Gali
galinilin
AI & ML interests
Deep Learning, Bioinformatics and Proteomics
Recent Activity
upvoted an article about 21 hours ago
The ML Engineer's Guide to Protein AI reacted to MaziyarPanahi's post with 🔥 about 21 hours ago
DNA, mRNA, proteins, AI. I spent the last year going deep into computational biology as an ML engineer. This is Part I of what I found. 🧬
In 2024, AlphaFold won the Nobel Prize in Chemistry.
By 2026, the open-source community had built alternatives that outperform it.
That's the story I find most interesting about protein AI right now. Not just the science (which is incredible), but the speed at which open-source caught up. Multiple teams, independently, reproduced and then exceeded AlphaFold 3's accuracy with permissive licenses. The field went from prediction to generation: we're not just modeling known proteins anymore, we're designing new ones.
I spent months mapping this landscape for ML engineers. What the architectures actually are (spoiler: transformers and diffusion models), which tools to use for what, and which ones you can actually ship commercially.
New post on the Hugging Face blog: https://huggingface.co/blog/MaziyarPanahi/protein-ai-landscape
Hope you all enjoy! 🤗 reacted to MaziyarPanahi's post with 🤗 about 21 hours ago
Training mRNA Language Models Across 25 Species for $165
We built an end-to-end protein AI pipeline covering structure prediction, sequence design, and codon optimization. After comparing multiple transformer architectures for codon-level language modeling, CodonRoBERTa-large-v2 emerged as the clear winner with a perplexity of 4.10 and a Spearman CAI correlation of 0.40, significantly outperforming ModernBERT. We then scaled to 25 species, trained 4 production models in 55 GPU-hours, and built a species-conditioned system that no other open-source project offers. Complete results, architectural decisions, and runnable code below.
https://huggingface.co/blog/OpenMed/training-mrna-models-25-speciesOrganizations
