Unlocking Cells' Secrets: Diffusion, Deconvolution, & Discovery with Siyu He, author of Squidiff & CORAL

In this episode of the Cognitive Revolution, we hear from Siyu He, a postdoc at Stanford specializing in biomedical data science. Siyu discusses the implications and methods behind their recent AI-driven biological research papers, Squidiff and CORAL. The conversation explores the use of AI models to analyze complex cellular systems and disease mechanisms, focusing on transcriptome and tissue sample analyses. Squidiff aims to simulate cellular transcriptomes to predict outcomes of various conditions, significantly expediting traditionally lengthy and expensive biological experiments. CORAL Project extends this by integrating different levels of biological data, enabling a more comprehensive understanding of tissue structures and cellular interactions. The discussion also delves into the challenges of using synthetic data for validating AI models and the potential acceleration of scientific discoveries through AI in biomedical research. The episode encapsulates the interplay between AI and biology, highlighting the future possibilities and current limitations of this innovative research front. Squidiff: https://www.biorxiv.org/content/10.1101/2024.11.16.623974v1.full.pdf CORAL: https://www.biorxiv.org/content/10.1101/2025.02.01.636038v1.full.pdf SPONSORS: Oracle Cloud Infrastructure (OCI): Oracle's next-generation cloud platform delivers blazing-fast AI and ML performance with 50% less for compute and 80% less for outbound networking compared to other cloud providers. OCI powers industry leaders like Vodafone and Thomson Reuters with secure infrastructure and application development capabilities. New U.S. customers can get their cloud bill cut in half by switching to OCI before March 31, 2024 at https://oracle.com/cognitive Shopify: Shopify is revolutionizing online selling with its market-leading checkout system and robust API ecosystem. Its exclusive library of cutting-edge AI apps empowers e-commerce businesses to thrive in a competitive market. Cognitive Revolution listeners can try Shopify for just $1 per month at https://shopify.com/cognitive NetSuite: Over 41,000 businesses trust NetSuite by Oracle, the #1 cloud ERP, to future-proof their operations. With a unified platform for accounting, financial management, inventory, and HR, NetSuite provides real-time insights and forecasting to help you make quick, informed decisions. Whether you're earning millions or hundreds of millions, NetSuite empowers you to tackle challenges and seize opportunities. Download the free CFO's guide to AI and machine learning at https://netsuite.com/cognitive PRODUCED BY: https://aipodcast.ing CHAPTERS: (00:00) About the Episode (03:37) Introduction and Guest Welcome (04:00) Setting the Big Picture Context (04:37) Exploring the Squidiff and CORAL Papers (08:31) Understanding Transcriptomes (11:17) Single Cell RNA Sequencing Technology (15:32) Motivation Behind Squidiff (Part 1) (17:14) Sponsors: Oracle Cloud Infrastructure (OCI) | Shopify (19:41) Motivation Behind Squidiff (Part 2) (25:56) Training Data and Model Architecture (Part 1) (31:38) Sponsors: NetSuite (33:11) Training Data and Model Architecture (Part 2) (37:18) Diffusion Models in Biology (46:07) In Silico Experiments and Applications (54:25) Clarifying the Validation Process (55:36) Validation Strategies and Real Data (58:26) Challenges in Modeling and Predictions (01:02:14) Accelerating Research with AI Models (01:07:31) Future Directions and Collaboration (01:10:46) Introduction to CORAL Paper (01:13:09) Spatial Transcriptomics and Proteomics (01:17:10) Challenges in Integrating Spatial Data (01:31:53) Synthetic Data and Model Validation (01:36:42) The Future of AI in Healthcare (01:43:31) Outro SOCIAL LINKS: Website: https://www.cognitiverevolution.ai Twitter (Podcast): https://x.com/cogrev_podcast Twitter (Nathan): https://x.com/labenz LinkedIn: https://linkedin.com/in/nathanlabenz/ Youtube: https://youtube.com/@CognitiveRevolutionPodcast