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| 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 | |
| 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 | |
| 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) | |
| 📂 **Full source**: [github.com/Rahul-Rajpurohitk/lysos](https://github.com/Rahul-Rajpurohitk/lysos) | |