sleap.nn.config.optimization

class sleap.nn.config.optimization.AugmentationConfig(rotate: bool = False, rotation_min_angle: float = -180, rotation_max_angle: float = 180, translate: bool = False, translate_min: int = -5, translate_max: int = 5, scale: bool = False, scale_min: float = 0.9, scale_max: float = 1.1, uniform_noise: bool = False, uniform_noise_min_val: float = 0.0, uniform_noise_max_val: float = 10.0, gaussian_noise: bool = False, gaussian_noise_mean: float = 5.0, gaussian_noise_stddev: float = 1.0, contrast: bool = False, contrast_min_gamma: float = 0.5, contrast_max_gamma: float = 2.0, brightness: bool = False, brightness_min_val: float = 0.0, brightness_max_val: float = 10.0, random_crop: bool = False, random_crop_height: int = 256, random_crop_width: int = 256, random_flip: bool = False, flip_horizontal: bool = True)

Parameters for configuring an augmentation stack.

The augmentations will be applied in the the order of the attributes.

rotate

If True, rotational augmentation will be applied. Rotation is relative to the center of the image. See imgaug.augmenters.geometric.Affine.

Type:

bool

rotation_min_angle

Minimum rotation angle in degrees in [-180, 180].

Type:

float

rotation_max_angle

Maximum rotation angle in degrees in [-180, 180].

Type:

float

translate

If True, translational augmentation will be applied. The values are sampled independently for x and y coordinates. See imgaug.augmenters.geometric.Affine.

Type:

bool

translate_min

Minimum translation in integer pixel units.

Type:

int

translate_max

Maximum translation in integer pixel units.

Type:

int

scale

If True, scaling augmentation will be applied. See imgaug.augmenters.geometric.Affine.

Type:

bool

scale_min

Minimum scaling factor.

Type:

float

scale_max

Maximum scaling factor.

Type:

float

uniform_noise

If True, uniformly distributed noise will be added to the image. This is effectively adding a different random value to each pixel to simulate shot noise. See imgaug.augmenters.arithmetic.AddElementwise.

Type:

bool

uniform_noise_min_val

Minimum value to add.

Type:

float

uniform_noise_max_val

Maximum value to add.

Type:

float

gaussian_noise

If True, normally distributed noise will be added to the image. This is similar to uniform noise, but can provide a tigher bound around a mean noise magnitude. This is applied independently to each pixel. See imgaug.augmenters.arithmetic.AdditiveGaussianNoise.

Type:

bool

gaussian_noise_mean

Mean of the distribution to sample from.

Type:

float

gaussian_noise_stddev

Standard deviation of the distribution to sample from.

Type:

float

contrast

If True, gamma constrast adjustment will be applied to the image. This scales all pixel values by x ** gamma where x is the pixel value in the [0, 1] range. Values in [0, 255] are first scaled to [0, 1]. See imgaug.augmenters.contrast.GammaContrast.

Type:

bool

contrast_min_gamma

Minimum gamma to use for augmentation. Reasonable values are in [0.5, 2.0].

Type:

float

contrast_max_gamma

Maximum gamma to use for augmentation. Reasonable values are in [0.5, 2.0].

Type:

float

brightness

If True, the image brightness will be augmented. This adjustment simply adds the same value to all pixels in the image to simulate broadfield illumination change. See imgaug.augmenters.arithmetic.Add.

Type:

bool

brightness_min_val

Minimum value to add to all pixels.

Type:

float

brightness_max_val

Maximum value to add to all pixels.

Type:

float

random_crop

If True, performs random crops on the image. This is useful for training efficiently on large resolution images, but may fail to learn global structure beyond the crop size. Random cropping will be applied after the augmentations above.

Type:

bool

random_crop_width

Width of random crops.

Type:

int

random_crop_height

Height of random crops.

Type:

int

random_flip

If True, images will be randomly reflected. The coordinates of the instances will be adjusted accordingly. Body parts that are left/right symmetric must be marked on the skeleton in order to be swapped correctly.

Type:

bool

flip_horizontal

If True, flip images left/right when randomly reflecting them. If False, flipping is down up/down instead.

Type:

bool

class sleap.nn.config.optimization.EarlyStoppingConfig(stop_training_on_plateau: bool = True, plateau_min_delta: float = 1e-06, plateau_patience: int = 10)

Configuration for early stopping.

stop_training_on_plateau

If True, the training will terminate automatically when the validation set loss plateaus. This can save time and compute resources when there are minimal improvements to be gained from further training, as well as to prevent training into the overfitting regime.

Type:

bool

plateau_min_delta

Minimum absolute decrease in the loss in order to consider an epoch as not in a plateau.

Type:

float

plateau_patience

Number of epochs without an improvement of at least plateau_min_delta in order for a plateau to be detected.

Type:

int

class sleap.nn.config.optimization.HardKeypointMiningConfig(online_mining: bool = False, hard_to_easy_ratio: float = 2.0, min_hard_keypoints: int = 2, max_hard_keypoints: Optional[int] = None, loss_scale: float = 5.0)

Configuration for online hard keypoint mining.

online_mining

If True, online hard keypoint mining (OHKM) will be enabled. When this is enabled, the loss is computed per keypoint (or edge for PAFs) and sorted from lowest (easy) to highest (hard). The hard keypoint loss will be scaled to have a higher weight in the total loss, encouraging the training to focus on tricky body parts that are more difficult to learn. If False, no mining will be performed and all keypoints will be weighted equally in the loss.

Type:

bool

hard_to_easy_ratio

The minimum ratio of the individual keypoint loss with respect to the lowest keypoint loss in order to be considered as “hard”. This helps to switch focus on across groups of keypoints during training.

Type:

float

min_hard_keypoints

The minimum number of keypoints that will be considered as “hard”, even if they are not below the hard_to_easy_ratio.

Type:

int

max_hard_keypoints

The maximum number of hard keypoints to apply scaling to. This can help when there are few very easy keypoints which may skew the ratio and result in loss scaling being applied to most keypoints, which can reduce the impact of hard mining altogether.

Type:

Optional[int]

loss_scale

Factor to scale the hard keypoint losses by.

Type:

float

class sleap.nn.config.optimization.LearningRateScheduleConfig(reduce_on_plateau: bool = True, reduction_factor: float = 0.5, plateau_min_delta: float = 1e-06, plateau_patience: int = 5, plateau_cooldown: int = 3, min_learning_rate: float = 1e-08)

Configuration for learning rate scheduling.

reduce_on_plateau

If True, learning rate will be reduced when the validation set loss plateaus. This improves training at later epochs when finer weight updates are required for fine-tuning the optimization, balancing out an initially high learning rate required for practical initial optimization.

Type:

bool

reduction_factor

Factor by which the learning rate will be scaled when a plateau is detected.

Type:

float

plateau_min_delta

Minimum absolute decrease in the loss in order to consider an epoch as not in a plateau.

Type:

float

plateau_patience

Number of epochs without an improvement of at least plateau_min_delta in order for a plateau to be detected.

Type:

int

plateau_cooldown

Number of epochs after a reduction step before epochs without improvement will begin to be counted again.

Type:

int

min_learning_rate

The minimum absolute value that the learning rate can be reduced to.

Type:

float

class sleap.nn.config.optimization.OptimizationConfig(preload_data: bool = True, augmentation_config: AugmentationConfig = _Nothing.NOTHING, online_shuffling: bool = True, shuffle_buffer_size: int = 128, prefetch: bool = True, batch_size: int = 8, batches_per_epoch: Optional[int] = None, min_batches_per_epoch: int = 200, val_batches_per_epoch: Optional[int] = None, min_val_batches_per_epoch: int = 10, epochs: int = 100, optimizer: str = 'adam', initial_learning_rate: float = 0.0001, learning_rate_schedule: LearningRateScheduleConfig = _Nothing.NOTHING, hard_keypoint_mining: HardKeypointMiningConfig = _Nothing.NOTHING, early_stopping: EarlyStoppingConfig = _Nothing.NOTHING)

Optimization configuration.

preload_data

If True, the data from the training/validation/test labels will be loaded into memory at the beginning of training. If False, the data will be loaded every time it is accessed. Preloading can considerably speed up the performance of data generation at the cost of memory as all the images will be loaded into memory. This is especially beneficial for datasets with few examples or when the raw data is on (slow) network storage.

Type:

bool

augmentation_config

Configuration options related to data augmentation.

Type:

sleap.nn.config.optimization.AugmentationConfig

online_shuffling

If True, data will be shuffled online by maintaining a buffer of examples that are sampled from at each step. This allows for randomization of data ordering, resulting in more varied mini-batch composition, which in turn can promote generalization. Note that the data are shuffled at the start of training regardless.

Type:

bool

shuffle_buffer_size

Number of examples to keep in a buffer to sample uniformly from. This should be set to relatively low number as it requires an additional copy of each data example to be stored in memory. If set to -1, the entire dataset will be used, which results in perfect randomization at the cost of increased memory usage.

Type:

int

prefetch

If True, data will generated in parallel to training to minimize the bottleneck of the preprocessing pipeline.

Type:

bool

batch_size

Number of examples per minibatch, i.e., a single step of training. Higher numbers can increase generalization performance by averaging model gradient updates over a larger number of examples at the cost of considerably more GPU memory, especially for larger sized images. Lower numbers may lead to overfitting, but may be beneficial to the optimization process when few but varied examples are available.

Type:

int

batches_per_epoch

Number of minibatches (steps) to train for in an epoch. If set to None, this is set to the number of batches in the training data or min_batches_per_epoch, whichever is largest. At the end of each epoch, the validation and test sets are evaluated, the model is saved if its performance improved, visualizations are generated, learning rate may be tuned, and several other non-optimization procedures executed. If this is set too low, training may be slowed down as these end-of-epoch procedures can take longer than the optimization itself, especially if model saving is enabled, which can take a while for larger models. If set too high, the training procedure may take longer, especially since several hyperparameter tuning heuristics only consider epoch-to-epoch performance.

Type:

Optional[int]

min_batches_per_epoch

The minimum number of batches per epoch if batches_per_epoch is set to None. No effect if the batches per epoch is explicitly specified. This should be set to 200-400 to compensate for short loops through the data when there are few examples.

Type:

int

val_batches_per_epoch

Same as batches_per_epoch, but for the validation set.

Type:

Optional[int]

min_val_batches_per_epoch

Same as min_batches_per_epoch, but for the validation set.

Type:

int

epochs

Maximum number of epochs to train for. Training can be stopped manually or automatically if early stopping is enabled and a plateau is detected.

Type:

int

optimizer

Name of the optimizer to use for training. This is typically “adam” but the name of any class from tf.keras.optimizers may be used. If “adam” is specified, the Adam optimizer will have AMSGrad enabled.

Type:

str

initial_learning_rate

The initial learning rate to use for the optimizer. This is typically set to 1e-3 or 1e-4, and can be decreased automatically if learning rate reduction on plateau is enabled. If this is too high or too low, the training may fail to find good initial local minima to descend.

Type:

float

learning_rate_schedule

Configuration options related to learning rate scheduling.

Type:

sleap.nn.config.optimization.LearningRateScheduleConfig

hard_keypoint_mining

Configuration options related to online hard keypoint mining.

Type:

sleap.nn.config.optimization.HardKeypointMiningConfig

early_stopping

Configuration options related to early stopping of training on plateau/convergence is detected.

Type:

sleap.nn.config.optimization.EarlyStoppingConfig