Hanbum Ko

Chanhui Lee, Hanbum Ko, Yuheon Song et al.

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

Hanbum Ko, Chanhui Lee, Ye Rin Kim et al.

Retrosynthesis prediction is a core task in organic synthesis that aims to predict reactants for a given product molecule. Traditionally, chemists select a plausible bond disconnection and derive corresponding reactants, which is time-consuming and requires substantial expertise. While recent advancements in molecular large language models (LLMs) have made progress, many methods either predict reactants without strategic reasoning or conduct only a generic product analysis, rather than reason explicitly about bond-disconnection strategies that logically lead to the choice of specific reactants. To overcome these limitations, we propose RetroReasoner, a retrosynthetic reasoning model that leverages chemists' strategic thinking. RetroReasoner is trained using both supervised fine-tuning (SFT) and reinforcement learning (RL). For SFT, we introduce SyntheticRetro, a framework that generates structured disconnection rationales alongside reactant predictions. In the case of RL, we apply a round-trip accuracy as reward, where predicted reactants are passed through a forward synthesis model, and predictions are rewarded when the forward-predicted product matches the original input product. Experimental results show that RetroReasoner not only outperforms prior baselines but also generates a broader range of feasible reactant proposals, particularly in handling more challenging reaction instances.

Aigerim Bogyrbayeva, Taehyun Yoon, Hanbum Ko et al.

Reinforcement learning has recently shown promise in learning quality solutions in many combinatorial optimization problems. In particular, the attention-based encoder-decoder models show high effectiveness on various routing problems, including the Traveling Salesman Problem (TSP). Unfortunately, they perform poorly for the TSP with Drone (TSP-D), requiring routing a heterogeneous fleet of vehicles in coordination -- a truck and a drone. In TSP-D, the two vehicles are moving in tandem and may need to wait at a node for the other vehicle to join. State-less attention-based decoder fails to make such coordination between vehicles. We propose a hybrid model that uses an attention encoder and a Long Short-Term Memory (LSTM) network decoder, in which the decoder's hidden state can represent the sequence of actions made. We empirically demonstrate that such a hybrid model improves upon a purely attention-based model for both solution quality and computational efficiency. Our experiments on the min-max Capacitated Vehicle Routing Problem (mmCVRP) also confirm that the hybrid model is more suitable for the coordinated routing of multiple vehicles than the attention-based model. The proposed model demonstrates comparable results as the operations research baseline methods.