Data updates: See the change log.

2026-08-21: vaccine_season and vaccine corrected/added for 16 studies in publicData.

2026-10-20: vaccine information added for 8 studies.

Here we describe the investigations that were collected from the public domain. The data from these investigations make up the training and challenge data for the CMI-Flu prediction challenge. An overview of all the data, including links to more detailed descriptions of the other data, may be found at CMI-x .

The Data

Change log

20260821 see https://www.kaggle.com/competitions/cmi-flu-first-prediction-challenge/discussion/736185

Following a screen of the training data studies, vaccine_season and vaccine have been updated, based on a manual review of all 152 arms across 59 studies.

Changes per column:

column changed cells
vaccine_season 22
vaccine 12

The majority of studies have had missing data completed, 4 studies have been corrected. The studies affected are: SDY3010 ; SDY3186 ; SDY3193, SDY3427 ; SDY270; SDY272 ; SDY305 ; SDY314 ; SDY404 ; SDY56 ; SDY1393 ; SDY80 ; SDY112 ; SDY212 ; EXT100

The vaccine_strains_per_season.txt reference file has also been updated: H3N2 A/Victoria/361/2011 in seasons 2013-14 and 2014-15 has been updated to A/Texas/50/2012. This information also affects the virus_in_vaccine flag in the serology data; the serology data has also been updated.

20261020

Changes per column:

column changed cells
vaccine 8

Vaccine information has now been added for 8 studies (16 arms) : 2016_UGA ; 2017_UGA ; 2018_UGA ; 2019_UGA ; 2020_UGA ; 2021_UGA ; 2022_UGA ; 2023_UGA ; 2024_UGA

Data tables

Investigations
Data dictionary
Column Description
study_accession Study identifier (links to the assay tables). One study may comprise multiple arms.
title Short title of the study.
description Free-text description of the study.
pubmed_ids PubMed IDs of publications associated with the study; semicolon-separated.
arm_id Identifier of the study arm/cohort (a group of participants receiving the same intervention). One row per arm.
arm_name Human-readable name of the arm.
arm_description Free-text description of the arm.
nr_participants Number of participants enrolled in the study.
vaccine_season Influenza season (year) in which the arm was vaccinated. NA where not recorded.
vaccine Vaccine type administered: TIV, QIV, IIV/IIV3/IIV8 (inactivated), or LAIV (live attenuated).
main_pubmed_id PubMed ID of the primary publication for the study.
year Publication year of the primary reference.
first_author First author of the primary publication.

Data preview:

invest = read_tsv('../datasets/260512/train_part2/investigations.tsv')
head(invest)
## # A tibble: 6 × 13
##   study_accession title   description pubmed_ids arm_id arm_name arm_description
##   <chr>           <chr>   <chr>       <chr>      <chr>  <chr>    <chr>          
## 1 2016_UGA        2016_U… Annual vac… 38917104;… 2016_… 2016 UG… 2016 UGA Stand…
## 2 2016_UGA        2016_U… Annual vac… 38917104;… 2016_… 2016 UG… 2016 UGA High …
## 3 2017_UGA        2017_U… Annual vac… 38917104;… 2017_… 2017 UG… 2017 UGA Stand…
## 4 2017_UGA        2017_U… Annual vac… 38917104;… 2017_… 2017 UG… 2017 UGA High …
## 5 2018_UGA        2018_U… Annual vac… 36366544;… 2018_… 2018 UG… 2018 UGA Stand…
## 6 2018_UGA        2018_U… Annual vac… 36366544;… 2018_… 2018 UG… 2018 UGA High …
## # ℹ 6 more variables: vaccine_season <dbl>, vaccine <chr>,
## #   main_pubmed_id <dbl>, year <dbl>, first_author <chr>, nr_participants <dbl>

Data exploration

Each study contributes a number of participants to the training data (left). The bar for the 2025LJI challenge cohort is highlighted in red; all other studies are shown in blue; the dashed line shows the mean number of participants per study. We have collected data from 4,805 participants across 59 studies. The heatmap (right) shows, for the same studies, the number of participants with data for each assay; grey cells indicate no data.

# Barplot, heatmap and the combined figure are built in participants_per_assay.R.
source("participants_per_assay_part2.R", local = TRUE)

combined