Cookbooks
Step-by-step guides for fine-tuning, deploying, and analyzing medical AI assets.
3D Medical Image Registration using SimpleITK
Tutorial 3D Medical Image Registration using SimpleITK Difficulty: Intermediate Time: 15 min read Introduction Medical Image Registration is the process of aligning two or more...
Accelerating Drug Discovery with Graph Neural Networks (GNNs)
Tutorial Accelerating Drug Discovery with Graph Neural Networks (GNNs) Difficulty: Advanced Time: 25 min read Introduction Traditional drug discovery is a slow, expensive process. By...
Analyzing Electronic Health Records with OMOP Common Data Model and Python
Tutorial Analyzing Electronic Health Records with OMOP Common Data Model and Python Difficulty: Intermediate Time: 20 min read Introduction Electronic Health Records (EHRs) are notoriously...
Automated Diagnosis of Retinal Diseases using Fundus Images and ResNet-50
Tutorial Automated Diagnosis of Retinal Diseases using Fundus Images and ResNet-50 Difficulty: Beginner Time: 12 min read Introduction Diabetic Retinopathy (DR) and Glaucoma are leading...
Automated Segmentation of Lung Nodules with LUNA16 and MONAI
Tutorial Automated Segmentation of Lung Nodules with LUNA16 and MONAI Difficulty: Advanced Time: 20 min read Introduction Lung cancer is the leading cause of cancer...
Brain Tumor Segmentation on MRI using nnU-Net
Tutorial Brain Tumor Segmentation on MRI using nnU-Net Difficulty: Advanced Time: 20 min read Introduction In the field of medical image segmentation, nnU-Net (no-new-Net) is...
Brain Tumor Segmentation on MRI with MONAI and UNet
Tutorial Brain Tumor Segmentation on MRI with MONAI and UNet Difficulty: Intermediate Time: 20 min read Introduction Medical imaging data is fundamentally different from standard...
Building a Clinical Knowledge Graph with BioBERT and Neo4j
Tutorial Building a Clinical Knowledge Graph with BioBERT and Neo4j Difficulty: Advanced Time: 20 min read Introduction In this cookbook, we will explore how to...
Cookbook 60: Offline Orthopedic Fracture & Joint Space Narrowing Classifier
Cookbook 60: Offline Orthopedic Fracture & Joint Space Narrowing Classifier This cookbook details how to deploy a localized orthopedic radiography engine to detect acute bone...
Cookbook 61: Offline Oncology Mammography Microcalcification & Tumor Classifier
Cookbook 61: Offline Oncology Mammography Microcalcification & Tumor Classifier This cookbook details how to deploy a localized oncology mammography analysis engine to detect pleomorphic microcalcifications,...
Cookbook 62: Offline Clinical Dermatology & Melanoma Dermoscopy Classifier
Cookbook 62: Offline Clinical Dermatology & Melanoma Dermoscopy Classifier This cookbook details how to deploy a localized dermatology classification engine to segment skin lesions, calculate...
Cookbook 63: Offline Emergency Cardiac ECG Arrhythmia & ST-Elevation Classifier
Cookbook 63: Offline Emergency Cardiac ECG Arrhythmia & ST-Elevation Classifier This cookbook details how to deploy a localized 12-lead electrocardiogram (ECG) processing engine to detect...
Cookbook 64: Offline Pulmonary CT Emphysema & COPD Quantitative Classifier
Cookbook 64: Offline Pulmonary CT Emphysema & COPD Quantitative Classifier This cookbook details how to deploy a localized pulmonology CT analysis engine to segment lung...
Cookbook 65: Offline Pediatric Bone Age & Skeletal Maturity Radiography Classifier
Cookbook 65: Offline Pediatric Bone Age & Skeletal Maturity Radiography Classifier This cookbook details how to deploy a localized pediatric radiography analysis engine to estimate...
Cookbook 66: Offline Ophthalmology Glaucoma Optic Disc & Cup Segmentation Engine
Cookbook 66: Offline Ophthalmology Glaucoma Optic Disc & Cup Segmentation Engine This cookbook details how to deploy a localized ophthalmology fundus image analysis engine to...
Cookbook 67: Offline Nephrology Renal Ultrasound Kidney Volume & Cyst Segmentor
Cookbook 67: Offline Nephrology Renal Ultrasound Kidney Volume & Cyst Segmentor This cookbook details how to deploy a localized renal ultrasound analysis engine to segment...
Cookbook 68: Offline Clinical Neurology Stroke Ischemic Core & Penumbra Perfusion Engine
Cookbook 68: Offline Clinical Neurology Stroke Ischemic Core & Penumbra Perfusion Engine This cookbook details how to deploy a localized neurology perfusion CT (CTP) analysis...
Cookbook 69: Offline Gastroenterology Endoscopy Polyps & Dysplasia Classifier Engine
Cookbook 69: Offline Gastroenterology Endoscopy Polyps & Dysplasia Classifier Engine This cookbook details how to deploy a localized gastroenterology video endoscopy analysis engine to detect...
Cookbook 70: Offline Hematology Blood Smear Leukocyte & Blast Cell Classifier
Cookbook 70: Offline Hematology Blood Smear Leukocyte & Blast Cell Classifier This cookbook details how to deploy a localized hematology microscopic image analysis engine to...
Cookbook 71: Offline Pathology Whole Slide Image Invasive Breast Carcinoma Engine
Cookbook 71: Offline Pathology Whole Slide Image Invasive Breast Carcinoma Engine This cookbook details how to deploy a localized gigapixel Whole Slide Image (WSI) histopathology...
Cookbook 72: Offline Otolaryngology Tympanic Membrane Otoscopy & Otitis Classifier
Cookbook 72: Offline Otolaryngology Tympanic Membrane Otoscopy & Otitis Classifier This cookbook details how to deploy a localized otolaryngology digital otoscopy analysis engine to segment...
De Novo Drug Design with Reinforcement Learning and REINVENT
Tutorial De Novo Drug Design with Reinforcement Learning and REINVENT Difficulty: Advanced Time: 25 min read Introduction Traditional high-throughput screening involves physically testing millions of...
De-identifying Clinical Text with Microsoft Presidio and NLP
Tutorial De-identifying Clinical Text with Microsoft Presidio and NLP Difficulty: Intermediate Time: 15 min read Introduction Before clinical notes can be shared for research or...
De-identifying Clinical Text with SpaCy and NLP
Tutorial De-identifying Clinical Text with SpaCy and NLP Difficulty: Intermediate Time: 18 min read Introduction Before clinical notes, discharge summaries, or pathology reports can be...
Deploying BioBERT as a Microservice with FastAPI and Docker
Tutorial Deploying BioBERT as a Microservice with FastAPI and Docker Difficulty: Intermediate Time: 15 min read Introduction Training a specialized clinical NLP model like BioBERT...
Deploying a Clinical LLM API with Docker and vLLM
Tutorial Deploying a Clinical LLM API with Docker and vLLM Difficulty: Intermediate Time: 12 min read Introduction In this cookbook, we will cover how to...
Deploying a Medical Chatbot with LlamaIndex and RAG
Tutorial Deploying a Medical Chatbot with LlamaIndex and RAG Difficulty: Intermediate Time: 20 min read Introduction Large Language Models (LLMs) like GPT-4 and Llama-3 are...
Diagnosing Diabetic Retinopathy from Fundus Images with PyTorch Lightning
Tutorial Diagnosing Diabetic Retinopathy from Fundus Images with PyTorch Lightning Difficulty: Intermediate Time: 20 min read Introduction Diabetic Retinopathy (DR) is a leading cause of...
Federated Learning for Medical Imaging using Flower and PyTorch
Tutorial Federated Learning for Medical Imaging using Flower and PyTorch Difficulty: Advanced Time: 25 min read Introduction In healthcare, data silos are a massive bottleneck....
Federated Learning for Medical Imaging with Flower and PyTorch
Tutorial Federated Learning for Medical Imaging with Flower and PyTorch Difficulty: Advanced Time: 25 min read Introduction In healthcare, patient data is highly sensitive and...
Fine-Tuning Clinical Llama-3 with PEFT
Tutorial Fine-Tuning Clinical Llama-3 with PEFT Difficulty: Intermediate Time: 15 min read Introduction In this cookbook, we will walk through how to fine-tune the Clinical...
Fine-Tuning Llama-3 for Medical Q&A using PEFT and LoRA
Tutorial Fine-Tuning Llama-3 for Medical Q&A using PEFT and LoRA Difficulty: Advanced Time: 22 min read Introduction General-purpose Large Language Models (LLMs) like Meta's Llama-3...
How to Train an EHR Mortality Prediction Model with PhysioNet 2012
Tutorial How to Train an EHR Mortality Prediction Model with PhysioNet 2012 Difficulty: Advanced Time: 25 min read Introduction In this cookbook, we will cover...
Identifying Anomalies in ECG Signals with Autoencoders
Tutorial Identifying Anomalies in ECG Signals with Autoencoders Difficulty: Intermediate Time: 15 min read Introduction Electrocardiogram (ECG) signals record the electrical activity of the heart...
Identifying Cell Types in Single-Cell RNA-Seq with Scanpy
Tutorial Identifying Cell Types in Single-Cell RNA-Seq with Scanpy Difficulty: Beginner Time: 15 min read Introduction Single-cell RNA sequencing (scRNA-seq) has transformed biology by allowing...
Identifying Cell Types in Spatial Transcriptomics using Giotto
Tutorial Identifying Cell Types in Spatial Transcriptomics using Giotto Difficulty: Advanced Time: 20 min read Introduction Single-cell RNA sequencing (scRNA-seq) tells us what genes are...
Identifying Gene Regulatory Networks from scRNA-seq using CellOracle
Tutorial Identifying Gene Regulatory Networks from scRNA-seq using CellOracle Difficulty: Advanced Time: 25 min read Introduction While single-cell RNA sequencing (scRNA-seq) provides a snapshot of...
Identifying Protein-Protein Interactions (PPIs) with Deep Learning using D-SCRIPT
Tutorial Identifying Protein-Protein Interactions (PPIs) with Deep Learning using D-SCRIPT Difficulty: Advanced Time: 20 min read Introduction Understanding which proteins interact with one another is...
Identifying Rare Disease Phenotypes with Human Phenotype Ontology (HPO)
Tutorial Identifying Rare Disease Phenotypes with Human Phenotype Ontology (HPO) Difficulty: Intermediate Time: 15 min read Introduction Diagnosing rare genetic diseases often resembles finding a...
In-Browser Clinical PII Redaction with Transformers.js
Tutorial In-Browser Clinical PII Redaction with Transformers.js Difficulty: Intermediate Time: 12 min read Introduction Removing Protected Health Information (PHI) from clinical notes is vital for...
Introduction to the BIDS Standard for Neuroimaging
Tutorial Introduction to the BIDS Standard for Neuroimaging Difficulty: Beginner Time: 10 min read Introduction The Brain Imaging Data Structure (BIDS) is a simple and...
Offline Critical Care Mechanical Ventilation & ARDS Trajectory Predictor
Tutorial Offline Critical Care Mechanical Ventilation & ARDS Trajectory Predictor Difficulty: Advanced Time: 25 min read Introduction Managing mechanical ventilation in intensive care units (ICUs)...
Offline Hematology Anemia & Bone Marrow Dysplasia Classifier
Tutorial Offline Hematology Anemia & Bone Marrow Dysplasia Classifier Difficulty: Advanced Time: 25 min read Introduction Hematologic evaluation of refractory anemias and suspected myelodysplastic syndromes...
Offline Hepatology Cirrhosis & Portal Hypertension Risk Predictor
Tutorial Offline Hepatology Cirrhosis & Portal Hypertension Risk Predictor Difficulty: Advanced Time: 25 min read Introduction Chronic liver disease and cirrhosis management requires continuous tracking...
Offline Neurology Epilepsy & Continuous EEG Seizure Prediction Engine
Tutorial Offline Neurology Epilepsy & Continuous EEG Seizure Prediction Engine Difficulty: Advanced Time: 25 min read Introduction Continuous electroencephalography (cEEG) monitoring in epilepsy monitoring units...
Offline Ophthalmic Retina & Macular Degeneration Diagnostic Engine
Tutorial Offline Ophthalmic Retina & Macular Degeneration Diagnostic Engine Difficulty: Advanced Time: 25 min read Introduction Optical Coherence Tomography (OCT) retinal imaging provides micrometric cross-sectional...
Offline Rheumatology Autoimmune Arthritis & Biologic Response Predictor
Tutorial Offline Rheumatology Autoimmune Arthritis & Biologic Response Predictor Difficulty: Advanced Time: 25 min read Introduction Rheumatoid arthritis (RA) and psoriatic arthritis management requires continuous...
Predicting Drug Toxicity with Tox21 and Chemprop
Tutorial Predicting Drug Toxicity with Tox21 and Chemprop Difficulty: Intermediate Time: 15 min read Introduction Before a new drug can reach clinical trials, it must...
Predicting Drug-Drug Interactions with Graph Neural Networks
Tutorial Predicting Drug-Drug Interactions with Graph Neural Networks Difficulty: Advanced Time: 25 min read Introduction Drug-Drug Interactions (DDIs) can cause severe adverse effects when multiple...
Predicting Drug-Target Binding Affinity with DeepPurpose
Tutorial Predicting Drug-Target Binding Affinity with DeepPurpose Difficulty: Intermediate Time: 15 min read Introduction In early-stage drug discovery, predicting how tightly a small molecule (drug)...
Predicting Heart Failure with Deep Survival Analysis (DeepSurv)
Tutorial Predicting Heart Failure with Deep Survival Analysis (DeepSurv) Difficulty: Advanced Time: 20 min read Introduction Traditional classification models predict if an event (like heart...
Predicting Patient Readmission with XGBoost and Claims Data
Tutorial Predicting Patient Readmission with XGBoost and Claims Data Difficulty: Intermediate Time: 15 min read Introduction Hospital readmission within 30 days is a critical quality...
Predicting Protein Secondary Structure with ProtT5
Tutorial Predicting Protein Secondary Structure with ProtT5 Difficulty: Intermediate Time: 15 min read Introduction While AlphaFold predicts full 3D atomic coordinates, there are many scenarios...
Predicting Protein-Ligand Binding Poses with DiffDock
Tutorial Predicting Protein-Ligand Binding Poses with DiffDock Difficulty: Advanced Time: 20 min read Introduction Molecular docking is the process of predicting the preferred orientation of...
Predicting Sepsis in the ICU with Recurrent Neural Networks (MIMIC-III)
Tutorial Predicting Sepsis in the ICU with Recurrent Neural Networks (MIMIC-III) Difficulty: Advanced Time: 25 min read Introduction Sepsis is a life-threatening condition that arises...
Privacy-Preserving Machine Learning with Differential Privacy and Opacus
Tutorial Privacy-Preserving Machine Learning with Differential Privacy and Opacus Difficulty: Advanced Time: 25 min read Introduction In healthcare AI, protecting patient data is paramount. Traditional...
Processing Whole Slide Images with OpenSlide and PyTorch
Tutorial Processing Whole Slide Images with OpenSlide and PyTorch Difficulty: Intermediate Time: 15 min read Introduction In computational pathology, Whole Slide Images (WSIs) are digitized...
Protein Structure Prediction with OpenFold
Tutorial Protein Structure Prediction with OpenFold Difficulty: Advanced Time: 25 min read Introduction AlphaFold2 revolutionized structural biology by predicting 3D protein structures from amino acid...
Run SmolVLM Locally on WebGPU for Radiological Analysis
Tutorial Run SmolVLM Locally on WebGPU for Radiological Analysis Difficulty: Advanced Time: 15 min read Introduction Multimodal vision-language models (VLMs) like SmolVLM are revolutionary for...
Simulating Molecular Dynamics with OpenMM
Tutorial Simulating Molecular Dynamics with OpenMM Difficulty: Advanced Time: 25 min read Introduction Molecular Dynamics (MD) simulations allow us to watch proteins fold, ligands bind...
Spatial Transcriptomics Analysis with Squidpy
Tutorial Spatial Transcriptomics Analysis with Squidpy Difficulty: Intermediate Time: 15 min read Introduction While scRNA-seq reveals cellular heterogeneity, it destroys the physical tissue architecture. Spatial...
Synthetic EHR Data Generation using GANs
Tutorial Synthetic EHR Data Generation using GANs Difficulty: Advanced Time: 25 min read Introduction Sharing Electronic Health Records (EHR) for research is severely restricted due...
Working with DICOM Images in Python for Deep Learning
Tutorial Working with DICOM Images in Python for Deep Learning Difficulty: Beginner Time: 15 min read Introduction DICOM (Digital Imaging and Communications in Medicine) is...
Zero-Shot Anomaly Detection in Brain MRIs using Diffusion Models
Tutorial Zero-Shot Anomaly Detection in Brain MRIs using Diffusion Models Difficulty: Advanced Time: 25 min read Introduction In this tutorial, we will explore how to...
Zero-Shot Medical Image Segmentation with MedSAM
Tutorial Zero-Shot Medical Image Segmentation with MedSAM Difficulty: Beginner Time: 15 min read Introduction In this cookbook, we will cover how to deploy MedSAM, a...