# Toward a Locally Deployable Agentic Co-Scientist: Small-Model Planning for Early-Stage Drug Discovery

arXiv: https://arxiv.org/abs/2610.04740 · HTML: https://mlsanity.com/paper/2610.04740/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 13 of its 44 references that are in the map.
- First posted on arXiv 3 Oct 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 13 of 13)

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- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields](https://mlsanity.com/paper/2206.07697/) (2022)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials](https://mlsanity.com/paper/2310.03121/) (2023)
- [DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration](https://mlsanity.com/paper/2411.15692/) (2024)
- [Docling Technical Report](https://mlsanity.com/paper/2408.09869/) (2024)
- [Agent AI with LangGraph: A Modular Framework for Enhancing Machine Translation Using Large Language Models](https://mlsanity.com/paper/2412.03801/) (2024)
- [LLM-IE: A Python Package for Generative Information Extraction with Large Language Models](https://mlsanity.com/paper/2411.11779/) (2024)
- [AI Agents in Drug Discovery](https://mlsanity.com/paper/2510.27130/) (2025)

## Abstract (arXiv)

Early-stage computational drug discovery requires coordinating heterogeneous scientific tools across multi-step workflows. We present a lightweight, tool-augmented framework in which a locally deployable compact language model plans calls to 18 modular tools. A Unified Molecular Schema maintains shared molecular records, while a plug-in interface supports tool replacement and extension. We construct 1,263 manually refined query-plan pairs through workflow-graph path coverage and apply LoRA fine-tuning to three compact model families. Under the query-level split, all fine-tuned models generate fully parseable and schema-compliant plans on 47 held-out cross-group queries. Llama 3.2-3B achieves a tool-selection F1 of 0.998, sequence exact match of 0.979, and argument F1 of 0.960. Under the stricter workflow-grouped split, which excludes identical ordered tool sequences across partitions, sequence exact match reaches 0.452 to 0.548, highlighting the remaining difficulty for compact models in generating complete workflow paths unseen during training. These results demonstrate the feasibility of compact, locally deployable planning while identifying compositional generalization as an important direction for further improvement.