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While GANs failed for protein systems, diffusion models became the key primitive. Now, the frontier of diffusion research is in specialized scientific areas like 3D structure prediction, surpassing the innovation seen in more mainstream AI applications like image generation.
The AI industry is hitting data limits for training massive, general-purpose models. The next wave of progress will likely come from creating highly specialized models for specific domains, similar to DeepMind's AlphaFold, which can achieve superhuman performance on narrow tasks.
Sergey Edunov, former Llama team lead, claims that LLM architectures have not fundamentally changed since the 2017 Transformer paper. He pivoted to drug discovery AI because the model architectures required for physical sciences are more diverse, complex, and present more interesting research challenges.
Similar to how an LLM uses a 'chain of thought' to reason, Genesis's model 'thinks' by iteratively refining an in-memory representation of a crystal structure. This process is guided by physics-based principles, significantly improving the final prediction's accuracy.
The next major AI breakthrough will come from applying generative models to complex systems beyond human language, such as biology. By treating biological processes as a unique "language," AI could discover novel therapeutics or research paths, leading to a "Move 37" moment in science.
Modern protein models use a generative approach (diffusion) instead of regression. Instead of predicting one "correct" structure, they model a distribution of possibilities. This better handles molecular dynamism and avoids averaging between multiple valid states, which is a flaw of regression models.
Instead of AI writing code that then gets rendered, future interfaces will be generated directly by diffusion models. This "intention-to-pixel" paradigm allows for hyper-personalized, real-time UIs, effectively making the diffusion model the new front-end.
A deep, non-obvious connection exists between generative AI (diffusion models, RL) and the physics of non-equilibrium systems. Prof. Max Welling notes their mathematical foundations are the same. This allows AI researchers to borrow theorems from physics and physicists to use AI models, fueling cross-disciplinary innovation.
Current AI for protein engineering relies on small public datasets like the PDB (~10,000 structures), causing models to "hallucinate" or default to known examples. This data bottleneck, orders of magnitude smaller than data used for LLMs, hinders the development of novel therapeutics.
AlphaFold 2 was a breakthrough for predicting single protein structures. However, this success highlighted the much larger, unsolved challenges of modeling protein interactions, their dynamic movements, and the actual folding process, which are critical for understanding disease and drug discovery.
Generative AI alone designs proteins that look correct on paper but often fail in the lab. DenovAI adds a physics layer to simulate molecular dynamics—the "jiggling and wiggling"—which weeds out false positives by modeling how proteins actually interact in the real world.