Add a MultiModal example Task

[sebffischer]

One of the strengths of mlr3torch is that it can easily handle multimodal data. This is because a neural network built out of PipeOpTorch operators can have multiple inputs (PipeOpTorchIngress).
To showcast this feature, we need a multimodal example dataset for which we can take this one: https://challenge2020.isic-archive.com/
Some predefined image tasks already exist in mlr3torch so integrating this new task will work similar to https://github.com/mlr-org/mlr3torch/blob/main/R/TaskClassif_mnist.R.

To add a new task to mlr3torch, we need to add a function that takes in an ID and returns task.

load_task_melanoma = function(id = "melanoma") {
  ...
  return(task)
}

Then, we need to add this function to the dictionary of tasks as below:

register_task("melanoma", load_task_melanoma)

Because the dataset is too large to be contained in the mlr3torch package, we use a DataBackendLazy as the tasks's backend.
Therefore, the load_task_melanoma function first needs to construct this DataBackendLazy and then create a TaskClassif from that DataBackendLazy.

The DataBackendLazy:

• implements the logic for downloading, processing and caching the dataset (for processing see the next issue).
  The caching is also implemented via the private cached() function, so only the download and processing needs to be implemented.
• hardcodes some metadata of the task that should be available even before downloading. This metadata should be stored in the .inst/col_info folder and can be loaded using the private load_column_info() (https://github.com/mlr-org/mlr3torch/tree/main/inst/col_info). The code that can be used to generate this hardcoded metadata should be located in ./data-raw

[sebffischer]

I also got sent some code for the preprocessing (not sure what we need from there but I am putting it here in case it is useful).

1. step in R:

preprocess-1.R - R
library(dplyr)
library(mgcv)

df <- read.csv2("data/ISIC_2020_Training_GroundTruth_v2.csv", sep=",")

### remove empty
keep_mask <- (df$sex != "") & (df$anatom_site_general_challenge != "") & !is.na(df$age_approx)
cat("removing", sum(!keep_mask), "rows with empty columns\n")
df <- df[keep_mask,]

### encode
df$sex <- factor(df$sex)
df$diagnosis <- factor(df$diagnosis)
df$site <- factor(df$anatom_site_general_challenge)
df$benign_malignant <- factor(df$benign_malignant)
df$patient_id <- factor(df$patient_id)

pats <- df %>% group_by(patient_id) %>% summarise(n=n()) %>% filter(n>=4)
df <- df[df$patient_id %in% pats$patient_id,]
cat("kept", nrow(df), "lesions from patients with at least four\n")
pats <- pats[sample(1:nrow(pats)),]

test_pats <- pats[1:170, "patient_id"]
tune_pats <- pats[171:340, "patient_id"]
train_pats <- pats[341:nrow(pats), "patient_id"]

test_df <- df %>% filter(patient_id %in% test_pats$patient_id)
tune_df <- df %>% filter(patient_id %in% tune_pats$patient_id)
train_df <- df %>% filter(patient_id %in% train_pats$patient_id)

cat("got", nrow(test_df), "patients for test\n")
cat("got", nrow(tune_df), "patients for tuning\n")
cat("got", nrow(train_df), "patients for training\n")

test_df$subset <- "test"
tune_df$subset <- "tune"
train_df$subset <- "trainval"

df_all <- rbind(train_df, tune_df, test_df)
saveRDS(df_all, "data/train-processed.RDS")

# model matrix for structured effects
#mdl <- gam(target ~ site + sex + s(age_approx), family = "binomial", data = df)
mdl <- bam(
    target ~ site + sex + s(age_approx, by=sex),
    family = "binomial", data = df_all, discrete = TRUE, nthreads = 4
)

x_struc <- as.data.frame(model.matrix(mdl))
x_struc$target <- df_all$target
x_struc$image <- df_all$image
x_struc$patient_id <- df_all$patient_id
x_struc$subset <- df_all$subset

write.csv2(x_struc, "data/x_struc.csv")

2. step in python:

import torch
import os
from tqdm import tqdm
import torchvision


images = []
files = []
tx = torchvision.transforms.Resize((128, 128))
for f in tqdm(os.listdir("train")):
    img = torchvision.io.read_image("train/" + f)
    images.append(tx(img.float() / 255))
    files.append(f)


torch.save({
    'names': files,
    'images': torch.stack(images),
}, 'x_train_resized_normalized.pt')

[cxzhang4]

eventual data representation is in a single table

entry1 = po("torch_ingress_ltnsr") %>>%
po("nn_linear_1")

entry2 = po("torch_ingress_num") %>>%
po("nn_linear_2")

list(entry1, entry2) %>>%
po("merge_sum") # takes multiple inputs, so handles multimodal data

more fine-grained control looks something like this

graph = Graph$new()

graph$add_pipeop()