Unlocking Cellular Mysteries with AI | 12min snip from "The Cognitive Revolution" | AI Builders, Researchers, and Live Player Analysis

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

"The Cognitive Revolution" | AI Builders, Researchers, and Live Player Analysis

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Unlocking Cellular Mysteries with AI

This chapter explores the complexities of biological systems, emphasizing the significance of the SquidDiff and CORAL papers in understanding cellular mechanisms. It discusses innovative AI models that analyze single-cell RNA transcriptomics and the intricate relationships that dictate cellular behavior. The conversation underscores the challenges in connecting molecular data to cellular functionalities while highlighting advancements in technology that enhance our insights into cellular evolution and heterogeneity.

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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

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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)