data: TBA

These files represent various medical imaging modalities and formats commonly used in clinical research and practice. They are intended for educational purposes, allowing students to practice image processing techniques, machine learning applications, and statistical analysis of medical images using Python libraries such as scikit-image, pydicom, and SimpleITK.