# Mol-MoE: Training Preference-Guided Routers for Molecule Generation

arXiv: https://arxiv.org/abs/2502.05633 · HTML: https://mlsanity.com/paper/2502.05633/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in MoE in reinforcement learning and robotics, one of 12 directions in Mixture-of-experts.
- Builds on 29 of its 48 references that are in the map.
- First posted on arXiv 8 Feb 2025.

## Placed in

- Mixture-of-experts / [MoE in reinforcement learning and robotics](https://mlsanity.com/moe/moe-in-reinforcement-learning-and-robotics/)
- Deep reinforcement learning methods / [RL for energy, networks and operations](https://mlsanity.com/deeprl/rl-for-energy-networks-and-operations/)

## Builds on (most cited first, 29 of 29)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Proximal Policy Optimization Algorithms](https://mlsanity.com/paper/1707.06347/) (2017)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Pythia: A Suite for Analyzing Large Language Models Across Training and Scaling](https://mlsanity.com/paper/2304.01373/) (2023)
- [Decision Transformer: Reinforcement Learning via Sequence Modeling](https://mlsanity.com/paper/2106.01345/) (2021)
- [TIES-Merging: Resolving Interference When Merging Models](https://mlsanity.com/paper/2306.01708/) (2023)
- [Language Models are Super Mario: Absorbing Abilities from Homologous Models as a Free Lunch](https://mlsanity.com/paper/2311.03099/) (2023)
- [Linear Mode Connectivity and the Lottery Ticket Hypothesis](https://mlsanity.com/paper/1912.05671/) (2019)
- [Mixture-of-Experts with Expert Choice Routing](https://mlsanity.com/paper/2202.09368/) (2022)
- [LoraHub: Efficient Cross-Task Generalization via Dynamic LoRA Composition](https://mlsanity.com/paper/2307.13269/) (2023)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Direct Language Model Alignment from Online AI Feedback](https://mlsanity.com/paper/2402.04792/) (2024)
- [A Practical Guide to Multi-Objective Reinforcement Learning and Planning](https://mlsanity.com/paper/2103.09568/) (2021)
- [Rewarded soups: towards Pareto-optimal alignment by interpolating weights fine-tuned on diverse rewards](https://mlsanity.com/paper/2306.04488/) (2023)
- [Sparse Upcycling: Training Mixture-of-Experts from Dense Checkpoints](https://mlsanity.com/paper/2212.05055/) (2022)
- [Arcee's MergeKit: A Toolkit for Merging Large Language Models](https://mlsanity.com/paper/2403.13257/) (2024)
- [A Generalized Algorithm for Multi-Objective Reinforcement Learning and Policy Adaptation](https://mlsanity.com/paper/1908.08342/) (2019)
- [Rewards-in-Context: Multi-objective Alignment of Foundation Models with Dynamic Preference Adjustment](https://mlsanity.com/paper/2402.10207/) (2024)
- [A Survey of Imitation Learning: Algorithms, Recent Developments, and Challenges](https://mlsanity.com/paper/2309.02473/) (2023)
- [Model Breadcrumbs: Scaling Multi-Task Model Merging with Sparse Masks](https://mlsanity.com/paper/2312.06795/) (2023)
- [Multi-Objective GFlowNets](https://mlsanity.com/paper/2210.12765/) (2022)
- [What Matters for Model Merging at Scale?](https://mlsanity.com/paper/2410.03617/) (2024)
- [LoRA Soups: Merging LoRAs for Practical Skill Composition Tasks](https://mlsanity.com/paper/2410.13025/) (2024)
- [Conditional Language Policy: A General Framework for Steerable Multi-Objective Finetuning](https://mlsanity.com/paper/2407.15762/) (2024)
- [Searching for High-Value Molecules Using Reinforcement Learning and Transformers](https://mlsanity.com/paper/2310.02902/) (2023)
- [SmileyLlama: Modifying Large Language Models for Directed Chemical Space Exploration](https://mlsanity.com/paper/2409.02231/) (2024)
- [Revisiting Single-gated Mixtures of Experts](https://mlsanity.com/paper/2304.05497/) (2023)

## Built on by (most cited first, 3 of 3)

- [A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization](https://mlsanity.com/paper/2505.16094/) (2025)
- [Round-trip Reinforcement Learning: Self-Consistent Training for Better Chemical LLMs](https://mlsanity.com/paper/2510.01527/) (2025)
- [Iterative Foundation Model Fine-Tuning on Multiple Rewards](https://mlsanity.com/paper/2511.00220/) (2025)

## Abstract (arXiv)

Recent advances in language models have enabled framing molecule generation as sequence modeling. However, existing approaches often rely on single-objective reinforcement learning, limiting their applicability to real-world drug design, where multiple competing properties must be optimized. Traditional multi-objective reinforcement learning (MORL) methods require costly retraining for each new objective combination, making rapid exploration of trade-offs impractical. To overcome these limitations, we introduce Mol-MoE, a mixture-of-experts (MoE) architecture that enables efficient test-time steering of molecule generation without retraining. Central to our approach is a preference-based router training objective that incentivizes the router to combine experts in a way that aligns with user-specified trade-offs. This provides improved flexibility in exploring the chemical property space at test time, facilitating rapid trade-off exploration. Benchmarking against state-of-the-art methods, we show that Mol-MoE achieves superior sample quality and steerability.