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6151 update feature highlights (#6571)
part of #6151 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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# What's new in 1.1 🎉🎉
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# What's new in 1.1
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- Digital pathology workflows
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- Experiment management for MONAI bundle

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# What's new in 1.2 🎉🎉
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- Auto3DSeg enhancements and benchmarks
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- nnUNet integration
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- TensorRT-optimized networks
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- MetricsReloaded integration
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- Bundle workflow APIs
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- Modular patch inference
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## Auto3DSeg enhancements and benchmarks
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Auto3DSeg is an innovative solution for 3D medical image segmentation, leveraging the advancements in MONAI and GPUs for algorithm development and deployment.
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Key improvements in this release include:
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- Several new modules to the training pipelines, such as automated GPU-based hyperparameter scaling, early stopping mechanisms, and dynamic validation frequency.
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- Multi-GPU parallelism has been activated for all GPU-related components including data analysis, model training, and model ensemble, to augment overall performance and capabilities.
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- The algorithms were benchmarked for computational efficiency on the TotalSegmentator dataset, containing over 1,000 CT images.
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- Multi-node training is implemented, reducing model training time significantly.
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## nnUNet integration
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The integration introduces a new class, `nnUNetV2Runner`, which leverages Python APIs to facilitate model training, validation,
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and ensemble, thereby simplifying the data conversion process for users.
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Benchmarking results from various public datasets confirm that nnUNetV2Runner performs as expected.
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Users are required to prepare a data list and create an `input.yaml` file to install and use the system.
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The framework also allows automatic execution of the entire nnU-Net pipeline, from model training to ensemble,
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with options to specify the number of epochs. Users can access APIs for training, dataset conversion, data preprocessing, and other components.
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Please check out [the tutorials](https://github.com/Project-MONAI/tutorials/tree/main/nnunet) for more details.
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## TensorRT-optimized networks
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[NVIDIA TensorRT](https://developer.nvidia.com/tensorrt) is an SDK for high-performance deep learning inference,
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includes a deep learning inference optimizer and runtime that delivers low latency and high throughput for inference applications.
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It can accelerate the deep learning model forward computation on the NVIDIA GPU.
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In this release, the `trt_export` API to export the TensorRT engine-based TorchScript model has been integrated into the MONAI bundle.
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Users can try to export bundles with it. A few bundles in the MONAI model zoo,
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like the [spleen_ct_segmentation](https://github.com/Project-MONAI/model-zoo/tree/dev/models/spleen_ct_segmentation)
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and [endoscopic_tool_segmentation](https://github.com/Project-MONAI/model-zoo/tree/dev/models/endoscopic_tool_segmentation) bundles,
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have already been exported and benchmarked. For more details about how to export and benchmark a model,
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please go to this [tutorial](https://github.com/Project-MONAI/tutorials/blob/main/acceleration/TensorRT_inference_acceleration.ipynb).
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## MetricsReloaded integration
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MetricsReloaded - a new recommendation framework for biomedical image analysis validation - is released publicly
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via https://github.com/Project-MONAI/MetricsReloaded. Binary and categorical metrics computing modules are included in this release,
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using MetricsReloaded as the backend. [Example scripts](https://github.com/Project-MONAI/tutorials/tree/main/modules/metrics_reloaded) are made available to demonstrate the usage.
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## Bundle workflow APIs
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`BundleWorkflow` abstracts the typical workflows (such as training, evaluation, and inference) of a bundle with three main interfaces:
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`initialize`, `run`, and `finalize`, applications use these APIs to execute a bundle.
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It unifies the required properties and optional properties for the workflows, downstream applications
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can invoke the components instead of parsing configs with keys.
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In this release, `ConfigWorkflow` class is also created for JSON and YAML config-based bundle workflows for improved Pythonic usability.
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## Modular patch inference
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In patch inference, patches are extracted from the image, the inference is run on those patches, and outputs are merged
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to construct the result image corresponding to the input image. Although depending on the task, model, and computational/memory resources,
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the exact implementations of a patch inference may vary, the overall process of splitting, running inference, and merging the results remains the same.
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In this release, we have created a modular design for patch inference, which defines the overall process while abstracting away the specific
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behavior of how to split the image into patches, how to pre and post process each patch, and how to merge the output patches.

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