Bonito model training

Bonito is a research-oriented model training tool designed for translating the raw-signals produced by Oxford Nanopore devices into genomic sequences.

Should I train a custom model for my data using bonito?

For the vast majority Oxford Nanopore sequencing use cases there is no need to train custom basecall models. Oxford Nanopore releases production basecall models through the Dorado project and these are incorporated into the MinKnow device software available on all Oxford Nanopore devices. These models are trained using a highly diverse pool of training samples and rigorously validated to ensure robust performance across a wide range of sample types, making them the recommended choice for general use cases.

Model training can be a complex and resource-intensive process, requiring a good understanding of machine learning principles, bioinformatics, and nanopore sequencing data. While Bonito provides tools to facilitate model training, it is important to note that we are unable to offer extensive support for custom model training. Users undertaking this should be prepared to troubleshoot and refine their workflows independently, the examples below are intended as a starting point for further development.

Training a model

Bonito models can be trained with the bonito train command. The choice of model design and hyperparameters for training will depend on the experiment and the data provided. Some default values are provided by Bonito, but these may need to be adjusted to fit your requirements.

The required arguments are shown below, for a full argument list including optional arguments please see bonito train --help

bonito train 
    {output_directory}                     # Positional argument. This is the directory that the output will be written to
    --directory {Path}                     # Path to the training data
    --epochs {int}                         # Number of epochs to train for
    --chunks {int}                         # Number of chunks read per epoch
    --valid-chunks {int}                   # Number of chunks used in validation at the end of each epoch
    ### One of the following arguments must be supplied
    --pretrained {Path}                    # Path to an existing model to finetune from. It is recommended to use a released model.
    --config {Path}                        # Path to a model definition file if training from scratch. Examples can be found in `bonito/models/configs`

Input data type and structure

Preparing training data with --save-ctc

The simplest way to prepare data for bonito training is using the --save-ctc flag with bonito basecaller:

bonito basecaller {initial_model} {input_data} --reference {ref.fasta} --save-ctc > basecalls.bam

In addition to the basecalls.bam output file this will generate a chunks.npy, references.npy and reference_lengths.npy file in the same output directory. This can be used immediately for basecaller training with bonito train ... --directory {basecaller_output_dir}

Understanding the data format

• chunks.npy is a numpy-array of shape num_chunks * chunksize where each row is a fixed size 'slice' of the raw signal data from the input pod5.
• references.npy is a numpy array of shape num_chunks * max_ref_len where each row contains a 'slice' of the reference-sequence which the chunk should align to. Bases are labelled as A=1, C=2, G=3, T=4. Since the number of reference bases will vary between chunks the reference array is zero-padded and the width of the array is the longest reference sequence in the sample
• reference_lengths.npy is a numpy-array of shape num_chunks. This is a helper array that indicates the start-index of the zero-padding in references.npy

Combining multiple datasets

In some cases it may be necessary to make several calls to bonito basecaller --save-ctc and combine the results. In these cases the output arrays can be combined by concatenation.

chunks_1 = np.load("dataset_1/chunks.npy")
chunks_2 = np.load("dataset_2/chunks.npy")
...

chunks_combined = np.concatenate([chunks_1, chunks_2, ...])
np.save("chunks.npy", chunks_combined)

In the case of the references.npy output each array must additionally be zero-padded to the width of the largest array.

refs_1 = np.load("ctc_data/dataset_1/references.npy")
refs_2 = np.load("ctc_data/dataset_2/references.npy")
...

max_width = max(refs_1.shape[1], refs_2.shape[1], ...)
refs_1_pad = np.pad(refs_1, ((0,0), (0, max_width - refs_1.shape[1])), mode='constant', constant_values=0)
refs_2_pad = np.pad(refs_2, ((0,0), (0, max_width - refs_2.shape[1])), mode='constant', constant_values=0)
... 

refs_combined = np.concatenate([refs_1_pad, refs_2_pad, ...])
np.save("references.npy", refs_combined)

Memory usage and limitations

During both the data generation with bonito basecaller --save-ctc and bonito train the entire dataset is loaded into RAM, which provides an upper bound to the amount of data which can be used for training by this method.

Providing data dynamically with dataset.py

:warning: WARNING: This method of feeding training data to bonito is provided for fleixbility in training and will require additional user development. The examples below are illustrative only and Oxford Nanopore is unable to support user implementations.

As an alternative to using the --save-ctc method described above data can alternatively be fed into Bonito training by dynamically loading a dataset.py file which serves chunks to the training module. This more advanced method allows for more flexible data loading, but requires the user to perform several intermediate steps such as the signal-reference mapping and creation of a DataLoader.

Interface

The data is loaded into bonito here: https://github.com/nanoporetech/bonito/blob/4bf419df/bonito/cli/data.py#L32

• There should be a module named dataset.py in the folder passed to the --directory argument of bonito train
• This module should have a callable named Loader which instantiates a class with the methods train_loader_kwargs and valid_loader_kwargs
• The train/valid_loader_kwargs should return a dict with the keys: dataset and sampler or shuffle
• The dataset should provide the same interface as a torch.utils.data.Dataset: https://pytorch.org/docs/stable/data.html#torch.utils.data.Dataset
• The sampler should provide the same interface as a torch.utils.data.Sampler: https://pytorch.org/docs/stable/data.html#torch.utils.data.Sampler

Example

This example shows how a dataset.py module can be used to load the default --save-ctc output format. It is possible to extend this method to utilise more complex datastructures for training.

"""
This is an example dataset.py file that can be loaded dynamically by bonito
"""

from functools import partial
from pathlib import Path

import numpy as np
from torch.utils.data import RandomSampler

from bonito.data import ChunkDataSet

class ChunkLoader:

    def __init__(self, train_data, valid_data, **kwargs):
        self.train_data = train_data
        self.valid_data = valid_data

    def train_loader_kwargs(self, **kwargs):
        train_ds = ChunkDataSet(*self.train_data)
        return {
            "dataset": train_ds,
            "sampler": RandomSampler(train_ds, num_samples=kwargs["chunks"]),
        }

    def valid_loader_kwargs(self, **kwargs):
        valid_ds = ChunkDataSet(*self.valid_data)
        return {
            "dataset": valid_ds,
            "shuffle": False,
        }


def load_chunks(input_folder):
    chunks = np.load(input_folder / "chunks.npy").astype(np.float32)
    refs = np.load(input_folder / "references.npy").astype(np.int64)
    ref_lens = np.load(input_folder / "reference_lengths.npy").astype(np.int64)
    return chunks, refs, ref_lens


chunks, refs, lens = load_chunks(Path("/data/ctc_output"))

# As an example, we take the first 1000 chunks for training and the last 100 for validation
# In practice more data will be required! 
train_data = chunks[:1000], refs[:1000], lens[:1000]
valid_data = chunks[100:], refs[100:], lens[100:]

Loader = partial(ChunkLoader, train_data, valid_data)