Why Pool When You Can Flow? Active Learning with GFlowNets
Authors: Renfei Zhang, Mohit Pandey, Artem Cherkasov, Martin Ester
Organizations: School of Computer Science, Simon Fraser University, Burnaby, BC, Canada · Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada · Diagen AI · Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
The scalability of pool-based active learning is limited by the computational cost of evaluating large unlabeled datasets, a challenge that is particularly acute in virtual screening for drug discovery. While active learning strategies such as Bayesian Active Learning by Disagreement (BALD) prioritize informative samples, it remains computationally intensive when scaled to libraries containing billions samples. In this work, we introduce BALD-GFlowNet, a generative active learning framework that circumvents this issue. Our method leverages Generative Flow Networks (GFlowNets) to directly sample objects in proportion to the BALD reward. By replacing traditional pool-based acquisition with generative sampling, BALD-GFlowNet achieves scalability that is independent of the size of the unlabeled pool. In our virtual screening experiment, we show that BALD-GFlowNet achieves a performance comparable to that of standard BALD baseline while generating more structurally diverse molecules, offering a promising direction for efficient and scalable molecular discovery.
Standard flow and diffusion pre-training matches the distribution of available data (e.g., molecules), which often covers only a small fraction of the valid design space. In generative discovery, however, one aims to sample valid new-to-nature designs, assigned negligible probability under, and thus inaccessible to, standard models fitted to the observed data. To overcome this limitation, we depart from data distribution matching and view a generative model through its generable set: the region it covers with non-negligible probability. This allows to introduce a new learning principle for out-of-distribution flow modeling: enlarging a model's generable set to increase coverage of the valid design space. We propose Active Flow Expansion (ActFlow), a continued pre-training method that employs verifier feedback to expand a pre-trained model over new valid regions by iteratively adapting to synthetic data generated through active exploration in the learned flow representation. Theoretically, we establish to our knowledge first-of-their-kind statistical learning guarantees for out-of-distribution flow modeling, analyzing generable set expansion as a local-to-global reachability process over a learned representation. Empirically, we assess ActFlow with suitable out-of-distribution generative modeling metrics across small organic molecules, mid-sized drug-like molecules, therapeutic peptides, and protein sequence design tasks. Results show that ActFlow expands valid coverage far beyond the region modeled by the initial pre-trained model, significantly outperforming widely adopted synthetic flow pre-training methods.
Riccardo De Santi, Bruce Lee, Cristian Perez Jensen +6
Generative Flow Networks (GFlowNets) have shown promising potential to generate high-scoring candidates with probability proportional to their rewards. As existing GFlowNets freely explore in state space, they encounter significant convergence challenges when scaling to large state spaces. Addressing this issue, this paper proposes to restrict the exploration of actor. A planner is introduced to partition the entire state space into overlapping partial state spaces. Given their limited size, these partial state spaces allow the actor to efficiently identify subregions with higher rewards. A heuristic strategy is introduced to switch partial regions thus preventing the actor from wasting time exploring fully explored or low-reward partial regions. By iteratively exploring these partial state spaces, the actor learns to converge towards the high-reward subregions within the entire state space. Experiments on several widely used datasets demonstrate that \modelname converges faster than existing works on large state spaces. Furthermore, \modelname not only generates candidates with higher rewards but also significantly improves their diversity.
The effectiveness of active learning hinges on the choice of the acquisition criterion by which a learning algorithm selects potentially informative data points whose label is subsequently queried. This paper proposes a novel gradient-based acquisition criterion, derived from a generalization bound introduced by Luo et al. (2022). This criterion can be applied in lieu of uncertainty measures in uncertainty sampling, or incorporated into diversity-based methods that consider the spread of sampled points in addition to the uncertainty of their labels. We provide a theoretical justification of the proposed acquisition criterion, and demonstrate its effectiveness in an empirical evaluation.