Topic

Diffusion Models

All digests tagged Diffusion Models

· 36:59

Stanford CS229 Machine Learning | Spring 2026 | Lecture 1: Introduction

This lecture provides a high-level introduction to Machine Learning fundamentals (Supervised, Unsupervised, and Reinforcement Learning) within the context of modern AI. The course emphasizes understanding the mathematical foundations and core techniques behind algorithms rather than focusing on programming implementation. Key topics include model training using large datasets, advanced concepts like embeddings, and the architectural differences between traditional ML tasks and general-purpose Large Language Models (LLMs). A critical focus for system builders is placed on the necessity of optimizing ML systems for hardware compatibility and speed.

Key takeaways

  1. ML Paradigm Shift 6:11

    The field has moved from specific, task-oriented models to general-purpose agents (LLMs). While traditional methods still apply, the focus is on tuning fundamental model capabilities rather than building complex data pipelines for every single use case.

  2. The Importance of ML Systems 33:00

    A planned lecture will cover 'ML system,' which addresses the critical need to make software and hardware compatible. Optimizing algorithms for speed (e.g., making them run 2x faster) is crucial due to the high cost associated with AI computation.

  3. Reinforcement Learning (RL) in LLMs 24:50

    RL can be used to train models dealing with stochastic sampling, such as text generation. Techniques like Policy Gradient and using human feedback (e.g., RLHF/RAG) are necessary because the generation process is not differentiable.

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· 1:29:47

Causal Models Need Causal Data - Xaira’s X-Cell model (Bo Wang & Ci Chu)

Xaira Therapeutics introduced X-Cell, a novel 4.9-billion-parameter diffusion language model designed as a virtual cell foundation model of biology. The model is trained on X-Atlas/Pisces—a massive dataset spanning 25.6 million single cells across 16 biological contexts and generated via the Perturb-seq platform. The core breakthrough lies in shifting from descriptive (observational) data to causal (interventional) data, allowing the model to predict how a cell will respond to genetic perturbations it has never encountered. This capability is crucial for advancing drug discovery by moving beyond trial-and-error methods.

Key takeaways

  1. Causality vs. Correlation in Biology 20:07

    Observational atlases (descriptive data) can describe biology, but they are fundamentally underpowered to learn causality. To predict the outcome of an intervention (e.g., knocking down a gene), causal data—generated through high-throughput perturbation screens—is required.

  2. X-Cell Architecture and Training 1:03:27

    X-Cell utilizes a diffusion language model approach, which treats gene expression prediction as an iterative 'editing' process rather than an autoregressive one. This architecture allows it to generate high-dimensional transcriptomic data by refining noisy representations until they minimize loss against the ground truth.

  3. Data Generation Scale and Engineering 1:16:47

    The model is powered by Perturb-seq, a technique combining high-throughput CRISPR perturbation with single-cell RNA sequencing. This process generates massive 2D datasets (perturbation on one axis, gene expression on the other) across millions of cells while minimizing batch effects.

  4. Generalization and Translational Potential 1:25:07

    X-Cell demonstrated impressive generalization by accurately predicting perturbation responses in active T-cells, even when the model was only trained on resting T-cell data. This suggests the potential to predict novel biology in unseen contexts.

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