Encrypt Your Dataset and Train Your Model with It Directly

In the ever-evolving landscape of biopharmaceutical technology and drug development, a recent effort in the field of Cell Analytics for Monoclonal Antibody Production has shed light on the crucial role of Edge AI Technology in navigating complex challenges of scaling and producing solutions.  

In this 2-part blog series, we will explore the use of Intel Edge AI Technology in biopharma and drug development, addressing challenges and providing insights into the development of AI pipelines for cell segmentation and analysis.

Intel has been involved in this process with a variety of partners. One of Intel’s contributions to the cell image project centers around processing brightfield¹ images using an AI pipeline containing multiple deep learning models. The pipeline's purpose is to identify cells and other biological components and provide feedback on dynamic biological characteristics such as cell morphology, viability, and phenotypic changes, among others. Throughout this process, working on cell-AI projects usually brings a unique set of challenges to the forefront.  

First, it is an interdisciplinary field and the knowledge gap between data scientists and biopharma experts requires more back-and-forth clear communications for planning and validity checks. Frequently when attempting to implement AI solutions in the laboratory, data scientists and bench scientists struggle to fully grasp the nature and needs of each other’s role. This lack of mutual understanding can also hinder the usability and scalability of an AI solution needing to be integrated into diverse lab environments.

The second challenge is instrument variability. Different plate reader² microscopes have different hardware, optics, and apertures which cause their produced images not to be consistent. This adds an extra layer of work to assess and address these inconsistencies along the way (like regular tracked calibration and adjustment). Additionally, equipment vendor-to-vendor differences, culture temperature, medium conditions, and genetic modifications can all affect the variability of data and the inherent transferability of the deep learning pipeline. This would drive the need to monitor the performance of DL models at the edge and cloud ML ops components.    

The third challenge is obtaining peer-review labels because the process is based on supervised Machine Learning and obtaining clean accurate labels is very costly and time-consuming.  

And the last challenge is about the model deployment. In most cases, cloud deployment is not an option due to data size and data privacy. Produced images from plate reader microscopes are huge and transferring data to the cloud and sending the results back would create high latency because a huge amount of data must be streamed (30Gb per hour). And more importantly, laboratories are usually not willing to share the data. Due to these two constraints, cloud deployments are not usually an option, and the pipeline must be deployed at the edge.  

Now, let’s talk about a specific application of this technology: the CHO Cell Segmentation Use Case.

CHO Cell Segmentation Use Case

CHO cells, or Chinese Hamster Ovary cells, are a cornerstone in the production of complex protein molecules such as monoclonal antibodies, fusion proteins, hormones, and coagulation factors. Unlike stem cells or CAR-T cells, where the cells themselves are the therapeutic product, in CHO cells, it is the proteins they produce that are of paramount importance. Monitoring the health, viability, and production capability of these cells is a critical step in commercial protein production.

Traditionally, assessing the condition of CHO cells involves a multi-step process that is not only time-consuming but also requires the use of expensive reagents and chemicals. Depending on the process, the workflow can be something like below.  

1. Culture cells  

2. Fix cells – wash in expensive reagents to remove the culture medium.  

3. Permeabilization – wash in more expensive chemicals to permeabilize the cell membrane (to stain for intercellular proteins).

4. Blocking – incubate cells in another expensive reagent to prevent binding of no specific antibodies.

5. Primary Antibody Incubation – antibody specifically to bind to a protein that is being produced.

6. Washing – removing unbound Primary Antibodies using more expensive chemicals.

7. Nuclear staining – use nuclear stain like DAPI to visualize cell nuclei then wash with the same chemicals from the washing step

8. Mounting – get ready to read in the microscope (plate reader¹)

9. Imaging – Stained cells …. count them up and determine the state in the protein production cycle and relative cell health (eventually they peter out and stop producing and the batch needs to be flushed. (Cell count, viability number, etc. are the output not the image)

From culturing to imaging, each step plays a vital role in ensuring the quality of the protein product. However, with the advent of AI and deep learning, there is an opportunity to streamline this workflow significantly. Using an AI pipeline including multiple Deep Learning models and data pre and post-processing, we can go from Step 1 directly to Step 9, removing the majority of the labor and latency in getting actionable results out of a staining workflow and bypassing expensive specialty chemicals requirement. Intel has put together a reference implementation for deploying said pipeline and inferencing of these images on the edge as part of the Cell Image project https://www.cellimage.ie/. OpenVINO Toolkit, OpenVINO Model Server, and AI Connect for Scientific Data are used in this design. Let’s briefly talk about each of these wonderful SW packages in part 2 of this article series. Stay tuned!

Conclusion

In conclusion, the integration of Intel Edge AI Technology into the biopharmaceutical sector represents a transformative step towards more efficient and scalable drug development processes. As we have seen in this first installment of our blog series, the deployment of AI pipelines for cell segmentation and analysis in monoclonal antibody production is not without its challenges. These include bridging the interdisciplinary knowledge gap, managing instrument variability, acquiring peer-reviewed labels, and overcoming the hurdles associated with model deployment.

Despite these challenges, the potential benefits of Edge AI in biopharma are substantial. By leveraging Intel's advanced AI technologies, we can significantly reduce the time and cost associated with traditional cell analysis methods, while also enhancing the accuracy and reliability of the results. The use of edge computing addresses the concerns of data size and privacy, allowing for real-time processing and analysis without the need for cloud transfer.

As we move forward in this blog series, we will delve deeper into the specifics of Intel's Edge AI solutions, including the OpenVINO toolkit, OpenVINO Model Server, and AI Connect for Scientific Data. We will explore how these tools are being applied in real-world scenarios to drive innovation and improve outcomes in the realm of biopharma and drug development in the next part of this series.

Reach out to Intel's Health and Life Sciences team at health.lifesciences@intel.com or learn more about what we do at https://www.intel.com/health.

We'd like to hear from you! Let us know in the comments or discuss – which AI use cases in health and life sciences do you think will have the greatest impact on global health?

If you enjoyed hearing from the Health and Life Sciences team and want to hear more, give this post a like and ensure you subscribe to get the latest updates from the team. 

About the Author

Nooshin Nabizadeh has Ph.D. in Electrical and Computer Engineering from the University of Miami and works at Intel Corporation as AI Solutions Architect. She enjoys photography, writing poetry, reading about psychology and philosophy, and optimizing solutions to run as fast as possible on a given piece of hardware. Connect with her on LinkedIn https://www.linkedin.com/in/nooshin-nabizadeh/ by mentioning this blog.

1. Brightfield microscopy is a widely used technique for observing the morphology of cells and tissues.

2. A plate reader is a laboratory instrument used to obtain images from samples in microtiter plates. The reader shines a specific calibrated frequency of light (UV, visible, fluorescence, etc.) through the samples in the wells of the plate. Plate reader microscopy data sets have inherent variability which drives the requirement of regular tracked calibration and adjustment.

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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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