| --- |
| title: Lysos |
| emoji: 🧬 |
| colorFrom: purple |
| colorTo: red |
| sdk: static |
| pinned: true |
| license: mit |
| short_description: Agentic antibiotic designer · Gemma 4 + MI300X |
| tags: |
| - antibiotic-discovery |
| - drug-design |
| - gemma |
| - mi300x |
| - amd |
| - amr |
| - agentic-ai |
| - antimicrobial-resistance |
| --- |
| |
| # Lysos · Open-source antibiotic designer for the AMR pandemic |
|
|
| > **Three-stage fine-tune of Gemma 4 31B-it on AMD MI300X. Multi-agent debate engine. End-to-end live agentic workspace.** |
|
|
| 🏆 **AMD Developer Hackathon 2026** · Track 2 — Fine-Tuning on AMD GPUs |
|
|
| --- |
|
|
| ## What it is |
|
|
| Lysos is an end-to-end open-source antibiotic discovery platform that takes Google's **Gemma 4 31B-it** and specializes it for antimicrobial-resistance (AMR) drug design via a three-stage fine-tune on a single AMD MI300X. The fine-tuned model drives a multi-agent debate engine and a live agentic workspace. |
|
|
| ## Live links |
|
|
| | Asset | Where | |
| |---|---| |
| | 📂 GitHub repo (full source) | <https://github.com/Rahul-Rajpurohitk/lysos> | |
| | 🤖 Stage 2.5 model (production) | <https://huggingface.co/rahul24raj/lysos-base-dpo> | |
| | 🤖 Stage 2 model | <https://huggingface.co/rahul24raj/lysos-base> | |
| | 🤖 Stage 1 model | <https://huggingface.co/rahul24raj/txgemma-4-31b> | |
| | 📊 Stage 2 SFT dataset (222,606 AMR examples) | <https://huggingface.co/datasets/rahul24raj/lysos-amr-stage2> | |
| | 🎬 Demo videos (release) | <https://github.com/Rahul-Rajpurohitk/lysos/releases/tag/v1.0-hackathon-submission> | |
| | 📺 Full walkthrough (9:08) | [lysos-demo-merged.mp4](https://github.com/Rahul-Rajpurohitk/lysos/releases/download/v1.0-hackathon-submission/lysos-demo-merged.mp4) | |
|
|
| ## The three-stage fine-tune |
|
|
| Every stage trains a LoRA adapter on top of `google/gemma-4-31B-it`. All adapters are public. |
|
|
| ``` |
| google/gemma-4-31B-it (62 GB base) |
| │ |
| ┌───────────────────────────────┼───────────────────────────────┐ |
| │ │ │ |
| STAGE 1 STAGE 2 STAGE 2.5 |
| TxGemma-4 31B lysos-base lysos-base-dpo |
| LoRA r=64, α=256 LoRA r=64, α=128 LoRA r=32, α=64 (β=0.1) |
| continued pretraining SFT on 222,606 AMR examples DPO on hard-negative pairs |
| for therapeutics (8 priority pathogens) (10 anti-correlated axes) |
| ~2 hr on 1× MI300X ~3 hr on 1× MI300X ~45 min on 1× MI300X |
| ``` |
|
|
| **Why DPO for the alignment stage**: DPO is the right tool for this objective. The downstream usage pattern — the Strategist agent picking among Designer-proposed candidates — is a discrete preference choice, exactly what DPO optimizes for. KL-bounded objective for stability, no axis to game, sample-efficient at 10K pairs in 45 min on 1× MI300X, full base capability preserved. |
|
|
| ## The agentic workspace |
|
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| When you fire `/wf design_with_debate`, four agent roles take turns — each is a separate LLM call: |
|
|
| ``` |
| ┌───────────┐ ┌───────────┐ ┌───────────┐ ┌─────────────┐ |
| │ DESIGNER │── 3 ───▶│ CRITIC │──────▶─▶│ EDITOR │──────▶─▶│ STRATEGIST │ |
| │ drafts │ smiles │ challenges│ critique│ refines │ fix │ picks winner│ |
| └───────────┘ └───────────┘ └───────────┘ └──────┬──────┘ |
| │ |
| winner SMILES auto-loads to 2D + 3D + radar |
| ``` |
|
|
| Plus 7 streaming workflows, 12+ slash commands, real-time per-atom resistance scoring against curated CARD clinical mutations, per-pathogen Champion table, Knowledge command-center with 4-tier resistance gene network. |
|
|
| ## Why MI300X |
|
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| 192 GB HBM3 lets us fit **Gemma 4 31B base in bf16 + LoRA adapter + KV cache + agent context coresident on one GPU**. Same GPU trains and serves. No tensor parallelism, no model sharding, no migration step. |
|
|
| ## Run it locally |
|
|
| ```bash |
| git clone https://github.com/Rahul-Rajpurohitk/lysos.git |
| cd lysos |
| python3 -m venv .venv && source .venv/bin/activate |
| pip install -e . |
| uvicorn workspace.api.server:app --host 0.0.0.0 --port 7860 & |
| |
| cd workspace/web && npm install && npm run dev |
| # open http://localhost:5173 |
| ``` |
|
|
| ## License |
|
|
| MIT (code) · Apache-2.0 / Gemma terms (weights) · CC-BY (datasets) |
|
|
| --- |
|
|
| 📺 **Watch the 9-minute demo**: [lysos-demo-merged.mp4](https://github.com/Rahul-Rajpurohitk/lysos/releases/download/v1.0-hackathon-submission/lysos-demo-merged.mp4) |
|
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| 📂 **Full source**: [github.com/Rahul-Rajpurohitk/lysos](https://github.com/Rahul-Rajpurohitk/lysos) |
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|
