arXiv subjects

Hyeonah Kim

Publications and source records attributed to Hyeonah Kim.

11 recordsLinked to original sources

arXiv2026

Synthesizable Molecular Generation via Soft-constrained GFlowNets with Rich Chemical Priors

The application of generative models for experimental drug discovery campaigns is severely limited by the difficulty of designing molecules de novo that can be synthesized in practice. Previous works have leveraged Generative Flow Networks (GFlowNets) to impose hard synthesizability constraints through the design of state and action spaces based on predefined reaction templates and building blocks. Despite the promising prospects of this approach, it currently lacks flexibility and scalability. As an alternative, we propose S3-GFN, which generates synthesizable SMILES molecules via simple soft regularization of a sequence-based GFlowNet. Our approach leverages rich molecular priors learned from large-scale SMILES corpora to steer molecular generation towards high-reward, synthesizable chemical spaces. The model induces constraints through off-policy replay training with a contrastive learning signal based on separate buffers of synthesizable and unsynthesizable samples. Our experiments show that S3-GFN learns to generate synthesizable molecules ($\geq 95\%$) with higher rewards in diverse tasks.

cs.LG↗

arXiv2025

Test-Time Search in Neural Graph Coarsening Procedures for the Capacitated Vehicle Routing Problem

The identification of valid inequalities, such as the rounded capacity inequalities (RCIs), is a key component of cutting plane methods for the Capacitated Vehicle Routing Problem (CVRP). While a deep learning-based separation method can learn to find high-quality cuts, our analysis reveals that the model produces fewer cuts than expected because it is insufficiently sensitive to generate a diverse set of generated subsets. This paper proposes an alternative: enhancing the performance of a trained model at inference time through a new test-time search with stochasticity. First, we introduce stochastic edge selection into the graph coarsening procedure, replacing the previously proposed greedy approach. Second, we propose the Graph Coarsening History-based Partitioning (GraphCHiP) algorithm, which leverages coarsening history to identify not only RCIs but also, for the first time, the Framed capacity inequalities (FCIs). Experiments on randomly generated CVRP instances demonstrate the effectiveness of our approach in reducing the dual gap compared to the existing neural separation method. Additionally, our method discovers effective FCIs on a specific instance, despite the challenging nature of identifying such cuts.

cs.AI↗

arXiv2025

RL4CO: an Extensive Reinforcement Learning for Combinatorial Optimization Benchmark

Combinatorial optimization (CO) is fundamental to several real-world applications, from logistics and scheduling to hardware design and resource allocation. Deep reinforcement learning (RL) has recently shown significant benefits in solving CO problems, reducing reliance on domain expertise and improving computational efficiency. However, the absence of a unified benchmarking framework leads to inconsistent evaluations, limits reproducibility, and increases engineering overhead, raising barriers to adoption for new researchers. To address these challenges, we introduce RL4CO, a unified and extensive benchmark with in-depth library coverage of 27 CO problem environments and 23 state-of-the-art baselines. Built on efficient software libraries and best practices in implementation, RL4CO features modularized implementation and flexible configurations of diverse environments, policy architectures, RL algorithms, and utilities with extensive documentation. RL4CO helps researchers build on existing successes while exploring and developing their own designs, facilitating the entire research process by decoupling science from heavy engineering. We finally provide extensive benchmark studies to inspire new insights and future work. RL4CO has already attracted numerous researchers in the community and is open-sourced at https://github.com/ai4co/rl4co.

cs.LG↗

arXiv2025

Improved Off-policy Reinforcement Learning in Biological Sequence Design

Designing biological sequences with desired properties is challenging due to vast search spaces and limited evaluation budgets. Although reinforcement learning methods use proxy models for rapid reward evaluation, insufficient training data can cause proxy misspecification on out-of-distribution inputs. To address this, we propose a novel off-policy search, $δ$-Conservative Search, that enhances robustness by restricting policy exploration to reliable regions. Starting from high-score offline sequences, we inject noise by randomly masking tokens with probability $δ$, then denoise them using our policy. We further adapt $δ$ based on proxy uncertainty on each data point, aligning the level of conservativeness with model confidence. Experimental results show that our conservative search consistently enhances the off-policy training, outperforming existing machine learning methods in discovering high-score sequences across diverse tasks, including DNA, RNA, protein, and peptide design.

cs.LG↗

arXiv2025

Neural Genetic Search in Discrete Spaces

Effective search methods are crucial for improving the performance of deep generative models at test time. In this paper, we introduce a novel test-time search method, Neural Genetic Search (NGS), which incorporates the evolutionary mechanism of genetic algorithms into the generation procedure of deep models. The core idea behind NGS is its crossover, which is defined as parent-conditioned generation using trained generative models. This approach offers a versatile and easy-to-implement search algorithm for deep generative models. We demonstrate the effectiveness and flexibility of NGS through experiments across three distinct domains: routing problems, adversarial prompt generation for language models, and molecular design.

cs.NE↗

arXiv2025

Ant Colony Sampling with GFlowNets for Combinatorial Optimization

We present the Generative Flow Ant Colony Sampler (GFACS), a novel meta-heuristic method that hierarchically combines amortized inference and parallel stochastic search. Our method first leverages Generative Flow Networks (GFlowNets) to amortize a \emph{multi-modal} prior distribution over combinatorial solution space that encompasses both high-reward and diversified solutions. This prior is iteratively updated via parallel stochastic search in the spirit of Ant Colony Optimization (ACO), leading to the posterior distribution that generates near-optimal solutions. Extensive experiments across seven combinatorial optimization problems demonstrate GFACS's promising performances.

cs.LG↗

arXiv2024

Genetic-guided GFlowNets for Sample Efficient Molecular Optimization

The challenge of discovering new molecules with desired properties is crucial in domains like drug discovery and material design. Recent advances in deep learning-based generative methods have shown promise but face the issue of sample efficiency due to the computational expense of evaluating the reward function. This paper proposes a novel algorithm for sample-efficient molecular optimization by distilling a powerful genetic algorithm into deep generative policy using GFlowNets training, the off-policy method for amortized inference. This approach enables the deep generative policy to learn from domain knowledge, which has been explicitly integrated into the genetic algorithm. Our method achieves state-of-the-art performance in the official molecular optimization benchmark, significantly outperforming previous methods. It also demonstrates effectiveness in designing inhibitors against SARS-CoV-2 with substantially fewer reward calls.

q-bio.BM↗

arXiv2024

Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial Optimization

Deep reinforcement learning (DRL) has significantly advanced the field of combinatorial optimization (CO). However, its practicality is hindered by the necessity for a large number of reward evaluations, especially in scenarios involving computationally intensive function assessments. To enhance the sample efficiency, we propose a simple but effective method, called symmetric replay training (SRT), which can be easily integrated into various DRL methods. Our method leverages high-reward samples to encourage exploration of the under-explored symmetric regions without additional online interactions - free. Through replay training, the policy is trained to maximize the likelihood of the symmetric trajectories of discovered high-rewarded samples. Experimental results demonstrate the consistent improvement of our method in sample efficiency across diverse DRL methods applied to real-world tasks, such as molecular optimization and hardware design.

cs.LG↗

arXiv2024

Equity-Transformer: Solving NP-hard Min-Max Routing Problems as Sequential Generation with Equity Context

Min-max routing problems aim to minimize the maximum tour length among multiple agents by having agents conduct tasks in a cooperative manner. These problems include impactful real-world applications but are known as NP-hard. Existing methods are facing challenges, particularly in large-scale problems that require the coordination of numerous agents to cover thousands of cities. This paper proposes Equity-Transformer to solve large-scale min-max routing problems. First, we employ sequential planning approach to address min-max routing problems, allowing us to harness the powerful sequence generators (e.g., Transformer). Second, we propose key inductive biases that ensure equitable workload distribution among agents. The effectiveness of Equity-Transformer is demonstrated through its superior performance in two representative min-max routing tasks: the min-max multi-agent traveling salesman problem (min-max mTSP) and the min-max multi-agent pick-up and delivery problem (min-max mPDP). Notably, our method achieves significant reductions of runtime, approximately 335 times, and cost values of about 53\% compared to a competitive heuristic (LKH3) in the case of 100 vehicles with 1,000 cities of mTSP. We provide reproducible source code: \url{https://github.com/kaist-silab/equity-transformer}.

cs.LG↗

arXiv2023

A Neural Separation Algorithm for the Rounded Capacity Inequalities

The cutting plane method is a key technique for successful branch-and-cut and branch-price-and-cut algorithms that find the exact optimal solutions for various vehicle routing problems (VRPs). Among various cuts, the rounded capacity inequalities (RCIs) are the most fundamental. To generate RCIs, we need to solve the separation problem, whose exact solution takes a long time to obtain; therefore, heuristic methods are widely used. We design a learning-based separation heuristic algorithm with graph coarsening that learns the solutions of the exact separation problem with a graph neural network (GNN), which is trained with small instances of 50 to 100 customers. We embed our separation algorithm within the cutting plane method to find a lower bound for the capacitated VRP (CVRP) with up to 1,000 customers. We compare the performance of our approach with CVRPSEP, a popular separation software package for various cuts used in solving VRPs. Our computational results show that our approach finds better lower bounds than CVRPSEP for large-scale problems with 400 or more customers, while CVRPSEP shows strong competency for problems with less than 400 customers.

cs.AI↗

arXiv2023

Meta-SAGE: Scale Meta-Learning Scheduled Adaptation with Guided Exploration for Mitigating Scale Shift on Combinatorial Optimization

This paper proposes Meta-SAGE, a novel approach for improving the scalability of deep reinforcement learning models for combinatorial optimization (CO) tasks. Our method adapts pre-trained models to larger-scale problems in test time by suggesting two components: a scale meta-learner (SML) and scheduled adaptation with guided exploration (SAGE). First, SML transforms the context embedding for subsequent adaptation of SAGE based on scale information. Then, SAGE adjusts the model parameters dedicated to the context embedding for a specific instance. SAGE introduces locality bias, which encourages selecting nearby locations to determine the next location. The locality bias gradually decays as the model is adapted to the target instance. Results show that Meta-SAGE outperforms previous adaptation methods and significantly improves scalability in representative CO tasks. Our source code is available at https://github.com/kaist-silab/meta-sage

cs.LG↗