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Changelog

March 2021

Container updated to 21.02
Change data format from tfrecord to npy and data loading for 2D

January 2021

Initial release
Add notebook with custom dataset loading

Known issues

There are no known issues in this release.

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The nnU-Net (\"no-new-Net\") refers to a robust and self-adapting framework for U-Net based medical image segmentation. This repository contains a nnU-Net implementation as described in the paper: nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation.

The differences between this nnU-net and original model are:

Dynamic selection of patch size is not supported, and it has to be set in data_preprocessing/configs.py file.
Cascaded U-Net is not supported.
The following data augmentations are not used: rotation, simulation of low resolution, gamma augmentation.

This model is trained with mixed precision using Tensor Cores on Volta, Turing, and the NVIDIA Ampere GPU architectures. Therefore, researchers can get results 2x faster than training without Tensor Cores, while experiencing the benefits of mixed precision training. This model is tested against each NGC monthly container release to ensure consistent accuracy and performance over time.

We developed the model using PyTorch Lightning, a new easy to use framework that ensures code readability and reproducibility without the boilerplate.

Model architecture

\nThe nnU-Net allows training two types of networks: 2D U-Net and 3D U-Net to perform semantic segmentation of 3D images, with high accuracy and performance.

The following figure shows the architecture of the 3D U-Net model and its different components. U-Net is composed of a contractive and an expanding path, that aims at building a bottleneck in its centremost part through a combination of convolution, instance norm and leaky relu operations. After this bottleneck, the image is reconstructed through a combination of convolutions and upsampling. Skip connections are added with the goal of helping the backward flow of gradients in order to improve the training.

Figure 1: The 3D U-Net architecture

Default configuration

All convolution blocks in U-Net in both encoder and decoder are using two convolution layers followed by instance normalization and a leaky ReLU nonlinearity. For downsampling we are using stride convolution whereas transposed convolution for upsampling.

All models were trained with Adam optimizer. For loss function we use the average of cross-entropy and dice coefficient.

Early stopping is triggered if validation dice score wasn't improved during the last 100 epochs.

Used data augmentation: crop with oversampling the foreground class, mirroring, zoom, Gaussian noise, Gaussian blur, brightness, contrast.

Feature support matrix

The following features are supported by this model:

\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

tr:nth-child(odd)]:bg-surface-sunken\">

Feature	nnUNet
DALI	Yes
Automatic mixed precision (AMP)	Yes
Distributed data parallel (DDP)	Yes

Features

DALI

NVIDIA DALI - DALI is a library accelerating data preparation pipeline. To accelerate your input pipeline, you only need to define your data loader\nwith the DALI library. For details, see example sources in this repository or see the DALI documentation

Automatic Mixed Precision (AMP)

This implementation uses native PyTorch AMP implementation of mixed precision training. It allows us to use FP16 training with FP32 master weights by modifying just a few lines of code.

DistributedDataParallel (DDP)

The model uses PyTorch Lightning implementation of distributed data parallelism at the module level which can run across multiple machines.

Mixed precision training

Mixed precision is the combined use of different numerical precisions in a computational method. Mixed precision training offers significant computational speedup by performing operations in half-precision format, while storing minimal information in single-precision to retain as much information as possible in critical parts of the network. Since the introduction of Tensor Cores in Volta, and following with both the Turing and Ampere architectures, significant training speedups are experienced by switching to mixed precision -- up to 3x overall speedup on the most arithmetically intense model architectures. Using mixed precision training requires two steps:

Porting the model to use the FP16 data type where appropriate.
Adding loss scaling to preserve small gradient values.

The ability to train deep learning networks with lower precision was introduced in the Pascal architecture and first supported in CUDA 8 in the NVIDIA Deep Learning SDK.

For information about:

How to train using mixed precision, see the Mixed Precision Training paper and Training With Mixed Precision documentation.
Techniques used for mixed precision training, see the Mixed-Precision Training of Deep Neural Networks blog.
APEX tools for mixed precision training, see the NVIDIA Apex: Tools for Easy Mixed-Precision Training in PyTorch.

Enabling mixed precision

For training and inference, mixed precision can be enabled by adding the --amp flag. Mixed precision is using native PyTorch implementation.

TF32

TensorFloat-32 (TF32) is the new math mode in NVIDIA A100 GPUs for handling the matrix math also called tensor operations. TF32 running on Tensor Cores in A100 GPUs can provide up to 10x speedups compared to single-precision floating-point math (FP32) on Volta GPUs.

TF32 Tensor Cores can speed up networks using FP32, typically with no loss of accuracy. It is more robust than FP16 for models which require high dynamic range for weights or activations.

For more information, refer to the TensorFloat-32 in the A100 GPU Accelerates AI Training, HPC up to 20x blog post.

TF32 is supported in the NVIDIA Ampere GPU architecture and is enabled by default.

Glossary

Test time augmentation

Test time augmentation is an inference technique which averages predictions from augmented images with its prediction. As a result, predictions are more accurate, but with the cost of slower inference process. For nnU-Net, we use all possible flip combinations for image augmenting. Test time augmentation can be enabled by adding the --tta flag.

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Aside from these dependencies, ensure you have the following components:\n- [NVIDIA Docker](https://github.com/NVIDIA/nvidia-docker)\n- PyTorch 21.11 NGC container\n- Supported GPUs:\n - [NVIDIA Volta architecture](https://www.nvidia.com/en-us/data-center/volta-gpu-architecture/)\n - [NVIDIA Turing architecture](https://www.nvidia.com/en-us/geforce/turing/)\n - [NVIDIA Ampere architecture](https://www.nvidia.com/en-us/data-center/nvidia-ampere-gpu-architecture/)\n\nFor more information about how to get started with NGC containers, see the following sections from the NVIDIA GPU Cloud Documentation and the Deep Learning Documentation:\n- [Getting Started Using NVIDIA GPU Cloud](https://docs.nvidia.com/ngc/ngc-getting-started-guide/index.html)\n- [Accessing And Pulling From The NGC Container Registry](https://docs.nvidia.com/deeplearning/frameworks/user-guide/index.html#accessing_registry)\n- Running [PyTorch](https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes/running.html#running)\n \nFor those unable to use the PyTorch NGC container, to set up the required environment or create your own container, see the versioned [NVIDIA Container Support Matrix](https://docs.nvidia.com/deeplearning/frameworks/support-matrix/index.html).","hasSetup","quickStartGuide","To train your model using mixed or TF32 precision with Tensor Cores or using FP32, perform the following steps using the default parameters of the nnUNet model on the [Medical Segmentation Decathlon](http://medicaldecathlon.com/) dataset. For the specifics concerning training and inference, see the [Advanced](#advanced) section.\n\n1. Clone the repository.\n\nExecuting this command will create your local repository with all the code to run nnU-Net.\n```\ngit clone https://github.com/NVIDIA/DeepLearningExamples\ncd DeepLearningExamples/PyTorch/Segmentation/nnUNet\n```\n \n2. Build the nnU-Net PyTorch NGC container.\n \nThis command will use the Dockerfile to create a Docker image named `nnunet`, downloading all the required components automatically.\n\n```\ndocker build -t nnunet .\n```\n \nThe NGC container contains all the components optimized for usage on NVIDIA hardware.\n \n3. Start an interactive session in the NGC container to run preprocessing/training/inference.\n \nThe following command will launch the container and mount the `./data` directory as a volume to the `/data` directory inside the container, and `./results` directory to the `/results` directory in the container.\n \n```\nmkdir data results\ndocker run -it --runtime=nvidia --shm-size=8g --ulimit memlock=-1 --ulimit stack=67108864 --rm -v ${PWD}/data:/data -v ${PWD}/results:/results nnunet:latest /bin/bash\n```\n\n4. Prepare BraTS dataset.\n\nTo download and preprocess the data run:\n```\npython download.py --task 01\npython preprocess.py --task 01 --dim 3\npython preprocess.py --task 01 --dim 2\n```\n\nThen `ls /data` should print:\n```\n01_3d 01_2d Task01_BrainTumour\n```\n\nFor the specifics concerning data preprocessing, see the [Getting the data](#getting-the-data) section.\n \n5. Start training.\n \nTraining can be started with:\n```\npython scripts/train.py --gpus --fold --dim [--amp]\n```\n\nTo see descriptions of the train script arguments run `python scripts/train.py --help`. You can customize the training process. For details, see the [Training process](#training-process) section.\n\n6. Start benchmarking.\n\nThe training and inference performance can be evaluated by using benchmarking scripts, such as:\n \n```\npython scripts/benchmark.py --mode {train,predict} --gpus --dim {2,3} --batch_size [--amp] \n```\n\nTo see descriptions of the benchmark script arguments run `python scripts/benchmark.py --help`.\n\n7. Start inference/predictions.\n \nInference can be started with:\n```\npython scripts/inference.py --data --dim --fold --ckpt_path [--amp] [--tta] [--save_preds]\n```\n\nNote: You have to prepare either validation or test dataset to run this script by running `python preprocess.py --task 01 --dim {2,3} --exec_mode {val,test}`. After preprocessing inside given task directory (e.g. `/data/01_3d/` for task 01 and dim 3) it will create `val` or `test` directory with preprocessed data ready for inference. Possible workflow:\n\n```\npython preprocess.py --task 01 --dim 3 --exec_mode val\npython scripts/inference.py --data /data/01_3d/val --dim 3 --fold 0 --ckpt_path --amp --tta --save_preds\n```\n\nThen if you have labels for predicted images you can evaluate it with `evaluate.py` script. For example:\n\n```\npython evaluate.py --preds /results/preds_task_01_dim_3_fold_0_tta --lbls /data/Task01_BrainTumour/labelsTr\n```\n\nTo see descriptions of the inference script arguments run `python scripts/inference.py --help`. You can customize the inference process. For details, see the [Inference process](#inference-process) section.\n\nNow that you have your model trained and evaluated, you can choose to compare your training results with our [Training accuracy results](#training-accuracy-results). You can also choose to benchmark yours performance to [Training performance benchmark](#training-performance-results), or [Inference performance benchmark](#inference-performance-results). Following the steps in these sections will ensure that you achieve the same accuracy and performance results as stated in the [Results](#results) section.","hasQuickStartGuide","advanced","The following sections provide greater details of the dataset, running training and inference, and the training results.\n\n### Scripts and sample code\n\nIn the root directory, the most important files are:\n\n* `main.py`: Entry point to the application. Runs training, evaluation, inference or benchmarking.\n* `preprocess.py`: Entry point to data preprocessing.\n* `download.py`: Downloads given dataset from [Medical Segmentation Decathlon](http://medicaldecathlon.com/).\n* `Dockerfile`: Container with the basic set of dependencies to run nnU-Net.\n* `requirements.txt:` Set of extra requirements for running nnU-Net.\n* `evaluate.py`: Compare predictions with ground truth and get final score.\n \nThe `data_preprocessing` folder contains information about the data preprocessing used by nnU-Net. Its contents are:\n \n* `configs.py`: Defines dataset configuration like patch size or spacing.\n* `preprocessor.py`: Implements data preprocessing pipeline.\n* `convert2tfrec.py`: Implements conversion from NumPy files to tfrecords.\n \nThe `data_loading` folder contains information about the data pipeline used by nnU-Net. Its contents are:\n \n* `data_module.py`: Defines `LightningDataModule` used by PyTorch Lightning.\n* `dali_loader.py`: Implements DALI data loader.\n \nThe `nnunet` folder contains information about the building blocks of nnU-Net and the way they are assembled. Its contents are:\n \n* `metrics.py`: Implements dice metric\n* `loss.py`: Implements loss function.\n* `nn_unet.py`: Implements training/validation/test logic and dynamic creation of U-Net architecture used by nnU-Net.\n \nThe `utils` folder includes:\n\n* `args.py`: Defines command line arguments.\n* `utils.py`: Defines utility functions.\n* `logger.py`: Defines logging callback for performance benchmarking.\n\nThe `notebooks` folder includes:\n\n* `BraTS21.ipynb`: Notebook with our solution for BraTS21 challenge.\n* `custom_dataset.ipynb`: Notebook which demonstrates how to use nnU-Net with custom dataset.\n\nOther folders included in the root directory are:\n\n* `images/`: Contains a model diagram.\n* `scripts/`: Provides scripts for training, benchmarking and inference of nnU-Net.\n\n### Command-line options\n\nTo see the full list of available options and their descriptions, use the `-h` or `--help` command-line option, for example:\n\n`python main.py --help`\n\nThe following example output is printed when running the model:\n\n```\nusage: main.py [-h] [--exec_mode {train,evaluate,predict}] [--data DATA] [--results RESULTS] [--logname LOGNAME] [--task TASK] [--gpus GPUS] [--learning_rate LEARNING_RATE] [--gradient_clip_val GRADIENT_CLIP_VAL] [--negative_slope NEGATIVE_SLOPE] [--tta] [--brats] [--deep_supervision] [--more_chn] [--invert_resampled_y] [--amp] [--benchmark] [--focal] [--sync_batchnorm] [--save_ckpt] [--nfolds NFOLDS] [--seed SEED] [--skip_first_n_eval SKIP_FIRST_N_EVAL] [--ckpt_path CKPT_PATH] [--fold FOLD] [--patience PATIENCE] [--batch_size BATCH_SIZE] [--val_batch_size VAL_BATCH_SIZE] [--profile] [--momentum MOMENTUM] [--weight_decay WEIGHT_DECAY] [--save_preds] [--dim {2,3}] [--resume_training] [--num_workers NUM_WORKERS] [--epochs EPOCHS] [--warmup WARMUP] [--norm {instance,batch,group}] [--nvol NVOL] [--depth DEPTH] [--min_fmap MIN_FMAP] [--deep_supr_num DEEP_SUPR_NUM] [--res_block] [--filters FILTERS [FILTERS ...]] [--data2d_dim {2,3}] [--oversampling OVERSAMPLING] [--overlap OVERLAP] [--affinity {socket,single_single,single_single_unique,socket_unique_interleaved,socket_unique_continuous,disabled}] [--scheduler] [--optimizer {sgd,adam}] [--blend {gaussian,constant}] [--train_batches TRAIN_BATCHES] [--test_batches TEST_BATCHES]\n\noptional arguments:\n -h, --help show this help message and exit\n --exec_mode {train,evaluate,predict}\n Execution mode to run the model (default: train)\n --data DATA Path to data directory (default: /data)\n --results RESULTS Path to results directory (default: /results)\n --logname LOGNAME Name of dlloger output (default: None)\n --task TASK Task number. MSD uses numbers 01-10 (default: None)\n --gpus GPUS Number of gpus (default: 1)\n --learning_rate LEARNING_RATE\n Learning rate (default: 0.0008)\n --gradient_clip_val GRADIENT_CLIP_VAL\n Gradient clipping norm value (default: 0)\n --negative_slope NEGATIVE_SLOPE\n Negative slope for LeakyReLU (default: 0.01)\n --tta Enable test time augmentation (default: False)\n --brats Enable BraTS specific training and inference (default: False)\n --deep_supervision Enable deep supervision (default: False)\n --more_chn Create encoder with more channels (default: False)\n --invert_resampled_y Resize predictions to match label size before resampling (default: False)\n --amp Enable automatic mixed precision (default: False)\n --benchmark Run model benchmarking (default: False)\n --focal Use focal loss instead of cross entropy (default: False)\n --sync_batchnorm Enable synchronized batchnorm (default: False)\n --save_ckpt Enable saving checkpoint (default: False)\n --nfolds NFOLDS Number of cross-validation folds (default: 5)\n --seed SEED Random seed (default: 1)\n --skip_first_n_eval SKIP_FIRST_N_EVAL\n Skip the evaluation for the first n epochs. (default: 0)\n --ckpt_path CKPT_PATH\n Path to checkpoint (default: None)\n --fold FOLD Fold number (default: 0)\n --patience PATIENCE Early stopping patience (default: 100)\n --batch_size BATCH_SIZE\n Batch size (default: 2)\n --val_batch_size VAL_BATCH_SIZE\n Validation batch size (default: 4)\n --profile Run dlprof profiling (default: False)\n --momentum MOMENTUM Momentum factor (default: 0.99)\n --weight_decay WEIGHT_DECAY\n Weight decay (L2 penalty) (default: 0.0001)\n --save_preds Enable prediction saving (default: False)\n --dim {2,3} UNet dimension (default: 3)\n --resume_training Resume training from the last checkpoint (default: False)\n --num_workers NUM_WORKERS\n Number of subprocesses to use for data loading (default: 8)\n --epochs EPOCHS Number of training epochs (default: 1000)\n --warmup WARMUP Warmup iterations before collecting statistics (default: 5)\n --norm {instance,batch,group}\n Normalization layer (default: instance)\n --nvol NVOL Number of volumes which come into single batch size for 2D model (default: 4)\n --depth DEPTH The depth of the encoder (default: 5)\n --min_fmap MIN_FMAP Minimal dimension of feature map in the bottleneck (default: 4)\n --deep_supr_num DEEP_SUPR_NUM\n Number of deep supervision heads (default: 2)\n --res_block Enable residual blocks (default: False)\n --filters FILTERS [FILTERS ...]\n [Optional] Set U-Net filters (default: None)\n --data2d_dim {2,3} Input data dimension for 2d model (default: 3)\n --oversampling OVERSAMPLING\n Probability of crop to have some region with positive label (default: 0.4)\n --overlap OVERLAP Amount of overlap between scans during sliding window inference (default: 0.5)\n --affinity {socket,single_single,single_single_unique,socket_unique_interleaved,socket_unique_continuous,disabled}\n type of CPU affinity (default: socket_unique_contiguous)\n --scheduler Enable cosine rate scheduler with warmup (default: False)\n --optimizer {sgd,adam}\n Optimizer (default: adam)\n --blend {gaussian,constant}\n How to blend output of overlapping windows (default: gaussian)\n --train_batches TRAIN_BATCHES\n Limit number of batches for training (used for benchmarking mode only) (default: 0)\n --test_batches TEST_BATCHES\n Limit number of batches for inference (used for benchmarking mode only) (default: 0)\n```\n\n### Getting the data\n\nThe nnU-Net model was trained on the [Medical Segmentation Decathlon](http://medicaldecathlon.com/) datasets. All datasets are in Neuroimaging Informatics Technology Initiative (NIfTI) format.\n\n#### Dataset guidelines\n\nTo train nnU-Net you will need to preprocess your dataset as a first step with `preprocess.py` script. Run `python scripts/preprocess.py --help` to see descriptions of the preprocess script arguments.\n\nFor example to preprocess data for 3D U-Net run: `python preprocess.py --task 01 --dim 3`.\n\nIn `data_preprocessing/configs.py` for each [Medical Segmentation Decathlon](http://medicaldecathlon.com/) task there are defined: patch size, precomputed spacings and statistics for CT datasets.\n\nThe preprocessing pipeline consists of the following steps:\n\n1. Cropping to the region of non-zero values.\n2. Resampling to the median voxel spacing of their respective dataset (exception for anisotropic datasets where the lowest resolution axis is selected to be the 10th percentile of the spacings).\n3. Padding volumes so that dimensions are at least as patch size.\n4. Normalizing:\n * For CT modalities the voxel values are clipped to 0.5 and 99.5 percentiles of the foreground voxels and then data is normalized with mean and standard deviation from collected from foreground voxels.\n * For MRI modalities z-score normalization is applied.\n\n#### Multi-dataset\n\nIt is possible to run nnUNet on custom dataset. If your dataset correspond to [Medical Segmentation Decathlon](http://medicaldecathlon.com/) (i.e. data should be `NIfTi` format and there should be `dataset.json` file where you need to provide fields: modality, labels and at least one of training, test) you need to perform the following:\n\n1. Mount your dataset to `/data` directory.\n \n2. In `data_preprocessing/config.py`:\n - Add to the `task_dir` dictionary your dataset directory name. For example, for Brain Tumour dataset, it corresponds to `\"01\": \"Task01_BrainTumour\"`.\n - Add the patch size that you want to use for training to the `patch_size` dictionary. For example, for Brain Tumour dataset it corresponds to `\"01_3d\": [128, 128, 128]` for 3D U-Net and `\"01_2d\": [192, 160]` for 2D U-Net. There are three types of suffixes `_3d, _2d` they correspond to 3D UNet and 2D U-Net.\n\n3. Preprocess your data with `preprocess.py` scripts. For example, to preprocess Brain Tumour dataset for 2D U-Net you should run `python preprocess.py --task 01 --dim 2`.\n\nIf you have dataset in other format or you want customize data preprocessing or data loading see `notebooks/custom_dataset.ipynb`.\n\n### Training process\n\nThe model trains for at least `--min_epochs` and at most `--max_epochs` epochs. After each epoch evaluation, the validation set is done and validation loss is monitored for early stopping (see `--patience` flag). Default training settings are:\n* Adam optimizer with learning rate of 0.0008 and weight decay 0.0001.\n* Training batch size is set to 2 for 3D U-Net and 16 for 2D U-Net.\n \nThis default parametrization is applied when running scripts from the `scripts/` directory and when running `main.py` without explicitly overriding these parameters. By default, the training is in full precision. To enable AMP, pass the `--amp` flag. AMP can be enabled for every mode of execution.\n\nThe default configuration minimizes a function `L = (1 - dice_coefficient) + cross_entropy` during training and reports achieved convergence as [dice coefficient](https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient) per class. The training, with a combination of dice and cross entropy has been proven to achieve better convergence than a training using only dice.\n\nThe training can be run directly without using the predefined scripts. The name of the training script is `main.py`. For example:\n\n```\npython main.py --exec_mode train --task 01 --fold 0 --gpus 1 --amp\n```\n \nTraining artifacts will be saved to `/results` in the container. Some important artifacts are:\n* `/results/logs.json`: Collected dice scores and loss values evaluated after each epoch during training on validation set.\n* `/results/checkpoints`: Saved checkpoints. By default, two checkpoints are saved - one after each epoch ('last.ckpt') and one with the highest validation dice (e.g 'epoch=5.ckpt' for if highest dice was at 5th epoch).\n\nTo load the pretrained model provide `--ckpt_path `.\n\n### Inference process\n\nInference can be launched by passing the `--exec_mode predict` flag. For example:\n\n```\npython main.py --exec_mode predict --task 01 --fold 0 --gpus 1 --amp --tta --save_preds --ckpt_path \n```\n\nThe script will then:\n\n* Load the checkpoint from the directory specified by the `` directory\n* Run inference on the preprocessed validation dataset corresponding to fold 0\n* Print achieved score to the console\n* If `--save_preds` is provided then resulting masks in the NumPy format will be saved in the `/results` directory","hasAdvanced","performance","### Benchmarking\n\nThe following section shows how to run benchmarks to measure the model performance in training and inference modes.\n\n#### Training performance benchmark\n\nTo benchmark training, run `scripts/benchmark.py` script with `--mode train`:\n\n```\npython scripts/benchmark.py --mode train --gpus --dim {2,3} --batch_size [--amp] \n```\n\nFor example, to benchmark 3D U-Net training using mixed-precision on 8 GPUs with batch size of 2, run:\n\n```\npython scripts/benchmark.py --mode train --gpus 8 --dim 3 --batch_size 2 --amp\n```\n\nEach of these scripts will by default run 1 warm-up epoch and start performance benchmarking during the second epoch.\n\nAt the end of the script, a line reporting the best train throughput and latency will be printed.\n\n#### Inference performance benchmark\n\nTo benchmark inference, run `scripts/benchmark.py` script with `--mode predict`:\n\n```\npython scripts/benchmark.py --mode predict --dim {2,3} --batch_size [--amp]\n```\n\nFor example, to benchmark inference using mixed-precision for 3D U-Net, with batch size of 4, run:\n\n```\npython scripts/benchmark.py --mode predict --dim 3 --amp --batch_size 4\n```\n\nEach of these scripts will by default run warm-up for 1 data pass and start inference benchmarking during the second pass.\n\nAt the end of the script, a line reporting the inference throughput and latency will be printed.\n\n### Results\n\nThe following sections provide details on how to achieve the same performance and accuracy in training and inference.\n\n#### Training accuracy results\n\n##### Training accuracy: NVIDIA DGX A100 (8x A100 80G)\n\nOur results were obtained by running the `python scripts/train.py --gpus {1,8} --fold {0,1,2,3,4} --dim {2,3} [--amp]` training scripts and averaging results in the PyTorch 21.11 NGC container on NVIDIA DGX with (8x A100 80G) GPUs.\n\n| Dimension | GPUs | Batch size / GPU | Accuracy - mixed precision | Accuracy - TF32 | Time to train - mixed precision | Time to train - TF32| Time to train speedup (TF32 to mixed precision) \n|:-:|:-:|:--:|:-----:|:-----:|:-----:|:-----:|:----:|\n| 2 | 1 | 2 | 73.21 | 73.11 | 33 min| 48 min| 1.46 |\n| 2 | 8 | 2 | 73.15 | 73.16 | 9 min| 13 min| 1.44 |\n| 3 | 1 | 2 | 74.35 | 74.34 |104 min|167 min| 1.61 |\n| 3 | 8 | 2 | 74.30 | 74.32 | 23min| 36 min| 1.57 |\n\n##### Training accuracy: NVIDIA DGX-1 (8x V100 16G)\n\nOur results were obtained by running the `python scripts/train.py --gpus {1,8} --fold {0,1,2,3,4} --dim {2,3} [--amp]` training scripts and averaging results in the PyTorch 21.11 NGC container on NVIDIA DGX-1 with (8x V100 16G) GPUs.\n\n| Dimension | GPUs | Batch size / GPU | Accuracy - mixed precision | Accuracy - FP32 | Time to train - mixed precision | Time to train - FP32 | Time to train speedup (FP32 to mixed precision) \n|:-:|:-:|:--:|:-----:|:-----:|:-----:|:-----:|:----:|\n| 2 | 1 | 2 | 73.18 | 73.22 | 60 min|114 min| 1.90 |\n| 2 | 8 | 2 | 73.15 | 73.18 | 13 min| 19 min| 1.46 |\n| 3 | 1 | 2 | 74.31 | 74.33 |201 min|680 min| 3.38 |\n| 3 | 8 | 2 | 74.35 | 74.39 | 41 min|153 min| 3.73 |\n\n#### Training performance results\n\n##### Training performance: NVIDIA DGX A100 (8x A100 80G)\n\nOur results were obtained by running the `python scripts/benchmark.py --mode train --gpus {1,8} --dim {2,3} --batch_size [--amp]` training script in the NGC container on NVIDIA DGX A100 (8x A100 80G) GPUs. Performance numbers (in volumes per second) were averaged over an entire training epoch.\n\n| Dimension | GPUs | Batch size / GPU | Throughput - mixed precision [img/s] | Throughput - TF32 [img/s] | Throughput speedup (TF32 - mixed precision) | Weak scaling - mixed precision | Weak scaling - TF32 |\n|:-:|:-:|:--:|:------:|:------:|:-----:|:-----:|:-----:|\n| 2 | 1 | 64 | 1129.48 | 702.82 | 1.607 | N/A | N/A |\n| 2 | 1 | 128 | 1234.69 | 741.01 | 1.666 | N/A | N/A |\n| 2 | 8 | 64 | 7015.45 | 4613.27 | 1.521 | 6.211 | 6.564 |\n| 2 | 8 | 128 | 8293.61 | 5498.78 | 1.508 | 6.717 | 7.421 |\n| 3 | 1 | 1 | 13.92 | 9.22 | 1.509 | N/A | N/A |\n| 3 | 1 | 2 | 17.68 | 10.72 | 1.649 | N/A | N/A |\n| 3 | 1 | 4 | 20.56 | 11.5 | 1.787 | N/A | N/A |\n| 3 | 8 | 1 | 92.97 | 61.68 | 1.416 | 6.679 | 7.119 |\n| 3 | 8 | 2 | 114.47 | 72.23 | 1.475 | 6.475 | 7.242 |\n| 3 | 8 | 4 | 140.55 | 85.53 | 1.643 | 6.836 | 7.437 |\n\nTo achieve these same results, follow the steps in the [Quick Start Guide](#quick-start-guide).\n\n##### Training performance: NVIDIA DGX-1 (8x V100 16G)\n\nOur results were obtained by running the `python scripts/benchmark.py --mode train --gpus {1,8} --dim {2,3} --batch_size [--amp]` training script in the PyTorch 21.11 NGC container on NVIDIA DGX-1 with (8x V100 16G) GPUs. Performance numbers (in volumes per second) were averaged over an entire training epoch.\n\n| Dimension | GPUs | Batch size / GPU | Throughput - mixed precision [img/s] | Throughput - FP32 [img/s] | Throughput speedup (FP32 - mixed precision) | Weak scaling - mixed precision | Weak scaling - FP32 |\n|:-:|:-:|:---:|:---------:|:-----------:|:--------:|:---------:|:-------------:|\n| 2 | 1 | 64 | 607.16 | 298.84 | 2.032 | N/A | N/A |\n| 2 | 1 | 128 | 653.44 | 307.01 | 2.128 | N/A | N/A |\n| 2 | 8 | 64 | 4058.79 | 2196.05 | 1.848 | 6.685 | 7.349 |\n| 2 | 8 | 128 | 4649.37 | 2388.46 | 1.848 | 7.115 | 7.779 |\n| 3 | 1 | 1 | 8.66 | 1.99 | 4.352 | N/A | N/A |\n| 3 | 1 | 2 | 9.65 | 2.07 | 4.662 | N/A | N/A |\n| 3 | 1 | 4 | 9.99 | OOM | N/A | N/A | N/A |\n| 3 | 8 | 1 | 58.45 | 15.55 | 3.756 | 6.749 | 7.819 |\n| 3 | 8 | 2 | 66.03 | 16.22 | 4.071 | 6.842 | 7.835 |\n| 3 | 8 | 4 | 67.37 | OOM | N/A | 6.743 | N/A |\n\nTo achieve these same results, follow the steps in the [Quick Start Guide](#quick-start-guide).\n\n#### Inference performance results\n\n##### Inference performance: NVIDIA DGX A100 (1x A100 80G)\n\nOur results were obtained by running the `python scripts/benchmark.py --mode predict --dim {2,3} --batch_size [--amp]` inferencing benchmarking script in the PyTorch 21.11 NGC container on NVIDIA DGX A100 (1x A100 80G) GPU.\n\nFP16\n\n| Dimension | Batch size | Resolution | Throughput Avg [img/s] | Latency Avg [ms] | Latency 90% [ms] | Latency 95% [ms] | Latency 99% [ms] |\n|:----------:|:---------:|:-------------:|:----------------------:|:----------------:|:----------------:|:----------------:|:----------------:|\n| 2 | 64 | 4x192x160 | 3211.23 | 19.93 | 20.24 | 20.38 | 20.84 |\n| 2 | 128 | 4x192x160 | 3465.45 | 36.94 | 38.35 | 38.72 | 38.95 |\n| 3 | 1 | 4x128x128x128 | 41.93 | 23.85 | 24.40 | 24.61 | 24.99 |\n| 3 | 2 | 4x128x128x128 | 44.24 | 45.21 | 47.08 | 47.38 | 48.24 |\n| 3 | 4 | 4x128x128x128 | 45.81 | 87.31 | 88.13 | 88.56 | 89.69 |\n\nTF32\n\n| Dimension | Batch size | Resolution | Throughput Avg [img/s] | Latency Avg [ms] | Latency 90% [ms] | Latency 95% [ms] | Latency 99% [ms] |\n|:----------:|:---------:|:-------------:|:----------------------:|:----------------:|:----------------:|:----------------:|:----------------:|\n| 2 | 64 | 4x192x160 | 2172.38 | 29.46 | 29.94 | 30.03 | 30.19 |\n| 2 | 128 | 4x192x160 | 1769.56 | 72.34 | 72.84 | 73.04 | 74.79 |\n| 3 | 1 | 4x128x128x128 | 23.83 | 41.97 | 42.71 | 42.76 | 42.87 |\n| 3 | 2 | 4x128x128x128 | 26.75 | 74.77 | 75.79 | 76.06 | 77.04 |\n| 3 | 4 | 4x128x128x128 | 27.10 | 147.62 | 147.81 | 149.14 | 190.08 |\n\nThroughput is reported in images per second. Latency is reported in milliseconds per batch.\nTo achieve these same results, follow the steps in the [Quick Start Guide](#quick-start-guide).\n\n##### Inference performance: NVIDIA DGX-1 (1x V100 16G)\n\nOur results were obtained by running the `python scripts/benchmark.py --mode predict --dim {2,3} --batch_size [--amp]` inferencing benchmarking script in the PyTorch 21.11 NGC container on NVIDIA DGX-1 with (1x V100 16G) GPU.\n\nFP16\n \n| Dimension | Batch size |Resolution| Throughput Avg [img/s] | Latency Avg [ms] | Latency 90% [ms] | Latency 95% [ms] | Latency 99% [ms] |\n|:----------:|:---------:|:-------------:|:----------------------:|:----------------:|:----------------:|:----------------:|:----------------:|\n| 2 | 64 | 4x192x160 | 1809.79 | 35.36 | 35.75 | 35.84 | 36.21 |\n| 2 | 128 | 4x192x160 | 1987.91 | 64.39 | 64.79 | 64.87 | 65.01 |\n| 3 | 1 | 4x128x128x128 | 26.75 | 37.38 | 37.66 | 37.74 | 38.17 |\n| 3 | 2 | 4x128x128x128 | 23.28 | 85.91 | 86.77 | 87.39 | 89.54 |\n| 3 | 4 | 4x128x128x128 | 23.83 | 167.83 | 169.41 | 170.30 | 173.47 |\n\nFP32\n \n| Dimension | Batch size |Resolution| Throughput Avg [img/s] | Latency Avg [ms] | Latency 90% [ms] | Latency 95% [ms] | Latency 99% [ms] |\n|:----------:|:---------:|:-------------:|:----------------------:|:----------------:|:----------------:|:----------------:|:----------------:|\n| 2 | 64 | 4x192x160 | 1007.91 | 63.50 | 63.93 | 64.03 | 64.19 |\n| 2 | 128 | 4x192x160 | 812.08 | 157.62 | 159.02 | 159.72 | 161.24 |\n| 3 | 1 | 4x128x128x128 | 8.23 | 121.45 | 122.84 | 123.93 | 124.69 |\n| 3 | 2 | 4x128x128x128 | 8.42 | 237.65 | 239.90 | 240.60 | 242.85 |\n| 3 | 4 | 4x128x128x128 | 8.37 | 478.01 | 482.70 | 483.43 | 484.84 |\n\nThroughput is reported in images per second. Latency is reported in milliseconds per batch.\nTo achieve these same results, follow the steps in the [Quick Start Guide](#quick-start-guide).","hasPerformance","policies",[],{"_188":211,"_190":212,"_149":-5,"_157":26,"_160":26,"_174":210,"_161":65},{"_188":209,"_190":209,"_149":-5,"_157":26,"_160":26,"_174":210,"_161":65},{"_188":207,"_190":207,"_149":-5,"_157":26,"_160":26,"_174":208,"_161":65},{"_188":205,"_190":205,"_149":-5,"_157":26,"_160":26,"_174":206,"_161":65},{"_188":14,"_190":14,"_149":-5,"_157":26,"_160":26,"_174":204,"_161":65},{"_188":202,"_190":202,"_149":-5,"_157":26,"_160":26,"_174":203,"_161":65},{"_188":200,"_190":200,"_149":-5,"_157":26,"_160":26,"_174":201,"_161":65},{"_188":198,"_190":198,"_149":-5,"_157":26,"_160":26,"_174":199,"_161":65},{"_188":196,"_190":196,"_149":-5,"_157":26,"_160":26,"_174":197,"_161":65},{"_188":194,"_190":194,"_149":-5,"_157":26,"_160":26,"_174":195,"_161":65},{"_188":192,"_190":192,"_149":-5,"_157":26,"_160":26,"_174":193,"_161":65},{"_188":189,"_190":189,"_149":-5,"_157":26,"_160":26,"_174":191,"_161":65},"id","20.12.0","name",[],"21.02.0",[],"21.02.2",[],"21.02.3",[],"21.02.4",[],"21.02.5",[],"21.02.6",[],[],"21.02.7",[],"21.02.9",[],"21.11.0",[],"-","Latest (21.11.0)","nvidia/nnunet_for_pytorch","key","nvidia/resources/nnunet_for_pytorch","resourceId","nnunet_for_pytorch","shortDescription","An optimized, robust and self-adapting framework for U-Net based medical image segmentation","The nnU-Net (\"no-new-Net\") refers to a robust and self-adapting framework for U-Net based medical image segmentation. This repository contains a nnU-Net implementation as described in the paper: [nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation](https://arxiv.org/abs/1809.10486). \n\nThe differences between this nnU-net and [original model](https://github.com/MIC-DKFZ/nnUNet) are:\n- Dynamic selection of patch size is not supported, and it has to be set in `data_preprocessing/configs.py` file.\n- Cascaded U-Net is not supported.\n- The following data augmentations are not used: rotation, simulation of low resolution, gamma augmentation.\n\nThis model is trained with mixed precision using Tensor Cores on Volta, Turing, and the NVIDIA Ampere GPU architectures. Therefore, researchers can get results 2x faster than training without Tensor Cores, while experiencing the benefits of mixed precision training. This model is tested against each NGC monthly container release to ensure consistent accuracy and performance over time.\n\nWe developed the model using [PyTorch Lightning](https://www.pytorchlightning.ai), a new easy to use framework that ensures code readability and reproducibility without the boilerplate.\n\n### Model architecture\n \nThe nnU-Net allows training two types of networks: 2D U-Net and 3D U-Net to perform semantic segmentation of 3D images, with high accuracy and performance.\n\nThe following figure shows the architecture of the 3D U-Net model and its different components. U-Net is composed of a contractive and an expanding path, that aims at building a bottleneck in its centremost part through a combination of convolution, instance norm and leaky relu operations. After this bottleneck, the image is reconstructed through a combination of convolutions and upsampling. Skip connections are added with the goal of helping the backward flow of gradients in order to improve the training.\n\n

\n \n*Figure 1: The 3D U-Net architecture*\n\n### Default configuration\n\nAll convolution blocks in U-Net in both encoder and decoder are using two convolution layers followed by instance normalization and a leaky ReLU nonlinearity. For downsampling we are using stride convolution whereas transposed convolution for upsampling.\n\nAll models were trained with Adam optimizer. For loss function we use the average of [cross-entropy](https://en.wikipedia.org/wiki/Cross_entropy) and [dice coefficient](https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient).\n\nEarly stopping is triggered if validation dice score wasn't improved during the last 100 epochs.\n\nUsed data augmentation: crop with oversampling the foreground class, mirroring, zoom, Gaussian noise, Gaussian blur, brightness, contrast.\n\n### Feature support matrix\n\nThe following features are supported by this model: \n\n| Feature | nnUNet \n|-----------------------|-------------------------- \n|[DALI](https://docs.nvidia.com/deeplearning/dali/release-notes/index.html) | Yes\n|Automatic mixed precision (AMP) | Yes \n|Distributed data parallel (DDP) | Yes\n \n#### Features\n\n**DALI**\n\nNVIDIA DALI - DALI is a library accelerating data preparation pipeline. To accelerate your input pipeline, you only need to define your data loader\nwith the DALI library. For details, see example sources in this repository or see the [DALI documentation](https://docs.nvidia.com/deeplearning/dali/index.html)\n\n**Automatic Mixed Precision (AMP)**\n\nThis implementation uses native PyTorch AMP implementation of mixed precision training. It allows us to use FP16 training with FP32 master weights by modifying just a few lines of code.\n\n**DistributedDataParallel (DDP)**\n\nThe model uses PyTorch Lightning implementation of distributed data parallelism at the module level which can run across multiple machines.\n \n### Mixed precision training\n\nMixed precision is the combined use of different numerical precisions in a computational method. [Mixed precision](https://arxiv.org/abs/1710.03740) training offers significant computational speedup by performing operations in half-precision format, while storing minimal information in single-precision to retain as much information as possible in critical parts of the network. Since the introduction of [Tensor Cores](https://developer.nvidia.com/tensor-cores) in Volta, and following with both the Turing and Ampere architectures, significant training speedups are experienced by switching to mixed precision -- up to 3x overall speedup on the most arithmetically intense model architectures. Using mixed precision training requires two steps:\n\n1. Porting the model to use the FP16 data type where appropriate.\n2. Adding loss scaling to preserve small gradient values.\n\nThe ability to train deep learning networks with lower precision was introduced in the Pascal architecture and first supported in [CUDA 8](https://devblogs.nvidia.com/parallelforall/tag/fp16/) in the NVIDIA Deep Learning SDK.\n\nFor information about:\n* How to train using mixed precision, see the [Mixed Precision Training](https://arxiv.org/abs/1710.03740) paper and [Training With Mixed Precision](https://docs.nvidia.com/deeplearning/performance/mixed-precision-training/index.html) documentation.\n* Techniques used for mixed precision training, see the [Mixed-Precision Training of Deep Neural Networks](https://devblogs.nvidia.com/mixed-precision-training-deep-neural-networks/) blog.\n* APEX tools for mixed precision training, see the [NVIDIA Apex: Tools for Easy Mixed-Precision Training in PyTorch](https://devblogs.nvidia.com/apex-pytorch-easy-mixed-precision-training/).\n\n#### Enabling mixed precision\n \nFor training and inference, mixed precision can be enabled by adding the `--amp` flag. Mixed precision is using [native PyTorch implementation](https://pytorch.org/blog/accelerating-training-on-nvidia-gpus-with-pytorch-automatic-mixed-precision/).\n\n#### TF32\n\nTensorFloat-32 (TF32) is the new math mode in [NVIDIA A100](https://www.nvidia.com/en-us/data-center/a100/) GPUs for handling the matrix math also called tensor operations. TF32 running on Tensor Cores in A100 GPUs can provide up to 10x speedups compared to single-precision floating-point math (FP32) on Volta GPUs. \n\nTF32 Tensor Cores can speed up networks using FP32, typically with no loss of accuracy. It is more robust than FP16 for models which require high dynamic range for weights or activations.\n\nFor more information, refer to the [TensorFloat-32 in the A100 GPU Accelerates AI Training, HPC up to 20x](https://blogs.nvidia.com/blog/2020/05/14/tensorfloat-32-precision-format/) blog post.\n\nTF32 is supported in the NVIDIA Ampere GPU architecture and is enabled by default.\n\n### Glossary\n\n**Test time augmentation**\n\nTest time augmentation is an inference technique which averages predictions from augmented images with its prediction. As a result, predictions are more accurate, but with the cost of slower inference process. For nnU-Net, we use all possible flip combinations for image augmenting. 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We and our advertising partners will use this information to make our websites and the advertising displayed on it, more relevant to your interests.",5,[491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528],[367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384],{"_385":486,"_221":486,"_147":387,"_357":487},{"_385":482,"_221":482,"_147":387,"_357":483},{"_385":477,"_221":477,"_147":387,"_357":478},{"_385":473,"_221":473,"_147":387,"_357":474},{"_385":468,"_221":468,"_147":387,"_357":469},{"_385":463,"_221":463,"_147":387,"_357":464},{"_385":456,"_221":456,"_147":387,"_357":457},{"_385":448,"_221":448,"_147":387,"_357":449},{"_385":443,"_221":443,"_147":387,"_357":444},{"_385":438,"_221":438,"_147":387,"_357":439},{"_385":430,"_221":430,"_147":387,"_357":431},{"_385":425,"_221":425,"_147":387,"_357":426},{"_385":420,"_221":420,"_147":387,"_357":421},{"_385":415,"_221":415,"_147":387,"_357":416},{"_385":408,"_221":408,"_147":387,"_357":409},{"_385":403,"_221":403,"_147":387,"_357":404},{"_385":396,"_221":396,"_147":387,"_357":397},{"_385":386,"_221":386,"_147":387,"_357":388},"hostName","amazon-adsystem.com","",[389,390],{"_190":395,"_392":386,"_393":26,"_147":394},{"_190":391,"_392":386,"_393":26,"_147":394},"ad-privacy","host","isSession","This domain is owned by online retailer Amazon and is used as part of its affiliate marketing programme.","ad-id","doubleclick.net",[398,399],{"_190":402,"_392":396,"_393":26,"_147":401},{"_190":400,"_392":396,"_393":26,"_147":401},"IDE","This domain is owned by Doubleclick (Google). 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It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","_uetsid","This cookie is used by Bing to determine what ads should be shown that may be relevant to the end user perusing the site. ","ai-podcast.nvidia.com","kndctr_F207D74D549850760A4C98C6_AdobeOrg_bc_session_id","ttcsid_XXXXXXXXXXXXXXXXXXXXCategory","This cookie name is associated with TikTok which is used to track your activity on the platform, including how you interact with their embedded services on other websites.This cookie is associated with TikTok. It helps track your activity on the platform, including how you interact with their embedded services on other websites.","_fbp","Used by Facebook to deliver a series of advertisement products such as real time bidding from third party advertisers","research.nvidia.com","_twpid","_gat_gtag_UA_141699104_1","_gat_gtag_UA_53775284_6","This cookie is typically associated with the use of Taptap Digital, a company specializing in digital advertising. It is used for tracking and ad personalization purposes.","_tt_enable_cookie","This cookie name is associated with TikTok which is used to collect data about behavior and purchases on the website and to measure the effect of advertising. It is also used to track website activity to help optimize advertising efforts.","AMCV_xxxxxAdobeOrg","This cookie is used to identify a unique visitor for tracking purposes by Adobe Experience Cloud.This is a pattern type cookie name associated with Adobe Marketing Cloud. It stores a unique visitor identifier, and uses an organisation identifier to allow a company to track users across their domains and services.","ttcsid","This cookie name is associated with TikTok which is used to enable TikTok Ads session tracking by assigning a unique session ID to users who click on TikTok ads, allowing for the attribution of user behavior and conversions within the same session.This cookie is associated with TikTok. It helps track your activity on the platform, including how you interact with their embedded services on other websites.","C0003","Personalization Cookies","These cookies collect data about how you have interacted with our website to help us improve your web experience, such as which pages you have visited. These cookies may store a unique ID so that our system will remember you when you return. They may be set by us or by third party providers whose services we have added to our pages. These cookies enable us to provide enhanced website functionality and personalization as well as make the marketing messages we send to you more relevant to your interests. If you do not allow these cookies, then some or all of these services may not function properly.",4,[617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647],[583,584,585,586,587,588],{"_385":468,"_221":468,"_147":387,"_357":612},{"_385":443,"_221":443,"_147":387,"_357":607},{"_385":602,"_221":602,"_147":387,"_357":603},{"_385":597,"_221":597,"_147":387,"_357":598},{"_385":593,"_221":593,"_147":387,"_357":594},{"_385":589,"_221":589,"_147":387,"_357":590},"nvcrm.my.site.com",[591],{"_190":592,"_392":589,"_393":26,"_147":387},"BrowserId","nvidia.partners",[595],{"_190":596,"_392":593,"_393":26,"_147":429},"edge","app.hushly.com",[599],{"_190":600,"_392":597,"_393":26,"_147":601},"*CORS","This domain is associated with Hushly, a platform that provides lead conversion solutions for content marketing by using personalization and content engagement strategies.","github.com",[604],{"_190":605,"_392":602,"_393":26,"_147":606},"_octo","This domain is owned by Github. 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These cookies may store a unique ID so that our system will remember you when you return. 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