Improved Off-policy Reinforcement Learning in Biological Sequence Design

Designing biological sequences with desired properties is a significant challenge due to the combinatorially vast search space and the high cost of evaluating each candidate sequence. To address these challenges, reinforcement learning (RL) methods, such as GFlowNets, utilize proxy models for rapid reward evaluation and annotated data for policy training. Although these approaches have shown promise in generating diverse and novel sequences, the limited training data relative to the vast search space often leads to the misspecification of proxy for out-of-distribution inputs. We introduce $\delta$-Conservative Search, a novel off-policy search method for training GFlowNets designed to improve robustness against proxy misspecification. The key idea is to incorporate conservativeness, controlled by parameter $\delta$, to constrain the search to reliable regions. Specifically, we inject noise into high-score offline sequences by randomly masking tokens with a Bernoulli distribution of parameter $\delta$ and then denoise masked tokens using the GFlowNet policy. Additionally, $\delta$ is adaptively adjusted based on the uncertainty of the proxy model for each data point. This enables the reflection of proxy uncertainty to determine the level of conservativeness. Experimental results demonstrate that our method consistently outperforms existing machine learning methods in discovering high-score sequences across diverse tasks-including DNA, RNA, protein, and peptide design-especially in large-scale scenarios.

Adaptive teachers for amortized samplers

Amortized inference is the task of training a parametric model, such as a neural network, to approximate a distribution with a given unnormalized density where exact sampling is intractable. When sampling is implemented as a sequential decision-making process, reinforcement learning (RL) methods, such as generative flow networks, can be used to train the sampling policy. Off-policy RL training facilitates the discovery of diverse, high-reward candidates, but existing methods still face challenges in efficient exploration. We propose to use an adaptive training distribution (the Teacher) to guide the training of the primary amortized sampler (the Student) by prioritizing high-loss regions. The Teacher, an auxiliary behavior model, is trained to sample high-error regions of the Student and can generalize across unexplored modes, thereby enhancing mode coverage by providing an efficient training curriculum. We validate the effectiveness of this approach in a synthetic environment designed to present an exploration challenge, two diffusion-based sampling tasks, and four biochemical discovery tasks demonstrating its ability to improve sample efficiency and mode coverage.

Ant Colony Sampling with GFlowNets for Combinatorial Optimization

This paper introduces the Generative Flow Ant Colony Sampler (GFACS), a novel neural-guided meta-heuristic algorithm for combinatorial optimization. GFACS integrates generative flow networks (GFlowNets) with the ant colony optimization (ACO) methodology. GFlowNets, a generative model that learns a constructive policy in combinatorial spaces, enhance ACO by providing an informed prior distribution of decision variables conditioned on input graph instances. Furthermore, we introduce a novel combination of training tricks, including search-guided local exploration, energy normalization, and energy shaping to improve GFACS. Our experimental results demonstrate that GFACS outperforms baseline ACO algorithms in seven CO tasks and is competitive with problem-specific heuristics for vehicle routing problems. The source code is available at \url{https://github.com/ai4co/gfacs}.

Genetic-guided GFlowNets: Advancing in Practical Molecular Optimization Benchmark

This paper proposes a novel variant of GFlowNet, genetic-guided GFlowNet (Genetic GFN), which integrates an iterative genetic search into GFlowNet. Genetic search effectively guides the GFlowNet to high-rewarded regions, addressing global over-exploration that results in training inefficiency and exploring limited regions. In addition, training strategies, such as rank-based replay training and unsupervised maximum likelihood pre-training, are further introduced to improve the sample efficiency of Genetic GFN. The proposed method shows a state-of-the-art score of 16.213, significantly outperforming the reported best score in the benchmark of 15.185, in practical molecular optimization (PMO), which is an official benchmark for sample-efficient molecular optimization. Remarkably, ours exceeds all baselines, including reinforcement learning, Bayesian optimization, generative models, GFlowNets, and genetic algorithms, in 14 out of 23 tasks.

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 agents as they collaboratively visit all cities, i.e., the completion time. 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 a new deep-learning framework to solve large-scale min-max routing problems. We model the simultaneous decision-making of multiple agents as a sequential generation process, allowing the utilization of scalable deep-learning models for sequential decision-making. In the sequentially approximated problem, we propose a scalable contextual Transformer model, Equity-Transformer, which generates sequential actions considering an equitable workload among other agents. The effectiveness of Equity-Transformer is demonstrated through its superior performance in two representative min-max routing tasks: the min-max multiple traveling salesman problem (min-max mTSP) and the min-max multiple 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: https://github.com/kaist-silab/equity-transformer