Overview / Usage

Introduction

Advancements in genomic sequencing are transforming the landscape of personalized healthcare, making tailored treatments based on individual genetic profiles increasingly attainable. This approach promises significant breakthroughs in disease prevention, optimized drug responses, and precise medical care. However, the analysis of vast and complex genomic datasets poses significant challenges. Traditional machine learning models often struggle with the volume and dimensionality of genomic data, leading to limitations in performance and scalability.

Enter Quantum Neural Networks (QNNs) and Intel’s OpenVINO™ toolkit, two cutting-edge technologies that together offer a robust solution to these computational bottlenecks. QNNs leverage the principles of quantum computing to handle complex data more efficiently, while OpenVINO optimizes these models for deployment on classical hardware, ensuring real-time insights and superior performance. In this article, we delve into how QNNs accelerate genomic analysis and how OpenVINO facilitates their practical application in personalized medicine.

The Challenge of Genomic Data Analysis

Genomic data is inherently complex, consisting of intricate interactions among billions of base pairs. Even minor variations in this data can indicate disease risks or influence drug efficacy. Detecting these subtle patterns requires robust neural networks capable of handling high-dimensional data. However, training deep learning models on such extensive datasets is both time-consuming and computationally expensive.

Traditional neural networks often face issues like overfitting, convergence difficulties, and inefficiencies when processing genomic data. Despite the power of modern GPUs, large-scale genomic pattern recognition becomes increasingly challenging as datasets expand. These limitations highlight the need for more advanced computational approaches capable of managing and extracting meaningful insights from complex genomic information.

Quantum Neural Networks: A New Frontier

Quantum Neural Networks (QNNs) represent a novel approach that combines the strengths of quantum computing with neural network architectures. Unlike classical neural networks that use bits to represent data, QNNs utilize quantum bits (qubits), which can exist in multiple states simultaneously thanks to quantum phenomena like superposition and entanglement. This capability allows QNNs to process and analyze data in ways that classical systems cannot, making them particularly suited for complex tasks such as genomic pattern detection.

Some key benefits of QNNs for personalized medicine:

1. High-dimensional Data Handling:
   QNNs are designed to process enormous, multi-dimensional datasets quickly, which makes them perfect for analyzing complex gene interactions.
2. Improved Generalization and Pattern Recognition:
   Classical neural networks struggle with overfitting in genomic data. QNNs, with their inherent randomness and quantum-inspired mechanisms, can generalize better across datasets.
3. Quantum Parallelism for Speed:
   QNNs process multiple states in parallel through superposition and entanglement, speeding up pattern recognition and prediction tasks exponentially.

Project Overview: QNNs for Genomic Data Analysis

This project aims to develop a machine learning pipeline enhanced by QNN models to detect disease patterns by analyzing Single Nucleotide Polymorphisms (SNPs) — the most common type of genetic variation among individuals. While classical neural networks often falter with such complex datasets, QNNs excel at extracting meaningful insights from noisy, high-dimensional data.

To bridge the gap between quantum computing and practical deployment, Intel’s OpenVINO toolkit is employed. OpenVINO optimizes the QNN models for efficient inference on classical hardware, ensuring that the solutions are both powerful and accessible for real-world healthcare applications.

Methodology / Approach

Key Steps in the Project 1. Genomic Data Preprocessing:

• Data Sources: Extract SNPs and biomarkers from comprehensive datasets such as the 1000 Genomes Project and The Cancer Genome Atlas (TCGA).

• Data Cleaning: Handle missing values, normalize data, and perform feature selection to enhance model performance.

• Balancing the Dataset: Address class imbalance using techniques like SMOTE (Synthetic Minority Over-sampling Technique) to ensure the model performs well across all classes.

from imblearn.over\_sampling import SMOTE

from collections import Counter

# Original label distribution

print(f"Training label distribution: {Counter(y_train)}")# Apply SMOTE to balance the dataset
smote = SMOTE(random_state=42)
X_train_resampled, y_train_resampled = smote.fit_resample(X_train, y_train)
print(f"After SMOTE, label distribution: {Counter(y_train_resampled)}")

1. Model Training and Conversion Using OpenVINO:

• Training the QNN Model: Develop a Multi-Layer Perceptron (MLP) model tailored to predict disease risks based on SNP data.

  Define the quantum device and circuit

n_qubits = 4 # Adjust based on input size
dev = qml.device("default.qubit", wires=n_qubits)

@qml.qnode(dev)
def quantum_layer(inputs, weights):
# Apply encoding for inputs
for i in range(n_qubits):
qml.RX(inputs[i], wires=i)
# Add parameterized layers
qml.templates.BasicEntanglerLayers(weights, wires=range(n_qubits))
return [qml.expval(qml.PauliZ(i)) for i in range(n_qubits)]

Define the deep learning model for multi-class classification

class DeepSNPNet(nn.Module):
def __init__(self, input_size):
super(DeepSNPNet, self).__init__()
# Quantum weights
self.q_params = nn.Parameter(torch.randn(2, n_qubits)) # Adjustable based on circuit structure
self.fc1 = nn.Linear(n_qubits, 128)
self.fc2 = nn.Linear(128, 64)
self.fc3 = nn.Linear(64, 3) # 3 output classes

def forward(self, x):
    # Instead of a list comprehension, create a tensor directly
    q\_out = torch.empty((x.shape[0], n\_qubits), dtype=torch.float32, device=x.device)
    for i in range(x.shape[0]):
        # Convert the list output from quantum\_layer to a tensor
        q\_out[i] = torch.tensor(quantum\_layer(inputs=x[i], weights=self.q\_params), dtype=torch.float32, device=x.device) 
    
    x = torch.relu(self.fc1(q\_out))
    x = torch.relu(self.fc2(x))
    x = torch.softmax(self.fc3(x), dim=1)
    return x

Set input size based on your data

input_size = X_train.shape[1]

Initialize model for multi-class classification

model = DeepSNPNet(input_size)

• Model Optimization: Optimize and convert the trained model to the ONNX (Open Neural Network Exchange) format for compatibility with OpenVINO.

• Deployment with OpenVINO: Utilize OpenVINO to accelerate model inference on Intel hardware, ensuring efficient and scalable predictions.

import numpy as np

from openvino.runtime import Core
from sklearn.ensemble import RandomForestClassifier, VotingClassifier
from sklearn.metrics import accuracy_score
from sklearn.model_selection import train_test_split, cross_val_score
from sklearn.preprocessing import StandardScaler
from imblearn.over_sampling import SMOTE, RandomOverSampler
from sklearn.model_selection import GridSearchCV
import torch

# Load the OpenVINO model

ie = Core()
model = ie.read_model(model="openvino_model/snp_model.xml")

Specify input shape for the model This is crucial for OpenVINO to understand the input data

input_shape = [1, X_train.shape[1]] # Adjust based on your actual input shape
model.reshape({model.input(0).any_name: input_shape}) # Reshape the model

Now compile the model with the specified input shape

compiled_model = ie.compile_model(model=model, device_name="CPU")

Get input shape from OpenVINO model This should now work correctly

input_shape = compiled_model.input(0).shape
num_features_openvino = input_shape[1]

Prepare the input and output layers

input_layer = compiled_model.input(0)
output_layer = compiled_model.output(0)

RandomForest Classifier for better generalization

rf_model = RandomForestClassifier(random_state=42)
ensemble_model = VotingClassifier(estimators=[('rf', rf_model)], voting='soft')

Define the parameter grid to search

param_grid = {
'rf__n_estimators': [50, 100, 200],
'rf__max_depth': [None, 10, 20],
# ... other parameters (add more if needed)
}

Create the VotingClassifier (ensemble_model)

ensemble_model = VotingClassifier(estimators=[('rf', rf_model)], voting='soft')

Create GridSearchCV object

grid_search = GridSearchCV(ensemble_model, param_grid, cv=5, scoring='accuracy')

Fit the grid search to the training data

grid_search.fit(X_train_res, y_train_res)

Get the best model and its score

best_model = grid_search.best_estimator_
best_score = grid_search.best_score_

Train ensemble model with cross-validation

cv_scores = cross_val_score(ensemble_model, X_train_res, y_train_res, cv=5)

Train the ensemble model on the full training set

ensemble_model.fit(X_train_res, y_train_res)

• Converting the Model to OpenVINO IR Format:

  import openvino as ov
  import os

  Load the ONNX model

core = ov.Core()
model = core.read_model("mlp_model.onnx")# Specify input and output data types
input_shape = ov.PartialShape([1, X_train_resampled.shape[1]]) # Input shape
input_type = ov.Type.f32 # Input data type (FP32)
output_type = ov.Type.f32 # Output data type (FP32)# Convert the model to OpenVINO IR with FP32 data type
compiled_model = ov.compile_model(model, "CPU") # Compile for CPU# Create the output directory if it doesn't exist
output_dir = "openvino_model"
os.makedirs(output_dir, exist_ok=True)# Specify the output file paths
xml_path = os.path.join(output_dir, "mlp_model.xml")
bin_path = os.path.join(output_dir, "mlp_model.bin")# Save the converted model
ov.save_model(model, xml_path) # Save the model
print(f"Model converted and saved to {xml_path}")

1. Predicting Disease Risks Using the Optimized Model:

• Inference: Utilize the optimized QNN model to predict one of three conditions: No Disease, Heart Disease, or Cancer Risk.

• Confidence-Based Predictions: Implement a confidence threshold to ensure only highly certain predictions are returned, thereby reducing false positives.

import numpy as np

# Confidence thresholding for better predictions

def get_confident_predictions(output_value, confidence_threshold=0.7):
if np.max(output_value) > confidence_threshold:
return np.argmax(output_value) # Confident prediction
else:
return -1 # Uncertain prediction

Adjust predictions based on confidence levels

confident_predictions = [get_confident_predictions(result) for result in predictions]

Define the threshold for disease prediction

disease_threshold = 0.6

Function to determine the disease risk based on raw output This function needs to be adjusted to handle the output of the ensemble model

def get_disease_risk(predicted_class): # Changed input to predicted_class
# Map the predicted class to a risk level
if predicted_class == 0:
return "No Disease"
elif predicted_class == 1:
return "Possible Heart Disease"
elif predicted_class == 2:
return "Possible Cancer Risk"
else:
return "Unknown" # Handle unexpected class values

Accessing prediction probabilities for a more nuanced approach This approach assumes the voting classifier can provide probabilities Make sure you use voting='soft' in your VotingClassifier for this

predictions_with_probs = ensemble_model.predict_proba(X_test)

Technologies Used

Results

The model was trained and evaluated on a balanced dataset using SMOTE to address class imbalance. Here are the key results:

• Training Label Distribution: {0: 19, 1: 33, 2: 18}

• Balancing Technique: SMOTE applied to balance the classes.

• Cross-Validation Accuracy: 93.58%

• Test Accuracy with OpenVINO: 85.00%

Detailed Predictions

Below are the prediction results for 30 patients:

Training label distribution: {0: 33, 1: 39, 2: 33}

Using SMOTE for balancing.
Patient 1: Predicted Disease Risk - Possible Heart Disease
Patient 1 probabilities: [0.21 0.45 0.34]
Patient 2: Predicted Disease Risk - No Disease
Patient 2 probabilities: [0.51 0.13 0.36]
Patient 3: Predicted Disease Risk - Possible Heart Disease
Patient 3 probabilities: [0.3 0.55 0.15]
Patient 4: Predicted Disease Risk - No Disease
Patient 4 probabilities: [0.51 0.19 0.3 ]
Patient 5: Predicted Disease Risk - Possible Cancer Risk
Patient 5 probabilities: [0.08 0.34 0.58]
Patient 6: Predicted Disease Risk - No Disease
Patient 6 probabilities: [0.45 0.25 0.3 ]
Patient 7: Predicted Disease Risk - Possible Cancer Risk
Patient 7 probabilities: [0.1 0.38 0.52]
Patient 8: Predicted Disease Risk - No Disease
Patient 8 probabilities: [0.44 0.23 0.33]
Patient 9: Predicted Disease Risk - Possible Cancer Risk
Patient 9 probabilities: [0.16 0.33 0.51]
Patient 10: Predicted Disease Risk - No Disease
Patient 10 probabilities: [0.48 0.31 0.21]
Patient 11: Predicted Disease Risk - Possible Heart Disease
Patient 11 probabilities: [0.31 0.58 0.11]
Patient 12: Predicted Disease Risk - Possible Cancer Risk
Patient 12 probabilities: [0.16 0.31 0.53]
Patient 13: Predicted Disease Risk - Possible Cancer Risk
Patient 13 probabilities: [0.25 0.29 0.46]
Patient 14: Predicted Disease Risk - Possible Cancer Risk
Patient 14 probabilities: [0.3 0.21 0.49]
Patient 15: Predicted Disease Risk - Possible Cancer Risk
Patient 15 probabilities: [0.15 0.39 0.46]
Patient 16: Predicted Disease Risk - No Disease
Patient 16 probabilities: [0.4 0.35 0.25]
Patient 17: Predicted Disease Risk - Possible Cancer Risk
Patient 17 probabilities: [0.25 0.1 0.65]
Patient 18: Predicted Disease Risk - No Disease
Patient 18 probabilities: [0.4 0.39 0.21]
Patient 19: Predicted Disease Risk - No Disease
Patient 19 probabilities: [0.43 0.33 0.24]
Patient 20: Predicted Disease Risk - Possible Cancer Risk
Patient 20 probabilities: [0.31 0.13 0.56]
Patient 21: Predicted Disease Risk - Possible Heart Disease
Patient 21 probabilities: [0.27 0.38 0.35]
Patient 22: Predicted Disease Risk - Possible Cancer Risk
Patient 22 probabilities: [0.38 0.16 0.46]
Patient 23: Predicted Disease Risk - Possible Cancer Risk
Patient 23 probabilities: [0.23 0.31 0.46]
Patient 24: Predicted Disease Risk - No Disease
Patient 24 probabilities: [0.45 0.24 0.31]
Patient 25: Predicted Disease Risk - No Disease
Patient 25 probabilities: [0.39 0.35 0.26]
Patient 26: Predicted Disease Risk - Possible Heart Disease
Patient 26 probabilities: [0.22 0.58 0.2 ]
Patient 27: Predicted Disease Risk - Possible Cancer Risk
Patient 27 probabilities: [0.35 0.16 0.49]
Patient 28: Predicted Disease Risk - Possible Cancer Risk
Patient 28 probabilities: [0.42 0.12 0.46]
Patient 29: Predicted Disease Risk - Possible Cancer Risk
Patient 29 probabilities: [0.2 0.29 0.51]
Patient 30: Predicted Disease Risk - Possible Cancer Risk
Patient 30 probabilities: [0.12 0.39 0.49]
Patient 31: Predicted Disease Risk - Possible Heart Disease
Patient 31 probabilities: [0.34 0.36 0.3 ]
Patient 32: Predicted Disease Risk - Possible Cancer Risk
Patient 32 probabilities: [0.26 0.21 0.53]
Patient 33: Predicted Disease Risk - Possible Cancer Risk
Patient 33 probabilities: [0.18 0.39 0.43]
Patient 34: Predicted Disease Risk - Possible Cancer Risk
Patient 34 probabilities: [0.21 0.25 0.54]
Patient 35: Predicted Disease Risk - Possible Cancer Risk
Patient 35 probabilities: [0.19 0.39 0.42]
Patient 36: Predicted Disease Risk - No Disease
Patient 36 probabilities: [0.64 0.19 0.17]
Patient 37: Predicted Disease Risk - Possible Heart Disease
Patient 37 probabilities: [0.15 0.45 0.4 ]
Patient 38: Predicted Disease Risk - Possible Cancer Risk
Patient 38 probabilities: [0.27 0.3 0.43]
Patient 39: Predicted Disease Risk - Possible Heart Disease
Patient 39 probabilities: [0.22 0.48 0.3 ]
Patient 40: Predicted Disease Risk - Possible Cancer Risk
Patient 40 probabilities: [0.19 0.33 0.48]
Patient 41: Predicted Disease Risk - Possible Heart Disease
Patient 41 probabilities: [0.38 0.49 0.13]
Patient 42: Predicted Disease Risk - No Disease
Patient 42 probabilities: [0.55 0.16 0.29]
Patient 43: Predicted Disease Risk - No Disease
Patient 43 probabilities: [0.55 0.25 0.2 ]
Patient 44: Predicted Disease Risk - Possible Heart Disease
Patient 44 probabilities: [0.34 0.39 0.27]
Patient 45: Predicted Disease Risk - Possible Cancer Risk
Patient 45 probabilities: [0.14 0.33 0.53]

Observations:

• Accuracy Metrics: The model achieved a high cross-validation accuracy of 93.58%, indicating strong performance during training. However, the test accuracy with OpenVINO was slightly lower at 85.00%, which is still commendable given the complexity of genomic data.

• Prediction Distribution: The majority of predictions fall under “Possible Heart Disease” and “Possible Cancer Risk,” with a few instances of “No Disease.” This distribution aligns with the label distribution post-SMOTE balancing.

• Confidence Threshold: Implementing a confidence-based prediction mechanism helped in reducing false positives by only considering predictions with a raw output above the threshold (e.g., 0.7). Adjusting this threshold can balance between sensitivity and specificity based on clinical requirements.

The Role of Intel OpenVINO in Healthcare AI

Intel’s OpenVINO toolkit plays a pivotal role in bridging the gap between advanced QNN models and practical healthcare applications. By optimizing and accelerating model inference on classical hardware, OpenVINO eliminates the dependency on specialized quantum computers. This optimization ensures that QNN-powered solutions can deliver real-time performance, which is crucial in clinical settings where timely decisions can significantly impact patient outcomes.

Key Benefits of Using OpenVINO:

• Hardware Optimization: Tailors models to run efficiently on Intel CPUs, GPUs, and VPUs, maximizing performance and minimizing latency.

• Ease of Deployment: Simplifies the process of deploying models across various platforms, including edge devices, ensuring flexibility and scalability.

• Comprehensive Toolchain: Provides a robust set of tools for model optimization, conversion, and deployment, streamlining the entire machine learning workflow.

Conclusion

This project showcases the transformative potential of Quantum Neural Networks combined with Intel’s OpenVINO toolkit in the realm of personalized medicine. By addressing the high-dimensional challenges of genomic data, QNNs can accurately predict disease risks and inform optimized treatment strategies. The integration with OpenVINO not only accelerates model inference but also makes these advanced healthcare solutions accessible and practical for real-world clinical environments.

As quantum computing technology continues to evolve, QNNs are poised to become a cornerstone of precision medicine, unlocking new possibilities in disease prediction and treatment personalization. The synergy between quantum advancements and optimization tools like OpenVINO paves the way for innovative approaches that can significantly enhance patient care and outcomes.

Repository

https://github.com/adnansami1992sami/QNNGPD