Graduate Project

Introduction

The graduate project is offered only to students enrolled in Data C200 or CS C200A. Other students are welcome to explore the questions and datasets in the project for personal learning, but their work will not be graded or counted towards their final grades.

The purpose of the project is to give students experience in both open-ended data science analysis and research in general. In this project, you will work with one or any combination of the following datasets provided to you to explore research questions that you define.

Project criteria: In addition to the general guidelines, each dataset option below has its own set of additional requirements for Report Format and Submission. Be sure to consult the correct section for your project option.

Grading: You will receive peer review feedback before the final deadline, and you are expected to incorporate the peer feedback into the final report and presentation. You will be graded on both the final report and presentation, as well as deliverables before the submission of the final reports, including your peer reviews.

Teamwork: You can work alone or in a group with at most two other students. If you are interested in working with others, we have an Ed post for teammate search. Everyone in the same group will receive the same grade. The group size will be taken into consideration when grading.

Timeline

Date (by EOD at 11:59pm Pacific) Event / Deliverable Link
9/30 Research proposal and project groups due Preliminary Form
10/14 Project checkpoint 1 Due  
11/18 Project checkpoint 2 Due  
12/2 First draft of final report due  
12/3 Peer review open  
12/7 Peer review due  
12/14 Revised final report due  
12/14 Presentation video due  
12/16 Presentation video released (at discretion)  

Late Policy: You may submit the final report and the presentation video late with a 10% penalty to that portion of your project for each day it is late. You may submit up to two days late. Submission times are rounded up to the next day. That is, 2 minutes late = 1 day late.

Deliverables and Grade Breakdown

Deliverable Weight
Research proposal and project groups 10%
Checkpoints 0%
Submission of first draft 10%
Peer review 15%
Final report: Analysis notebook 20%
Final report: Project writeup 30%
Final presentation video 15%

The project checkpoint is a quick Google Form to assess if you are making progress towards your goals.

Datasets

This section contains the datasets we will provide to you to explore your research questions.

  • You must incorporate at least one of the provided datasets.
  • You are welcome to bring in additional datasets to complement the datasets provided here, but you must cite the sources and clearly describe the content of any additional data you use in the final report.

Should you need to connect together multiple datasets, please be sure to consult the extra resource on causal inference.

Accessing Datasets

All the datasets provided by us can be found inside the following link on Google Drive:

Graduate Project Datasets Google Drive

If you wish to work on Datahub, use the following instructions on how to easily move the data from Google Drive onto Datahub (keep in mind that your Datahub kernel can only manage 2GB of memory at maximum).

If you wish to work on the project locally, you can also download the zip files containing the datasets for each topic.

How to Pull Data from Google Drive directly onto Datahub

  1. Get the Google Drive ID of the file. You can do this by first getting the URL of the file. You do this by right-clicking on the file in Google Drive and pressing ‘Get Link’. Once you have the URL, you can find the ID by looking for the set of characters after the /d/ in the url. For example, in the following url: https://drive.google.com/file/d/16-4O_lJGioPC5G9il4vR_XrCgJ3J9_zK/view?usp=sharing , the Google Drive ID would be 16-4O_lJGioPC5G9il4vR_XrCgJ3J9_zK.
  2. Download the data. Once you have the Google Drive ID of the file, you can use the utils.py file inside the grad_proj directory on your Datahub. This file has a number of useful functions for downloading data. You’ll want to use fetch_and_cache_gdrive. You will call the function in a notebook. The function takes in two arguments: (1) Google Drive ID that you got in the previous step, and (2) name of the file. Calling the function will generate a data folder and place the file into that folder, using the name you came up with as the second argument of the function.

Hopefully the above steps help you to access the data on Google Drive. There are other ways to move the data onto Datahub. Consider looking into gdown or just downloading the data from Google Drive and uploading it to Datahub manually.

Take a look at the other functions in utils.py if you’d like to use other data sources to supplement your project.

Topic 1: COVID-19

Dataset A: Testing and Mortality Statistics

This dataset contains US reports on COVID-19 testing and cases from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University and CDC (Centers for Disease Control and Prevention). You can access all the data within the Topic 1/Dataset A directory on Google Drive:

  • csse_covid_19_daily_reports_us.csv contains US daily reports (documentation)
  • cdc_death_counts_by_sex_age_state.csv contains US weekly reports on deaths involving COVID-19, pneumonia, and influenza reported to NCHS by sex, age, group, and state. (documentation)
  • cdc_death_counts_by_conditons.csv contains US weekly reports on health conditions and contributing causes mentioned in conjunction with deaths involving COVID-19. (documentation)

You must choose to work with at least 2 of the reports above in your analysis.

Dataset B: Impact on Health Care

This dataset contains reports from the Household Pulse Survey launched by NCHS in partnership with the U.S. Census Bureau; it focuses on how COVID-19 has affected survey correspondents’ mental health and their access to health care. In addition, it provides statistics on usage of telemedicine by healthcare providers. You can access all the data within the Topic 1/Dataset B directory on Google Drive:

  • nchs_covid_indicators_of_anxiety_depression.csv contains survey estimates of responses to questions that are indicators of anxiety or depression based on reported frequency of symptoms within the past week. (documentation)
  • nchs_covid_mental_health_care.csv contains survey estimates of responses to questions that ask if participants have accessed mental health care in the past 4 weeks. (documentation)
  • nchs_covid_health_insurance_coverage.csv contains survey estimates of responses to questions that ask about participants’ health insurance coverage. (documentation)
  • nchs_covid_reduced_access_to_health_care.csv contains survey estimates of responses to questions that ask if participants have experienced delay or been refused health care due to COVID-19. (documentation)
  • nchs_covid_telemedicine_usage.csv contains survey estimates of responses to questions that ask if healthcare providers offered telemedicine (including video and telephone appointments) – both during and before the pandemic – and about the use of telemedicine during the pandemic. (documentation)

You must choose to work with at least 3 of the reports above in your analysis.

Dataset C: Ongoing Researches

This dataset contains (in full-text and metadata form) scholarly articles related to COVID-19. The data are optimized for machine readability and made available for use by the global research community. The dataset is intended to mobilize researchers to generate new insights from the articles in support of the fight against this infectious disease. You can access all the data within the Topic 1/Dataset C directory on Google Drive:

  • covid_open_research_dataset.txt contains the link that will guide you to obtain the full-text and metadata dataset of COVID-related research articles. (documentation)

Topic 2: Climate and the Environment

Dataset A: General Measurements and Statistics

This dataset contains some general statistics and measurements of various aspects of the climate and the environment. You can access all the data within the Topic 2/Dataset A directory on Google Drive. It includes the following reports:

  • daily_global_weather_2020.csv contains data on daily temperature and precipitation measurements. To learn how to use the data from this file, please read the following section on the first report.
  • us_greenhouse_gas_emissions_direct_emitter_facilities.csv and us_greenhouse_gas_emission_direct_emitter_gas_type.csv contain data reported by EPA (Environment Protection Agency) on greenhouse gas emissions, detailing the specific types of gas reported by facilities and general information about the facilities themselves. The dataset is made available through EPA’s GHGRP (Greenhouse Gas Reporting Program).
  • us_air_quality_measures.csv contains data from the EPA’s AQS (Air Quality System) that measures air quality on a county level from approximately 4000 monitoring stations around the country. (source)
  • aqi_data contains more data from the EPA from a number of sites across a multitude of different metrics. (source)

The following subsection contains more details on how to work with the first report on global daily temperature and precipitation:

The first report on daily temperature and precipitation is measured by weather stations in the Global Historical Climatology Network for January to December 2020.

The data in daily_global_weather_2020.csv is derived from the source file at https://www1.ncdc.noaa.gov/pub/data/ghcn/daily/by_year/2020.csv.gz.

To help you get started with a dataset of manageable size, we have preprocessed the GHCN dataset to include only the average temperature and precipitation measurements from stations that have both measurements. Each row in the preprocessed dataset contains both the average temperature and precipitation measurements for a given station on a given date.

If you wish to explore the climate data for a different year, you can use the GHCN_data_preprocessing.ipynb notebook to download and perform the preprocessing described above. Please be advised that depending on the dataset size for a given year, GHCN_data_preprocessing.ipynb may not run on DataHub. We will not be providing infrastructural support for running the notebook, but you are welcome to run it on a different machine you have access to or ask a GSI to dump the data for you.

The data contains only the (latitude, longitude) coordinates for the weather stations. To map the coordinates to geographical locations, the reverse-geocoder package mentioned in the References section might be helpful.

Dataset B: Biodiversity in the Ecosystem

This dataset contains studies focused specifically on the impact of environmental and climate changes on biodiversity and the local ecosystems. You can access all the data within the Topic 2/Dataset B directory on Google Drive. It includes the following reports:

  • bioCON_plant_diversity.csv contains data collected as part of an ecological experiment, BioCON (Biodiversity, CO2, and Nitrogen), that started in 1997 and focused on studying biodiversity within the plant species at Cedar Creek Ecosystem Science Preserve. (documentation)
  • plant_pollinator_diversity_set1.csv and plant_pollinator_diversity_set2.csv contain ecological data collected from a long-term observation study from 2011 to 2018 that focuses on plant-pollinator interaction and its impact on local biodiversity. (documentation)
  • national_parks_biodiversity_parks.csv and national_parks_biodiversity_species.csv contain data published by the National Park Service on animal and plant species identified in individual national parks.

Topic 3: Emerging Researches and Technologies

Dataset A: Space Exploration

This dataset contains a set of reports from pioneering researches that explore the outer space. Much of the data from these studies have provided a rich foundation for a variety of large-scale research projects that explore widely discussed topics such as habitable exoplanets or search for extraterrestrial life.

You can access all the data within the Topic 3/Dataset A directory on Google Drive. It includes the following reports:

  • kepler_exoplanet_search.csv contains data collected by NASA from the Kepler Space Observatory as part of a long-term study on finding habitable exoplanets from over 10,000 candidates. (source)
  • kelper_planetary_system_composite.csv contains data collected by NASA from the Kelper Space Observatory as part of an ongoing study that tabulates all confirmed planetary systems outside the solar system. You are encouraged to use the composite data in conjunction with the exoplanet search results above. (source)
  • nasa_neows.csv contains data collected from NASA’s NeoWs (Near Earth Object Web Service) that collects information on near earth asteroids.

Dataset B: Recommender Systems

A recommender system is an information filtering system that focuses on predicting the preference a user would give to an item by predicting its rank; it is used in a variety of areas, such as search engines, online shopping platforms, etc. This dataset contains a set of reports on various tools using a recommender system.

You can access all the data within the Topic 3/Dataset B directory on Google Drive. It includes the following reports:

  • fitness_recommendation.txt contains a link to access the fitness data from sequential sensors for various workouts. (documentation)
  • amazon_reviews.txt contains a link to access the data on a subset of Amazon product reviews. The report includes metadata such as ratings and text on the reviews and general information about the product. (documentation)

Extra Resources: Causal Inference

When studying the relationship between datasets, you might want to consult the following references on causality vs. correlation. Oftentimes, it is tempting to make claims about causal relationships when there is not enough evidence from the data to support such claims. Please review the following references, or other reputable references that you find on the topic to familiarize yourself with relevant concepts and methods.