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import torch
from rdkit.Chem import Draw
from moses.metrics import mol_passes_filters, QED, SA, logP
from moses.metrics.utils import get_n_rings, get_mol
torch.cuda.set_device(0)
torch.cuda.set_device(0)
Model initialization
Next, initialize an RNN-based encoder (enc) and a dilated convolutional decoder (dec).
These components are used to build the GENTRL model.
enc = gentrl.RNNEncoder(latent_size=50)
dec = gentrl.DilConvDecoder(latent_input_size=50)
model = gentrl.GENTRL(enc, dec, 50 * [('c', 20)], [('c', 20)], beta=0.001)
model.cuda();
Loading the trained model
Load the pre-trained GENTRL model that has been previously saved in the
‘saved_gentrl_after_rl/’ directory and move it to the CUDA device for GPU acceleration.
model.load('saved_gentrl_after_rl/')
model.cuda();
Define the utility functions
Now, we have to define two helper functions for calculating the number of rings with more
than six atoms in a molecule and computing a penalized LogP value for a given molecule or
SMILES string. These functions can be part of a broader pipeline for molecule analysis,
property optimization, or generating molecules that satisfy certain criteria.
def get_num_rings_6(mol):
r = mol.GetRingInfo()
return len([x for x in r.AtomRings() if len(x) > 6])
def penalized_logP(mol_or_smiles, masked=True, default=-5):](https://image.slidesharecdn.com/generativeaiinhealthcare-231030161104-cb27273f/85/generative-AI-in-healthcare-pdf-10-320.jpg)
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mol = get_mol(mol_or_smiles)
if mol is None:
return default
reward = logP(mol) - SA(mol) - get_num_rings_6(mol)
if masked and not mol_passes_filters(mol):
return default
return reward
Molecule generation loop
Next, we need to generate a list of 1000 valid molecules using the ‘model’ object. The loop
should continue until the desired number of valid molecules is reached. This process can be
part of a molecule generation or optimization pipeline, where the objective is to obtain a set
of valid molecules for further analysis, screening, or other purposes.
generated = []
while len(generated) < 1000:
sampled = model.sample(100)
sampled_valid = [s for s in sampled if get_mol(s)]
generated += sampled_valid
Molecule visualization
Finally, to visualize the generated molecules, run the following command. This will generate
a grid image of molecules and their corresponding penalized logP values.
Draw.MolsToGridImage([get_mol(s) for s in sampled_valid],
legends=[str(penalized_logP(s)) for s in sampled_valid])
Endnote
The advent of generative AI has brought forth transformative advancements and
opportunities in the healthcare field. With its ability to generate novel data, improve
diagnostics, optimize treatment strategies, and expedite drug discovery, generative AI is
reshaping the healthcare landscape. From enhancing medical imaging and patient care to
enabling personalized medicine and streamlining drug development, this powerful](https://image.slidesharecdn.com/generativeaiinhealthcare-231030161104-cb27273f/85/generative-AI-in-healthcare-pdf-11-320.jpg)
generative AI in healthcare.pdf
- 1. 1/12 Applications of generative AI in healthcare leewayhertz.com/generative-ai-in-healthcare The emergence of generative AI has ushered in a new era of possibilities in multiple domains and industries. This ever-evolving technology has the potential to reshape the way we approach and solve complex problems, offering transformative solutions and innovative outcomes that were once unimaginable. With its ability to generate, simulate, and optimize, generative AI opens up new horizons and propels us into an era of limitless potential. Like many other industries embracing technological advancements, the healthcare landscape is on the cusp of transformative progress driven by the emergence of generative AI. As advanced machine learning algorithms continue to evolve, they are reshaping multiple aspects of the healthcare industry, transcending the boundaries of traditional approaches. From diagnosis and treatment to drug discovery and personalized medicine, generative AI is poised to transform how healthcare professionals approach complex medical challenges. By harnessing the capabilities of generative AI, the healthcare industry is poised to witness remarkable advancements that have the capability to enhance patient outcomes, improve medical research, and reshape the entire healthcare landscape. This article will dive deep into the profound impact of generative AI in healthcare and delve into its applications, benefits and other key areas. What is generative AI? Prominent generative AI models
- 2. 2/12 Generative AI in healthcare Benefits of generative AI in healthcare Applications of generative AI in healthcare Generative AI in healthcare: Real world examples How does generative AI help in drug discovery? How does GENTRL work? What is generative AI? Generative AI, or generative artificial intelligence, refers to a branch of AI that focuses on creating models capable of generating new and original content. Unlike traditional AI models that rely on predefined rules and patterns, generative AI models have the ability to learn from existing data and generate new outputs that mimic the characteristics of the training data. At the core of generative AI is the concept of generative models. These models are designed to learn the underlying patterns and structures within a dataset and use that knowledge to generate new instances that resemble the original data. Generative models are trained using large datasets and use probabilistic techniques to capture the training data distribution. Generative AI models have various applications, including image synthesis, text generation, music composition, and even video generation. These models have the ability to generate new and unique content that exhibits the characteristics and style of the training data. However, it’s important to note that generative AI models are not simply copying existing data but learning underlying patterns and structures to generate novel outputs. Prominent generative AI models Several prominent generative AI models have made significant contributions to the field of artificial intelligence. Here are a few examples and a brief overview of how they work: Generative Adversarial Networks (GANs) GANs consist of two components: a generator and a discriminator. The generator aims to generate synthetic data samples, such as images or text, that resemble real data samples. The discriminator, on the other hand, tries to distinguish between the real and generated samples. Through an adversarial training process, the generator learns to produce increasingly realistic samples, while the discriminator learns to become more accurate in distinguishing between real and generated samples. GANs have been successfully applied in various domains, including image synthesis, text generation, and video generation. Variational Autoencoders (VAEs)
- 3. 3/12 VAEs are generative models that learn to encode and decode data samples. They consist of an encoder network that maps input data to a latent space representation and a decoder network that reconstructs the original data from the latent space. VAEs are trained by maximizing the Evidence Lower Bound (ELBO), which encourages the learned latent space to capture meaningful and continuous data representations. VAEs can generate new samples by sampling from the latent space and decoding the samples back into the original data space. VAEs have been widely used for image generation, text generation, and anomaly detection tasks. Transformer models Transformer models, such as the GPT (Generative Pre-trained Transformer) series, have transformed natural language processing and text generation tasks. Transformers employ a self-attention mechanism that allows the model to capture long-range dependencies in the input data. These models are typically trained in an unsupervised or semi-supervised manner on large amounts of text data to learn the statistical properties of language. Once trained, they can generate coherent and contextually relevant text by conditioning on an input prompt or by autonomously generating text from scratch. Autoregressive models Autoregressive models, including models like LSTM (Long Short-term Memory) and GRU (Gated Recurrent Unit), generate sequences by modeling the conditional probability of each element in the sequence given the previous elements. These models have a recurrent structure that allows them to capture dependencies over time or sequence. During training, the models are exposed to input sequences and learn to predict the next element in the sequence. Autoregressive models have been used for tasks such as language modeling, speech recognition, and music generation. These are only a handful of prominent examples of generative AI models, each with its own unique approach to generating new data samples. The field of generative AI is constantly evolving, and researchers continue to develop new models and techniques for generating realistic and creative outputs in various domains. Generative AI in healthcare Generative AI in healthcare refers to the application of generative artificial intelligence techniques and models in various aspects of the healthcare industry. It involves using machine learning algorithms to generate new and original content that is relevant to healthcare, such as medical images, personalized treatment plans, and more. Benefits of generative AI in healthcare
- 4. 4/12 The benefits of generative AI in healthcare are numerous, some of which include: Improved efficiency and cost reduction 1. Automating repetitive tasks: Generative AI can automate routine and repetitive tasks in healthcare, such as data entry, administrative processes, and image analysis. This automation saves time for healthcare professionals, enabling them to give attention to more complex and critical aspects of patient care. 2. Streamlined workflows and resource utilization: Generative AI can optimize healthcare workflows by allocating resources and prioritizing tasks intelligently. It can assist in scheduling appointments, managing patient flow, and coordinating care, leading to smoother operations and efficient resource utilization. This can result in cost reduction and improved patient satisfaction. Enhanced accuracy and precision 1. Reduction of human error and biases: Human errors and biases are inherent in healthcare, and they can impact diagnoses, treatment decisions, and patient outcomes. Generative AI models, when properly trained and validated, can minimize these errors by providing objective and consistent analysis. They can mitigate the effects of human biases and ensure more accurate and unbiased predictions and diagnoses. 2. More accurate predictions and diagnoses: Generative AI models can analyze vast amounts of patient data, including medical records, genetic information, and environmental factors. By integrating and analyzing these data points, AI models can identify patterns and relationships that may not be apparent to humans. This can lead to more accurate disease progression predictions, personalized treatment plans, and early detection of potential risks. Facilitation of medical education and training 1. Virtual simulations and training scenarios: Generative AI can create realistic virtual simulations and training scenarios for medical education. These simulations offer healthcare professionals the opportunity to replicate a wide range of medical conditions and procedures, creating a safe and controlled environment for skill practice and refinement. It enables hands-on training without risking patient safety and provides opportunities for repeated practice and feedback. 2. Access to diverse case studies and expert knowledge: Generative AI can generate synthetic medical data, including patient profiles, medical images, and clinical scenarios. This synthetic data can be used for educational purposes, providing access to diverse case studies and rare conditions. It enables healthcare professionals to enhance their knowledge, learn from experts, and develop expertise in specialized areas that may be limited in real-world patient encounters.
- 5. 5/12 Generative AI has shown significant potential in various applications within the healthcare industry. Let us explore each of these applications in detail: Medical imaging Generative AI techniques have been extensively used to enhance medical imaging analysis and diagnostics. Prominent image-generating models like DALL.E and Stable Diffusion, among others, can be effectively used for this purpose. Here are some key aspects of the impact of generative AI in medical imaging: 1. Improved diagnostic accuracy: Generative models, such as Generative Adversarial Networks (GANs), can generate synthetic medical images that closely resemble real patient images. This helps in training models to improve accuracy in diagnosing diseases, such as cancer or abnormalities in MRI or CT scans. 2. Faster and more precise image analysis: Generative AI can assist in automating image analysis tasks, such as segmentation, lesion detection, or organ identification. Utilizing generative models makes it possible to process images more quickly and with higher precision, reducing the workload on radiologists and improving efficiency. Drug discovery and development Generative AI techniques can potentially reinvent the drug discovery and development process, leading to faster and more efficient drug development pipelines. Here is how generative AI is applied: 1. Accelerated identification of potential drug candidates: Generative models can generate novel molecules with desired properties, helping researchers explore the vast chemical space efficiently. These generated molecules can be further analyzed for drug-like properties, potentially leading to the discovery of new drug candidates. 2. Optimization of drug formulations and dosages: Generative AI can assist in optimizing drug formulations and dosages by simulating the interactions between drugs and the human body. This allows for personalized medicine and tailoring treatments based on individual patient characteristics, improving therapeutic outcomes. Personalized medicine Generative AI is crucial in advancing personalized medicine, which aims to provide tailored treatment plans based on individual patient data. Here is how generative AI is utilized: 1. Tailored treatment plans: Generative models can analyze patient data, including genetic information, medical history, and clinical data, to generate personalized treatment plans. This can aid in selecting the most effective therapies and predicting individual patient responses.
- 6. 6/12 2. Predictive analytics for disease progression and treatment response: By analyzing large datasets and integrating various patient factors, generative AI can generate predictive models that estimate disease progression and treatment outcomes. This helps healthcare professionals make informed decisions regarding treatment strategies and optimize patient care. Medical research and data analysis Generative AI techniques have immense potential in medical research and data analysis. Here are two key aspects: 1. Mining large datasets for insights and patterns: Generative models can analyze vast amounts of medical data, including electronic health records, research papers, and clinical trials, to extract valuable insights and identify patterns that may lead to new discoveries or medical breakthroughs. 2. Generating synthetic data for privacy-preserving research: To address privacy concerns, generative AI can generate synthetic medical data that closely resembles real patient data while preserving privacy. This synthetic data can be utilized for research purposes without exposing sensitive patient information. Clinical decision-making processes Generative AI in healthcare holds significant potential to enhance clinical decision-making processes and assist healthcare professionals in making accurate and informed diagnoses, as demonstrated by solutions like Glass.Health. By analyzing vast amounts of patient data,
- 7. 7/12 including medical records, lab results, previous treatments, and medical imaging such as MRIs and X-rays, generative AI algorithms can identify patterns and correlations that may not be immediately apparent to human clinicians. Generative AI algorithms can assist in detecting potential problem areas, highlighting concerns and suggesting further diagnostic tests or treatment approaches. By considering a broader range of patient data and drawing upon extensive medical knowledge, generative AI systems can act as valuable decision-support tools, empowering healthcare professionals with additional information and recommendations. Population health management Generative AI in healthcare can enhance population health management strategies greatly. By leveraging generative AI, policymakers can access more detailed demographic information, enabling them to gain deeper insights into specific populations’ health profiles and needs. They can analyze large datasets and identify these populations’ patterns, trends, and disparities. This level of granularity enables the design and implementation of targeted public health initiatives, like preventive measures and early intervention programs, that address the unique challenges faced by underserved communities. By understanding the specific health needs and social determinants of health affecting different populations, policymakers can allocate resources more efficiently and effectively to improve population health outcomes. Risk prediction of pandemic preparedness Generative AI models have become invaluable resources for scientists studying the societal- scale effects of catastrophic events, such as pandemics. By leveraging large datasets and advanced algorithms, generative AI can simulate and model the spread of infectious diseases, providing insights into potential outbreak scenarios and their implications. These models can help identify key factors that contribute to the rapid escalation of a virus, allowing policymakers and healthcare organizations to develop targeted preventive measures and response strategies. One significant application of generative AI in pandemic preparedness is the training of models on vast amounts of protein sequences. By analyzing these sequences, generative AI algorithms can identify and generate new antibodies or antiviral compounds that can potentially address infectious diseases. This approach enables researchers to expedite the development of targeted treatments and therapeutic interventions for emerging pathogens, bolstering the arsenal against future pandemics. These applications of generative AI in healthcare demonstrate its potential to improve diagnostics, drug development, personalized medicine, and medical research, among others. By leveraging generative AI techniques, healthcare professionals can enhance decision-
- 8. 8/12 making, optimize treatment strategies, and ultimately improve patient outcomes. Generative AI in healthcare: Real-world examples Some examples of solutions built using generative AI in healthcare are: Chest-gan A generative AI model that utilizes GANs to produce realistic chest X-rays that can be used to train other machine learning models used for diagnosing chest pathologies. The project aims to augment the existing dataset by generating synthetic chest X-ray images and providing more training examples for classification models. This could enhance the performance of the models in accurately classifying different chest pathologies. The focus is on five specific pathology classes: Atelectasis, effusion, pneumothorax, cardiomegaly, and no finding (Normal). GENTRL GENTRL (Generative Tensorial Reinforcement Learning) model is a variational autoencoder that combines generative models and reinforcement learning to optimize molecules with desired properties. The main objective of GENTRL is to generate novel molecules with specific characteristics or properties that can be used in various applications like drug discovery. Unlike traditional generative models, GENTRL takes into account both the chemical structure and the desired properties of the molecules. It uses a combination of reinforcement learning algorithms and deep neural networks to optimize the generation process. By training on a dataset of molecules with known properties, the model acquires the ability to generate novel molecules that optimize the desired properties. Med-PaLM Med-PaLM and Med-PaLM 2 are large language models developed by Google for answering medical questions and providing accurate information in the medical domain. The original Med-PaLM model was introduced in 2022 and was the first AI system to surpass the pass mark on US Medical License Exam (USMLE) style questions. It utilizes Google’s powerful LLMs, which have been trained and fine-tuned using expert demonstrations from the medical field. Med-PaLM can generate comprehensive and reliable answers to consumer health questions, as evaluated by panels of physicians and users. Med-PaLM 2, the latest version of the model, achieves an impressive accuracy of 85.4% on USMLE questions, which is comparable to the performance of “expert” test takers. Additionally, it became the first AI system to achieve a passing score on the MedMCQA dataset, which consists of Indian AIIMS and NEET medical examination questions, with a score of 72.3%.
- 9. 9/12 Glass.Health Glass.Health is an advanced platform that utilizes AI-assisted diagnosis and clinical decision- making to assist healthcare practitioners. Through their generative AI tool, they have created a system capable of generating diagnoses and clinical plans based on input symptoms. By leveraging generative AI, this tool can process patient symptoms and compare them with a vast knowledge base, providing physicians with additional insights and potential treatment options. How does generative AI help in drug discovery? With the remarkable progress of generative AI in healthcare, its impact on drug discovery cannot be overlooked. In this context, we delve into the application of the pre-trained GENTRL model, which enables the generation and visualization of valid molecules. Let us explore its detailed mechanism to gain a comprehensive understanding of GENTRL’s functioning. How does GENTRL work? GENTRL consists of an encoder network that encodes the molecular structure into a latent space, a decoder network that generates molecules from the latent space, and a reinforcement learning module that guides the generation process based on the desired properties. The reinforcement learning module provides rewards or penalties to the model based on how well the generated molecules match the desired properties. GENTRL improves its ability to generate molecules with the desired properties by iteratively generating and evaluating molecules. It can be used in various healthcare applications, including drug discovery, where the goal is to find molecules with specific drug-like properties or optimize existing molecules to enhance their efficacy or safety. Now that we have understood the working mechanism of GENTRL, let us go through the step-by-step process of molecule generation and visualization using it. First, we must load the dataset, perform data preprocessing, and initialize and pre-train the GENTRL model using the dataset. For this, you can run the code from this Github file. Then, we must initialize and load the pre-trained GENTRL model, train it using the RL approach with a specific reward function, and save the model. The codes for this can be accessed in this Github file. We can now use the saved GENTRL model for molecule generation and visualization. Import the necessities Begin by importing the required modules and setting the CUDA device for GPU acceleration. import gentrl
- 10. 10/12 import torch from rdkit.Chem import Draw from moses.metrics import mol_passes_filters, QED, SA, logP from moses.metrics.utils import get_n_rings, get_mol torch.cuda.set_device(0) torch.cuda.set_device(0) Model initialization Next, initialize an RNN-based encoder (enc) and a dilated convolutional decoder (dec). These components are used to build the GENTRL model. enc = gentrl.RNNEncoder(latent_size=50) dec = gentrl.DilConvDecoder(latent_input_size=50) model = gentrl.GENTRL(enc, dec, 50 * [('c', 20)], [('c', 20)], beta=0.001) model.cuda(); Loading the trained model Load the pre-trained GENTRL model that has been previously saved in the ‘saved_gentrl_after_rl/’ directory and move it to the CUDA device for GPU acceleration. model.load('saved_gentrl_after_rl/') model.cuda(); Define the utility functions Now, we have to define two helper functions for calculating the number of rings with more than six atoms in a molecule and computing a penalized LogP value for a given molecule or SMILES string. These functions can be part of a broader pipeline for molecule analysis, property optimization, or generating molecules that satisfy certain criteria. def get_num_rings_6(mol): r = mol.GetRingInfo() return len([x for x in r.AtomRings() if len(x) > 6]) def penalized_logP(mol_or_smiles, masked=True, default=-5):
- 11. 11/12 mol = get_mol(mol_or_smiles) if mol is None: return default reward = logP(mol) - SA(mol) - get_num_rings_6(mol) if masked and not mol_passes_filters(mol): return default return reward Molecule generation loop Next, we need to generate a list of 1000 valid molecules using the ‘model’ object. The loop should continue until the desired number of valid molecules is reached. This process can be part of a molecule generation or optimization pipeline, where the objective is to obtain a set of valid molecules for further analysis, screening, or other purposes. generated = [] while len(generated) < 1000: sampled = model.sample(100) sampled_valid = [s for s in sampled if get_mol(s)] generated += sampled_valid Molecule visualization Finally, to visualize the generated molecules, run the following command. This will generate a grid image of molecules and their corresponding penalized logP values. Draw.MolsToGridImage([get_mol(s) for s in sampled_valid], legends=[str(penalized_logP(s)) for s in sampled_valid]) Endnote The advent of generative AI has brought forth transformative advancements and opportunities in the healthcare field. With its ability to generate novel data, improve diagnostics, optimize treatment strategies, and expedite drug discovery, generative AI is reshaping the healthcare landscape. From enhancing medical imaging and patient care to enabling personalized medicine and streamlining drug development, this powerful
- 12. 12/12 technology holds immense potential for improving healthcare outcomes. As we continue to harness the capabilities of generative AI and address the associated challenges, we are poised to witness a new era of innovation and breakthroughs in the realm of healthcare. Partner with LeewayHertz to build robust generative AI solutions tailored to your business- specific use case in healthcare and stay at the forefront of technological advancements for improved healthcare delivery.