Creating AI Pipeline for Cell Image Analysis: Insights, Challenges, and CHO Use Case (Part 1 of 2, Intel Edge AI in the Realm of Biopharma and Drug Development)

Authors: Nikita Savelyev, Alexander Kozlov, Ekaterina Aidova, Maxim Proshin

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Introduction

Whisper is a general-purpose speech recognition model from OpenAI. The model can transcribe speech across dozens of languages and even handle poor audio quality or excessive background noise. You can find more information about this model in the research paper, OpenAI blog, model card and GitHub repository.

Recently, a distilled variant of the model called Distil-Whisper has been proposed in the paper Robust Knowledge Distillation via Large-Scale Pseudo Labelling. Compared to Whisper, Distil-Whisper runs several times faster with 50% fewer parameters, while performing to within 1% word error rate (WER) on out-of-distribution evaluation data.

Whisper is a Transformer-based encoder-decoder model, also referred to as a sequence-to-sequence model. It maps a sequence of audio spectrogram features to a sequence of text tokens. First, the raw audio inputs are converted to a log-Mel spectrogram by action of the feature extractor. Then, the Transformer encoder encodes the spectrogram to form a sequence of encoder hidden states. Finally, the decoder autoregressively predicts text tokens, conditional on both the previous tokens and the encoder's hidden states.

You can see the model architecture in the diagram below:

In this article, we would like to demonstrate how to improve Whisper and Distil-Whisper inference speed with OpenVINO for Intel hardware. Additionally, we show how to make models even faster by applying 8-bit Post-training Quantization with Neural Network Compression Framework (NNCF). In the end we present evaluation results from accuracy and performance standpoints on a large-scale dataset.

All code snippets presented in this article are from the Automatic speech recognition using Distil-Whisper and OpenVINO Jupyter notebook, so you can follow along.

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Converting Model to OpenVINO format

We are going to load models from Hugging Face Hub with the help of Optimum Intel library which makes it easier to load and run OpenVINO-optimized models. For more details, pleaes refer to the Hugging Face Optimum documentation.

For example, the following code loads the Distil-Whisper large-v2 model ready for inference with OpenVINO.

from optimum.intel.openvino import OVModelForSpeechSeq2Seq

model_id = "distil-whisper/distil-large-v2"
model_path = Path(model_id)
if not model_path.exists():
    ov_model = OVModelForSpeechSeq2Seq.from_pretrained(
        model_id, export=True, compile=False, load_in_8bit=False)
    ov_model.half()
    ov_model.save_pretrained(model_path)
else:
    ov_model = OVModelForSpeechSeq2Seq.from_pretrained(
        model_path, compile=False)

Models from the Distil-Whisper family are available at Distil-Whisper Models collection and Whisper models are available at OpenAI Hugging Face page.

To transcribe an input audio with the loaded model, we first compile the model to the device of choice and then call generate() method on input features prepared by corresponding processor.

from transformers import AutoProcessor

processor = AutoProcessor.from_pretrained(model_id)

ov_model.to("AUTO")
ov_model.compile()

# ... load input audio and reference text
input_features = processor(input_audio).input_features
predicted_ids = ov_model.generate(input_features)
transcription = processor.batch_decode(predicted_ids, skip_special_tokens=True)[0]
print(f"Reference: {reference_text}")
print(f"Result: {transcription}")

The output is the following. As you can see the transcription equals the reference text.

Reference: MISTER QUILTER IS THE APOSTLE OF THE MIDDLE CLASSES AND WE ARE GLAD TO WELCOME HIS GOSPEL
Result:  Mr. Quilter is the apostle of the middle classes, and we are glad to welcome his gospel.

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Running Post-Training Quantization with NNCF

NNCF enables post-training quantization by adding quantization layers into the model graph and then using a subset of the training dataset to initialize parameters of these additional quantization layers. During quantization, some layers (e.g., MatMuls, Convolutions) are transformed to be executed in INT8 instead of FP16/FP32. If a quantized operation is parameterized then its corresponding weight variable is also converted to INT8.

In general, the optimization process contains the following steps:

1. Create a calibration dataset for quantization.
2. Run nncf.quantize() to obtain quantized encoder and decoder models.
3. Serialize the INT8 models using openvino.save_model() function.

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Whisper model consists of an encoder and decoder submodels. Furthermore, for the decoder model its forward() signature is different for the first call compared to all subsequent calls. During the first call, key-value cache is empty and is not needed for decoder inference. Starting from the second call, key-value cache is fed to the decoder. Because of this, these two cases are represented by two separate OpenVINO models: openvino_decoder_model.xml and openvino_decoder_with_past_model.xml. Since the first decoder model is inferred only once it does not make much sense to quantize it. So, we apply quantization to the encoder and the decoder with past models.

The first step towards quantization is collecting calibration data. For that, we need to collect some number of model inputs for both models. To do that, we patch OpenVINO model request objects with an InferRequestWrapper class instance that will intercept model inputs during inference and store them in a list. We infer the model on about 50 samples from validation split of librispeech_asr dataset.

def collect_calibration_dataset(ov_model: OVModelForSpeechSeq2Seq, calibration_dataset_size: int):
    # Overwrite model request properties, saving the original ones for restoring later
    original_encoder_request = ov_model.encoder.request
    original_decoder_with_past_request = ov_model.decoder_with_past.request
    encoder_calibration_data = []
    decoder_calibration_data = []
    ov_model.encoder.request = InferRequestWrapper(original_encoder_request, encoder_calibration_data)
    ov_model.decoder_with_past.request = InferRequestWrapper(original_decoder_with_past_request,
                                                             decoder_calibration_data)

    calibration_dataset = load_dataset("librispeech_asr", "clean", split="validation", streaming=True)
    for sample in islice(calibration_dataset, calibration_dataset_size):
        input_features = extract_input_features(sample)
        ov_model.generate(input_features)

    ov_model.encoder.request = original_encoder_request
    ov_model.decoder_with_past.request = original_decoder_with_past_request

    return encoder_calibration_data, decoder_calibration_data

With the collected calibration data for encoder and decoder models we can proceed to quantization itself. Let's examine the quantization call for the encoder model. For the decoder model, it is similar.

quantized_encoder = nncf.quantize(
    ov_model.encoder.model,                     # ov.Model object of the encoder model
    nncf.Dataset(encoder_calibration_data),     # calibration data wrapped in a nncf.Dataset object
    subset_size=len(encoder_calibration_data),  # number of samples to calibrate on (all are chosen)
    model_type=nncf.ModelType.TRANSFORMER,      # providing the information that Whisper encoder is of
    # a Transformer architecture
    advanced_parameters=nncf.AdvancedQuantizationParameters(smooth_quant_alpha=0.50)    # Smooth Quant 
    # algorithm reduces activation quantization error; optimal alpha was obtained through grid search
)
ov.save_model(quantized_encoder, quantized_model_path / "openvino_encoder_model.xml")

After both models are quantized and saved, the quantized Whisper model can be loaded and run the same way as shown previously. Comparing the transcriptions produced by original and quantized models results in the following.

Original :  Mr. Quilter is the apostle of the middle classes, and we are glad to welcome his gospel.
Quantized:  Mr. Quilter is the apostle of the middle classes, and we are glad to welcome his gospel.

As you can see for the quantized distil-whisper-large-v2 transcription is the same.

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Evaluating on Common Voice Dataset

We evaluate Whisper and Distil-Whisper large-v2 model variants on a Common Voice 13.0 speech-to-text dataset. We use en/test split containing 16372 audio samples amounting to about 27 hours of recordings.

The evaluation is done across three model types: original PyTorch model, original OpenVINO model and quantized OpenVINO model. Additionally, we run tests on three Intel CPUs: Cascade Lake Intel(R) Core(TM) i9-10980XE, Ice Lake Intel(R) Xeon(R) Gold 6338 and Sapphire Rapids Intel(R) Xeon(R) Gold 6430L.

For all combinations above we measure transcription time and accuracy. When measuring time for a model we sum up generate() call durations for all audio samples. Transcription accuracy is represented as Accuracy = (100 - WER), WER stands for Word Error Rate. We compute accuracy for each audio sample and then take the average value across the dataset. The results are given in the table below.

Please note that we report transcription time in relative terms such that the values for each CPU are normalized over its corresponding column. The duration of audio data in the dataset is 27.06 hours and the absolute transcription time values for Whisper large-v2 PyTorch on each CPU are:

• 20.35 hours for Core i9-10980XE
• 14.09 hours for Xeon Gold 6338
• 15.03 hours for Xeon Gold 6430L

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Based on the results we can conclude that:

1. OpenVINO models execute 1.4x - 5.1x faster than PyTorch models with pretty much the same accuracy across all cases.
2. When compared to original PyTorch models, quantized OpenVINO models provide 2.1x - 6.1x performance boost with 1-2% accuracy drop.

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NOTE: in terms of this article we focus on presenting performance values. Accuracy of quantized models can be improved with a more careful selection of calibration data.

Notices and Disclaimers:

Performance varies by use, configuration, and other factors. Learn more at www.intel.com/PerformanceIndex. Performance results are based on testing as of dates shown in configurations and may not reflect all publicly available updates. No product or component can be absolutely secure. Intel technologies may require enabled hardware, software or service activation.

The products described may contain design defects or errors known as errata which may cause the product to deviate from published specifications. Current characterized errata are available on request.

Test Configuration: Intel® Core™ i9-10980XE CPU Processor at 3.00GHz with DDR4 128 GB at 3000MHz, OS: Ubuntu 20.04.3 LTS; Intel® Xeon® Gold 6338 CPU Processor at 2.00GHz with DDR4 256 GB at 3200MHz, OS: Ubuntu 20.04.3 LTS; Intel® Xeon® Gold 6430L CPU Processor at 1.90GHz with DDR5 1024 GB at 4800MHz, OS: Ubuntu 20.04.6 LTS. Testing was performed using distil-whisper-asr notebook for model export and whisper evaluation notebook for model evaluation.

The test was conducted by Intel in December 2023.

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Conclusion

We demonstrated how to load and run Whisper and Distil-Whisper models for audio transcription task with OpenVINO and Optimum Intel, and how to perform INT8 post-training quantization of these models with NNCF. Further we evaluated these models on a large scale speech-to-text dataset across multiple CPU devices. The evaluation results show a significant performance boost of OpenVINO vs PyTorch models without loss of transcription quality, and even a larger boost with a tolerable accuracy drop when we apply INT8 quantization.

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Introduction

Latent Consistency Models (LCMs) is the next generation of generative models after Latent Diffusion Models (LDMs). While Latent Diffusion Models (LDMs) like Stable Diffusion are capable of achieving the outstanding quality of generation, they often suffer from the slowness of the iterative image denoising process. LCM is an optimized version of LDM. Inspired by Consistency Models (CM), Latent Consistency Models (LCMs) enabled swift inference with minimal steps on any pre-trained LDMs, including Stable Diffusion. The Consistency Models is a new family of generative models that enables one-step or few-step generation. More details about the proposed approach and models can be found using the following resources: project page, paper, original repository.

This article will demonstrate a C++ application of the LCM model with Intel’s OpenVINO™ C++ API on Linux systems. For model inference performance and accuracy, the C++ pipeline is well aligned with the Python implementation.

The full implementation of the LCM C++ demo described in this post is available on the GitHub: openvino.genai/lcm_dreamshaper_v7.

Model Conversion

To leverage efficient inference with OpenVINO™ runtime on Intel platforms, the original model should be converted to OpenVINO™ Intermediate Representation (IR).

LCM model

Optimum Intel can be used to load SimianLuo/LCM_Dreamshaper_v7 model from Hugging Face Hub and convert PyTorch checkpoint to the OpenVINO™ IR on-the-fly, by setting export=True when loading the model, like:

from optimum.intel.openvino import OVLatentConsistencyModelPipeline

model = OVLatentConsistencyModelPipeline.from_pretrained("SimianLuo/LCM_Dreamshaper_v7", export=True)
model.save_pretrained("ov_lcm_model")

Tokenizer

OpenVINO Tokenizers is an extension that adds text processing operations to OpenVINO Inference Engine. In addition, the OpenVINO Tokenizers project has a tool to convert a HuggingFace tokenizer into OpenVINO IR model tokenizer and detokenizer: it provides the convert_tokenizer function that accepts a tokenizer Python object and returns an OpenVINO Model object:

from transformers import AutoTokenizer
from openvino_tokenizers import convert_tokenizer
from openvino import compile_model, save_model

hf_tokenizer = AutoTokenizer.from_pretrained(tokenizer_path)
ov_tokenizer_encoder = convert_tokenizer(hf_tokenizer)
save_model(ov_tokenizer_encoder, "ov_tokenizer.xml")

Note: Currently OpenVINO Tokenizers can be inferred on CPU devices only.

Conversion step

You can find the full script for model conversion at the original repo.

Note: The tutorial assumes that the current working directory is and <openvino.genai repo>/image_generation/lcm_ dreamshaper_v7/cpp all paths are relative to this folder.

Let’s prepare a Python environment and install dependencies:

conda create -n openvino_lcm_cpp python==3.10
conda activate openvino_lcm_cpp
conda install -c conda-forge 'openvino>=2023.3.0'
python -m pip install -r scripts/requirements.txt
python -m pip install ../../../thirdparty/openvino_contrib/modules/custom_operations/[transformers]

Now we can use the script scripts/convert_model.py to download and convert models:

cd scripts
python convert_model.py -lcm "SimianLuo/LCM_Dreamshaper_v7" -t FP16

C++ Pipeline

Pipeline flow

Let’s now talk about the logical structure of the LCM model pipeline.

Just like the classic Stable Diffusion pipeline, the LCM pipeline consists of three important parts:
- A text encoder to create a condition to generate an image from a text prompt.
- U-Net for step-by-step denoising the latent image representation.
- Autoencoder (VAE) for decoding the latent space to an image.

The pipeline takes a latent image representation and a text prompt transformed to text embedding via CLIP’s text encoder as an input. The initial latent image representation is generated using random noise generator. LCM uses a guidance scale for getting time step conditional embeddings as input for the diffusion process, while in Stable Diffusion, it used for scaling output latents.

Next, the U-Net iteratively denoises the random latent image representations while being conditioned on the text embeddings. The output of the U-Net, being the noise residual, is used to compute a denoised latent image representation via a scheduler algorithm. LCM introduces its own scheduling algorithm that extends the denoising procedure introduced by denoising diffusion probabilistic models (DDPMs) with non-Markovian guidance. The denoising process is repeated for a given number of times to step-by-step retrieve better latent image representations. When complete, the latent image representation is decoded by the decoder part of the variational auto encoder.

The C++ implementations of the scheduler algorithm and LCM pipeline are available at the following links: LCM Scheduler, LCM Pipeline.

LoRA support

LoRA (Low-Rank Adaptation) is a training technique for fine-tuning Stable Diffusion models. There are various LoRA models available on https://civitai.com/tag/lora.

The main idea for LoRA weights enabling, is to append weights onto the OpenVINO LCM models at runtime before compiling the Unet/text_encoder model. The method is to extract LoRA weights from safetensors file, find the corresponding weights in Unet/text_encoder model and insert the LoRA bias weights. The common approach to add LoRA weights looks like:

The original LoRA safetensor model is loaded via safetensors.h. The layer name and weight of LoRA are modified with Eigen Lib and inserted into Unet/text_encoder OpenVINO model using ov::pass::MatcherPass - you can see the implementation in the file common/diffusers/src/lora.cpp.

To run the LCM demo with the LoRA model, first download LoRA, for example: LoRa/Soulcard.

Build and Run LCM demo

Let’s start with the dependencies installation:‍

conda activate openvino_lcm_cpp
conda install -c conda-forge eigen c-compiler cxx-compiler make

Now we can build the application:

cmake -DCMAKE_BUILD_TYPE=Release -S . -B build
cmake --build build --config Release --parallel
cd build

‍‍And finally we’re ready to run the LCM demo. By default the positive prompt is set to: “a beautiful pink unicorn”.

Please note, that the quality of the resulting image depends on the quality of the random noise generator, so there is a difference for output images generated by the C++ noise generator and the PyTorch generator. Use oprion -r to read the PyTorch generated noise from the provided textfiles for the alignment with Python pipeline.
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Note: Run ./lcm_dreamshaper -h to see all the available demo options

Let’s try to run the application in a few modes:

Read the numpy latent input and noise for scheduler instead of C++ std lib for the alignment with Python pipeline: ./lcm_dreamshaper -r‍

Generate image with C++ std lib generated latent and noise : ./lcm_dreamshaper

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Generate image with Soulcard LoRa and C++ generated latent and noise: ./lcm_dreamshaper -r -l path/to/soulcard.safetensors

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See Also

1. Optimizing Latent Consistency Model for Image Generation with OpenVINO™ and NNCF
2. Image generation with Latent Consistency Model and OpenVINO
3. C++ Pipeline for Stable Diffusion v1.5 with Pybind for Lora Enabling
4. Enable LoRA weights with Stable Diffusion Controlnet Pipeline

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Authors: Fiona Zhao, Xiake Sun, Su Yang

The purpose is to demonstrate the use of C++ native OpenVINO API.

For model inference performance and accuracy, the pipelines of C++ and python are well aligned.

Source code github: OV_SD_CPP.

Step 1: Prepare Environment

Setup in Linux:

C++ pipeline loads the Lora safetensors via Pybind

conda create -n SD-CPP python==3.10
conda activate SD-CPP
conda install numpy safetensors pybind11 

C++ Dependencies:

• OpenVINO: Tested with OpenVINO 2023.1.0.dev20230811 pre-release
• Boost: Install with sudo apt-get install libboost-all-dev for LMSDiscreteScheduler's integration
• OpenCV: Install with sudo apt install libopencv-dev for image saving

Notice:

SD Preparation in two steps above could be auto implemented with build_dependencies.sh in the scripts directory.

cd scripts
chmod +x build_dependencies.sh
./build_dependencies.sh

Step 2: Prepare SD model and Tokenizer Model

• SD v1.5 model:

Refer this link to generate SD v1.5 model, reshape to (1,3,512,512) for best performance.

With downloaded models, the model conversion from PyTorch model to OpenVINO IR could be done with script convert_model.py in the scripts directory.

python -m convert_model.py -b 1 -t <INT8|FP16|FP32> -sd Path_to_your_SD_model

Lora enabling with safetensors, refer this blog.

SD model dreamlike-anime-1.0 and Lora soulcard are tested in this pipeline.

• Tokenizer model:

1. The script convert_sd_tokenizer.py in the scripts dir could serialize the tokenizer model IR
2. Build OpenVINO extension:

git clone https://github.com/apaniukov/openvino_contrib/  -b tokenizer-fix-decode

Refer to PR OpenVINO custom extension ( new feature still in experiments )

3. read model with extension in the SD pipeline

Step 3: Build Pipeline

source /Path_to_your_OpenVINO_package/setupvars.sh
conda activate SD-CPP
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

Step 4: Run Pipeline

./SD-generate -p <posPromp> -n <negPrompt> -d <device> -s <seed> --height <output image> --width <output image> --log <use logger> -c <use cache> -e <useOVExtension> -r <readNPLatent> -m <modelPath> -t <type of model IR> -l <lora.safetensors> -a <alpha> -h <help>

Usage: OV_SD_CPP [OPTION...]

• -p, --posPrompt arg Initial positive prompt for SD (default: cyberpunk cityscape like Tokyo New York with tall buildings at dusk golden hour cinematic lighting)
• -n, --negPrompt arg Default negative prompt is empty with space (default: )
• -d, --device arg AUTO, CPU, or GPU (default: CPU)
• -s, --seed arg Number of random seed to generate latent (default: 42)
• --height arg height of output image (default: 512)
• --width arg width of output image (default: 512)‍
• --log arg Generate logging into log.txt for debug
• -c, --useCache Use model caching
• -e, --useOVExtension Use OpenVINO extension for tokenizer‍
• -r, --readNPLatent Read numpy generated latents from file‍
• -m, --modelPath arg Specify path of SD model IR (default: /YOUR_PATH/SD_ctrlnet/dreamlike-anime-1.0)‍
• -t, --type arg Specify precision of SD model IR (default: FP16_static)‍
• -l, --loraPath arg Specify path of lora file. (*.safetensors). (default: /YOUR_PATH/soulcard.safetensors)‍
• -a, --alpha arg alpha for lora (default: 0.75)
• -h, --help Print usage

Example:

Positive prompt: cyberpunk cityscape like Tokyo New York with tall buildings at dusk golden hour cinematic lighting.

Negative prompt: (empty, here couldn't use OV tokenizer, check the issues for details).

Read the numpy latent instead of C++ std lib for the alignment with Python pipeline.

• Generate image without lora

./SD-generate -r -l ""

• Generate image with Soulcard Lora

./SD-generate -r

• Generate the debug logging into log.txt

./SD-generate --log

Benchmark:

The performance and image quality of C++ pipeline are aligned with Python.

To align the performance with Python SD pipeline, C++ pipeline will print the duration of each model inferencing only.

For the diffusion part, the duration is for all the steps of Unet inferencing, which is the bottleneck.

For the generation quality, be careful with the negative prompt and random latent generation.

Limitation:

• Pipeline features:

- Batch size 1
- LMS Discrete Scheduler
- Text to image

• Program optimization: now parallel optimization with std::for_each only and add_compile_options(-O3 -march=native -Wall) with CMake
• The pipeline with INT8 model IR not improve the performance
• Lora enabling only for FP16

• Random generation fails to align, C++ random with MT19937 results is differ from numpy.random.randn(). Hence, please use -r, --readNPLatent for the alignment with Python
• OV extension tokenizer cannot recognize the special character, like “.”, ”,”, “”, etc. When write prompt, need to use space to split words, and cannot accept empty negative prompt. So use default tokenizer without config -e, --useOVExtension, when negative prompt is empty

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Setup in Windows 10 with VS2019:

1. Python env: Setup Conda env SD-CPP with the anaconda prompt terminal

2. C++ dependencies:

• OpenVINO and OpenCV:

Download and setup Environment Variable: add the path of bin and lib (System Properties -> System Properties -> Environment Variables -> System variables -> Path )

• Boost:

- Download from sourceforge

- Unzip

- Setup: bootstrap.bat

- Build: b2.exe

- Install: b2.exe install

Installed boost in the path C:/Boost, add CMakeList with "SET(BOOST_ROOT"C:/Boost")"

3. Setup of conda env SD-CPP and Setup OpenVINO with setupvars.bat

4. CMake with build.bat like:

rmdir /Q /S build
mkdir build
cd build
cmake -G "Visual Studio 16 2019" -A x64 ^
 -DCMAKE_BUILD_TYPE=Release ^
      ..
cmake --build . --config Release
cd ..

5. Setup of Visual Studio with release and x64, and build: open .sln file in the build Dir

6. Run the SD_generate.exe

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