R/train.R
In GenomeNet/deepG: Deep Learning for Genome Sequence Data
Defines functions
set_new_run_name
get_seed
load_model
get_mc
resume_training_from_model_card
get_run_name
train_model
Documented in
resume_training_from_model_card
train_model
#' @title Train neural network on genomic data
#'
#' @description
#' Train a neural network on genomic data. Data can be fasta/fastq files, rds files or a prepared data set.
#' If the data is given as collection of fasta, fastq or rds files, function will create a data generator that extracts training and validation batches
#' from files. Function includes several options to determine the sampling strategy of the generator and preprocessing of the data.
#' Training progress can be visualized in tensorboard. Model weights can be stored during training using checkpoints.
#'
#' @inheritParams generator_fasta_lm
#' @inheritParams generator_fasta_label_folder
#' @inheritParams generator_fasta_label_header_csv
#' @inheritParams get_generator
#' @param train_type Either `"lm"`, `"lm_rds"`, `"masked_lm"` for language model; `"label_header"`, `"label_folder"`, `"label_csv"`, `"label_rds"` for classification or `"dummy_gen"`.
#' \itemize{
#' \item Language model is trained to predict character(s) in a sequence. \cr
#' \item `"label_header"`/`"label_folder"`/`"label_csv"` are trained to predict a corresponding class given a sequence as input.
#' \item If `"label_header"`, class will be read from fasta headers.
#' \item If `"label_folder"`, class will be read from folder, i.e. all files in one folder must belong to the same class.
#' \item If `"label_csv"`, targets are read from a csv file. This file should have one column named "file". The targets then correspond to entries in that row (except "file"
#' column). Example: if we are currently working with a file called "a.fasta" and corresponding label is "label_1", there should be a row in our csv file
#'
#' | file | label_1 | label_2 |
#' | --- | --- | --- |
#' | "a.fasta" | 1 | 0 |
#'
#' \item If `"label_rds"`, generator will iterate over set of .rds files containing each a list of input and target tensors. Not implemented for model
#' with multiple inputs.
#' \item If `"lm_rds"`, generator will iterate over set of .rds files and will split tensor according to `target_len` argument
#' (targets are last `target_len` nucleotides of each sequence).
#' \item If `"dummy_gen"`, generator creates random data once and repeatedly feeds these to model.
#' \item If `"masked_lm"`, generator maskes some parts of the input. See `masked_lm` argument for details.
#' }
#' @param model A keras model.
#' @param path Path to training data. If \code{train_type} is \code{label_folder}, should be a vector or list
#' where each entry corresponds to a class (list elements can be directories and/or individual files). If \code{train_type} is not \code{label_folder},
#' can be a single directory or file or a list of directories and/or files.
#' @param path_val Path to validation data. See `path` argument for details.
#' @param dataset List of training data holding training samples in RAM instead of using generator. Should be list with two entries called `"X"` and `"Y"`.
#' @param dataset_val List of validation data. Should have two entries called `"X"` and `"Y"`.
#' @param path_checkpoint Path to checkpoints folder or `NULL`. If `NULL`, checkpoints don't get stored.
#' @param path_log Path to directory to write training scores. File name is `run_name` + `".csv"`. No output if `NULL`.
#' @param train_val_ratio For generator defines the fraction of batches that will be used for validation (compared to size of training data), i.e. one validation iteration
#' processes \code{batch_size} \eqn{*} \code{steps_per_epoch} \eqn{*} \code{train_val_ratio} samples. If you use dataset instead of generator and \code{dataset_val} is `NULL`, splits \code{dataset}
#' into train/validation data.
#' @param run_name Name of the run. Name will be used to identify output from callbacks. If `NULL`, will use date as run name.
#' If name already present, will add `"_2"` to name or `"_{x+1}"` if name ends with `_x`, where `x` is some integer.
#' @param batch_size Number of samples used for one network update.
#' @param epochs Number of iterations.
#' @param max_queue_size Maximum size for the generator queue.
#' @param reduce_lr_on_plateau Whether to use learning rate scheduler.
#' @param lr_plateau_factor Factor of decreasing learning rate when plateau is reached.
#' @param patience Number of epochs waiting for decrease in validation loss before reducing learning rate.
#' @param cooldown Number of epochs without changing learning rate.
#' @param steps_per_epoch Number of training batches per epoch.
#' @param step Frequency of sampling steps.
#' @param shuffle_file_order Boolean, whether to go through files sequentially or shuffle beforehand.
#' @param vocabulary Vector of allowed characters. Characters outside vocabulary get encoded as specified in \code{ambiguous_nuc}.
#' @param initial_epoch Epoch at which to start training. Note that network
#' will run for (\code{epochs} - \code{initial_epochs}) rounds and not \code{epochs} rounds.
#' @param path_tensorboard Path to tensorboard directory or `NULL`. If `NULL`, training not tracked on tensorboard.
#' @param save_best_only Only save model that improved on some score. Not applied if argument is `NULL`. Otherwise must be
#' list with argument `monitor` or `save_freq` (can only use one option). `moniter` specifies what metric to use.
#' `save_freq`, integer specifying how often to store a checkpoint (in epochs).
#' @param save_weights_only Whether to save weights only.
#' @param seed Sets seed for reproducible results.
#' @param shuffle_input Whether to shuffle entries in file.
#' @param tb_images Whether to show custom images (confusion matrix) in tensorboard "IMAGES" tab.
#' @param format File format, `"fasta"`, `"fastq"`, `"rds"` or `"fasta.tar.gz"`, `"fastq.tar.gz"` for `tar.gz` files.
#' @param path_file_log Write name of files used for training to csv file if path is specified.
#' @param vocabulary_label Character vector of possible targets. Targets outside \code{vocabulary_label} will get discarded if
#' \code{train_type = "label_header"}.
#' @param file_limit Integer or `NULL`. If integer, use only specified number of randomly sampled files for training. Ignored if greater than number of files in \code{path}.
#' @param reverse_complement_encoding Whether to use both original sequence and reverse complement as two input sequences.
#' @param output_format Determines shape of output tensor for language model.
#' Either `"target_right"`, `"target_middle_lstm"`, `"target_middle_cnn"` or `"wavenet"`.
#' Assume a sequence `"AACCGTA"`. Output correspond as follows
#' \itemize{
#' \item `"target_right": X = "AACCGT", Y = "A"`
#' \item `"target_middle_lstm": X = (X_1 = "AAC", X_2 = "ATG"), Y = "C"` (note reversed order of X_2)
#' \item `"target_middle_cnn": X = "AACGTA", Y = "C"`
#' \item `"wavenet": X = "AACCGT", Y = "ACCGTA"`
#' }
#' @param reset_states Whether to reset hidden states of RNN layer at every new input file and before/after validation.
#' @param use_quality_score Whether to use fastq quality scores. If `TRUE` input is not one-hot-encoding but corresponds to probabilities.
#' For example (0.97, 0.01, 0.01, 0.01) instead of (1, 0, 0, 0).
#' @param padding Whether to pad sequences too short for one sample with zeros.
#' @param early_stopping_time Time in seconds after which to stop training.
#' @param validation_only_after_training Whether to skip validation during training and only do one validation iteration after training.
#' @param skip_amb_nuc Threshold of ambiguous nucleotides to accept in fasta entry. Complete entry will get discarded otherwise.
#' @param class_weight List of weights for output. Order should correspond to \code{vocabulary_label}.
#' You can use \code{\link{get_class_weight}} function to estimate class weights:
#'
#' \code{class_weights <- get_class_weights(path = path, train_type = train_type)}
#'
#' If \code{train_type = "label_csv"} you need to add path to csv file:
#'
#' \code{class_weights <- get_class_weights(path = path, train_type = train_type, csv_path = target_from_csv)}
#' @param print_scores Whether to print train/validation scores during training.
#' @param train_val_split_csv A csv file specifying train/validation split. csv file should contain one column named `"file"` and one column named
#' `"type"`. The `"file"` column contains names of fasta/fastq files and `"type"` column specifies if file is used for training or validation.
#' Entries in `"type"` must be named `"train"` or `"val"`, otherwise file will not be used for either. `path` and `path_val` arguments should be the same.
#' Not implemented for `train_type = "label_folder"`.
#' @param set_learning When you want to assign one label to set of samples. Only implemented for `train_type = "label_folder"`.
#' Input is a list with the following parameters
#' \itemize{
#' \item `samples_per_target`: how many samples to use for one target.
#' \item `maxlen`: length of one sample.
#' \item `reshape_mode`: `"time_dist", "multi_input"` or `"concat"`.
#' \itemize{
#' \item
#' If `reshape_mode` is `"multi_input"`, generator will produce `samples_per_target` separate inputs, each of length `maxlen` (model should have
#' `samples_per_target` input layers).
#' \item If reshape_mode is `"time_dist"`, generator will produce a 4D input array. The dimensions correspond to
#' `(batch_size, samples_per_target, maxlen, length(vocabulary))`.
#' \item If `reshape_mode` is `"concat"`, generator will concatenate `samples_per_target` sequences
#' of length `maxlen` to one long sequence.
#' }
#' \item If `reshape_mode` is `"concat"`, there is an additional `buffer_len`
#' argument. If `buffer_len` is an integer, the subsequences are interspaced with `buffer_len` rows. The input length is
#' (`maxlen` \eqn{*} `samples_per_target`) + `buffer_len` \eqn{*} (`samples_per_target` - 1).
#' }
#' @param random_sampling Whether samples should be taken from random positions when using `max_samples` argument. If `FALSE` random
#' samples are taken from a consecutive subsequence.
#' @param n_gram_stride Step size for n-gram encoding. For AACCGGTT with `n_gram = 4` and `n_gram_stride = 2`, generator encodes
#' `(AACC), (CCGG), (GGTT)`; for `n_gram_stride = 4` generator encodes `(AACC), (GGTT)`.
#' @param callback_list Add additional callbacks to `keras::fit` call.
#' @param model_card List of arguments for training parameters of training run. Must contain at least an entry `path_model_card`, i.e. the
#' directory where parameters are stored. List can contain additional (optional) arguments, for example
#' `model_card = list(path_model_card = "/path/to/logs", description = "transfer learning with BERT model on virus data", ...)`
#' @param return_gen Whether to return the train and validation generators (instead of training).
#' @examplesIf reticulate::py_module_available("tensorflow")
#' # create dummy data
#' path_train_1 <- tempfile()
#' path_train_2 <- tempfile()
#' path_val_1 <- tempfile()
#' path_val_2 <- tempfile()
#'
#' for (current_path in c(path_train_1, path_train_2,
#' path_val_1, path_val_2)) {
#' dir.create(current_path)
#' create_dummy_data(file_path = current_path,
#' num_files = 3,
#' seq_length = 10,
#' num_seq = 5,
#' vocabulary = c("a", "c", "g", "t"))
#' }
#'
#' # create model
#' model <- create_model_lstm_cnn(layer_lstm = 8, layer_dense = 2, maxlen = 5)
#'
#' # train model
#' hist <- train_model(train_type = "label_folder",
#' model = model,
#' path = c(path_train_1, path_train_2),
#' path_val = c(path_val_1, path_val_2),
#' batch_size = 8,
#' epochs = 3,
#' steps_per_epoch = 6,
#' step = 5,
#' format = "fasta",
#' vocabulary_label = c("label_1", "label_2"))
#'
#' @returns A list of training metrics.
#' @export
train_model <- function(model = NULL,
dataset = NULL,
dataset_val = NULL,
# training args
train_val_ratio = 0.2,
run_name = "run_1",
initial_epoch = 0,
class_weight = NULL,
print_scores = TRUE,
epochs = 10,
max_queue_size = 100,
steps_per_epoch = 1000,
# callbacks
path_checkpoint = NULL,
path_tensorboard = NULL,
path_log = NULL,
save_best_only = NULL,
save_weights_only = FALSE,
tb_images = FALSE,
path_file_log = NULL,
reset_states = FALSE,
early_stopping_time = NULL,
validation_only_after_training = FALSE,
train_val_split_csv = NULL,
reduce_lr_on_plateau = TRUE,
lr_plateau_factor = 0.9,
patience = 20,
cooldown = 1,
model_card = NULL,
callback_list = NULL,
# generator args
train_type = "label_folder",
path = NULL,
path_val = NULL,
batch_size = 64,
step = NULL,
shuffle_file_order = TRUE,
vocabulary = c("a", "c", "g", "t"),
format = "fasta",
ambiguous_nuc = "zero",
seed = c(1234, 4321),
file_limit = NULL,
use_coverage = NULL,
set_learning = NULL,
proportion_entries = NULL,
sample_by_file_size = FALSE,
n_gram = NULL,
n_gram_stride = 1,
masked_lm = NULL,
random_sampling = FALSE,
add_noise = NULL,
return_int = FALSE,
maxlen = NULL,
reverse_complement = FALSE,
reverse_complement_encoding = FALSE,
output_format = "target_right",
proportion_per_seq = NULL,
read_data = FALSE,
use_quality_score = FALSE,
padding = FALSE,
concat_seq = NULL,
target_len = 1,
skip_amb_nuc = NULL,
max_samples = NULL,
added_label_path = NULL,
add_input_as_seq = NULL,
target_from_csv = NULL,
target_split = NULL,
shuffle_input = TRUE,
vocabulary_label = NULL,
delete_used_files = FALSE,
reshape_xy = NULL,
return_gen = FALSE) {
if (!is.null(model_card)) {
if (!is.list(model_card)) {
stop("model_card must be a list and contain at least an entry called 'path_model_card'")
}
}
# initialize metrics, temporary fix
model <- manage_metrics(model)
run_name <- get_run_name(run_name, path_tensorboard, path_checkpoint, path_log,
path_model_card = model_card$path_model_card,
auto_extend = TRUE)
train_with_gen <- is.null(dataset)
output <- list(tensorboard = FALSE, checkpoints = FALSE)
if (!is.null(path_tensorboard)) output$tensorboard <- TRUE
if (!is.null(path_checkpoint)) output$checkpoints <- TRUE
wavenet_format <- FALSE ; target_middle <- FALSE ; cnn_format <- FALSE
if (train_type != "label_csv") target_from_csv <- NULL
if (train_with_gen) {
stopifnot(train_type %in% c("lm", "label_header", "label_folder", "label_csv", "label_rds", "lm_rds", "dummy_gen", "masked_lm"))
stopifnot(ambiguous_nuc %in% c("zero", "equal", "discard", "empirical"))
stopifnot(length(vocabulary) == length(unique(vocabulary)))
stopifnot(length(vocabulary_label) == length(unique(vocabulary_label)))
labelByFolder <- FALSE
labelGen <- ifelse(train_type == "lm", FALSE, TRUE)
if (train_type == "label_header") target_from_csv <- NULL
if (train_type == "label_csv") {
#train_type <- "label_header"
if (is.null(target_from_csv)) {
stop('You need to add a path to csv file for target_from_csv when using train_type = "label_csv"')
}
if (!is.null(vocabulary_label)) {
message("Reading vocabulary_label from csv header")
if (!is.data.frame(target_from_csv)) {
output_label_csv <- utils::read.csv2(target_from_csv, header = TRUE, stringsAsFactors = FALSE)
if (dim(output_label_csv)[2] == 1) {
output_label_csv <- utils::read.csv(target_from_csv, header = TRUE, stringsAsFactors = FALSE)
}
} else {
output_label_csv <- target_from_csv
}
vocabulary_label <- names(output_label_csv)
vocabulary_label <- vocabulary_label[vocabulary_label != "file"]
}
}
if (!is.null(skip_amb_nuc)) {
if((skip_amb_nuc > 1) | (skip_amb_nuc <0)) {
stop("skip_amb_nuc should be between 0 and 1 or NULL")
}
}
if (!is.null(proportion_per_seq)) {
if(any(proportion_per_seq > 1) | any(proportion_per_seq < 0)) {
stop("proportion_per_seq should be between 0 and 1 or NULL")
}
}
# TODO: adjust for multi output model
# if (!is.null(class_weight) && (length(class_weight) != length(vocabulary_label))) {
# stop("class_weight and vocabulary_label must have same length")
# }
if (!is.null(concat_seq)) {
if (!is.null(use_coverage)) stop("Coverage encoding not implemented for concat_seq")
}
# train train_val_ratio via csv file
if (!is.null(train_val_split_csv)) {
train_val_file <- utils::read.csv2(train_val_split_csv, header = TRUE, stringsAsFactors = FALSE)
if (is.null(path)) {
path <- train_val_file %>% dplyr::filter(type %in% c("train", "val", "validation")) %>%
dplyr::select(file) %>% as.list()
}
if (train_type == "label_folder") {
stop('train_val_split_csv not implemented for train_type = "label_folder"')
}
if (is.null(path_val)) {
path_val <- path
} else {
if (!all(unlist(path_val) %in% unlist(path))) {
warning("Train/validation split done via file in train_val_split_csv. Only using files from path argument.")
}
path_val <- path
}
if (dim(train_val_file)[2] == 1) {
train_val_file <- utils::read.csv(train_val_split_csv, header = TRUE, stringsAsFactors = FALSE)
}
train_val_file <- dplyr::distinct(train_val_file)
if (!all(c("file", "type") %in% names(train_val_file))) {
stop("Column names of train_val_split_csv file must be 'file' and 'type'")
}
if (length(train_val_file$file) != length(unique(train_val_file$file))) {
stop("In train_val_split_csv all entires in 'file' column must be unique")
}
train_files <- train_val_file %>% dplyr::filter(type == "train")
train_files <- as.character(train_files$file)
val_files <- train_val_file %>% dplyr::filter(type == "val" | type == "validation")
val_files <- as.character(val_files$file)
} else {
train_files <- NULL
val_files <- NULL
}
if (train_type == "lm") {
stopifnot(output_format %in% c("target_right", "target_middle_lstm", "target_middle_cnn", "wavenet"))
if (output_format == "target_middle_lstm") target_middle <- TRUE
if (output_format == "target_middle_cnn") cnn_format <- TRUE
if (output_format == "wavenet") wavenet_format <- TRUE
}
if (train_type == "label_header" & is.null(target_from_csv)) {
stopifnot(!is.null(vocabulary_label))
}
if (train_type == "label_folder") {
labelByFolder <- TRUE
stopifnot(!is.null(vocabulary_label))
stopifnot(length(path) == length(vocabulary_label))
}
}
model_weights <- model$get_weights()
# function arguments
argumentList <- as.list(match.call(expand.dots=FALSE))
#argumentList <- c(as.list(environment()), list(...)) log default args too
argumentList <- argumentList[names(argumentList) != ""]
argumentList <- lapply(argumentList, eval, envir = parent.frame())
# extract maxlen from model
if (is.null(maxlen)) {
maxlen <- get_maxlen(model, set_learning, target_middle, read_data)
}
if (is.null(step)) step <- maxlen
vocabulary_label_size <- length(vocabulary_label)
vocabulary_size <- length(vocabulary)
if (is.null(dataset) && labelByFolder) {
if (length(path) == 1) warning("Training with just one label")
}
# add empty hparam dict if non exists
if (!reticulate::py_has_attr(model, "hparam")) {
model$hparam <- reticulate::dict()
}
# tempory file to log training data
removeLog <- FALSE
if (is.null(path_file_log)) {
removeLog <- TRUE
path_file_log <- tempfile(pattern = "", fileext = ".csv")
} else {
if (!endsWith(path_file_log, ".csv")) path_file_log <- paste0(path_file_log, ".csv")
#path_file_logVal <- tempfile(pattern = "", fileext = ".csv")
}
if (reset_states) {
path_file_logVal <- tempfile(pattern = "", fileext = ".csv")
} else {
path_file_logVal <- NULL
}
# if no dataset is supplied, external fasta generator will generate batches
if (train_with_gen) {
#message("Starting fasta generator...")
gen <- get_generator(path = path, batch_size = batch_size, model = model,
maxlen = maxlen, step = step, shuffle_file_order = shuffle_file_order,
vocabulary = vocabulary, seed = seed[1], proportion_entries = proportion_entries,
shuffle_input = shuffle_input, format = format, reshape_xy = reshape_xy,
path_file_log = path_file_log, reverse_complement = reverse_complement, n_gram_stride = n_gram_stride,
output_format = output_format, ambiguous_nuc = ambiguous_nuc,
proportion_per_seq = proportion_per_seq, skip_amb_nuc = skip_amb_nuc,
use_quality_score = use_quality_score, padding = padding, n_gram = n_gram,
added_label_path = added_label_path, add_input_as_seq = add_input_as_seq,
max_samples = max_samples, concat_seq = concat_seq, target_len = target_len,
file_filter = train_files, use_coverage = use_coverage, random_sampling = random_sampling,
train_type = train_type, set_learning = set_learning, file_limit = file_limit,
reverse_complement_encoding = reverse_complement_encoding, read_data = read_data,
sample_by_file_size = sample_by_file_size, add_noise = add_noise, target_split = target_split,
target_from_csv = target_from_csv, masked_lm = masked_lm, return_int = return_int,
path_file_logVal = path_file_logVal, delete_used_files = delete_used_files,
vocabulary_label = vocabulary_label, val = FALSE)
if (!is.null(path_val)) {
gen.val <- get_generator(path = path_val, batch_size = batch_size, model = model,
maxlen = maxlen, step = step, shuffle_file_order = shuffle_file_order,
vocabulary = vocabulary, seed = seed[2], proportion_entries = proportion_entries,
shuffle_input = shuffle_input, format = format, delete_used_files = FALSE,
path_file_log = path_file_logVal, reverse_complement = reverse_complement, n_gram_stride = n_gram_stride,
output_format = output_format, ambiguous_nuc = ambiguous_nuc, reshape_xy = reshape_xy,
proportion_per_seq = proportion_per_seq, skip_amb_nuc = skip_amb_nuc,
use_quality_score = use_quality_score, padding = padding, n_gram = n_gram,
added_label_path = added_label_path, add_input_as_seq = add_input_as_seq,
max_samples = max_samples, concat_seq = concat_seq, target_len = target_len,
file_filter = val_files, use_coverage = use_coverage, random_sampling = random_sampling,
train_type = train_type, set_learning = set_learning, file_limit = file_limit,
reverse_complement_encoding = reverse_complement_encoding, read_data = read_data,
sample_by_file_size = sample_by_file_size, add_noise = add_noise, target_split = target_split,
target_from_csv = target_from_csv, masked_lm = masked_lm, return_int = return_int,
path_file_logVal = path_file_logVal, vocabulary_label = vocabulary_label,
val = TRUE)
} else {
gen.val <- NULL
}
}
# skip validation callback
if (validation_only_after_training | is.null(train_val_ratio) || train_val_ratio == 0) {
validation_data <- NULL
} else {
if (train_with_gen) {
if (is.null(path_val)) {
validation_data <- NULL
} else {
validation_data <- gen.val
}
} else {
validation_data <- dataset_val
}
}
if (is.null(validation_data)) {
validation_steps <- NULL
} else {
validation_steps <- ceiling(steps_per_epoch * train_val_ratio)
}
callbacks <- get_callbacks(default_arguments = NULL, model = model, path_tensorboard = path_tensorboard, run_name = run_name, train_type = train_type,
path = path, train_val_ratio = train_val_ratio, batch_size = batch_size, epochs = epochs,
max_queue_size = max_queue_size, lr_plateau_factor = lr_plateau_factor, patience = patience, cooldown = cooldown, format = format,
steps_per_epoch = steps_per_epoch, step = step, shuffle_file_order = shuffle_file_order, initial_epoch = initial_epoch, vocabulary = vocabulary,
learning_rate = model$optimizer$learning_rate$numpy(), solver = stringr::str_to_lower(model$optimizer$get_config()["name"]),
shuffle_input = shuffle_input, vocabulary_label = vocabulary_label,
file_limit = file_limit, reverse_complement = reverse_complement, wavenet_format = wavenet_format, cnn_format = cnn_format,
train_val_split_csv = train_val_split_csv, n_gram = n_gram, path_file_logVal = path_file_logVal, validation_steps = validation_steps,
create_model_function = NULL, vocabulary_size = vocabulary_size, gen_cb = NULL, argumentList = argumentList, output = output,
maxlen = maxlen, labelGen = labelGen, labelByFolder = labelByFolder, vocabulary_label_size = vocabulary_label_size, tb_images = tb_images,
target_middle = target_middle, path_file_log = path_file_log, proportion_per_seq = proportion_per_seq,
skip_amb_nuc = skip_amb_nuc, max_samples = max_samples, proportion_entries = proportion_entries, path_log = path_log,
train_with_gen = train_with_gen, random_sampling = random_sampling, reduce_lr_on_plateau = reduce_lr_on_plateau,
save_weights_only = save_weights_only, path_checkpoint = path_checkpoint, save_best_only = save_best_only, gen.val = gen.val,
target_from_csv = target_from_csv, reset_states = reset_states, early_stopping_time = early_stopping_time,
validation_only_after_training = validation_only_after_training, model_card = model_card, dataset_val = dataset_val)
# training
if (train_with_gen) {
if (!is.null(dataset_val)) {
validation_data <- dataset_val
validation_steps <- NULL
}
if (return_gen) {
return(list(gen = gen, gen.val = gen.val))
}
model <- keras::set_weights(model, model_weights)
history <-
model %>% keras::fit(
x = gen,
validation_data = validation_data,
validation_steps = validation_steps,
steps_per_epoch = steps_per_epoch,
max_queue_size = max_queue_size,
epochs = epochs,
initial_epoch = initial_epoch,
callbacks = c(callbacks, callback_list),
class_weight = class_weight,
batch_size = batch_size,
verbose = print_scores)
if (validation_only_after_training) {
history$val_loss <- model$val_loss
history$val_acc <- model$val_acc
model$val_loss <- NULL
model$val_acc <- NULL
}
} else {
model <- keras::set_weights(model, model_weights)
if (!is.null(dataset_val)) {
validation_data <- list(dataset_val[[1]], dataset_val[[2]])
} else {
validation_data <- NULL
}
history <- keras::fit(
object = model,
x = dataset[[1]],
y = dataset[[2]],
batch_size = batch_size,
validation_split = train_val_ratio,
validation_data = validation_data,
callbacks = c(callbacks, callback_list),
epochs = epochs,
class_weight = class_weight,
verbose = print_scores)
}
if (removeLog & file.exists(path_file_log)) {
file.remove(path_file_log)
}
message("Training done.")
return(history)
}
#' Generate run_name if none is given or is already present.
#'
#' If no run name is given, will use date as run name. If run name is already present will add _2 to name or
#' _x+1 if name ends with _x and x is integer.
#'
#' @param auto_extend If run_name is already present, add "_2" to name. If name already ends with "_x" replace x with x+1.
#' @noRd
get_run_name <- function(run_name = NULL, path_tensorboard, path_checkpoint, path_log, path_model_card, auto_extend = FALSE) {
if (is.null(run_name)) {
run_name_new <- as.character(Sys.time()) %>% stringr::str_replace_all(" ", "_")
}
tb_names <- ""
cp_names <- ""
log_names <- ""
mc_names <- ""
name_present_tb <- FALSE
name_present_cp <- FALSE
name_present_log <- FALSE
name_present_mc <- FALSE
if (!is.null(path_tensorboard)) {
tb_names <- list.files(path_tensorboard)
name_present_tb <- (run_name %in% tb_names) # & any(stringr::str_detect(tb_names, run_name))
}
if (!is.null(path_checkpoint)) {
cp_names <- list.files(path_checkpoint)
name_present_cp <- (run_name %in% cp_names) # & any(stringr::str_detect(cp_names, run_name))
}
if (!is.null(path_log)) {
log_names <- list.files(path_log)
name_present_log <- (run_name %in% log_names) # & any(stringr::str_detect(log_names, run_name))
}
if (!is.null(path_model_card)) {
mc_names <- list.files(path_model_card)
name_present_mc <- (run_name %in% mc_names) # & any(stringr::str_detect(log_names, run_name))
}
name_present <- name_present_tb | name_present_cp | name_present_log | name_present_mc
if (name_present & auto_extend) {
ends_with_int <- stringr::str_detect(run_name, "_\\d+$")
if (ends_with_int) {
int_ending <- stringr::str_extract(run_name, "\\d+$") %>% as.integer()
run_name_new <- paste0(stringr::str_remove(run_name, "\\d+$"), int_ending + 1)
} else {
run_name_new <- paste0(run_name, "_2")
}
int_ending <- stringr::str_subset(c(tb_names, cp_names, log_names, mc_names),
paste0("^", stringr::str_remove(run_name, "_\\d+$"))) %>% unique()
int_ending <- stringr::str_subset(int_ending, "_\\d+$")
if (length(int_ending) > 0) {
max_int_ending <- stringr::str_extract(int_ending, "_\\d+$") %>% stringr::str_remove("_") %>% as.integer() %>% max()
if (!ends_with_int) {
run_name_new <- paste0(run_name, "_", max_int_ending + 1)
} else {
run_name_new <- paste0(stringr::str_remove(run_name, "\\d+$"), max_int_ending + 1)
}
}
if (length(int_ending) > 0) {
name_order <- stringr::str_extract(int_ending, "\\d+$") %>% as.integer() %>% order()
prev_names <- unique(c(run_name, int_ending[name_order]))
if (ends_with_int) {
name_order <- stringr::str_extract(prev_names, "\\d+$") %>% as.integer() %>% order()
prev_names <- prev_names[name_order]
}
if (length(prev_names) > 8) {
old_names_start <- paste(prev_names[1:2], collapse = ", ")
old_names_end <- paste(prev_names[(length(prev_names)-1) : length(prev_names)], collapse = ", ")
#old_names <- paste(old_names_start, ",...,", old_names_end) # outputs range of previously used names
old_names <- run_name
} else {
old_names <- paste(prev_names, collapse = ", ")
}
message(paste("run_name", old_names, "already present, setting run_name to", run_name_new))
} else {
message(paste("run_name", run_name, "already present, setting run_name to", run_name_new))
}
}
if (name_present & !auto_extend) {
stop("run_name already present, please give your run a unique name")
}
if (!name_present) {
return(run_name)
}
return(run_name_new)
}
#' Continue training from model card
#'
#' Use information from model card to resume from the corresponding checkpoint using the same training arguments.
#'
#' @param path_model_card Path to model card to resume training from.
#' @param seed Seed for reproducible results. If `NULL`, set random seed.
#' @param epoch Epoch to resume from. If `NULL`, use last epoch.
#' @param new_run_name New run name. If `NULL`, new run name is old run name + '_cont'.
#' @param new_args Named list of arguments to overwrite. Will use previous arguments from model card otherwise.
#' For example, if you want to change the batch size and padding option:
#' `new_args = list(batch_size = 6, padding = TRUE)`.
#' @param new_compile List of arguments to compile the model again. If `NULL`, use compiled model from checkpoint.
#' Example: `new_compile = list(loss = 'binary_crossentropy', metrics = 'acc', optimizer = keras::optimizer_adam())`
#' @param use_mirrored_strategy Whether to use distributed mirrored strategy.
#' If NULL, will use distributed mirrored strategy only if >1 GPU available.
#' @param unfreeze If `TRUE`, set trainable attribute of model to `TRUE` (unfreeze weights).
#' @param verbose Whether to print all training arguments.
#' @examples
#' \donttest{
#' library(keras)
#' # create dummy data and temp directories
#' path_train_1 <- tempfile()
#' path_train_2 <- tempfile()
#' path_val_1 <- tempfile()
#' path_val_2 <- tempfile()
#' path_checkpoint <- tempfile()
#' dir.create(path_checkpoint)
#' path_model_card <- tempfile()
#' dir.create(path_model_card)
#'
#' for (current_path in c(path_train_1, path_train_2,
#' path_val_1, path_val_2)) {
#' dir.create(current_path)
#' create_dummy_data(file_path = current_path,
#' num_files = 3,
#' seq_length = 10,
#' num_seq = 5,
#' vocabulary = c("a", "c", "g", "t"))
#' }
#'
#' # create model
#' model <- create_model_lstm_cnn(layer_lstm = 8, layer_dense = 2, maxlen = 5)
#'
#' # train model
#' run_name <- 'test_run_1'
#' hist <- train_model(train_type = "label_folder",
#' run_name = run_name,
#' path_checkpoint = path_checkpoint,
#' model_card = list(path_model_card = path_model_card, description = 'test run'),
#' model = model,
#' path = c(path_train_1, path_train_2),
#' path_val = c(path_val_1, path_val_2),
#' batch_size = 8,
#' epochs = 3,
#' steps_per_epoch = 6,
#' vocabulary_label = c("label_1", "label_2"))
#'
#' # resume training
#' resume_training_from_model_card(path_model_card = file.path(path_model_card, run_name))
#' }
#' @returns A list of training metrics.
#' @export
resume_training_from_model_card <- function(path_model_card,
seed = NULL,
epoch = NULL,
new_run_name = NULL,
new_args = NULL,
new_compile = NULL,
use_mirrored_strategy = NULL,
unfreeze = FALSE,
verbose = FALSE) {
if (is.null(use_mirrored_strategy)) use_mirrored_strategy <- ifelse(count_gpu() > 1, TRUE, FALSE)
info <- file.info(path_model_card)
is_directory <- info$isdir
if (is.na(is_directory)) {
stop("model_card path does not exist.\n")
} else if (is_directory) {
mc <- get_mc(path_model_card = path_model_card, epoch = epoch)
} else {
mc <- path_model_card
}
mc_args <- readRDS(mc)
train_args_mc <- mc_args$train_model_args
new_train_args <- train_args_mc
if (is.null(new_run_name)) {
new_train_args$run_name <- set_new_run_name(train_args_mc$run_name)
} else {
new_train_args$run_name <- new_run_name
}
# overwrite args
if (is.null(seed)) seed <- get_seed()
new_train_args$seed <- seed
# load checkpoint to resume from
if (is.null(train_args_mc$path_checkpoint)) {
stop('Did not save checkpoints in the run from model card')
}
if (unfreeze) {
model$trainable <- TRUE
}
if (use_mirrored_strategy) {
mirrored_strategy <- tensorflow::tf$distribute$MirroredStrategy()
with(mirrored_strategy$scope(), {
model <- load_model(cp_path = file.path(train_args_mc$path_checkpoint, train_args_mc$run_name),
ep_index = epoch,
new_compile = new_compile)
})
} else {
model <- load_model(cp_path = file.path(train_args_mc$path_checkpoint, train_args_mc$run_name),
ep_index = epoch,
new_compile = new_compile)
}
new_train_args$model <- model
if (!is.null(new_args)) {
stopifnot(is.list(new_args))
for (n in names(new_args))
new_train_args[[n]] <- new_args[[n]]
}
new_train_args$model_card[['cont_train_info']] <- paste0('run continues training from run ',
train_args_mc, ' and epoch ',
max(mc_args$logs$processing_step))
if (verbose) {
print(new_train_args)
}
do.call(train_model, new_train_args)
}
get_mc <- function(path_model_card, epoch = NULL) {
all_cards <- list.files(path_model_card, full.names = TRUE)
all_epochs <- vector("integer", length(all_cards))
for (i in seq_along(all_cards)) {
split_string <- all_cards[i] %>% basename() %>% stringr::str_split("_")
all_epochs[i] <- split_string[[1]][2] %>% as.integer()
}
if (is.null(epoch)) epoch <- max(all_epochs)
index <- all_epochs == epoch
if (sum(index) == 0) {
error_message <- paste('epoch not found in model card directory, possible values:',
paste(all_epochs, collapse = ", "))
stop(error_message)
}
mc <- all_cards[index]
return(mc)
}
load_model <- function(cp_path,
ep_index,
new_compile) {
model <- load_cp(cp_path,
ep_index = ep_index,
mirrored_strategy = FALSE,
compile = ifelse(is.null(new_compile), TRUE, FALSE))
if (!is.null(new_compile)) {
model <- keras::compile(model,
optimizer = new_compile$optimizer,
loss = new_compile$loss,
metrics = new_compile$metrics)
}
return(model)
}
get_seed <- function() {
current_time <- Sys.time()
current_time <- as.numeric(current_time) * 1e2
seed_value <- (current_time %% 10^5) %>% as.integer()
set.seed(seed_value)
return(sample(1:10^6, 2))
}
set_new_run_name <- function(run_name_old) {
run_name_new <- paste0(run_name_old, '_cont')
return(run_name_new)
}
GenomeNet/deepG documentation built on Dec. 24, 2024, 12:11 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions set_new_run_name get_seed load_model get_mc resume_training_from_model_card get_run_name train_model
Documented in resume_training_from_model_card train_model
#' @title Train neural network on genomic data
#'
#' @description
#' Train a neural network on genomic data. Data can be fasta/fastq files, rds files or a prepared data set.
#' If the data is given as collection of fasta, fastq or rds files, function will create a data generator that extracts training and validation batches
#' from files. Function includes several options to determine the sampling strategy of the generator and preprocessing of the data.
#' Training progress can be visualized in tensorboard. Model weights can be stored during training using checkpoints.
#'
#' @inheritParams generator_fasta_lm
#' @inheritParams generator_fasta_label_folder
#' @inheritParams generator_fasta_label_header_csv
#' @inheritParams get_generator
#' @param train_type Either `"lm"`, `"lm_rds"`, `"masked_lm"` for language model; `"label_header"`, `"label_folder"`, `"label_csv"`, `"label_rds"` for classification or `"dummy_gen"`.
#' \itemize{
#' \item Language model is trained to predict character(s) in a sequence. \cr
#' \item `"label_header"`/`"label_folder"`/`"label_csv"` are trained to predict a corresponding class given a sequence as input.
#' \item If `"label_header"`, class will be read from fasta headers.
#' \item If `"label_folder"`, class will be read from folder, i.e. all files in one folder must belong to the same class.
#' \item If `"label_csv"`, targets are read from a csv file. This file should have one column named "file". The targets then correspond to entries in that row (except "file"
#' column). Example: if we are currently working with a file called "a.fasta" and corresponding label is "label_1", there should be a row in our csv file
#'
#' | file | label_1 | label_2 |
#' | --- | --- | --- |
#' | "a.fasta" | 1 | 0 |
#'
#' \item If `"label_rds"`, generator will iterate over set of .rds files containing each a list of input and target tensors. Not implemented for model
#' with multiple inputs.
#' \item If `"lm_rds"`, generator will iterate over set of .rds files and will split tensor according to `target_len` argument
#' (targets are last `target_len` nucleotides of each sequence).
#' \item If `"dummy_gen"`, generator creates random data once and repeatedly feeds these to model.
#' \item If `"masked_lm"`, generator maskes some parts of the input. See `masked_lm` argument for details.
#' }
#' @param model A keras model.
#' @param path Path to training data. If \code{train_type} is \code{label_folder}, should be a vector or list
#' where each entry corresponds to a class (list elements can be directories and/or individual files). If \code{train_type} is not \code{label_folder},
#' can be a single directory or file or a list of directories and/or files.
#' @param path_val Path to validation data. See `path` argument for details.
#' @param dataset List of training data holding training samples in RAM instead of using generator. Should be list with two entries called `"X"` and `"Y"`.
#' @param dataset_val List of validation data. Should have two entries called `"X"` and `"Y"`.
#' @param path_checkpoint Path to checkpoints folder or `NULL`. If `NULL`, checkpoints don't get stored.
#' @param path_log Path to directory to write training scores. File name is `run_name` + `".csv"`. No output if `NULL`.
#' @param train_val_ratio For generator defines the fraction of batches that will be used for validation (compared to size of training data), i.e. one validation iteration
#' processes \code{batch_size} \eqn{*} \code{steps_per_epoch} \eqn{*} \code{train_val_ratio} samples. If you use dataset instead of generator and \code{dataset_val} is `NULL`, splits \code{dataset}
#' into train/validation data.
#' @param run_name Name of the run. Name will be used to identify output from callbacks. If `NULL`, will use date as run name.
#' If name already present, will add `"_2"` to name or `"_{x+1}"` if name ends with `_x`, where `x` is some integer.
#' @param batch_size Number of samples used for one network update.
#' @param epochs Number of iterations.
#' @param max_queue_size Maximum size for the generator queue.
#' @param reduce_lr_on_plateau Whether to use learning rate scheduler.
#' @param lr_plateau_factor Factor of decreasing learning rate when plateau is reached.
#' @param patience Number of epochs waiting for decrease in validation loss before reducing learning rate.
#' @param cooldown Number of epochs without changing learning rate.
#' @param steps_per_epoch Number of training batches per epoch.
#' @param step Frequency of sampling steps.
#' @param shuffle_file_order Boolean, whether to go through files sequentially or shuffle beforehand.
#' @param vocabulary Vector of allowed characters. Characters outside vocabulary get encoded as specified in \code{ambiguous_nuc}.
#' @param initial_epoch Epoch at which to start training. Note that network
#' will run for (\code{epochs} - \code{initial_epochs}) rounds and not \code{epochs} rounds.
#' @param path_tensorboard Path to tensorboard directory or `NULL`. If `NULL`, training not tracked on tensorboard.
#' @param save_best_only Only save model that improved on some score. Not applied if argument is `NULL`. Otherwise must be
#' list with argument `monitor` or `save_freq` (can only use one option). `moniter` specifies what metric to use.
#' `save_freq`, integer specifying how often to store a checkpoint (in epochs).
#' @param save_weights_only Whether to save weights only.
#' @param seed Sets seed for reproducible results.
#' @param shuffle_input Whether to shuffle entries in file.
#' @param tb_images Whether to show custom images (confusion matrix) in tensorboard "IMAGES" tab.
#' @param format File format, `"fasta"`, `"fastq"`, `"rds"` or `"fasta.tar.gz"`, `"fastq.tar.gz"` for `tar.gz` files.
#' @param path_file_log Write name of files used for training to csv file if path is specified.
#' @param vocabulary_label Character vector of possible targets. Targets outside \code{vocabulary_label} will get discarded if
#' \code{train_type = "label_header"}.
#' @param file_limit Integer or `NULL`. If integer, use only specified number of randomly sampled files for training. Ignored if greater than number of files in \code{path}.
#' @param reverse_complement_encoding Whether to use both original sequence and reverse complement as two input sequences.
#' @param output_format Determines shape of output tensor for language model.
#' Either `"target_right"`, `"target_middle_lstm"`, `"target_middle_cnn"` or `"wavenet"`.
#' Assume a sequence `"AACCGTA"`. Output correspond as follows
#' \itemize{
#' \item `"target_right": X = "AACCGT", Y = "A"`
#' \item `"target_middle_lstm": X = (X_1 = "AAC", X_2 = "ATG"), Y = "C"` (note reversed order of X_2)
#' \item `"target_middle_cnn": X = "AACGTA", Y = "C"`
#' \item `"wavenet": X = "AACCGT", Y = "ACCGTA"`
#' }
#' @param reset_states Whether to reset hidden states of RNN layer at every new input file and before/after validation.
#' @param use_quality_score Whether to use fastq quality scores. If `TRUE` input is not one-hot-encoding but corresponds to probabilities.
#' For example (0.97, 0.01, 0.01, 0.01) instead of (1, 0, 0, 0).
#' @param padding Whether to pad sequences too short for one sample with zeros.
#' @param early_stopping_time Time in seconds after which to stop training.
#' @param validation_only_after_training Whether to skip validation during training and only do one validation iteration after training.
#' @param skip_amb_nuc Threshold of ambiguous nucleotides to accept in fasta entry. Complete entry will get discarded otherwise.
#' @param class_weight List of weights for output. Order should correspond to \code{vocabulary_label}.
#' You can use \code{\link{get_class_weight}} function to estimate class weights:
#'
#' \code{class_weights <- get_class_weights(path = path, train_type = train_type)}
#'
#' If \code{train_type = "label_csv"} you need to add path to csv file:
#'
#' \code{class_weights <- get_class_weights(path = path, train_type = train_type, csv_path = target_from_csv)}
#' @param print_scores Whether to print train/validation scores during training.
#' @param train_val_split_csv A csv file specifying train/validation split. csv file should contain one column named `"file"` and one column named
#' `"type"`. The `"file"` column contains names of fasta/fastq files and `"type"` column specifies if file is used for training or validation.
#' Entries in `"type"` must be named `"train"` or `"val"`, otherwise file will not be used for either. `path` and `path_val` arguments should be the same.
#' Not implemented for `train_type = "label_folder"`.
#' @param set_learning When you want to assign one label to set of samples. Only implemented for `train_type = "label_folder"`.
#' Input is a list with the following parameters
#' \itemize{
#' \item `samples_per_target`: how many samples to use for one target.
#' \item `maxlen`: length of one sample.
#' \item `reshape_mode`: `"time_dist", "multi_input"` or `"concat"`.
#' \itemize{
#' \item
#' If `reshape_mode` is `"multi_input"`, generator will produce `samples_per_target` separate inputs, each of length `maxlen` (model should have
#' `samples_per_target` input layers).
#' \item If reshape_mode is `"time_dist"`, generator will produce a 4D input array. The dimensions correspond to
#' `(batch_size, samples_per_target, maxlen, length(vocabulary))`.
#' \item If `reshape_mode` is `"concat"`, generator will concatenate `samples_per_target` sequences
#' of length `maxlen` to one long sequence.
#' }
#' \item If `reshape_mode` is `"concat"`, there is an additional `buffer_len`
#' argument. If `buffer_len` is an integer, the subsequences are interspaced with `buffer_len` rows. The input length is
#' (`maxlen` \eqn{*} `samples_per_target`) + `buffer_len` \eqn{*} (`samples_per_target` - 1).
#' }
#' @param random_sampling Whether samples should be taken from random positions when using `max_samples` argument. If `FALSE` random
#' samples are taken from a consecutive subsequence.
#' @param n_gram_stride Step size for n-gram encoding. For AACCGGTT with `n_gram = 4` and `n_gram_stride = 2`, generator encodes
#' `(AACC), (CCGG), (GGTT)`; for `n_gram_stride = 4` generator encodes `(AACC), (GGTT)`.
#' @param callback_list Add additional callbacks to `keras::fit` call.
#' @param model_card List of arguments for training parameters of training run. Must contain at least an entry `path_model_card`, i.e. the
#' directory where parameters are stored. List can contain additional (optional) arguments, for example
#' `model_card = list(path_model_card = "/path/to/logs", description = "transfer learning with BERT model on virus data", ...)`
#' @param return_gen Whether to return the train and validation generators (instead of training).
#' @examplesIf reticulate::py_module_available("tensorflow")
#' # create dummy data
#' path_train_1 <- tempfile()
#' path_train_2 <- tempfile()
#' path_val_1 <- tempfile()
#' path_val_2 <- tempfile()
#'
#' for (current_path in c(path_train_1, path_train_2,
#' path_val_1, path_val_2)) {
#' dir.create(current_path)
#' create_dummy_data(file_path = current_path,
#' num_files = 3,
#' seq_length = 10,
#' num_seq = 5,
#' vocabulary = c("a", "c", "g", "t"))
#' }
#'
#' # create model
#' model <- create_model_lstm_cnn(layer_lstm = 8, layer_dense = 2, maxlen = 5)
#'
#' # train model
#' hist <- train_model(train_type = "label_folder",
#' model = model,
#' path = c(path_train_1, path_train_2),
#' path_val = c(path_val_1, path_val_2),
#' batch_size = 8,
#' epochs = 3,
#' steps_per_epoch = 6,
#' step = 5,
#' format = "fasta",
#' vocabulary_label = c("label_1", "label_2"))
#'
#' @returns A list of training metrics.
#' @export
train_model <- function(model = NULL,
dataset = NULL,
dataset_val = NULL,
# training args
train_val_ratio = 0.2,
run_name = "run_1",
initial_epoch = 0,
class_weight = NULL,
print_scores = TRUE,
epochs = 10,
max_queue_size = 100,
steps_per_epoch = 1000,
# callbacks
path_checkpoint = NULL,
path_tensorboard = NULL,
path_log = NULL,
save_best_only = NULL,
save_weights_only = FALSE,
tb_images = FALSE,
path_file_log = NULL,
reset_states = FALSE,
early_stopping_time = NULL,
validation_only_after_training = FALSE,
train_val_split_csv = NULL,
reduce_lr_on_plateau = TRUE,
lr_plateau_factor = 0.9,
patience = 20,
cooldown = 1,
model_card = NULL,
callback_list = NULL,
# generator args
train_type = "label_folder",
path = NULL,
path_val = NULL,
batch_size = 64,
step = NULL,
shuffle_file_order = TRUE,
vocabulary = c("a", "c", "g", "t"),
format = "fasta",
ambiguous_nuc = "zero",
seed = c(1234, 4321),
file_limit = NULL,
use_coverage = NULL,
set_learning = NULL,
proportion_entries = NULL,
sample_by_file_size = FALSE,
n_gram = NULL,
n_gram_stride = 1,
masked_lm = NULL,
random_sampling = FALSE,
add_noise = NULL,
return_int = FALSE,
maxlen = NULL,
reverse_complement = FALSE,
reverse_complement_encoding = FALSE,
output_format = "target_right",
proportion_per_seq = NULL,
read_data = FALSE,
use_quality_score = FALSE,
padding = FALSE,
concat_seq = NULL,
target_len = 1,
skip_amb_nuc = NULL,
max_samples = NULL,
added_label_path = NULL,
add_input_as_seq = NULL,
target_from_csv = NULL,
target_split = NULL,
shuffle_input = TRUE,
vocabulary_label = NULL,
delete_used_files = FALSE,
reshape_xy = NULL,
return_gen = FALSE) {
if (!is.null(model_card)) {
if (!is.list(model_card)) {
stop("model_card must be a list and contain at least an entry called 'path_model_card'")
}
}
# initialize metrics, temporary fix
model <- manage_metrics(model)
run_name <- get_run_name(run_name, path_tensorboard, path_checkpoint, path_log,
path_model_card = model_card$path_model_card,
auto_extend = TRUE)
train_with_gen <- is.null(dataset)
output <- list(tensorboard = FALSE, checkpoints = FALSE)
if (!is.null(path_tensorboard)) output$tensorboard <- TRUE
if (!is.null(path_checkpoint)) output$checkpoints <- TRUE
wavenet_format <- FALSE ; target_middle <- FALSE ; cnn_format <- FALSE
if (train_type != "label_csv") target_from_csv <- NULL
if (train_with_gen) {
stopifnot(train_type %in% c("lm", "label_header", "label_folder", "label_csv", "label_rds", "lm_rds", "dummy_gen", "masked_lm"))
stopifnot(ambiguous_nuc %in% c("zero", "equal", "discard", "empirical"))
stopifnot(length(vocabulary) == length(unique(vocabulary)))
stopifnot(length(vocabulary_label) == length(unique(vocabulary_label)))
labelByFolder <- FALSE
labelGen <- ifelse(train_type == "lm", FALSE, TRUE)
if (train_type == "label_header") target_from_csv <- NULL
if (train_type == "label_csv") {
#train_type <- "label_header"
if (is.null(target_from_csv)) {
stop('You need to add a path to csv file for target_from_csv when using train_type = "label_csv"')
}
if (!is.null(vocabulary_label)) {
message("Reading vocabulary_label from csv header")
if (!is.data.frame(target_from_csv)) {
output_label_csv <- utils::read.csv2(target_from_csv, header = TRUE, stringsAsFactors = FALSE)
if (dim(output_label_csv)[2] == 1) {
output_label_csv <- utils::read.csv(target_from_csv, header = TRUE, stringsAsFactors = FALSE)
}
} else {
output_label_csv <- target_from_csv
}
vocabulary_label <- names(output_label_csv)
vocabulary_label <- vocabulary_label[vocabulary_label != "file"]
}
}
if (!is.null(skip_amb_nuc)) {
if((skip_amb_nuc > 1) | (skip_amb_nuc <0)) {
stop("skip_amb_nuc should be between 0 and 1 or NULL")
}
}
if (!is.null(proportion_per_seq)) {
if(any(proportion_per_seq > 1) | any(proportion_per_seq < 0)) {
stop("proportion_per_seq should be between 0 and 1 or NULL")
}
}
# TODO: adjust for multi output model
# if (!is.null(class_weight) && (length(class_weight) != length(vocabulary_label))) {
# stop("class_weight and vocabulary_label must have same length")
# }
if (!is.null(concat_seq)) {
if (!is.null(use_coverage)) stop("Coverage encoding not implemented for concat_seq")
}
# train train_val_ratio via csv file
if (!is.null(train_val_split_csv)) {
train_val_file <- utils::read.csv2(train_val_split_csv, header = TRUE, stringsAsFactors = FALSE)
if (is.null(path)) {
path <- train_val_file %>% dplyr::filter(type %in% c("train", "val", "validation")) %>%
dplyr::select(file) %>% as.list()
}
if (train_type == "label_folder") {
stop('train_val_split_csv not implemented for train_type = "label_folder"')
}
if (is.null(path_val)) {
path_val <- path
} else {
if (!all(unlist(path_val) %in% unlist(path))) {
warning("Train/validation split done via file in train_val_split_csv. Only using files from path argument.")
}
path_val <- path
}
if (dim(train_val_file)[2] == 1) {
train_val_file <- utils::read.csv(train_val_split_csv, header = TRUE, stringsAsFactors = FALSE)
}
train_val_file <- dplyr::distinct(train_val_file)
if (!all(c("file", "type") %in% names(train_val_file))) {
stop("Column names of train_val_split_csv file must be 'file' and 'type'")
}
if (length(train_val_file$file) != length(unique(train_val_file$file))) {
stop("In train_val_split_csv all entires in 'file' column must be unique")
}
train_files <- train_val_file %>% dplyr::filter(type == "train")
train_files <- as.character(train_files$file)
val_files <- train_val_file %>% dplyr::filter(type == "val" | type == "validation")
val_files <- as.character(val_files$file)
} else {
train_files <- NULL
val_files <- NULL
}
if (train_type == "lm") {
stopifnot(output_format %in% c("target_right", "target_middle_lstm", "target_middle_cnn", "wavenet"))
if (output_format == "target_middle_lstm") target_middle <- TRUE
if (output_format == "target_middle_cnn") cnn_format <- TRUE
if (output_format == "wavenet") wavenet_format <- TRUE
}
if (train_type == "label_header" & is.null(target_from_csv)) {
stopifnot(!is.null(vocabulary_label))
}
if (train_type == "label_folder") {
labelByFolder <- TRUE
stopifnot(!is.null(vocabulary_label))
stopifnot(length(path) == length(vocabulary_label))
}
}
model_weights <- model$get_weights()
# function arguments
argumentList <- as.list(match.call(expand.dots=FALSE))
#argumentList <- c(as.list(environment()), list(...)) log default args too
argumentList <- argumentList[names(argumentList) != ""]
argumentList <- lapply(argumentList, eval, envir = parent.frame())
# extract maxlen from model
if (is.null(maxlen)) {
maxlen <- get_maxlen(model, set_learning, target_middle, read_data)
}
if (is.null(step)) step <- maxlen
vocabulary_label_size <- length(vocabulary_label)
vocabulary_size <- length(vocabulary)
if (is.null(dataset) && labelByFolder) {
if (length(path) == 1) warning("Training with just one label")
}
# add empty hparam dict if non exists
if (!reticulate::py_has_attr(model, "hparam")) {
model$hparam <- reticulate::dict()
}
# tempory file to log training data
removeLog <- FALSE
if (is.null(path_file_log)) {
removeLog <- TRUE
path_file_log <- tempfile(pattern = "", fileext = ".csv")
} else {
if (!endsWith(path_file_log, ".csv")) path_file_log <- paste0(path_file_log, ".csv")
#path_file_logVal <- tempfile(pattern = "", fileext = ".csv")
}
if (reset_states) {
path_file_logVal <- tempfile(pattern = "", fileext = ".csv")
} else {
path_file_logVal <- NULL
}
# if no dataset is supplied, external fasta generator will generate batches
if (train_with_gen) {
#message("Starting fasta generator...")
gen <- get_generator(path = path, batch_size = batch_size, model = model,
maxlen = maxlen, step = step, shuffle_file_order = shuffle_file_order,
vocabulary = vocabulary, seed = seed[1], proportion_entries = proportion_entries,
shuffle_input = shuffle_input, format = format, reshape_xy = reshape_xy,
path_file_log = path_file_log, reverse_complement = reverse_complement, n_gram_stride = n_gram_stride,
output_format = output_format, ambiguous_nuc = ambiguous_nuc,
proportion_per_seq = proportion_per_seq, skip_amb_nuc = skip_amb_nuc,
use_quality_score = use_quality_score, padding = padding, n_gram = n_gram,
added_label_path = added_label_path, add_input_as_seq = add_input_as_seq,
max_samples = max_samples, concat_seq = concat_seq, target_len = target_len,
file_filter = train_files, use_coverage = use_coverage, random_sampling = random_sampling,
train_type = train_type, set_learning = set_learning, file_limit = file_limit,
reverse_complement_encoding = reverse_complement_encoding, read_data = read_data,
sample_by_file_size = sample_by_file_size, add_noise = add_noise, target_split = target_split,
target_from_csv = target_from_csv, masked_lm = masked_lm, return_int = return_int,
path_file_logVal = path_file_logVal, delete_used_files = delete_used_files,
vocabulary_label = vocabulary_label, val = FALSE)
if (!is.null(path_val)) {
gen.val <- get_generator(path = path_val, batch_size = batch_size, model = model,
maxlen = maxlen, step = step, shuffle_file_order = shuffle_file_order,
vocabulary = vocabulary, seed = seed[2], proportion_entries = proportion_entries,
shuffle_input = shuffle_input, format = format, delete_used_files = FALSE,
path_file_log = path_file_logVal, reverse_complement = reverse_complement, n_gram_stride = n_gram_stride,
output_format = output_format, ambiguous_nuc = ambiguous_nuc, reshape_xy = reshape_xy,
proportion_per_seq = proportion_per_seq, skip_amb_nuc = skip_amb_nuc,
use_quality_score = use_quality_score, padding = padding, n_gram = n_gram,
added_label_path = added_label_path, add_input_as_seq = add_input_as_seq,
max_samples = max_samples, concat_seq = concat_seq, target_len = target_len,
file_filter = val_files, use_coverage = use_coverage, random_sampling = random_sampling,
train_type = train_type, set_learning = set_learning, file_limit = file_limit,
reverse_complement_encoding = reverse_complement_encoding, read_data = read_data,
sample_by_file_size = sample_by_file_size, add_noise = add_noise, target_split = target_split,
target_from_csv = target_from_csv, masked_lm = masked_lm, return_int = return_int,
path_file_logVal = path_file_logVal, vocabulary_label = vocabulary_label,
val = TRUE)
} else {
gen.val <- NULL
}
}
# skip validation callback
if (validation_only_after_training | is.null(train_val_ratio) || train_val_ratio == 0) {
validation_data <- NULL
} else {
if (train_with_gen) {
if (is.null(path_val)) {
validation_data <- NULL
} else {
validation_data <- gen.val
}
} else {
validation_data <- dataset_val
}
}
if (is.null(validation_data)) {
validation_steps <- NULL
} else {
validation_steps <- ceiling(steps_per_epoch * train_val_ratio)
}
callbacks <- get_callbacks(default_arguments = NULL, model = model, path_tensorboard = path_tensorboard, run_name = run_name, train_type = train_type,
path = path, train_val_ratio = train_val_ratio, batch_size = batch_size, epochs = epochs,
max_queue_size = max_queue_size, lr_plateau_factor = lr_plateau_factor, patience = patience, cooldown = cooldown, format = format,
steps_per_epoch = steps_per_epoch, step = step, shuffle_file_order = shuffle_file_order, initial_epoch = initial_epoch, vocabulary = vocabulary,
learning_rate = model$optimizer$learning_rate$numpy(), solver = stringr::str_to_lower(model$optimizer$get_config()["name"]),
shuffle_input = shuffle_input, vocabulary_label = vocabulary_label,
file_limit = file_limit, reverse_complement = reverse_complement, wavenet_format = wavenet_format, cnn_format = cnn_format,
train_val_split_csv = train_val_split_csv, n_gram = n_gram, path_file_logVal = path_file_logVal, validation_steps = validation_steps,
create_model_function = NULL, vocabulary_size = vocabulary_size, gen_cb = NULL, argumentList = argumentList, output = output,
maxlen = maxlen, labelGen = labelGen, labelByFolder = labelByFolder, vocabulary_label_size = vocabulary_label_size, tb_images = tb_images,
target_middle = target_middle, path_file_log = path_file_log, proportion_per_seq = proportion_per_seq,
skip_amb_nuc = skip_amb_nuc, max_samples = max_samples, proportion_entries = proportion_entries, path_log = path_log,
train_with_gen = train_with_gen, random_sampling = random_sampling, reduce_lr_on_plateau = reduce_lr_on_plateau,
save_weights_only = save_weights_only, path_checkpoint = path_checkpoint, save_best_only = save_best_only, gen.val = gen.val,
target_from_csv = target_from_csv, reset_states = reset_states, early_stopping_time = early_stopping_time,
validation_only_after_training = validation_only_after_training, model_card = model_card, dataset_val = dataset_val)
# training
if (train_with_gen) {
if (!is.null(dataset_val)) {
validation_data <- dataset_val
validation_steps <- NULL
}
if (return_gen) {
return(list(gen = gen, gen.val = gen.val))
}
model <- keras::set_weights(model, model_weights)
history <-
model %>% keras::fit(
x = gen,
validation_data = validation_data,
validation_steps = validation_steps,
steps_per_epoch = steps_per_epoch,
max_queue_size = max_queue_size,
epochs = epochs,
initial_epoch = initial_epoch,
callbacks = c(callbacks, callback_list),
class_weight = class_weight,
batch_size = batch_size,
verbose = print_scores)
if (validation_only_after_training) {
history$val_loss <- model$val_loss
history$val_acc <- model$val_acc
model$val_loss <- NULL
model$val_acc <- NULL
}
} else {
model <- keras::set_weights(model, model_weights)
if (!is.null(dataset_val)) {
validation_data <- list(dataset_val[[1]], dataset_val[[2]])
} else {
validation_data <- NULL
}
history <- keras::fit(
object = model,
x = dataset[[1]],
y = dataset[[2]],
batch_size = batch_size,
validation_split = train_val_ratio,
validation_data = validation_data,
callbacks = c(callbacks, callback_list),
epochs = epochs,
class_weight = class_weight,
verbose = print_scores)
}
if (removeLog & file.exists(path_file_log)) {
file.remove(path_file_log)
}
message("Training done.")
return(history)
}
#' Generate run_name if none is given or is already present.
#'
#' If no run name is given, will use date as run name. If run name is already present will add _2 to name or
#' _x+1 if name ends with _x and x is integer.
#'
#' @param auto_extend If run_name is already present, add "_2" to name. If name already ends with "_x" replace x with x+1.
#' @noRd
get_run_name <- function(run_name = NULL, path_tensorboard, path_checkpoint, path_log, path_model_card, auto_extend = FALSE) {
if (is.null(run_name)) {
run_name_new <- as.character(Sys.time()) %>% stringr::str_replace_all(" ", "_")
}
tb_names <- ""
cp_names <- ""
log_names <- ""
mc_names <- ""
name_present_tb <- FALSE
name_present_cp <- FALSE
name_present_log <- FALSE
name_present_mc <- FALSE
if (!is.null(path_tensorboard)) {
tb_names <- list.files(path_tensorboard)
name_present_tb <- (run_name %in% tb_names) # & any(stringr::str_detect(tb_names, run_name))
}
if (!is.null(path_checkpoint)) {
cp_names <- list.files(path_checkpoint)
name_present_cp <- (run_name %in% cp_names) # & any(stringr::str_detect(cp_names, run_name))
}
if (!is.null(path_log)) {
log_names <- list.files(path_log)
name_present_log <- (run_name %in% log_names) # & any(stringr::str_detect(log_names, run_name))
}
if (!is.null(path_model_card)) {
mc_names <- list.files(path_model_card)
name_present_mc <- (run_name %in% mc_names) # & any(stringr::str_detect(log_names, run_name))
}
name_present <- name_present_tb | name_present_cp | name_present_log | name_present_mc
if (name_present & auto_extend) {
ends_with_int <- stringr::str_detect(run_name, "_\\d+$")
if (ends_with_int) {
int_ending <- stringr::str_extract(run_name, "\\d+$") %>% as.integer()
run_name_new <- paste0(stringr::str_remove(run_name, "\\d+$"), int_ending + 1)
} else {
run_name_new <- paste0(run_name, "_2")
}
int_ending <- stringr::str_subset(c(tb_names, cp_names, log_names, mc_names),
paste0("^", stringr::str_remove(run_name, "_\\d+$"))) %>% unique()
int_ending <- stringr::str_subset(int_ending, "_\\d+$")
if (length(int_ending) > 0) {
max_int_ending <- stringr::str_extract(int_ending, "_\\d+$") %>% stringr::str_remove("_") %>% as.integer() %>% max()
if (!ends_with_int) {
run_name_new <- paste0(run_name, "_", max_int_ending + 1)
} else {
run_name_new <- paste0(stringr::str_remove(run_name, "\\d+$"), max_int_ending + 1)
}
}
if (length(int_ending) > 0) {
name_order <- stringr::str_extract(int_ending, "\\d+$") %>% as.integer() %>% order()
prev_names <- unique(c(run_name, int_ending[name_order]))
if (ends_with_int) {
name_order <- stringr::str_extract(prev_names, "\\d+$") %>% as.integer() %>% order()
prev_names <- prev_names[name_order]
}
if (length(prev_names) > 8) {
old_names_start <- paste(prev_names[1:2], collapse = ", ")
old_names_end <- paste(prev_names[(length(prev_names)-1) : length(prev_names)], collapse = ", ")
#old_names <- paste(old_names_start, ",...,", old_names_end) # outputs range of previously used names
old_names <- run_name
} else {
old_names <- paste(prev_names, collapse = ", ")
}
message(paste("run_name", old_names, "already present, setting run_name to", run_name_new))
} else {
message(paste("run_name", run_name, "already present, setting run_name to", run_name_new))
}
}
if (name_present & !auto_extend) {
stop("run_name already present, please give your run a unique name")
}
if (!name_present) {
return(run_name)
}
return(run_name_new)
}
#' Continue training from model card
#'
#' Use information from model card to resume from the corresponding checkpoint using the same training arguments.
#'
#' @param path_model_card Path to model card to resume training from.
#' @param seed Seed for reproducible results. If `NULL`, set random seed.
#' @param epoch Epoch to resume from. If `NULL`, use last epoch.
#' @param new_run_name New run name. If `NULL`, new run name is old run name + '_cont'.
#' @param new_args Named list of arguments to overwrite. Will use previous arguments from model card otherwise.
#' For example, if you want to change the batch size and padding option:
#' `new_args = list(batch_size = 6, padding = TRUE)`.
#' @param new_compile List of arguments to compile the model again. If `NULL`, use compiled model from checkpoint.
#' Example: `new_compile = list(loss = 'binary_crossentropy', metrics = 'acc', optimizer = keras::optimizer_adam())`
#' @param use_mirrored_strategy Whether to use distributed mirrored strategy.
#' If NULL, will use distributed mirrored strategy only if >1 GPU available.
#' @param unfreeze If `TRUE`, set trainable attribute of model to `TRUE` (unfreeze weights).
#' @param verbose Whether to print all training arguments.
#' @examples
#' \donttest{
#' library(keras)
#' # create dummy data and temp directories
#' path_train_1 <- tempfile()
#' path_train_2 <- tempfile()
#' path_val_1 <- tempfile()
#' path_val_2 <- tempfile()
#' path_checkpoint <- tempfile()
#' dir.create(path_checkpoint)
#' path_model_card <- tempfile()
#' dir.create(path_model_card)
#'
#' for (current_path in c(path_train_1, path_train_2,
#' path_val_1, path_val_2)) {
#' dir.create(current_path)
#' create_dummy_data(file_path = current_path,
#' num_files = 3,
#' seq_length = 10,
#' num_seq = 5,
#' vocabulary = c("a", "c", "g", "t"))
#' }
#'
#' # create model
#' model <- create_model_lstm_cnn(layer_lstm = 8, layer_dense = 2, maxlen = 5)
#'
#' # train model
#' run_name <- 'test_run_1'
#' hist <- train_model(train_type = "label_folder",
#' run_name = run_name,
#' path_checkpoint = path_checkpoint,
#' model_card = list(path_model_card = path_model_card, description = 'test run'),
#' model = model,
#' path = c(path_train_1, path_train_2),
#' path_val = c(path_val_1, path_val_2),
#' batch_size = 8,
#' epochs = 3,
#' steps_per_epoch = 6,
#' vocabulary_label = c("label_1", "label_2"))
#'
#' # resume training
#' resume_training_from_model_card(path_model_card = file.path(path_model_card, run_name))
#' }
#' @returns A list of training metrics.
#' @export
resume_training_from_model_card <- function(path_model_card,
seed = NULL,
epoch = NULL,
new_run_name = NULL,
new_args = NULL,
new_compile = NULL,
use_mirrored_strategy = NULL,
unfreeze = FALSE,
verbose = FALSE) {
if (is.null(use_mirrored_strategy)) use_mirrored_strategy <- ifelse(count_gpu() > 1, TRUE, FALSE)
info <- file.info(path_model_card)
is_directory <- info$isdir
if (is.na(is_directory)) {
stop("model_card path does not exist.\n")
} else if (is_directory) {
mc <- get_mc(path_model_card = path_model_card, epoch = epoch)
} else {
mc <- path_model_card
}
mc_args <- readRDS(mc)
train_args_mc <- mc_args$train_model_args
new_train_args <- train_args_mc
if (is.null(new_run_name)) {
new_train_args$run_name <- set_new_run_name(train_args_mc$run_name)
} else {
new_train_args$run_name <- new_run_name
}
# overwrite args
if (is.null(seed)) seed <- get_seed()
new_train_args$seed <- seed
# load checkpoint to resume from
if (is.null(train_args_mc$path_checkpoint)) {
stop('Did not save checkpoints in the run from model card')
}
if (unfreeze) {
model$trainable <- TRUE
}
if (use_mirrored_strategy) {
mirrored_strategy <- tensorflow::tf$distribute$MirroredStrategy()
with(mirrored_strategy$scope(), {
model <- load_model(cp_path = file.path(train_args_mc$path_checkpoint, train_args_mc$run_name),
ep_index = epoch,
new_compile = new_compile)
})
} else {
model <- load_model(cp_path = file.path(train_args_mc$path_checkpoint, train_args_mc$run_name),
ep_index = epoch,
new_compile = new_compile)
}
new_train_args$model <- model
if (!is.null(new_args)) {
stopifnot(is.list(new_args))
for (n in names(new_args))
new_train_args[[n]] <- new_args[[n]]
}
new_train_args$model_card[['cont_train_info']] <- paste0('run continues training from run ',
train_args_mc, ' and epoch ',
max(mc_args$logs$processing_step))
if (verbose) {
print(new_train_args)
}
do.call(train_model, new_train_args)
}
get_mc <- function(path_model_card, epoch = NULL) {
all_cards <- list.files(path_model_card, full.names = TRUE)
all_epochs <- vector("integer", length(all_cards))
for (i in seq_along(all_cards)) {
split_string <- all_cards[i] %>% basename() %>% stringr::str_split("_")
all_epochs[i] <- split_string[[1]][2] %>% as.integer()
}
if (is.null(epoch)) epoch <- max(all_epochs)
index <- all_epochs == epoch
if (sum(index) == 0) {
error_message <- paste('epoch not found in model card directory, possible values:',
paste(all_epochs, collapse = ", "))
stop(error_message)
}
mc <- all_cards[index]
return(mc)
}
load_model <- function(cp_path,
ep_index,
new_compile) {
model <- load_cp(cp_path,
ep_index = ep_index,
mirrored_strategy = FALSE,
compile = ifelse(is.null(new_compile), TRUE, FALSE))
if (!is.null(new_compile)) {
model <- keras::compile(model,
optimizer = new_compile$optimizer,
loss = new_compile$loss,
metrics = new_compile$metrics)
}
return(model)
}
get_seed <- function() {
current_time <- Sys.time()
current_time <- as.numeric(current_time) * 1e2
seed_value <- (current_time %% 10^5) %>% as.integer()
set.seed(seed_value)
return(sample(1:10^6, 2))
}
set_new_run_name <- function(run_name_old) {
run_name_new <- paste0(run_name_old, '_cont')
return(run_name_new)
}
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