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The Next Frontier: Large Language Models In Biology
mmhamdy
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Nick Doiron
monsoon-nlp
AI & ML interests
biology and multilingual models
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I never really posted about my DaisyChain project because it's still work in progress. I decided to post a small bit about it and the demo.
DaisyChain Genomics: four small DNA/RNA specialists chained behind a learned router that behave like one big genomics model, at ~7× less active compute.
I built a modular genomics model chasing a 500M-parameter foundation model, then caught myself measuring it wrong. Here's the honest version.
DaisyChain is a different bet: instead of one monolithic DNA model, it's four ~74M specialists (eukaryote, prokaryote, mRNA, splice) chained behind a learned router, each distilled per-domain from HuggingFaceBio's Carbon-500M. Every specialist reports how surprised it is (bits/base) and the router hands each sequence to the link most at home with it. In lineage it's a cluster Branch-Train-Merge mixture of experts, so you can chain on a new domain without retraining the others.
The pitch: ~295M total params (under Carbon-500M), but only one ~74M specialist runs per query, so ~7× cheaper per token, routing at 100% held-out.
The mistake: Carbon works in 6-mers, and I'd been scoring likelihood as 6-mer cross-entropy. By that number I was +0.043 bits/base behind, splice even "beating" Carbon. But Carbon scores at the base-pair level, which is harder and more honest. Re-run their way:
Real gap: 1.862 vs 1.787 bits/base, +0.089 behind, not +0.043
No domain actually beats Carbon; the "splice win" was an artifact
Seq recovery: euk 31.5% vs 38.9%, bacteria 40.9% vs 54.1%
DaisyChain is still behind Carbon-500M (itself a draft model, not built to top benchmarks), but by a number I can defend, and the gap closes with every per-domain pass. 🌼
DaisyChainAI
DaisyChainAI/Daisychain-Genomics-Demo
DaisyChainAI/daisychain-genomics
DaisyChain Genomics: four small DNA/RNA specialists chained behind a learned router that behave like one big genomics model, at ~7× less active compute.
I built a modular genomics model chasing a 500M-parameter foundation model, then caught myself measuring it wrong. Here's the honest version.
DaisyChain is a different bet: instead of one monolithic DNA model, it's four ~74M specialists (eukaryote, prokaryote, mRNA, splice) chained behind a learned router, each distilled per-domain from HuggingFaceBio's Carbon-500M. Every specialist reports how surprised it is (bits/base) and the router hands each sequence to the link most at home with it. In lineage it's a cluster Branch-Train-Merge mixture of experts, so you can chain on a new domain without retraining the others.
The pitch: ~295M total params (under Carbon-500M), but only one ~74M specialist runs per query, so ~7× cheaper per token, routing at 100% held-out.
The mistake: Carbon works in 6-mers, and I'd been scoring likelihood as 6-mer cross-entropy. By that number I was +0.043 bits/base behind, splice even "beating" Carbon. But Carbon scores at the base-pair level, which is harder and more honest. Re-run their way:
Real gap: 1.862 vs 1.787 bits/base, +0.089 behind, not +0.043
No domain actually beats Carbon; the "splice win" was an artifact
Seq recovery: euk 31.5% vs 38.9%, bacteria 40.9% vs 54.1%
DaisyChain is still behind Carbon-500M (itself a draft model, not built to top benchmarks), but by a number I can defend, and the gap closes with every per-domain pass. 🌼
DaisyChainAI/Daisychain-Genomics-Demo
DaisyChainAI/daisychain-genomics
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Human brains don't recreate every pixel to understand the world!
Most current models in genomics, proteomics, and single-cell transcriptomics rely on generative objectives like masked language modeling or next token prediction. While effective, these architectures waste significant capacity reconstructing raw, noisy sequence details that may not carry functional biological meaning.
But a promising, more efficient alternative is emerging: Joint-Embedding Predictive Architecture (JEPA)
Originally introduced by Yann LeCun for computer vision, JEPA is a non-generative, self-supervised learning (SSL) framework. Instead of predicting raw inputs, it operates as a world model that predicts abstract semantic embeddings in latent space.
Recently, the JEPA framework (and its more efficient LeJEPA variant) has been adapted into the biological sciences to develop performing foundation models and to improve on already existing ones.
It's interesting how each adaptation modified and tailored JEPA to suit its specific biological domain, whether by experimenting with different backbones or complementing the objective with other loss terms.
For example, JEPA-DNA and ProteinJEPA used JEPA as a continual pre-training framework to enhance existing foundation models without training from scratch, while Cell-JEPA and JEPA-DNA employed a hybrid objective that combines the JEPA loss with a traditional language modeling loss.
The article below provides an overview of these implementations, along with others that came out this year. As always, your thoughts and feedback are welcome and highly appreciated!
Link to the article is in the first comment 👇
Most current models in genomics, proteomics, and single-cell transcriptomics rely on generative objectives like masked language modeling or next token prediction. While effective, these architectures waste significant capacity reconstructing raw, noisy sequence details that may not carry functional biological meaning.
But a promising, more efficient alternative is emerging: Joint-Embedding Predictive Architecture (JEPA)
Originally introduced by Yann LeCun for computer vision, JEPA is a non-generative, self-supervised learning (SSL) framework. Instead of predicting raw inputs, it operates as a world model that predicts abstract semantic embeddings in latent space.
Recently, the JEPA framework (and its more efficient LeJEPA variant) has been adapted into the biological sciences to develop performing foundation models and to improve on already existing ones.
It's interesting how each adaptation modified and tailored JEPA to suit its specific biological domain, whether by experimenting with different backbones or complementing the objective with other loss terms.
For example, JEPA-DNA and ProteinJEPA used JEPA as a continual pre-training framework to enhance existing foundation models without training from scratch, while Cell-JEPA and JEPA-DNA employed a hybrid objective that combines the JEPA loss with a traditional language modeling loss.
The article below provides an overview of these implementations, along with others that came out this year. As always, your thoughts and feedback are welcome and highly appreciated!
Link to the article is in the first comment 👇
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reacted to pankajpandey-dev's post with 🔥 about 2 months ago
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🇮🇳 Qwen3-4B Hindi Instruct v2 — a Hindi LLM that runs on your own machine
Most strong Hindi-capable models are either huge or cloud-only. I wanted one that's small enough to run locally but actually follows instructions in Hindi — so I fine-tuned Qwen3-4B on 10K Hindi instruction pairs and shipped it with a full GGUF quant ladder.
✅ Fine-tune (16-bit): huggingface.co/pankajpandey-dev/Qwen3-4B-Hindi-Instruct-v2
✅ GGUF (Q4/Q5/Q8): huggingface.co/pankajpandey-dev/Qwen3-4B-Hindi-Instruct-v2-GGUF
Runs in Ollama, llama.cpp, and LM Studio. The Q4_K_M is just 2.5 GB — fits comfortably on a laptop, CPU or GPU.
Part of my Hindi LLM Series — building openly-licensed Indic models for local and edge use. More coming (Gemma next). Feedback welcome 🙏
#Hindi #IndicNLP #GGUF #LocalLLM #Qwen
Most strong Hindi-capable models are either huge or cloud-only. I wanted one that's small enough to run locally but actually follows instructions in Hindi — so I fine-tuned Qwen3-4B on 10K Hindi instruction pairs and shipped it with a full GGUF quant ladder.
✅ Fine-tune (16-bit): huggingface.co/pankajpandey-dev/Qwen3-4B-Hindi-Instruct-v2
✅ GGUF (Q4/Q5/Q8): huggingface.co/pankajpandey-dev/Qwen3-4B-Hindi-Instruct-v2-GGUF
Runs in Ollama, llama.cpp, and LM Studio. The Q4_K_M is just 2.5 GB — fits comfortably on a laptop, CPU or GPU.
Part of my Hindi LLM Series — building openly-licensed Indic models for local and edge use. More coming (Gemma next). Feedback welcome 🙏
#Hindi #IndicNLP #GGUF #LocalLLM #Qwen
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